#399 by GitHub stars
FreedomIntelligence/OpenClaw-Medical-Skills
The largest open-source medical AI skills library for OpenClaw🦞.
History
Review weekly changes to SKILL.md before updating. Dates mark the weeks in which we observed each version; checks apply to the recorded commits.
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skills/aav-vector-design-agent/SKILL.md
Week of Oct 26, 2026 · +0 / −0 lines
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skills/adaptyv/SKILL.md
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skills/adhd-daily-planner/SKILL.md
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skills/aeon/SKILL.md
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skills/agent-browser/SKILL.md
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skills/agentd-drug-discovery/SKILL.md
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skills/ai-analyzer/SKILL.md
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skills/alphafold/SKILL.md
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skills/alphafold-database/SKILL.md
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skills/anndata/SKILL.md
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skills/antibody-design-agent/SKILL.md
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skills/antibody-design-agent/MAGE/SKILL.md
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skills/arboreto/SKILL.md
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skills/armored-cart-design-agent/SKILL.md
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skills/arxiv-search/SKILL.md
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skills/autonomous-oncology-agent/SKILL.md
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skills/bayesian-optimizer/SKILL.md
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skills/benchling-integration/SKILL.md
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skills/bgpt-paper-search/SKILL.md
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skills/bindcraft/SKILL.md
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skills/binder-design/SKILL.md
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skills/binding-characterization/SKILL.md
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skills/bindingdb-database/SKILL.md
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skills/bio-admet-prediction/SKILL.md
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skills/bio-alignment-files-bam-statistics/SKILL.md
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skills/bio-alignment-filtering/SKILL.md
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skills/bio-alignment-indexing/SKILL.md
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skills/bio-alignment-io/SKILL.md
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skills/bio-alignment-msa-parsing/SKILL.md
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skills/bio-alignment-msa-statistics/SKILL.md
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skills/bio-alignment-pairwise/SKILL.md
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skills/bio-alignment-sorting/SKILL.md
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skills/bio-alignment-validation/SKILL.md
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skills/bio-atac-seq-atac-peak-calling/SKILL.md
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skills/bio-atac-seq-atac-qc/SKILL.md
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skills/bio-atac-seq-differential-accessibility/SKILL.md
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skills/bio-atac-seq-footprinting/SKILL.md
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skills/bio-atac-seq-motif-deviation/SKILL.md
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skills/bio-atac-seq-nucleosome-positioning/SKILL.md
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skills/bio-basecalling/SKILL.md
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skills/bio-batch-downloads/SKILL.md
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skills/bio-batch-processing/SKILL.md
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skills/bio-bedgraph-handling/SKILL.md
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skills/bio-blast-searches/SKILL.md
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skills/bio-causal-genomics-colocalization-analysis/SKILL.md
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skills/bio-causal-genomics-fine-mapping/SKILL.md
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skills/bio-causal-genomics-mediation-analysis/SKILL.md
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skills/bio-causal-genomics-mendelian-randomization/SKILL.md
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skills/bio-causal-genomics-pleiotropy-detection/SKILL.md
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skills/bio-cfdna-preprocessing/SKILL.md
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skills/bio-chipseq-differential-binding/SKILL.md
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skills/bio-chipseq-motif-analysis/SKILL.md
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skills/bio-chipseq-peak-annotation/SKILL.md
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skills/bio-chipseq-peak-calling/SKILL.md
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skills/bio-chipseq-qc/SKILL.md
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skills/bio-chipseq-super-enhancers/SKILL.md
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skills/bio-chipseq-visualization/SKILL.md
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skills/bio-clinical-databases-clinvar-lookup/SKILL.md
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skills/bio-clinical-databases-dbsnp-queries/SKILL.md
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skills/bio-clinical-databases-gnomad-frequencies/SKILL.md
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skills/bio-clinical-databases-hla-typing/SKILL.md
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skills/bio-clinical-databases-myvariant-queries/SKILL.md
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skills/bio-clinical-databases-pharmacogenomics/SKILL.md
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skills/bio-clinical-databases-polygenic-risk/SKILL.md
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skills/bio-clinical-databases-somatic-signatures/SKILL.md
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skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md
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skills/bio-clinical-databases-variant-prioritization/SKILL.md
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skills/bio-clip-seq-binding-site-annotation/SKILL.md
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skills/bio-clip-seq-clip-alignment/SKILL.md
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skills/bio-clip-seq-clip-motif-analysis/SKILL.md
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skills/bio-clip-seq-clip-peak-calling/SKILL.md
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skills/bio-clip-seq-clip-preprocessing/SKILL.md
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skills/bio-codon-usage/SKILL.md
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skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md
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skills/bio-comparative-genomics-hgt-detection/SKILL.md
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skills/bio-comparative-genomics-ortholog-inference/SKILL.md
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skills/bio-comparative-genomics-positive-selection/SKILL.md
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skills/bio-comparative-genomics-synteny-analysis/SKILL.md
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skills/bio-compressed-files/SKILL.md
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skills/bio-consensus-sequences/SKILL.md
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skills/bio-copy-number-cnv-annotation/SKILL.md
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skills/bio-copy-number-cnv-visualization/SKILL.md
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skills/bio-copy-number-cnvkit-analysis/SKILL.md
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skills/bio-copy-number-gatk-cnv/SKILL.md
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skills/bio-crispr-screens-base-editing-analysis/SKILL.md
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skills/bio-crispr-screens-batch-correction/SKILL.md
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skills/bio-crispr-screens-crispresso-editing/SKILL.md
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skills/bio-crispr-screens-hit-calling/SKILL.md
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skills/bio-crispr-screens-jacks-analysis/SKILL.md
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skills/bio-crispr-screens-library-design/SKILL.md
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skills/bio-crispr-screens-mageck-analysis/SKILL.md
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skills/bio-crispr-screens-screen-qc/SKILL.md
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skills/bio-ctdna-mutation-detection/SKILL.md
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skills/bio-data-visualization-circos-plots/SKILL.md
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skills/bio-data-visualization-color-palettes/SKILL.md
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skills/bio-data-visualization-genome-browser-tracks/SKILL.md
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skills/bio-data-visualization-genome-tracks/SKILL.md
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skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md
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skills/bio-data-visualization-heatmaps-clustering/SKILL.md
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skills/bio-data-visualization-interactive-visualization/SKILL.md
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skills/bio-data-visualization-multipanel-figures/SKILL.md
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skills/bio-data-visualization-specialized-omics-plots/SKILL.md
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skills/bio-data-visualization-upset-plots/SKILL.md
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skills/bio-data-visualization-volcano-customization/SKILL.md
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skills/bio-de-deseq2-basics/SKILL.md
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skills/bio-de-edger-basics/SKILL.md
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skills/bio-de-results/SKILL.md
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skills/bio-de-visualization/SKILL.md
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skills/bio-differential-expression-batch-correction/SKILL.md
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skills/bio-differential-expression-timeseries-de/SKILL.md
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skills/bio-differential-splicing/SKILL.md
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skills/bio-duplicate-handling/SKILL.md
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skills/bio-entrez-fetch/SKILL.md
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skills/bio-entrez-link/SKILL.md
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skills/bio-entrez-search/SKILL.md
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skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md
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skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md
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skills/bio-epidemiological-genomics-phylodynamics/SKILL.md
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skills/bio-epidemiological-genomics-transmission-inference/SKILL.md
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skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md
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skills/bio-epitranscriptomics-m6a-differential/SKILL.md
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skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md
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skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md
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skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md
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skills/bio-epitranscriptomics-modification-visualization/SKILL.md
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skills/bio-experimental-design-batch-design/SKILL.md
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skills/bio-experimental-design-multiple-testing/SKILL.md
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skills/bio-experimental-design-power-analysis/SKILL.md
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skills/bio-experimental-design-sample-size/SKILL.md
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skills/bio-expression-matrix-counts-ingest/SKILL.md
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skills/bio-expression-matrix-gene-id-mapping/SKILL.md
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skills/bio-expression-matrix-metadata-joins/SKILL.md
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skills/bio-expression-matrix-sparse-handling/SKILL.md
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skills/bio-fastq-quality/SKILL.md
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skills/bio-filter-sequences/SKILL.md
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skills/bio-flow-cytometry-bead-normalization/SKILL.md
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skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md
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skills/bio-flow-cytometry-compensation-transformation/SKILL.md
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skills/bio-flow-cytometry-cytometry-qc/SKILL.md
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skills/bio-flow-cytometry-differential-analysis/SKILL.md
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skills/bio-flow-cytometry-doublet-detection/SKILL.md
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skills/bio-flow-cytometry-fcs-handling/SKILL.md
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skills/bio-flow-cytometry-gating-analysis/SKILL.md
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skills/bio-format-conversion/SKILL.md
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skills/bio-fragment-analysis/SKILL.md
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skills/bio-gatk-variant-calling/SKILL.md
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skills/bio-genome-assembly-assembly-polishing/SKILL.md
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skills/bio-genome-assembly-assembly-qc/SKILL.md
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skills/bio-genome-assembly-contamination-detection/SKILL.md
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skills/bio-genome-assembly-hifi-assembly/SKILL.md
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skills/bio-genome-assembly-long-read-assembly/SKILL.md
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skills/bio-genome-assembly-metagenome-assembly/SKILL.md
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skills/bio-genome-assembly-scaffolding/SKILL.md
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skills/bio-genome-assembly-short-read-assembly/SKILL.md
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skills/bio-genome-engineering-base-editing-design/SKILL.md
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skills/bio-genome-engineering-grna-design/SKILL.md
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skills/bio-genome-engineering-hdr-template-design/SKILL.md
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skills/bio-genome-engineering-off-target-prediction/SKILL.md
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skills/bio-genome-engineering-prime-editing-design/SKILL.md
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skills/bio-genome-intervals-bed-file-basics/SKILL.md
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skills/bio-genome-intervals-bigwig-tracks/SKILL.md
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skills/bio-genome-intervals-coverage-analysis/SKILL.md
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skills/bio-genome-intervals-gtf-gff-handling/SKILL.md
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skills/bio-genome-intervals-interval-arithmetic/SKILL.md
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skills/bio-genome-intervals-proximity-operations/SKILL.md
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skills/bio-geo-data/SKILL.md
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skills/bio-hi-c-analysis-compartment-analysis/SKILL.md
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skills/bio-hi-c-analysis-contact-pairs/SKILL.md
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skills/bio-hi-c-analysis-hic-data-io/SKILL.md
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skills/bio-hi-c-analysis-hic-differential/SKILL.md
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skills/bio-hi-c-analysis-hic-visualization/SKILL.md
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skills/bio-hi-c-analysis-loop-calling/SKILL.md
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skills/bio-hi-c-analysis-matrix-operations/SKILL.md
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skills/bio-hi-c-analysis-tad-detection/SKILL.md
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skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md
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skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md
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skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md
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skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md
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skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md
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skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md
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skills/bio-immunoinformatics-epitope-prediction/SKILL.md
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skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md
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skills/bio-multi-omics-similarity-network/SKILL.md
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skills/bio-pathway-enrichment-visualization/SKILL.md
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skills/bio-pathway-kegg-pathways/SKILL.md
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skills/bio-pdb-geometric-analysis/SKILL.md
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skills/bio-pdb-structure-navigation/SKILL.md
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skills/bio-phasing-imputation-genotype-imputation/SKILL.md
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skills/bio-phylo-distance-calculations/SKILL.md
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skills/bio-phylo-modern-tree-inference/SKILL.md
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skills/bio-phylo-tree-manipulation/SKILL.md
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skills/bio-phylo-tree-visualization/SKILL.md
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skills/bio-pileup-generation/SKILL.md
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skills/bio-population-genetics-association-testing/SKILL.md
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skills/bio-population-genetics-plink-basics/SKILL.md
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skills/bio-population-genetics-population-structure/SKILL.md
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skills/bio-population-genetics-selection-statistics/SKILL.md
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skills/bio-primer-design-primer-basics/SKILL.md
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skills/bio-primer-design-primer-validation/SKILL.md
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skills/bio-primer-design-qpcr-primers/SKILL.md
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skills/bio-proteomics-data-import/SKILL.md
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skills/bio-proteomics-dia-analysis/SKILL.md
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skills/bio-proteomics-differential-abundance/SKILL.md
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skills/bio-proteomics-peptide-identification/SKILL.md
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skills/bio-proteomics-protein-inference/SKILL.md
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skills/bio-proteomics-proteomics-qc/SKILL.md
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skills/bio-proteomics-ptm-analysis/SKILL.md
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3.1kGitHub stars
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Individual skills in this repository
- aav-vector-design-agent
skills/aav-vector-design-agent - adaptyv
skills/adaptyv - adhd-daily-planner
skills/adhd-daily-planner - aeon
skills/aeon - agent-browser
skills/agent-browser - agentd-drug-discovery
skills/agentd-drug-discovery - ai-analyzer
skills/ai-analyzer - alphafold
skills/alphafold - alphafold-database
skills/alphafold-database - anndata
skills/anndata - antibody-design-agent
skills/antibody-design-agent - MAGE
skills/antibody-design-agent/MAGE - arboreto
skills/arboreto - armored-cart-design-agent
skills/armored-cart-design-agent - arxiv-search
skills/arxiv-search - autonomous-oncology-agent
skills/autonomous-oncology-agent - bayesian-optimizer
skills/bayesian-optimizer - benchling-integration
skills/benchling-integration - bgpt-paper-search
skills/bgpt-paper-search - bindcraft
skills/bindcraft - binder-design
skills/binder-design - binding-characterization
skills/binding-characterization - bindingdb-database
skills/bindingdb-database - bio-admet-prediction
skills/bio-admet-prediction - bio-alignment-files-bam-statistics
skills/bio-alignment-files-bam-statistics - bio-alignment-filtering
skills/bio-alignment-filtering - bio-alignment-indexing
skills/bio-alignment-indexing - bio-alignment-io
skills/bio-alignment-io - bio-alignment-msa-parsing
skills/bio-alignment-msa-parsing - bio-alignment-msa-statistics
skills/bio-alignment-msa-statistics - bio-alignment-pairwise
skills/bio-alignment-pairwise - bio-alignment-sorting
skills/bio-alignment-sorting - bio-alignment-validation
skills/bio-alignment-validation - bio-atac-seq-atac-peak-calling
skills/bio-atac-seq-atac-peak-calling - bio-atac-seq-atac-qc
skills/bio-atac-seq-atac-qc - bio-atac-seq-differential-accessibility
skills/bio-atac-seq-differential-accessibility - bio-atac-seq-footprinting
skills/bio-atac-seq-footprinting - bio-atac-seq-motif-deviation
skills/bio-atac-seq-motif-deviation - bio-atac-seq-nucleosome-positioning
skills/bio-atac-seq-nucleosome-positioning - bio-basecalling
skills/bio-basecalling - bio-batch-downloads
skills/bio-batch-downloads - bio-batch-processing
skills/bio-batch-processing - bio-bedgraph-handling
skills/bio-bedgraph-handling - bio-blast-searches
skills/bio-blast-searches - bio-causal-genomics-colocalization-analysis
skills/bio-causal-genomics-colocalization-analysis - bio-causal-genomics-fine-mapping
skills/bio-causal-genomics-fine-mapping - bio-causal-genomics-mediation-analysis
skills/bio-causal-genomics-mediation-analysis - bio-causal-genomics-mendelian-randomization
skills/bio-causal-genomics-mendelian-randomization - bio-causal-genomics-pleiotropy-detection
skills/bio-causal-genomics-pleiotropy-detection - bio-cfdna-preprocessing
skills/bio-cfdna-preprocessing - bio-chipseq-differential-binding
skills/bio-chipseq-differential-binding - bio-chipseq-motif-analysis
skills/bio-chipseq-motif-analysis - bio-chipseq-peak-annotation
skills/bio-chipseq-peak-annotation - bio-chipseq-peak-calling
skills/bio-chipseq-peak-calling - bio-chipseq-qc
skills/bio-chipseq-qc - bio-chipseq-super-enhancers
skills/bio-chipseq-super-enhancers - bio-chipseq-visualization
skills/bio-chipseq-visualization - bio-clinical-databases-clinvar-lookup
skills/bio-clinical-databases-clinvar-lookup - bio-clinical-databases-dbsnp-queries
skills/bio-clinical-databases-dbsnp-queries - bio-clinical-databases-gnomad-frequencies
skills/bio-clinical-databases-gnomad-frequencies - bio-clinical-databases-hla-typing
skills/bio-clinical-databases-hla-typing - bio-clinical-databases-myvariant-queries
skills/bio-clinical-databases-myvariant-queries - bio-clinical-databases-pharmacogenomics
skills/bio-clinical-databases-pharmacogenomics - bio-clinical-databases-polygenic-risk
skills/bio-clinical-databases-polygenic-risk - bio-clinical-databases-somatic-signatures
skills/bio-clinical-databases-somatic-signatures - bio-clinical-databases-tumor-mutational-burden
skills/bio-clinical-databases-tumor-mutational-burden - bio-clinical-databases-variant-prioritization
skills/bio-clinical-databases-variant-prioritization - bio-clip-seq-binding-site-annotation
skills/bio-clip-seq-binding-site-annotation - bio-clip-seq-clip-alignment
skills/bio-clip-seq-clip-alignment - bio-clip-seq-clip-motif-analysis
skills/bio-clip-seq-clip-motif-analysis - bio-clip-seq-clip-peak-calling
skills/bio-clip-seq-clip-peak-calling - bio-clip-seq-clip-preprocessing
skills/bio-clip-seq-clip-preprocessing - bio-codon-usage
skills/bio-codon-usage - bio-comparative-genomics-ancestral-reconstruction
skills/bio-comparative-genomics-ancestral-reconstruction - bio-comparative-genomics-hgt-detection
skills/bio-comparative-genomics-hgt-detection - bio-comparative-genomics-ortholog-inference
skills/bio-comparative-genomics-ortholog-inference - bio-comparative-genomics-positive-selection
skills/bio-comparative-genomics-positive-selection - bio-comparative-genomics-synteny-analysis
skills/bio-comparative-genomics-synteny-analysis - bio-compressed-files
skills/bio-compressed-files - bio-consensus-sequences
skills/bio-consensus-sequences - bio-copy-number-cnv-annotation
skills/bio-copy-number-cnv-annotation - bio-copy-number-cnv-visualization
skills/bio-copy-number-cnv-visualization - bio-copy-number-cnvkit-analysis
skills/bio-copy-number-cnvkit-analysis - bio-copy-number-gatk-cnv
skills/bio-copy-number-gatk-cnv - bio-crispr-screens-base-editing-analysis
skills/bio-crispr-screens-base-editing-analysis - bio-crispr-screens-batch-correction
skills/bio-crispr-screens-batch-correction - bio-crispr-screens-crispresso-editing
skills/bio-crispr-screens-crispresso-editing - bio-crispr-screens-hit-calling
skills/bio-crispr-screens-hit-calling - bio-crispr-screens-jacks-analysis
skills/bio-crispr-screens-jacks-analysis - bio-crispr-screens-library-design
skills/bio-crispr-screens-library-design - bio-crispr-screens-mageck-analysis
skills/bio-crispr-screens-mageck-analysis - bio-crispr-screens-screen-qc
skills/bio-crispr-screens-screen-qc - bio-ctdna-mutation-detection
skills/bio-ctdna-mutation-detection - bio-data-visualization-circos-plots
skills/bio-data-visualization-circos-plots - bio-data-visualization-color-palettes
skills/bio-data-visualization-color-palettes - bio-data-visualization-genome-browser-tracks
skills/bio-data-visualization-genome-browser-tracks - bio-data-visualization-genome-tracks
skills/bio-data-visualization-genome-tracks - bio-data-visualization-ggplot2-fundamentals
skills/bio-data-visualization-ggplot2-fundamentals - bio-data-visualization-heatmaps-clustering
skills/bio-data-visualization-heatmaps-clustering - bio-data-visualization-interactive-visualization
skills/bio-data-visualization-interactive-visualization - bio-data-visualization-multipanel-figures
skills/bio-data-visualization-multipanel-figures - bio-data-visualization-specialized-omics-plots
skills/bio-data-visualization-specialized-omics-plots - bio-data-visualization-upset-plots
skills/bio-data-visualization-upset-plots - bio-data-visualization-volcano-customization
skills/bio-data-visualization-volcano-customization - bio-de-deseq2-basics
skills/bio-de-deseq2-basics - bio-de-edger-basics
skills/bio-de-edger-basics - bio-de-results
skills/bio-de-results - bio-de-visualization
skills/bio-de-visualization - bio-differential-expression-batch-correction
skills/bio-differential-expression-batch-correction - bio-differential-expression-timeseries-de
skills/bio-differential-expression-timeseries-de - bio-differential-splicing
skills/bio-differential-splicing - bio-duplicate-handling
skills/bio-duplicate-handling - bio-entrez-fetch
skills/bio-entrez-fetch - bio-entrez-link
skills/bio-entrez-link - bio-entrez-search
skills/bio-entrez-search - bio-epidemiological-genomics-amr-surveillance
skills/bio-epidemiological-genomics-amr-surveillance - bio-epidemiological-genomics-pathogen-typing
skills/bio-epidemiological-genomics-pathogen-typing - bio-epidemiological-genomics-phylodynamics
skills/bio-epidemiological-genomics-phylodynamics - bio-epidemiological-genomics-transmission-inference
skills/bio-epidemiological-genomics-transmission-inference - bio-epidemiological-genomics-variant-surveillance
skills/bio-epidemiological-genomics-variant-surveillance - bio-epitranscriptomics-m6a-differential
skills/bio-epitranscriptomics-m6a-differential - bio-epitranscriptomics-m6a-peak-calling
skills/bio-epitranscriptomics-m6a-peak-calling - bio-epitranscriptomics-m6anet-analysis
skills/bio-epitranscriptomics-m6anet-analysis - bio-epitranscriptomics-merip-preprocessing
skills/bio-epitranscriptomics-merip-preprocessing - bio-epitranscriptomics-modification-visualization
skills/bio-epitranscriptomics-modification-visualization - bio-experimental-design-batch-design
skills/bio-experimental-design-batch-design - bio-experimental-design-multiple-testing
skills/bio-experimental-design-multiple-testing - bio-experimental-design-power-analysis
skills/bio-experimental-design-power-analysis - bio-experimental-design-sample-size
skills/bio-experimental-design-sample-size - bio-expression-matrix-counts-ingest
skills/bio-expression-matrix-counts-ingest - bio-expression-matrix-gene-id-mapping
skills/bio-expression-matrix-gene-id-mapping - bio-expression-matrix-metadata-joins
skills/bio-expression-matrix-metadata-joins - bio-expression-matrix-sparse-handling
skills/bio-expression-matrix-sparse-handling - bio-fastq-quality
skills/bio-fastq-quality - bio-filter-sequences
skills/bio-filter-sequences - bio-flow-cytometry-bead-normalization
skills/bio-flow-cytometry-bead-normalization - bio-flow-cytometry-clustering-phenotyping
skills/bio-flow-cytometry-clustering-phenotyping - bio-flow-cytometry-compensation-transformation
skills/bio-flow-cytometry-compensation-transformation - bio-flow-cytometry-cytometry-qc
skills/bio-flow-cytometry-cytometry-qc - bio-flow-cytometry-differential-analysis
skills/bio-flow-cytometry-differential-analysis - bio-flow-cytometry-doublet-detection
skills/bio-flow-cytometry-doublet-detection - bio-flow-cytometry-fcs-handling
skills/bio-flow-cytometry-fcs-handling - bio-flow-cytometry-gating-analysis
skills/bio-flow-cytometry-gating-analysis - bio-format-conversion
skills/bio-format-conversion - bio-fragment-analysis
skills/bio-fragment-analysis - bio-gatk-variant-calling
skills/bio-gatk-variant-calling - bio-genome-assembly-assembly-polishing
skills/bio-genome-assembly-assembly-polishing - bio-genome-assembly-assembly-qc
skills/bio-genome-assembly-assembly-qc - bio-genome-assembly-contamination-detection
skills/bio-genome-assembly-contamination-detection - bio-genome-assembly-hifi-assembly
skills/bio-genome-assembly-hifi-assembly - bio-genome-assembly-long-read-assembly
skills/bio-genome-assembly-long-read-assembly - bio-genome-assembly-metagenome-assembly
skills/bio-genome-assembly-metagenome-assembly - bio-genome-assembly-scaffolding
skills/bio-genome-assembly-scaffolding - bio-genome-assembly-short-read-assembly
skills/bio-genome-assembly-short-read-assembly - bio-genome-engineering-base-editing-design
skills/bio-genome-engineering-base-editing-design - bio-genome-engineering-grna-design
skills/bio-genome-engineering-grna-design - bio-genome-engineering-hdr-template-design
skills/bio-genome-engineering-hdr-template-design - bio-genome-engineering-off-target-prediction
skills/bio-genome-engineering-off-target-prediction - bio-genome-engineering-prime-editing-design
skills/bio-genome-engineering-prime-editing-design - bio-genome-intervals-bed-file-basics
skills/bio-genome-intervals-bed-file-basics - bio-genome-intervals-bigwig-tracks
skills/bio-genome-intervals-bigwig-tracks - bio-genome-intervals-coverage-analysis
skills/bio-genome-intervals-coverage-analysis - bio-genome-intervals-gtf-gff-handling
skills/bio-genome-intervals-gtf-gff-handling - bio-genome-intervals-interval-arithmetic
skills/bio-genome-intervals-interval-arithmetic - bio-genome-intervals-proximity-operations
skills/bio-genome-intervals-proximity-operations - bio-geo-data
skills/bio-geo-data - bio-hi-c-analysis-compartment-analysis
skills/bio-hi-c-analysis-compartment-analysis - bio-hi-c-analysis-contact-pairs
skills/bio-hi-c-analysis-contact-pairs - bio-hi-c-analysis-hic-data-io
skills/bio-hi-c-analysis-hic-data-io - bio-hi-c-analysis-hic-differential
skills/bio-hi-c-analysis-hic-differential - bio-hi-c-analysis-hic-visualization
skills/bio-hi-c-analysis-hic-visualization - bio-hi-c-analysis-loop-calling
skills/bio-hi-c-analysis-loop-calling - bio-hi-c-analysis-matrix-operations
skills/bio-hi-c-analysis-matrix-operations - bio-hi-c-analysis-tad-detection
skills/bio-hi-c-analysis-tad-detection - bio-imaging-mass-cytometry-cell-segmentation
skills/bio-imaging-mass-cytometry-cell-segmentation - bio-imaging-mass-cytometry-data-preprocessing
skills/bio-imaging-mass-cytometry-data-preprocessing - bio-imaging-mass-cytometry-interactive-annotation
skills/bio-imaging-mass-cytometry-interactive-annotation - bio-imaging-mass-cytometry-phenotyping
skills/bio-imaging-mass-cytometry-phenotyping - bio-imaging-mass-cytometry-quality-metrics
skills/bio-imaging-mass-cytometry-quality-metrics - bio-imaging-mass-cytometry-spatial-analysis
skills/bio-imaging-mass-cytometry-spatial-analysis - bio-immunoinformatics-epitope-prediction
skills/bio-immunoinformatics-epitope-prediction - bio-immunoinformatics-immunogenicity-scoring
skills/bio-immunoinformatics-immunogenicity-scoring - bio-immunoinformatics-mhc-binding-prediction
skills/bio-immunoinformatics-mhc-binding-prediction - bio-immunoinformatics-neoantigen-prediction
skills/bio-immunoinformatics-neoantigen-prediction - bio-immunoinformatics-tcr-epitope-binding
skills/bio-immunoinformatics-tcr-epitope-binding - bio-isoform-switching
skills/bio-isoform-switching - bio-liquid-biopsy-pipeline
skills/bio-liquid-biopsy-pipeline - bio-local-blast
skills/bio-local-blast - bio-long-read-sequencing-clair3-variants
skills/bio-long-read-sequencing-clair3-variants - bio-long-read-sequencing-isoseq-analysis
skills/bio-long-read-sequencing-isoseq-analysis - bio-long-read-sequencing-nanopore-methylation
skills/bio-long-read-sequencing-nanopore-methylation - bio-longitudinal-monitoring
skills/bio-longitudinal-monitoring - bio-longread-alignment
skills/bio-longread-alignment - bio-longread-medaka
skills/bio-longread-medaka - bio-longread-qc
skills/bio-longread-qc - bio-longread-structural-variants
skills/bio-longread-structural-variants - bio-machine-learning-atlas-mapping
skills/bio-machine-learning-atlas-mapping - bio-machine-learning-biomarker-discovery
skills/bio-machine-learning-biomarker-discovery - bio-machine-learning-model-validation
skills/bio-machine-learning-model-validation - bio-machine-learning-omics-classifiers
skills/bio-machine-learning-omics-classifiers - bio-machine-learning-prediction-explanation
skills/bio-machine-learning-prediction-explanation - bio-machine-learning-survival-analysis
skills/bio-machine-learning-survival-analysis - bio-metabolomics-lipidomics
skills/bio-metabolomics-lipidomics - bio-metabolomics-metabolite-annotation
skills/bio-metabolomics-metabolite-annotation - bio-metabolomics-msdial-preprocessing
skills/bio-metabolomics-msdial-preprocessing - bio-metabolomics-normalization-qc
skills/bio-metabolomics-normalization-qc - bio-metabolomics-pathway-mapping
skills/bio-metabolomics-pathway-mapping - bio-metabolomics-statistical-analysis
skills/bio-metabolomics-statistical-analysis - bio-metabolomics-targeted-analysis
skills/bio-metabolomics-targeted-analysis - bio-metabolomics-xcms-preprocessing
skills/bio-metabolomics-xcms-preprocessing - bio-metagenomics-abundance
skills/bio-metagenomics-abundance - bio-metagenomics-amr-detection
skills/bio-metagenomics-amr-detection - bio-metagenomics-functional-profiling
skills/bio-metagenomics-functional-profiling - bio-metagenomics-kraken
skills/bio-metagenomics-kraken - bio-metagenomics-metaphlan
skills/bio-metagenomics-metaphlan - bio-metagenomics-strain-tracking
skills/bio-metagenomics-strain-tracking - bio-metagenomics-visualization
skills/bio-metagenomics-visualization - bio-methylation-based-detection
skills/bio-methylation-based-detection - bio-methylation-bismark-alignment
skills/bio-methylation-bismark-alignment - bio-methylation-calling
skills/bio-methylation-calling - bio-methylation-dmr-detection
skills/bio-methylation-dmr-detection - bio-methylation-methylkit
skills/bio-methylation-methylkit - bio-microbiome-amplicon-processing
skills/bio-microbiome-amplicon-processing - bio-microbiome-differential-abundance
skills/bio-microbiome-differential-abundance - bio-microbiome-diversity-analysis
skills/bio-microbiome-diversity-analysis - bio-microbiome-functional-prediction
skills/bio-microbiome-functional-prediction - bio-microbiome-qiime2-workflow
skills/bio-microbiome-qiime2-workflow - bio-microbiome-taxonomy-assignment
skills/bio-microbiome-taxonomy-assignment - bio-molecular-descriptors
skills/bio-molecular-descriptors - bio-molecular-io
skills/bio-molecular-io - bio-motif-search
skills/bio-motif-search - bio-multi-omics-data-harmonization
skills/bio-multi-omics-data-harmonization - bio-multi-omics-mixomics-analysis
skills/bio-multi-omics-mixomics-analysis - bio-multi-omics-mofa-integration
skills/bio-multi-omics-mofa-integration - bio-multi-omics-similarity-network
skills/bio-multi-omics-similarity-network - bio-orchestrator
skills/bio-orchestrator - bio-paired-end-fastq
skills/bio-paired-end-fastq - bio-pathway-enrichment-visualization
skills/bio-pathway-enrichment-visualization - bio-pathway-go-enrichment
skills/bio-pathway-go-enrichment - bio-pathway-gsea
skills/bio-pathway-gsea - bio-pathway-kegg-pathways
skills/bio-pathway-kegg-pathways - bio-pathway-reactome
skills/bio-pathway-reactome - bio-pathway-wikipathways
skills/bio-pathway-wikipathways - bio-pdb-geometric-analysis
skills/bio-pdb-geometric-analysis - bio-pdb-structure-io
skills/bio-pdb-structure-io - bio-pdb-structure-modification
skills/bio-pdb-structure-modification - bio-pdb-structure-navigation
skills/bio-pdb-structure-navigation - bio-phasing-imputation-genotype-imputation
skills/bio-phasing-imputation-genotype-imputation - bio-phasing-imputation-haplotype-phasing
skills/bio-phasing-imputation-haplotype-phasing - bio-phasing-imputation-imputation-qc
skills/bio-phasing-imputation-imputation-qc - bio-phasing-imputation-reference-panels
skills/bio-phasing-imputation-reference-panels - bio-phylo-distance-calculations
skills/bio-phylo-distance-calculations - bio-phylo-modern-tree-inference
skills/bio-phylo-modern-tree-inference - bio-phylo-tree-io
skills/bio-phylo-tree-io - bio-phylo-tree-manipulation
skills/bio-phylo-tree-manipulation - bio-phylo-tree-visualization
skills/bio-phylo-tree-visualization - bio-pileup-generation
skills/bio-pileup-generation - bio-population-genetics-association-testing
skills/bio-population-genetics-association-testing - bio-population-genetics-linkage-disequilibrium
skills/bio-population-genetics-linkage-disequilibrium - bio-population-genetics-plink-basics
skills/bio-population-genetics-plink-basics - bio-population-genetics-population-structure
skills/bio-population-genetics-population-structure - bio-population-genetics-scikit-allel-analysis
skills/bio-population-genetics-scikit-allel-analysis - bio-population-genetics-selection-statistics
skills/bio-population-genetics-selection-statistics - bio-primer-design-primer-basics
skills/bio-primer-design-primer-basics - bio-primer-design-primer-validation
skills/bio-primer-design-primer-validation - bio-primer-design-qpcr-primers
skills/bio-primer-design-qpcr-primers - bio-proteomics-data-import
skills/bio-proteomics-data-import - bio-proteomics-dia-analysis
skills/bio-proteomics-dia-analysis - bio-proteomics-differential-abundance
skills/bio-proteomics-differential-abundance - bio-proteomics-peptide-identification
skills/bio-proteomics-peptide-identification - bio-proteomics-protein-inference
skills/bio-proteomics-protein-inference - bio-proteomics-proteomics-qc
skills/bio-proteomics-proteomics-qc - bio-proteomics-ptm-analysis
skills/bio-proteomics-ptm-analysis - bio-proteomics-quantification
skills/bio-proteomics-quantification - bio-proteomics-spectral-libraries
skills/bio-proteomics-spectral-libraries - bio-reaction-enumeration
skills/bio-reaction-enumeration - bio-read-alignment-bowtie2-alignment
skills/bio-read-alignment-bowtie2-alignment - bio-read-alignment-bwa-alignment
skills/bio-read-alignment-bwa-alignment - bio-read-alignment-hisat2-alignment
skills/bio-read-alignment-hisat2-alignment - bio-read-alignment-star-alignment
skills/bio-read-alignment-star-alignment - bio-read-qc-adapter-trimming
skills/bio-read-qc-adapter-trimming - bio-read-qc-contamination-screening
skills/bio-read-qc-contamination-screening - bio-read-qc-fastp-workflow
skills/bio-read-qc-fastp-workflow - bio-read-qc-quality-filtering
skills/bio-read-qc-quality-filtering - bio-read-qc-quality-reports
skills/bio-read-qc-quality-reports - bio-read-qc-umi-processing
skills/bio-read-qc-umi-processing - bio-read-sequences
skills/bio-read-sequences - bio-reference-operations
skills/bio-reference-operations - bio-reporting-automated-qc-reports
skills/bio-reporting-automated-qc-reports - bio-reporting-figure-export
skills/bio-reporting-figure-export - bio-reporting-jupyter-reports
skills/bio-reporting-jupyter-reports - bio-reporting-quarto-reports
skills/bio-reporting-quarto-reports - bio-reporting-rmarkdown-reports
skills/bio-reporting-rmarkdown-reports - bio-research-tools-biomarker-signature-studio
skills/bio-research-tools-biomarker-signature-studio - bio-restriction-enzyme-selection
skills/bio-restriction-enzyme-selection - bio-restriction-fragment-analysis
skills/bio-restriction-fragment-analysis - bio-restriction-mapping
skills/bio-restriction-mapping - bio-restriction-sites
skills/bio-restriction-sites - bio-reverse-complement
skills/bio-reverse-complement - bio-ribo-seq-orf-detection
skills/bio-ribo-seq-orf-detection - bio-ribo-seq-riboseq-preprocessing
skills/bio-ribo-seq-riboseq-preprocessing - bio-ribo-seq-ribosome-periodicity
skills/bio-ribo-seq-ribosome-periodicity - bio-ribo-seq-ribosome-stalling
skills/bio-ribo-seq-ribosome-stalling - bio-ribo-seq-translation-efficiency
skills/bio-ribo-seq-translation-efficiency - bio-rna-quantification-alignment-free-quant
skills/bio-rna-quantification-alignment-free-quant - bio-rna-quantification-count-matrix-qc
skills/bio-rna-quantification-count-matrix-qc - bio-rna-quantification-featurecounts-counting
skills/bio-rna-quantification-featurecounts-counting - bio-rna-quantification-tximport-workflow
skills/bio-rna-quantification-tximport-workflow - bio-rnaseq-qc
skills/bio-rnaseq-qc - bio-sam-bam-basics
skills/bio-sam-bam-basics - bio-sashimi-plots
skills/bio-sashimi-plots - bio-seq-objects
skills/bio-seq-objects - bio-sequence-properties
skills/bio-sequence-properties - bio-sequence-similarity
skills/bio-sequence-similarity - bio-sequence-slicing
skills/bio-sequence-slicing - bio-sequence-statistics
skills/bio-sequence-statistics - bio-similarity-searching
skills/bio-similarity-searching - bio-single-cell-batch-integration
skills/bio-single-cell-batch-integration - bio-single-cell-cell-annotation
skills/bio-single-cell-cell-annotation - bio-single-cell-cell-communication
skills/bio-single-cell-cell-communication - bio-single-cell-clustering
skills/bio-single-cell-clustering - bio-single-cell-data-io
skills/bio-single-cell-data-io - bio-single-cell-doublet-detection
skills/bio-single-cell-doublet-detection - bio-single-cell-lineage-tracing
skills/bio-single-cell-lineage-tracing - bio-single-cell-markers-annotation
skills/bio-single-cell-markers-annotation - bio-single-cell-metabolite-communication
skills/bio-single-cell-metabolite-communication - bio-single-cell-multimodal-integration
skills/bio-single-cell-multimodal-integration - bio-single-cell-perturb-seq
skills/bio-single-cell-perturb-seq - bio-single-cell-preprocessing
skills/bio-single-cell-preprocessing - bio-single-cell-scatac-analysis
skills/bio-single-cell-scatac-analysis - bio-single-cell-splicing
skills/bio-single-cell-splicing - bio-single-cell-trajectory-inference
skills/bio-single-cell-trajectory-inference - bio-small-rna-seq-differential-mirna
skills/bio-small-rna-seq-differential-mirna - bio-small-rna-seq-mirdeep2-analysis
skills/bio-small-rna-seq-mirdeep2-analysis - bio-small-rna-seq-mirge3-analysis
skills/bio-small-rna-seq-mirge3-analysis - bio-small-rna-seq-smrna-preprocessing
skills/bio-small-rna-seq-smrna-preprocessing - bio-small-rna-seq-target-prediction
skills/bio-small-rna-seq-target-prediction - bio-spatial-transcriptomics-image-analysis
skills/bio-spatial-transcriptomics-image-analysis - bio-spatial-transcriptomics-spatial-communication
skills/bio-spatial-transcriptomics-spatial-communication - bio-spatial-transcriptomics-spatial-data-io
skills/bio-spatial-transcriptomics-spatial-data-io - bio-spatial-transcriptomics-spatial-deconvolution
skills/bio-spatial-transcriptomics-spatial-deconvolution - bio-spatial-transcriptomics-spatial-domains
skills/bio-spatial-transcriptomics-spatial-domains - bio-spatial-transcriptomics-spatial-multiomics
skills/bio-spatial-transcriptomics-spatial-multiomics - bio-spatial-transcriptomics-spatial-neighbors
skills/bio-spatial-transcriptomics-spatial-neighbors - bio-spatial-transcriptomics-spatial-preprocessing
skills/bio-spatial-transcriptomics-spatial-preprocessing - bio-spatial-transcriptomics-spatial-proteomics
skills/bio-spatial-transcriptomics-spatial-proteomics - bio-spatial-transcriptomics-spatial-statistics
skills/bio-spatial-transcriptomics-spatial-statistics - bio-spatial-transcriptomics-spatial-visualization
skills/bio-spatial-transcriptomics-spatial-visualization - bio-splicing-pipeline
skills/bio-splicing-pipeline - bio-splicing-qc
skills/bio-splicing-qc - bio-splicing-quantification
skills/bio-splicing-quantification - bio-sra-data
skills/bio-sra-data - bio-structural-biology-alphafold-predictions
skills/bio-structural-biology-alphafold-predictions - bio-structural-biology-modern-structure-prediction
skills/bio-structural-biology-modern-structure-prediction - bio-substructure-search
skills/bio-substructure-search - bio-systems-biology-context-specific-models
skills/bio-systems-biology-context-specific-models - bio-systems-biology-flux-balance-analysis
skills/bio-systems-biology-flux-balance-analysis - bio-systems-biology-gene-essentiality
skills/bio-systems-biology-gene-essentiality - bio-systems-biology-metabolic-reconstruction
skills/bio-systems-biology-metabolic-reconstruction - bio-systems-biology-model-curation
skills/bio-systems-biology-model-curation - bio-tcr-bcr-analysis-immcantation-analysis
skills/bio-tcr-bcr-analysis-immcantation-analysis - bio-tcr-bcr-analysis-mixcr-analysis
skills/bio-tcr-bcr-analysis-mixcr-analysis - bio-tcr-bcr-analysis-repertoire-visualization
skills/bio-tcr-bcr-analysis-repertoire-visualization - bio-tcr-bcr-analysis-scirpy-analysis
skills/bio-tcr-bcr-analysis-scirpy-analysis - bio-tcr-bcr-analysis-vdjtools-analysis
skills/bio-tcr-bcr-analysis-vdjtools-analysis - bio-transcription-translation
skills/bio-transcription-translation - bio-tumor-fraction-estimation
skills/bio-tumor-fraction-estimation - bio-uniprot-access
skills/bio-uniprot-access - bio-variant-annotation
skills/bio-variant-annotation - bio-variant-calling
skills/bio-variant-calling - bio-variant-calling-clinical-interpretation
skills/bio-variant-calling-clinical-interpretation - bio-variant-calling-deepvariant
skills/bio-variant-calling-deepvariant - bio-variant-calling-filtering-best-practices
skills/bio-variant-calling-filtering-best-practices - bio-variant-calling-joint-calling
skills/bio-variant-calling-joint-calling - bio-variant-calling-structural-variant-calling
skills/bio-variant-calling-structural-variant-calling - bio-variant-normalization
skills/bio-variant-normalization - bio-vcf-basics
skills/bio-vcf-basics - bio-vcf-manipulation
skills/bio-vcf-manipulation - bio-vcf-statistics
skills/bio-vcf-statistics - bio-virtual-screening
skills/bio-virtual-screening - bio-workflow-management-cwl-workflows
skills/bio-workflow-management-cwl-workflows - bio-workflow-management-nextflow-pipelines
skills/bio-workflow-management-nextflow-pipelines - bio-workflow-management-snakemake-workflows
skills/bio-workflow-management-snakemake-workflows - bio-workflow-management-wdl-workflows
skills/bio-workflow-management-wdl-workflows - bio-workflows-atacseq-pipeline
skills/bio-workflows-atacseq-pipeline - bio-workflows-biomarker-pipeline
skills/bio-workflows-biomarker-pipeline - bio-workflows-chipseq-pipeline
skills/bio-workflows-chipseq-pipeline - bio-workflows-clip-pipeline
skills/bio-workflows-clip-pipeline - bio-workflows-cnv-pipeline
skills/bio-workflows-cnv-pipeline - bio-workflows-crispr-editing-pipeline
skills/bio-workflows-crispr-editing-pipeline - bio-workflows-crispr-screen-pipeline
skills/bio-workflows-crispr-screen-pipeline - bio-workflows-cytometry-pipeline
skills/bio-workflows-cytometry-pipeline - bio-workflows-expression-to-pathways
skills/bio-workflows-expression-to-pathways - bio-workflows-fastq-to-variants
skills/bio-workflows-fastq-to-variants - bio-workflows-genome-assembly-pipeline
skills/bio-workflows-genome-assembly-pipeline - bio-workflows-gwas-pipeline
skills/bio-workflows-gwas-pipeline - bio-workflows-hic-pipeline
skills/bio-workflows-hic-pipeline - bio-workflows-imc-pipeline
skills/bio-workflows-imc-pipeline - bio-workflows-longread-sv-pipeline
skills/bio-workflows-longread-sv-pipeline - bio-workflows-merip-pipeline
skills/bio-workflows-merip-pipeline - bio-workflows-metabolic-modeling-pipeline
skills/bio-workflows-metabolic-modeling-pipeline - bio-workflows-metabolomics-pipeline
skills/bio-workflows-metabolomics-pipeline - bio-workflows-metagenomics-pipeline
skills/bio-workflows-metagenomics-pipeline - bio-workflows-methylation-pipeline
skills/bio-workflows-methylation-pipeline - bio-workflows-microbiome-pipeline
skills/bio-workflows-microbiome-pipeline - bio-workflows-multi-omics-pipeline
skills/bio-workflows-multi-omics-pipeline - bio-workflows-multiome-pipeline
skills/bio-workflows-multiome-pipeline - bio-workflows-neoantigen-pipeline
skills/bio-workflows-neoantigen-pipeline - bio-workflows-outbreak-pipeline
skills/bio-workflows-outbreak-pipeline - bio-workflows-proteomics-pipeline
skills/bio-workflows-proteomics-pipeline - bio-workflows-riboseq-pipeline
skills/bio-workflows-riboseq-pipeline - bio-workflows-rnaseq-to-de
skills/bio-workflows-rnaseq-to-de - bio-workflows-scrnaseq-pipeline
skills/bio-workflows-scrnaseq-pipeline - bio-workflows-smrna-pipeline
skills/bio-workflows-smrna-pipeline - bio-workflows-somatic-variant-pipeline
skills/bio-workflows-somatic-variant-pipeline - bio-workflows-spatial-pipeline
skills/bio-workflows-spatial-pipeline - bio-workflows-tcr-pipeline
skills/bio-workflows-tcr-pipeline - bio-write-sequences
skills/bio-write-sequences - bioinformatics-singlecell
skills/bioinformatics-singlecell - biokernel
skills/biokernel - biologist-analyst
skills/biologist-analyst - biomaster-workflows
skills/biomaster-workflows - biomcp-server
skills/biomcp-server - biomedical-data-analysis
skills/biomedical-data-analysis - biomedical-search
skills/biomedical-search - biomni
skills/biomni - biomni-general-agent
skills/biomni-general-agent - biomni-research-agent
skills/biomni-research-agent - biopython
skills/biopython - biorxiv-database
skills/biorxiv-database - bioservices
skills/bioservices - boltz
skills/boltz - boltzgen
skills/boltzgen - bone-marrow-ai-agent
skills/bone-marrow-ai-agent - brainstorming
skills/brainstorming - brenda-database
skills/brenda-database - bulk-rna-seq-batch-correction-with-combat
skills/bulk-combat-correction - bulk-rna-seq-differential-expression-with-omicverse
skills/bulk-deg-analysis - bulk-rna-seq-deseq2-analysis-with-omicverse
skills/bulk-deseq2-analysis - string-protein-interaction-analysis-with-omicverse
skills/bulk-stringdb-ppi - bulk-rna-seq-deconvolution-with-bulk2single
skills/bulk-to-single-deconvolution - bulktrajblend-trajectory-interpolation
skills/bulk-trajblend-interpolation - bulk-wgcna-analysis-with-omicverse
skills/bulk-wgcna-analysis - cancer-metabolism-agent
skills/cancer-metabolism-agent - care-coordination
skills/care-coordination - cart-design-optimizer-agent
skills/cart-design-optimizer-agent - cbioportal-database
skills/cbioportal-database - cell-free-expression
skills/cell-free-expression - cellagent-annotation
skills/cellagent-annotation - cellfree-rna-agent
skills/cellfree-rna-agent - cellular-senescence-agent
skills/cellular-senescence-agent - cellxgene-census
skills/cellxgene-census - chai
skills/chai - chatehr-clinician-assistant
skills/chatehr-clinician-assistant - chematagent-drug-discovery
skills/chematagent-drug-discovery - chembl-database
skills/chembl-database - chembl-search
skills/chembl-search - chemcrow-drug-discovery
skills/chemcrow-drug-discovery - chemical-property-lookup
skills/chemical-property-lookup - chemist-analyst
skills/chemist-analyst - chemistry-agent
skills/chemistry-agent - chip-clonal-hematopoiesis-agent
skills/chip-clonal-hematopoiesis-agent - chromosomal-instability-agent
skills/chromosomal-instability-agent - citation-management
skills/citation-management - claims-appeals
skills/claims-appeals - claw-ancestry-pca
skills/claw-ancestry-pca - claw-metagenomics
skills/claw-metagenomics - claw-semantic-sim
skills/claw-semantic-sim - clinical-decision-support
skills/clinical-decision-support - clinical-diagnostic-reasoning
skills/clinical-diagnostic-reasoning - clinical-nlp-extractor
skills/clinical-nlp-extractor - clinical-note-summarization
skills/clinical-note-summarization - clinical-reports
skills/clinical-reports - clinical-trial-protocol-skill
skills/clinical-trial-protocol-skill - clinical-trials-search
skills/clinical-trials-search - clinicaltrials-database
skills/clinicaltrials-database - clinpgx
skills/clinpgx - clinpgx-database
skills/clinpgx-database - clinvar-database
skills/clinvar-database - cnv-caller-agent
skills/cnv-caller-agent - coagulation-thrombosis-agent
skills/coagulation-thrombosis-agent - cobrapy
skills/cobrapy - compbioagent-explorer
skills/compbioagent-explorer - computational-pathology-agent
skills/computational-pathology-agent - convergence-study
skills/convergence-study - cosmic-database
skills/cosmic-database - crisis-detection-intervention-ai
skills/crisis-detection-intervention-ai - crisis-response-protocol
skills/crisis-response-protocol - crispr-guide-design
skills/crispr-guide-design - crispr-offtarget-predictor
skills/crispr-offtarget-predictor - cryoem-ai-drug-design-agent
skills/cryoem-ai-drug-design-agent - ctdna-dynamics-mrd-agent
skills/ctdna-dynamics-mrd-agent - cytokine-storm-analysis-agent
skills/cytokine-storm-analysis-agent - dask
skills/dask - data-stats-analysis
skills/data-stats-analysis - data-transform
skills/data-transform - data-visualization-biomedical
skills/data-visualization-biomedical - data-visualization-expert
skills/data-visualization-expert - data-viz-plots
skills/data-viz-plots - datacommons-client
skills/datacommons-client - datamol
skills/datamol - deep-research
skills/deep-research - deep-research-swarm
skills/deep-research-swarm - deep-visual-proteomics-agent
skills/deep-visual-proteomics-agent - deepchem
skills/deepchem - deeptools
skills/deeptools - depmap
skills/depmap - diffdock
skills/diffdock - differentiation-schemes
skills/differentiation-schemes - digital-twin-clinical-agent
skills/digital-twin-clinical-agent - dispatching-parallel-agents
skills/dispatching-parallel-agents - dnanexus-integration
skills/dnanexus-integration - doc-coauthoring
skills/doc-coauthoring - docx
skills/docx - docx
skills/docx-official - drug-discovery-search
skills/drug-discovery-search - drug-interaction-checker
skills/drug-interaction-checker - drug-labels-search
skills/drug-labels-search - drug-photo
skills/drug-photo - drugbank-database
skills/drugbank-database - drugbank-search
skills/drugbank-search - ehr-fhir-integration
skills/ehr-fhir-integration - emergency-card
skills/emergency-card - ena-database
skills/ena-database - ensembl-database
skills/ensembl-database - epidemiologist-analyst
skills/epidemiologist-analyst - epigenomics-methylgpt-agent
skills/epigenomics-methylgpt-agent - equity-scorer
skills/equity-scorer - esm
skills/esm - etetoolkit
skills/etetoolkit - executing-plans
skills/executing-plans - exosome-ev-analysis-agent
skills/exosome-ev-analysis-agent - exploratory-data-analysis
skills/exploratory-data-analysis - family-health-analyzer
skills/family-health-analyzer - fastq-analysis-pipeline
skills/fastq-analysis - fda-database
skills/fda-database - fhir-developer-skill
skills/fhir-developer-skill - fhir-development
skills/fhir-development - find-skills
skills/find-skills - finishing-a-development-branch
skills/finishing-a-development-branch - fitness-analyzer
skills/fitness-analyzer - flowio
skills/flowio - foldseek
skills/foldseek - galaxy-bridge
skills/galaxy-bridge - gene-database
skills/gene-database - gene-panel-design-agent
skills/gene-panel-design-agent - geniml
skills/geniml - genome-compare
skills/genome-compare - geo-database
skills/geo-database - geopandas
skills/geopandas - gget
skills/gget - ginkgo-cloud-lab
skills/ginkgo-cloud-lab - glycoengineering
skills/glycoengineering - gnomad-database
skills/gnomad-database - goal-analyzer
skills/goal-analyzer - grief-companion
skills/grief-companion - gsea-enrichment-analysis
skills/gsea-enrichment - gtars
skills/gtars - gtex-database
skills/gtex-database - gwas-database
skills/gwas-database - gwas-lookup
skills/gwas-lookup - gwas-prs
skills/gwas-prs - health-trend-analyzer
skills/health-trend-analyzer - hemoglobinopathy-analysis-agent
skills/hemoglobinopathy-analysis-agent - hipaa-compliance
skills/hipaa-compliance - histolab
skills/histolab - hmdb-database
skills/hmdb-database - hrd-analysis-agent
skills/hrd-analysis-agent - hrv-alexithymia-expert
skills/hrv-alexithymia-expert - hypogenic
skills/hypogenic - hypothesis-generation
skills/hypothesis-generation - imaging-data-commons
skills/imaging-data-commons - immune-checkpoint-combination-agent
skills/immune-checkpoint-combination-agent - infographics
skills/infographics - instrument-data-to-allotrope
skills/instrument-data-to-allotrope - interpro-database
skills/interpro-database - ipsae
skills/ipsae - iso-13485-certification
skills/iso-13485-certification - jaspar-database
skills/jaspar-database - jungian-psychologist
skills/jungian-psychologist - kegg-database
skills/kegg-database - knowledge-synthesis
skills/knowledge-synthesis - kragen-knowledge-graph
skills/kragen-knowledge-graph - lab-results
skills/lab-results - labarchive-integration
skills/labarchive-integration - labstep
skills/labstep - lamindb
skills/lamindb - latchbio-integration
skills/latchbio-integration - latex-posters
skills/latex-posters - leads-literature-mining
skills/leads-literature-mining - ligandmpnn
skills/ligandmpnn - linear-solvers
skills/linear-solvers - liquid-biopsy-analytics-agent
skills/liquid-biopsy-analytics-agent - lit-synthesizer
skills/lit-synthesizer - literature-review
skills/literature-review - literature-search
skills/literature-search - lobster-bioinformatics
skills/lobster-bioinformatics - long-read-sequencing-agent
skills/long-read-sequencing-agent - mage-antibody-generator
skills/mage-antibody-generator - markdown-mermaid-writing
skills/markdown-mermaid-writing - markitdown
skills/markitdown - matchms
skills/matchms - matplotlib
skills/matplotlib - mcpmed-bioinformatics-server
skills/mcpmed-bioinformatics-server - medchem
skills/medchem - medea-therapeutic-discovery
skills/medea-therapeutic-discovery - medical-entity-extractor
skills/medical-entity-extractor - medical-imaging-review
skills/medical-imaging-review - medical-research-toolkit
skills/medical-research-toolkit - medical-specialty-briefs
skills/medical-specialty-briefs - medrxiv-search
skills/medrxiv-search - mental-health-analyzer
skills/mental-health-analyzer - mesh-generation
skills/mesh-generation - metabolomics-workbench-database
skills/metabolomics-workbench-database - microbiome-cancer-agent
skills/microbiome-cancer-agent - modern-drug-rehab-computer
skills/modern-drug-rehab-computer - molecular-dynamics
skills/molecular-dynamics - molecular-glue-discovery-agent
skills/molecular-glue-discovery-agent - molecule-evolution-agent
skills/molecule-evolution-agent - molfeat
skills/molfeat - monarch-database
skills/monarch-database - mpn-progression-monitor-agent
skills/mpn-progression-monitor-agent - mpn-research-assistant
skills/mpn-research-assistant - mrd-edge-detection-agent
skills/mrd-edge-detection-agent - multi-ancestry-prs-agent
skills/multi-ancestry-prs-agent - multi-search-engine
skills/multi-search-engine - multimodal-medical-imaging
skills/multimodal-medical-imaging - multimodal-radpath-fusion-agent
skills/multimodal-radpath-fusion-agent - myeloma-mrd-agent
skills/myeloma-mrd-agent - networkx
skills/networkx - neurokit2
skills/neurokit2 - neuropixels-analysis
skills/neuropixels-analysis - nextflow-development
skills/nextflow-development - ngs-analysis
skills/ngs-analysis - nicheformer-spatial-agent
skills/nicheformer-spatial-agent - nk-cell-therapy-agent
skills/nk-cell-therapy-agent - nonlinear-solvers
skills/nonlinear-solvers - numerical-integration
skills/numerical-integration - numerical-stability
skills/numerical-stability - nutrition-analyzer
skills/nutrition-analyzer - occupational-health-analyzer
skills/occupational-health-analyzer - omero-integration
skills/omero-integration - ontology-explorer
skills/ontology-explorer - ontology-mapper
skills/ontology-mapper - ontology-validator
skills/ontology-validator - open-notebook
skills/open-notebook - open-targets-search
skills/open-targets-search - openalex-database
skills/openalex-database - opentargets-database
skills/opentargets-database - opentrons-integration
skills/opentrons-integration - opentrons-protocol-agent
skills/opentrons-protocol-agent - organoid-drug-response-agent
skills/organoid-drug-response-agent - pan-cancer-multiomics-agent
skills/pan-cancer-multiomics-agent - paper-2-web
skills/paper-2-web - parameter-optimization
skills/parameter-optimization - patents-search
skills/patents-search - pathml
skills/pathml - patiently-ai
skills/patiently-ai - pdb
skills/pdb - pdb-database
skills/pdb-database - pdf
skills/pdf - pdf
skills/pdf-anthropic - pdf-processing
skills/pdf-processing - pdf-processing-pro
skills/pdf-processing-pro - pdx-model-analysis-agent
skills/pdx-model-analysis-agent - peer-review
skills/peer-review - performance-profiling
skills/performance-profiling - perplexity-search
skills/perplexity-search - pharmacogenomics-agent
skills/pharmacogenomics-agent - pharmgx-reporter
skills/pharmgx-reporter - phylogenetics
skills/phylogenetics - plotly
skills/plotly - polars
skills/polars - popeve-variant-predictor-agent
skills/popeve-variant-predictor-agent - post-processing
skills/post-processing - pptx
skills/pptx - pptx
skills/pptx-official - pptx-posters
skills/pptx-posters - precision-oncology-agent
skills/precision-oncology-agent - prior-auth-coworker
skills/prior-auth-coworker - prior-auth-review-skill
skills/prior-auth-review-skill - profile-report
skills/profile-report - protac-design-agent
skills/protac-design-agent - protein-design-workflow
skills/protein-design-workflow - protein-qc
skills/protein-qc - protein-structure-prediction
skills/protein-structure-prediction - proteinmpnn
skills/proteinmpnn - protocolsio-integration
skills/protocolsio-integration - prs-net-deep-learning-agent
skills/prs-net-deep-learning-agent - psychologist-analyst
skills/psychologist-analyst - pubchem-database
skills/pubchem-database - pubmed-database
skills/pubmed-database - pubmed-search
skills/pubmed-search - pydeseq2
skills/pydeseq2 - pydicom
skills/pydicom - pyhealth
skills/pyhealth - pylabrobot
skills/pylabrobot - pymc-bayesian-modeling
skills/pymc - pymoo
skills/pymoo - pyopenms
skills/pyopenms - pysam
skills/pysam - pytdc
skills/pytdc - pytorch-lightning
skills/pytorch-lightning - pyzotero
skills/pyzotero - radgpt-radiology-reporter
skills/radgpt-radiology-reporter - radiomics-pathomics-fusion-agent
skills/radiomics-pathomics-fusion-agent - rdkit
skills/rdkit - reactome-database
skills/reactome-database - receiving-code-review
skills/receiving-code-review - recovery-community-moderator
skills/recovery-community-moderator - regulatory-drafter
skills/regulatory-drafter - regulatory-drafting
skills/regulatory-drafting - rehabilitation-analyzer
skills/rehabilitation-analyzer - repro-enforcer
skills/repro-enforcer - requesting-code-review
skills/requesting-code-review - research-grants
skills/research-grants - research-literature
skills/research-literature - research-lookup
skills/research-lookup - rfdiffusion
skills/rfdiffusion - rna-velocity-agent
skills/rna-velocity-agent - scanpy
skills/scanpy - scfoundation-model-agent
skills/scfoundation-model-agent - scientific-brainstorming
skills/scientific-brainstorming - scientific-critical-thinking
skills/scientific-critical-thinking - scientific-manuscript
skills/scientific-manuscript - scientific-problem-selection
skills/scientific-problem-selection - scientific-schematics
skills/scientific-schematics - scientific-slides
skills/scientific-slides - scientific-visualization
skills/scientific-visualization - scientific-writing
skills/scientific-writing - scikit-bio
skills/scikit-bio - scikit-learn
skills/scikit-learn - scikit-survival
skills/scikit-survival - scrna-orchestrator
skills/scrna-orchestrator - scrna-qc
skills/scrna-qc - scvelo
skills/scvelo - scvi-tools
skills/scvi-tools - seaborn
skills/seaborn - search-strategy
skills/search-strategy - seq-wrangler
skills/seq-wrangler - shap
skills/shap - simo-multiomics-integration-agent
skills/simo-multiomics-integration-agent - simpy
skills/simpy - simulation-orchestrator
skills/simulation-orchestrator - simulation-validator
skills/simulation-validator - single-cell-annotation-skills-with-omicverse
skills/single-annotation - single-cell-rna-qc
skills/single-cell-rna-qc - single-cell-cellphonedb-communication-mapping
skills/single-cellphone-db - single-cell-clustering-and-batch-correction-with-omicverse
skills/single-clustering - single-cell-downstream-analysis
skills/single-downstream-analysis - single-cell-multi-omics-integration
skills/single-multiomics - single-cell-preprocessing-with-omicverse
skills/single-preprocessing - single2spatial-spatial-mapping
skills/single-to-spatial-mapping - single-trajectory-analysis
skills/single-trajectory - sleep-analyzer
skills/sleep-analyzer - slurm-job-script-generator
skills/slurm-job-script-generator - solublempnn
skills/solublempnn - spatial-agent
skills/spatial-agent - spatial-epigenomics-agent
skills/spatial-epigenomics-agent - spatial-transcriptomics-agent
skills/spatial-transcriptomics-agent - spatial-transcriptomics-analysis
skills/spatial-transcriptomics-analysis - STAgent
skills/spatial-transcriptomics-analysis/STAgent - SpatialAgent
skills/spatial-transcriptomics-analysis/SpatialAgent - image-analysis
skills/spatial-transcriptomics-analysis/bioSkills/image-analysis - spatial-communication
skills/spatial-transcriptomics-analysis/bioSkills/spatial-communication - spatial-data-io
skills/spatial-transcriptomics-analysis/bioSkills/spatial-data-io - spatial-deconvolution
skills/spatial-transcriptomics-analysis/bioSkills/spatial-deconvolution - spatial-domains
skills/spatial-transcriptomics-analysis/bioSkills/spatial-domains - spatial-multiomics
skills/spatial-transcriptomics-analysis/bioSkills/spatial-multiomics - spatial-neighbors
skills/spatial-transcriptomics-analysis/bioSkills/spatial-neighbors - spatial-preprocessing
skills/spatial-transcriptomics-analysis/bioSkills/spatial-preprocessing - spatial-proteomics
skills/spatial-transcriptomics-analysis/bioSkills/spatial-proteomics - spatial-statistics
skills/spatial-transcriptomics-analysis/bioSkills/spatial-statistics - spatial-visualization
skills/spatial-transcriptomics-analysis/bioSkills/spatial-visualization - spatial-transcriptomics-tutorials-with-omicverse
skills/spatial-tutorials - speech-pathology-ai
skills/speech-pathology-ai - statistical-analysis
skills/statistical-analysis - statsmodels
skills/statsmodels - string-database
skills/string-database - struct-predictor
skills/struct-predictor - subagent-driven-development
skills/subagent-driven-development - systematic-debugging
skills/systematic-debugging - tcell-exhaustion-analysis-agent
skills/tcell-exhaustion-analysis-agent - tcga-bulk-data-preprocessing-with-omicverse
skills/tcga-preprocessing - tcm-constitution-analyzer
skills/tcm-constitution-analyzer - tcr-pmhc-prediction-agent
skills/tcr-pmhc-prediction-agent - tcr-repertoire-analysis-agent
skills/tcr-repertoire-analysis-agent - test-driven-development
skills/test-driven-development - tiledbvcf
skills/tiledbvcf - time-resolved-cryoem-agent
skills/time-resolved-cryoem-agent - time-stepping
skills/time-stepping - timesfm-forecasting
skills/timesfm-forecasting - tme-immune-profiling-agent
skills/tme-immune-profiling-agent - tooluniverse-adverse-event-detection
skills/tooluniverse-adverse-event-detection - tooluniverse-antibody-engineering
skills/tooluniverse-antibody-engineering - tooluniverse-binder-discovery
skills/tooluniverse-binder-discovery - tooluniverse-cancer-variant-interpretation
skills/tooluniverse-cancer-variant-interpretation - tooluniverse-chemical-compound-retrieval
skills/tooluniverse-chemical-compound-retrieval - tooluniverse-chemical-safety
skills/tooluniverse-chemical-safety - tooluniverse-clinical-guidelines
skills/tooluniverse-clinical-guidelines - tooluniverse-clinical-trial-design
skills/tooluniverse-clinical-trial-design - tooluniverse-clinical-trial-matching
skills/tooluniverse-clinical-trial-matching - tooluniverse-crispr-screen-analysis
skills/tooluniverse-crispr-screen-analysis - tooluniverse-disease-research
skills/tooluniverse-disease-research - tooluniverse-drug-drug-interaction
skills/tooluniverse-drug-drug-interaction - tooluniverse-drug-repurposing
skills/tooluniverse-drug-repurposing - tooluniverse-drug-research
skills/tooluniverse-drug-research - tooluniverse-drug-target-validation
skills/tooluniverse-drug-target-validation - tooluniverse-epigenomics
skills/tooluniverse-epigenomics - tooluniverse-expression-data-retrieval
skills/tooluniverse-expression-data-retrieval - tooluniverse-gene-enrichment
skills/tooluniverse-gene-enrichment - tooluniverse-gwas-drug-discovery
skills/tooluniverse-gwas-drug-discovery - tooluniverse-gwas-finemapping
skills/tooluniverse-gwas-finemapping - tooluniverse-gwas-snp-interpretation
skills/tooluniverse-gwas-snp-interpretation - tooluniverse-gwas-study-explorer
skills/tooluniverse-gwas-study-explorer - tooluniverse-gwas-trait-to-gene
skills/tooluniverse-gwas-trait-to-gene - tooluniverse-image-analysis
skills/tooluniverse-image-analysis - tooluniverse-immune-repertoire-analysis
skills/tooluniverse-immune-repertoire-analysis - tooluniverse-immunotherapy-response-prediction
skills/tooluniverse-immunotherapy-response-prediction - tooluniverse-infectious-disease
skills/tooluniverse-infectious-disease - tooluniverse-literature-deep-research
skills/tooluniverse-literature-deep-research - tooluniverse-metabolomics
skills/tooluniverse-metabolomics - tooluniverse-metabolomics-analysis
skills/tooluniverse-metabolomics-analysis - tooluniverse-multi-omics-integration
skills/tooluniverse-multi-omics-integration - tooluniverse-multiomic-disease-characterization
skills/tooluniverse-multiomic-disease-characterization - tooluniverse-network-pharmacology
skills/tooluniverse-network-pharmacology - tooluniverse-pharmacovigilance
skills/tooluniverse-pharmacovigilance - tooluniverse-phylogenetics
skills/tooluniverse-phylogenetics - tooluniverse-polygenic-risk-score
skills/tooluniverse-polygenic-risk-score - tooluniverse-precision-medicine-stratification
skills/tooluniverse-precision-medicine-stratification - tooluniverse-precision-oncology
skills/tooluniverse-precision-oncology - protein-interaction-network-analysis
skills/tooluniverse-protein-interactions - tooluniverse-protein-structure-retrieval
skills/tooluniverse-protein-structure-retrieval - tooluniverse-protein-therapeutic-design
skills/tooluniverse-protein-therapeutic-design - tooluniverse-proteomics-analysis
skills/tooluniverse-proteomics-analysis - tooluniverse-rare-disease-diagnosis
skills/tooluniverse-rare-disease-diagnosis - tooluniverse-rnaseq-deseq2
skills/tooluniverse-rnaseq-deseq2 - tooluniverse-sequence-retrieval
skills/tooluniverse-sequence-retrieval - tooluniverse-single-cell
skills/tooluniverse-single-cell - tooluniverse-spatial-omics-analysis
skills/tooluniverse-spatial-omics-analysis - tooluniverse-spatial-transcriptomics
skills/tooluniverse-spatial-transcriptomics - tooluniverse-statistical-modeling
skills/tooluniverse-statistical-modeling - tooluniverse-structural-variant-analysis
skills/tooluniverse-structural-variant-analysis - tooluniverse-systems-biology
skills/tooluniverse-systems-biology - tooluniverse-target-research
skills/tooluniverse-target-research - tooluniverse-variant-analysis
skills/tooluniverse-variant-analysis - tooluniverse-variant-interpretation
skills/tooluniverse-variant-interpretation - torch-geometric
skills/torch-geometric - torch-geometric
skills/torch_geometric - torchdrug
skills/torchdrug - tpd-ternary-complex-agent
skills/tpd-ternary-complex-agent - transformers
skills/transformers - travel-health-analyzer
skills/travel-health-analyzer - treatment-plans
skills/treatment-plans - trial-eligibility-agent
skills/trial-eligibility-agent - trialgpt-matching
skills/trialgpt-matching - tumor-clonal-evolution-agent
skills/tumor-clonal-evolution-agent - tumor-heterogeneity-agent
skills/tumor-heterogeneity-agent - tumor-mutational-burden-agent
skills/tumor-mutational-burden-agent - ukb-navigator
skills/ukb-navigator - umap-learn
skills/umap-learn - uniprot-database
skills/uniprot-database - universal-single-cell-annotator
skills/universal-single-cell-annotator - using-git-worktrees
skills/using-git-worktrees - using-superpowers
skills/using-superpowers - usmle
skills/usmle - uspto-database
skills/uspto-database - vaex
skills/vaex - varcadd-pathogenicity
skills/varcadd-pathogenicity - variant-interpretation-acmg
skills/variant-interpretation-acmg - clinical-interpretation
skills/variant-interpretation-acmg/bioSkills/clinical-interpretation - consensus-sequences
skills/variant-interpretation-acmg/bioSkills/consensus-sequences - deepvariant
skills/variant-interpretation-acmg/bioSkills/deepvariant - filtering-best-practices
skills/variant-interpretation-acmg/bioSkills/filtering-best-practices - gatk-variant-calling
skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling - joint-calling
skills/variant-interpretation-acmg/bioSkills/joint-calling - structural-variant-calling
skills/variant-interpretation-acmg/bioSkills/structural-variant-calling - variant-annotation
skills/variant-interpretation-acmg/bioSkills/variant-annotation - variant-calling
skills/variant-interpretation-acmg/bioSkills/variant-calling - variant-normalization
skills/variant-interpretation-acmg/bioSkills/variant-normalization - vcf-basics
skills/variant-interpretation-acmg/bioSkills/vcf-basics - vcf-manipulation
skills/variant-interpretation-acmg/bioSkills/vcf-manipulation - vcf-statistics
skills/variant-interpretation-acmg/bioSkills/vcf-statistics - varCADD
skills/variant-interpretation-acmg/varCADD - vcf-annotator
skills/vcf-annotator - verification-before-completion
skills/verification-before-completion - virtual-lab-agent
skills/virtual-lab-agent - wearable-analysis-agent
skills/wearable-analysis-agent - weightloss-analyzer
skills/weightloss-analyzer - wellally-tech
skills/wellally-tech - wikipedia-search
skills/wikipedia-search - writing-plans
skills/writing-plans - writing-skills
skills/writing-skills - xlsx
skills/xlsx - xlsx
skills/xlsx-official - zarr-python
skills/zarr-python - zinc-database
skills/zinc-database
How it works
When your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,518 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Core Capabilities
- AAV Serotype Tropism
- Workflow
- Example Usage
- Expression Cassette Components
- Capsid Engineering Strategies
- Immunogenicity Considerations
- AI/ML Components
- Manufacturing Considerations
- Prerequisites
- Related Skills
- Regulatory Considerations
- Author
Files
SKILL.mdcore5,894 bytesSKILL.mdcore5,894 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubadaptyv
When your agent uses it
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
What it loads into context
Frontmatter
113 tokensAlways available to the agent
SKILL.md
806 tokensWhen the skill is activated
Reference documents
13,585 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Quick Start
- Available Experiment Types
- Protein Sequence Optimization
- API Reference
- Examples
- Important Notes
Files
SKILL.mdcore3,742 bytesSKILL.mdcore3,742 bytesSKILL.mdcore3,742 bytesSKILL.mdcore3,742 bytesreference/api_reference.mddoc6,665 bytesreference/examples.mddoc23,091 bytesreference/experiments.mddoc9,947 bytesreference/protein_optimization.mddoc17,861 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubadhd-daily-planner
When your agent uses it
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that actually work for neurodivergent minds.
What it loads into context
Frontmatter
160 tokensAlways available to the agent
SKILL.md
2,207 tokensWhen the skill is activated
Reference documents
5,279 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Philosophy
- The ADHD Planning Paradox
- Decision Tree
- Time Blindness Strategies
- Daily Planning Template
- Executive Function Support
- The Doom Box Strategy
- Anti-Patterns (Things That Don't Work)
- Good Days vs Bad Days
- Tools That Actually Help
- The Shutdown Ritual (5 min)
- Integration with Other Skills
- Remember
Files
SKILL.mdcore10,373 bytesreferences/dopamine-menu.mddoc9,859 bytesreferences/executive-function-toolkit.mddoc15,125 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubaeon
When your agent uses it
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
What it loads into context
Frontmatter
97 tokensAlways available to the agent
SKILL.md
2,509 tokensWhen the skill is activated
Reference documents
15,062 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Installation
- Core Capabilities
- Feature Extraction and Transformations
- Distance Metrics
- Deep Learning Networks
- Datasets and Benchmarking
- Common Workflows
- Best Practices
- Reference Documentation
- Additional Resources
Files
SKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesSKILL.mdcore10,587 bytesreferences/anomaly_detection.mddoc4,912 bytesreferences/classification.mddoc5,377 bytesreferences/clustering.mddoc3,744 bytesreferences/datasets_benchmarking.mddoc8,871 bytesreferences/distances.mddoc6,409 bytesreferences/forecasting.mddoc3,879 bytesreferences/networks.mddoc7,849 bytesreferences/regression.mddoc3,960 bytesreferences/segmentation.mddoc4,924 bytesreferences/similarity_search.mddoc5,242 bytesreferences/transformations.mddoc7,725 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubagent-browser
When your agent uses it
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test web pages. Use whenever a browser would be useful, not just when the user explicitly asks.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,104 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Quick start
- Core workflow
- Commands
- Example: Form submission
- Example: Data extraction
Files
SKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytesSKILL.mdcore4,828 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
497 tokensWhen the skill is activated
Reference documents
1,335 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- At-a-Glance
- Inputs
- Outputs
- Workflow
- Guardrails
- References
Scripts executed separately
agent_d.py
Files
README.mddoc2,685 bytesSKILL.mdcore2,072 bytesSKILL.mdcore2,072 bytesagent_d.pyruns3,807 bytesprompt.mddoc2,524 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubai-analyzer
When your agent uses it
AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
2,121 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- 核心功能
- 使用说明
- 数据源
- 算法说明
- 安全与合规
- 相关命令
- 技术实现
Files
SKILL.mdcore7,394 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubalphafold
When your agent uses it
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
What it loads into context
Frontmatter
145 tokensAlways available to the agent
SKILL.md
1,408 tokensWhen the skill is activated
Reference documents
965 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Prerequisites
- How to run
- Key parameters
- Output format
- Sample output
- Decision tree
- Typical performance
- Verify
- Troubleshooting
Files
SKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesSKILL.mdcore4,804 bytesreferences/multimer.mddoc3,545 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubalphafold-database
When your agent uses it
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
3,898 tokensWhen the skill is activated
Reference documents
3,884 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Core Capabilities
- Installation and Setup
- Common Use Cases
- Key Concepts
- Confidence Interpretation Guidelines
- Resources
- Important Notes
- Additional Resources
Files
SKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesSKILL.mdcore15,806 bytesreferences/api_reference.mddoc12,557 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubanndata
When your agent uses it
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,745 tokensWhen the skill is activated
Reference documents
14,415 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Installation
- Quick Start
- Core Capabilities
- Integration with Scverse Ecosystem
- Common Workflows
- Troubleshooting
- Additional Resources
Files
SKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesSKILL.mdcore10,185 bytesreferences/best_practices.mddoc12,106 bytesreferences/concatenation.mddoc10,504 bytesreferences/data_structure.mddoc8,744 bytesreferences/io_operations.mddoc9,456 bytesreferences/manipulation.mddoc11,866 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
682 tokensWhen the skill is activated
Reference documents
374 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Core Capabilities
- Workflow
- Example Usage
Files
MAGE_Agent/README.mddoc1,472 bytesSKILL.mdcore2,759 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
424 tokensWhen the skill is activated
Reference documents
1,336 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Workflow
- Guardrails
- References
Scripts executed separately
repo/Data cleaning/CoVAbDab/covabdab_gen_curation_allBinders_allVariants_v2_24-03-12.ipynbrepo/Data cleaning/Other_notebooks/10618/10618_antigen_alignment_v1_24-03-06.ipynbrepo/Data cleaning/Other_notebooks/10618/AA_10618_LLM-clean_24-03-06.ipynbrepo/Data cleaning/Other_notebooks/SAbDab/SAbDab_final_clean_v1_24-03-04.ipynbrepo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynbrepo/Data cleaning/Other_notebooks/atlas_antigen_alignment_v1_24-03-04.ipynbrepo/Data cleaning/Other_notebooks/published_LIBRA-seq_concatenation_24-05-31.ipynbrepo/Data cleaning/Other_notebooks/signalP/detagging_nonSAbDab_24-03-12.ipynbrepo/Data cleaning/PlAbDab/ebola_Bornholdt_24-03-07.ipynbrepo/Data cleaning/PlAbDab/ebola_EhrHardt_24-01-03.ipynbrepo/Data cleaning/PlAbDab/gilman_RSV_24-01-04.ipynbrepo/Data cleaning/PlAbDab/hcv_24-01-03.ipynbrepo/Data cleaning/crowe_ebola/crowe_ebola_processing_24-03-07.ipynbrepo/Data cleaning/denovo_absci/denovo_trastuzamab_24-02-29.ipynbrepo/Data cleaning/final_processing/detagging_script_24-03-04.ipynbrepo/Data cleaning/final_processing/final_concat_v2_24-03-12.ipynbrepo/Data cleaning/flu_LLM_paper/wang_preprint_flu_cleaning_24-01-03.ipynbrepo/Data cleaning/zurbuchen/zurbuchen_data_23-03-08.ipynbrepo/Fine_tuning/full_model_training_24-03-12.pyrepo/Fine_tuning/selected_abs_Figure_2-3_24-06-10.ipynbrepo/Output_analysis/figure1_plots_24-06-10.ipynbrepo/Output_analysis/output_filtering_annotation.ipynbrepo/Output_analysis/selected_abs_Figure_2-3_24-06-10.ipynbrepo/Output_analysis/selection_pipeline_24-03-16.ipynbrepo/generate_antibodies.py
Files
README.mddoc1,657 bytesSKILL.mdcore1,749 bytesSKILL.mdcore1,749 bytesrepo/Data cleaning/ASAb_database_metadata_v2_24-03-12.xlsxasset31,843 bytesrepo/Data cleaning/CoVAbDab/NTD_SA.npyasset563,696 bytesrepo/Data cleaning/CoVAbDab/RBD_SA.npyasset337,632 bytesrepo/Data cleaning/CoVAbDab/covabdab_gen_curation_allBinders_allVariants_v2_24-03-12.ipynbruns42,069 bytesrepo/Data cleaning/Other_notebooks/10618/10618_antigen_alignment_v1_24-03-06.ipynbruns27,420 bytesrepo/Data cleaning/Other_notebooks/10618/AA_10618_LLM-clean_24-03-06.ipynbruns36,492 bytesrepo/Data cleaning/Other_notebooks/SAbDab/SAbDab_final_clean_v1_24-03-04.ipynbruns17,354 bytesrepo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynbruns239,056 bytesrepo/Data cleaning/Other_notebooks/atlas_antigen_alignment_v1_24-03-04.ipynbruns11,110 bytesrepo/Data cleaning/Other_notebooks/published_LIBRA-seq_concatenation_24-05-31.ipynbruns23,302 bytesrepo/Data cleaning/Other_notebooks/signalP/detagging_nonSAbDab_24-03-12.ipynbruns26,819 bytesrepo/Data cleaning/Other_notebooks/signalP/signalP_summary_output_24-03-12.txtdoc6,370 bytesrepo/Data cleaning/PlAbDab/ebola_Bornholdt_24-03-07.ipynbruns7,323 bytesrepo/Data cleaning/PlAbDab/ebola_EhrHardt_24-01-03.ipynbruns67,113 bytesrepo/Data cleaning/PlAbDab/gilman_RSV_24-01-04.ipynbruns9,146 bytesrepo/Data cleaning/PlAbDab/hcv_24-01-03.ipynbruns3,226 bytesrepo/Data cleaning/crowe_ebola/crowe_ebola_processing_24-03-07.ipynbruns7,240 bytesrepo/Data cleaning/denovo_absci/denovo_trastuzamab_24-02-29.ipynbruns7,988 bytesrepo/Data cleaning/final_processing/detagging_script_24-03-04.ipynbruns195,802 bytesrepo/Data cleaning/final_processing/final_concat_v2_24-03-12.ipynbruns6,550 bytesrepo/Data cleaning/flu_LLM_paper/wang_preprint_flu_cleaning_24-01-03.ipynbruns39,988 bytesrepo/Data cleaning/zurbuchen/zurbuchen_data_23-03-08.ipynbruns57,376 bytesrepo/Fine_tuning/example_training_data.csvasset759,041 bytesrepo/Fine_tuning/full_model_training_24-03-12.pyruns8,162 bytesrepo/Fine_tuning/selected_abs_Figure_2-3_24-06-10.ipynbruns217,128 bytesrepo/LICENSEasset11,357 bytesrepo/MAGE_annotated_training_data.zipasset2,236,165 bytesrepo/Output_analysis/RBD_1K_sequences_24-03-16.csvasset1,627,358 bytesrepo/Output_analysis/figure1_plots_24-06-10.ipynbruns332,263 bytesrepo/Output_analysis/output_filtering_annotation.ipynbruns14,902 bytesrepo/Output_analysis/selected_abs_Figure_2-3_24-06-10.ipynbruns216,935 bytesrepo/Output_analysis/selected_abs_for_testing.csvasset27,396 bytesrepo/Output_analysis/selection_pipeline_24-03-16.ipynbruns11,411 bytesrepo/README.mddoc3,514 bytesrepo/generate_antibodies.pyruns2,987 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubarboreto
When your agent uses it
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
1,623 tokensWhen the skill is activated
Reference documents
3,496 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- Quick Start
- Core Capabilities
- Installation
- Common Use Cases
- Output Interpretation
- Integration with pySCENIC
- Reproducibility
- Troubleshooting
Scripts executed separately
scripts/basic_grn_inference.py
Files
SKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesSKILL.mdcore6,857 bytesreferences/algorithms.mddoc4,361 bytesreferences/basic_inference.mddoc3,811 bytesreferences/distributed_computing.mddoc6,734 bytesscripts/basic_grn_inference.pyruns2,969 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,920 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Core Capabilities
- Armoring Strategies
- Construct Architecture Options
- Workflow
- Example Usage
- Output Components
- IL-12 Armoring Details
- IL-18 Armoring Details
- IL-15 Armoring Details
- AI/ML Components
- Safety Considerations
- Clinical Trials (2025-2026)
- Prerequisites
- Related Skills
- Manufacturing Considerations
- Special Considerations
- Efficacy Enhancement Mechanisms
- Author
Files
SKILL.mdcore7,901 bytesSKILL.mdcore7,901 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubarxiv-search
When your agent uses it
Search arXiv physics, math, and computer science preprints using natural language queries. Powered by Valyu semantic search.
What it loads into context
Frontmatter
73 tokensAlways available to the agent
SKILL.md
1,368 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Skill is Powerful
- Requirements
- CRITICAL: Script Path Resolution
- API Key Setup Flow
- When to Use This Skill
- Output Format
- Processing Results
- Common Use Cases
- Error Handling
- API Endpoint
- Architecture
- Adding to Your Project
Scripts executed separately
scripts/searchscripts/search.mjs
Files
SKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesSKILL.mdcore5,485 bytesscripts/searchruns387 bytesscripts/search.mjsruns3,646 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
759 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Core Capabilities
- Workflow
- Example Usage
Files
SKILL.mdcore3,050 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
499 tokensWhen the skill is activated
Reference documents
1,101 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Core Capabilities
- Workflow
- Example Usage
Scripts executed separately
bayesian_optimization.pystats_essentials.py
Files
README.mddoc1,361 bytesSKILL.mdcore1,971 bytesSKILL.mdcore1,971 bytesTUTORIAL_SELF_DRIVING_LAB_OPTIMIZER.mddoc3,007 bytesbayesian_optimization.pyruns6,695 bytesstats_essentials.pyruns2,019 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbenchling-integration
When your agent uses it
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
What it loads into context
Frontmatter
49 tokensAlways available to the agent
SKILL.md
2,845 tokensWhen the skill is activated
Reference documents
10,851 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Core Capabilities
- Best Practices
- Resources
- Common Use Cases
- Additional Resources
Files
SKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesSKILL.mdcore12,950 bytesreferences/api_endpoints.mddoc14,226 bytesreferences/authentication.mddoc10,124 bytesreferences/sdk_reference.mddoc17,624 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbgpt-paper-search
When your agent uses it
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.
What it loads into context
Frontmatter
113 tokensAlways available to the agent
SKILL.md
638 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Setup
- Usage
- Pricing
- Complementary Skills
Files
SKILL.mdcore2,872 bytesSKILL.mdcore2,872 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbindcraft
When your agent uses it
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
What it loads into context
Frontmatter
172 tokensAlways available to the agent
SKILL.md
1,519 tokensWhen the skill is activated
Reference documents
1,345 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Prerequisites
- How to run
- Key parameters
- Protocols
- Output format
- Sample output
- Decision tree
- Typical performance
- Verify
- Troubleshooting
Files
SKILL.mdcore5,225 bytesSKILL.mdcore5,225 bytesSKILL.mdcore5,225 bytesSKILL.mdcore5,225 bytesSKILL.mdcore5,225 bytesreferences/protocols.mddoc2,422 bytesreferences/troubleshooting.mddoc2,394 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbinder-design
When your agent uses it
Guidance for choosing the right protein binder design tool. Use this skill when: (1) Deciding between BoltzGen, BindCraft, or RFdiffusion, (2) Planning a binder design campaign, (3) Understanding trade-offs between different approaches, (4) Selecting tools for specific target types. For specific tool parameters, use the individual tool skills (boltzgen, bindcraft, rfdiffusion, etc.).
What it loads into context
Frontmatter
123 tokensAlways available to the agent
SKILL.md
1,229 tokensWhen the skill is activated
Reference documents
946 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Decision tree
- Tool comparison
- Recommended Pipeline: BoltzGen → Chai → QC
- Number of designs
- Common mistakes
- Timeline guide
Files
SKILL.mdcore4,626 bytesSKILL.mdcore4,626 bytesSKILL.mdcore4,626 bytesSKILL.mdcore4,626 bytesSKILL.mdcore4,626 bytesreferences/tool-comparison.mddoc3,691 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbinding-characterization
When your agent uses it
Guidance for SPR and BLI binding characterization experiments. Use when: (1) Planning binding kinetics experiments, (2) Troubleshooting poor/no binding signal, (3) Interpreting kinetic data artifacts, (4) Choosing between SPR vs BLI platforms.
What it loads into context
Frontmatter
85 tokensAlways available to the agent
SKILL.md
2,281 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- SPR vs BLI Decision Matrix
- Key differences
- Troubleshooting: Why BLI works but SPR doesn't
- Mass transport considerations
- Nonspecific binding mitigation
- Regeneration conditions
- Common artifacts and solutions
- Kinetic data quality checklist
- References
Files
SKILL.mdcore8,840 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbindingdb-database
When your agent uses it
Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.
What it loads into context
Frontmatter
93 tokensAlways available to the agent
SKILL.md
3,135 tokensWhen the skill is activated
Reference documents
1,682 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- When to Use This Skill
- Core Capabilities
- Query Workflows
- Key Data Fields
- Affinity Interpretation
- Best Practices
- Additional Resources
Files
SKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesSKILL.mdcore12,069 bytesreferences/affinity_queries.mddoc5,835 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-admet-prediction
When your agent uses it
Predicts ADMET properties using ADMETlab 3.0 API or DeepChem models. Estimates bioavailability, CYP inhibition, hERG liability, and 119 toxicity endpoints with uncertainty quantification. Filters for PAINS and other structural alerts. Use when filtering compounds for drug-likeness or prioritizing leads by predicted safety.
What it loads into context
Frontmatter
88 tokensAlways available to the agent
SKILL.md
1,773 tokensWhen the skill is activated
Reference documents
423 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- ADMETlab 3.0 API
- Key ADMET Endpoints
- DeepChem Models
- PAINS Filter
- Lipinski and Beyond
- Prioritization Pipeline
- Related Skills
Scripts executed separately
examples/predict_admet.py
Files
SKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesSKILL.mdcore7,031 bytesexamples/predict_admet.pyruns4,334 bytesusage-guide.mddoc1,774 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,342 tokensWhen the skill is activated
Reference documents
1,910 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Quick Summary Commands
- samtools flagstat
- samtools idxstats
- samtools stats
- samtools depth
- samtools coverage
- pysam Python Alternative
- Quick Reference
- Common Metrics
- Related Skills
Scripts executed separately
examples/qc_report.py
Files
SKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesSKILL.mdcore8,189 bytesexamples/qc_report.pyruns2,332 bytesusage-guide.mddoc7,008 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,400 tokensWhen the skill is activated
Reference documents
2,161 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Filter Flags
- Common FLAG Values
- Filter by FLAG
- Filter by Mapping Quality
- Filter by Region
- Combined Filters
- Subsample Reads
- pysam Python Alternative
- Quick Reference
- Common Filter Combinations
- Related Skills
Scripts executed separately
examples/filter_bam.py
Files
SKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesSKILL.mdcore8,086 bytesexamples/filter_bam.pyruns2,743 bytesusage-guide.mddoc7,799 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,746 tokensWhen the skill is activated
Reference documents
1,470 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Index Types
- samtools index
- Index Requirements
- Using Indices for Region Access
- pysam Python Alternative
- Index File Locations
- idxstats - Index Statistics
- FASTA Index (faidx)
- Quick Reference
- Common Errors
- Related Skills
Scripts executed separately
examples/fetch_regions.py
Files
SKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesSKILL.mdcore6,075 bytesexamples/fetch_regions.pyruns1,534 bytesusage-guide.mddoc5,359 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-alignment-io
When your agent uses it
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
What it loads into context
Frontmatter
79 tokensAlways available to the agent
SKILL.md
2,406 tokensWhen the skill is activated
Reference documents
519 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Supported Formats
- Reading Alignments
- Writing Alignments
- Format Conversion
- Accessing Alignment Data
- Working with Alignment Objects
- Creating Alignments Programmatically
- Format-Specific Notes
- Batch Processing Multiple Files
- Alternative: Bio.Align Module I/O
- Quick Reference: Common Operations
- Common Errors
- Related Skills
Scripts executed separately
examples/batch_convert.pyexamples/convert_formats.pyexamples/read_alignment.pyexamples/slice_alignment.py
Files
SKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesSKILL.mdcore9,687 bytesexamples/batch_convert.pyruns645 bytesexamples/convert_formats.pyruns615 bytesexamples/read_alignment.pyruns499 bytesexamples/sample_alignment.alnasset237 bytesexamples/slice_alignment.pyruns686 bytesusage-guide.mddoc2,211 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-alignment-msa-parsing
When your agent uses it
Parse and analyze multiple sequence alignments using Biopython. Extract sequences, identify conserved regions, analyze gaps, work with annotations, and manipulate alignment data for downstream analysis. Use when parsing or manipulating multiple sequence alignments.
What it loads into context
Frontmatter
67 tokensAlways available to the agent
SKILL.md
2,573 tokensWhen the skill is activated
Reference documents
450 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Loading Alignments
- Extracting Sequence Information
- Column-wise Analysis
- Gap Analysis
- Consensus Sequence
- Extracting Regions
- Sequence Filtering
- Working with Annotations
- Position Mapping
- Quick Reference: Common Operations
- Common Errors
- Related Skills
Scripts executed separately
examples/analyze_alignment.pyexamples/clean_alignment.pyexamples/consensus_sequence.pyexamples/find_conserved.pyexamples/gap_analysis.py
Files
SKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesSKILL.mdcore11,504 bytesexamples/analyze_alignment.pyruns675 bytesexamples/clean_alignment.pyruns2,035 bytesexamples/consensus_sequence.pyruns1,447 bytesexamples/find_conserved.pyruns1,122 bytesexamples/gap_analysis.pyruns778 bytesusage-guide.mddoc2,153 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-alignment-msa-statistics
When your agent uses it
Calculate alignment statistics including sequence identity, conservation scores, substitution matrices, and similarity metrics. Use when comparing alignment quality, measuring sequence divergence, and analyzing evolutionary patterns.
What it loads into context
Frontmatter
54 tokensAlways available to the agent
SKILL.md
3,044 tokensWhen the skill is activated
Reference documents
508 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Pairwise Identity
- Conservation Score
- Substitution Counts
- Information Content
- Gap Statistics
- Alignment Quality Metrics
- Position-Specific Score Matrix (PSSM)
- Note on Bio.Align.AlignInfo
- Quick Reference: Metrics
- Common Errors
- Related Skills
Scripts executed separately
examples/conservation_profile.pyexamples/entropy_analysis.pyexamples/gap_statistics.pyexamples/identity_matrix.pyexamples/substitution_counts.py
Files
SKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesSKILL.mdcore12,990 bytesexamples/conservation_profile.pyruns1,255 bytesexamples/entropy_analysis.pyruns1,462 bytesexamples/gap_statistics.pyruns1,642 bytesexamples/identity_matrix.pyruns1,100 bytesexamples/substitution_counts.pyruns1,390 bytesusage-guide.mddoc2,563 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-alignment-pairwise
When your agent uses it
Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. Use when comparing two sequences, finding optimal alignments, scoring similarity, and identifying local or global matches between DNA, RNA, or protein sequences.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
2,258 tokensWhen the skill is activated
Reference documents
467 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Core Concepts
- Creating an Aligner
- Performing Alignments
- Alignment Output Format
- Accessing Alignment Data
- Alignment Counts (Identities, Mismatches, Gaps)
- Common Scoring Configurations
- Available Substitution Matrices
- Working with SeqRecord Objects
- Iterating Over Multiple Alignments
- Substitution Matrix from Alignment
- Export Alignment to Different Formats
- Quick Reference: Scoring Parameters
- Common Errors
- Decision Tree: Choosing Alignment Mode
- Related Skills
Scripts executed separately
examples/alignment_from_file.pyexamples/global_alignment.pyexamples/local_alignment.pyexamples/protein_alignment.py
Files
SKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesSKILL.mdcore9,470 bytesexamples/alignment_from_file.pyruns662 bytesexamples/global_alignment.pyruns2,045 bytesexamples/local_alignment.pyruns723 bytesexamples/protein_alignment.pyruns692 bytesusage-guide.mddoc2,129 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,088 tokensWhen the skill is activated
Reference documents
1,361 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Sort Orders
- samtools sort
- samtools collate
- Check Sort Order
- pysam Python Alternative
- samtools merge
- Common Workflows
- Performance Tips
- Quick Reference
- Common Errors
- Related Skills
Scripts executed separately
examples/sort_pipeline.sh
Files
SKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesSKILL.mdcore7,158 bytesexamples/sort_pipeline.shruns712 bytesusage-guide.mddoc4,935 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,770 tokensWhen the skill is activated
Reference documents
2,280 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Insert Size Distribution
- Proper Pairing Rate
- GC Bias
- Strand Balance
- Mapping Quality Distribution
- Chromosome Coverage Balance
- Mismatch Rate
- Comprehensive Validation Script
- Python Validation Module
- Quality Thresholds Summary
- Related Skills
Scripts executed separately
examples/validate_alignment.pyexamples/validate_alignment.sh
Files
SKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesSKILL.mdcore9,617 bytesexamples/validate_alignment.pyruns3,183 bytesexamples/validate_alignment.shruns1,112 bytesusage-guide.mddoc9,255 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-atac-peak-calling
When your agent uses it
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
What it loads into context
Frontmatter
73 tokensAlways available to the agent
SKILL.md
1,775 tokensWhen the skill is activated
Reference documents
580 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic MACS3 for ATAC-seq
- Key ATAC-seq Parameters
- Why These Parameters?
- Paired-End vs Single-End
- Call Peaks on NFR Only
- Broad Peaks (Optional)
- Batch Processing
- Output Files
- narrowPeak Format
- Convert to BigWig
- Merge Replicates
- IDR for Replicate Consistency
- Related Skills
Scripts executed separately
examples/call_atac_peaks.sh
Files
SKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesSKILL.mdcore6,192 bytesexamples/call_atac_peaks.shruns728 bytesusage-guide.mddoc2,349 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-atac-qc
When your agent uses it
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library complexity. Use when assessing ATAC-seq library quality before or after peak calling to identify problematic samples.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
2,553 tokensWhen the skill is activated
Reference documents
600 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Fragment Size Distribution
- TSS Enrichment Score
- Calculate TSS Enrichment Score
- FRiP (Fraction of Reads in Peaks)
- Mitochondrial Read Fraction
- Library Complexity (NRF, PBC1, PBC2)
- deepTools QC
- ATACseqQC (R)
- Comprehensive QC Report
- QC Thresholds
- Related Skills
Scripts executed separately
examples/atac_qc_metrics.R
Files
SKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesSKILL.mdcore8,921 bytesexamples/atac_qc_metrics.Rruns1,733 bytesusage-guide.mddoc2,436 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-differential-accessibility
When your agent uses it
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq experiments.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
2,058 tokensWhen the skill is activated
Reference documents
678 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- DiffBind Workflow
- DiffBind with Consensus Peaks
- DiffBind Visualizations
- Using DESeq2 Directly
- Count Reads in Peaks
- Python Alternative
- Annotate Differential Peaks
- Filter Results
- Multi-factor Designs
- Related Skills
Scripts executed separately
examples/diff_accessibility.R
Files
SKILL.mdcore7,367 bytesSKILL.mdcore7,367 bytesSKILL.mdcore7,367 bytesexamples/diff_accessibility.Rruns1,213 bytesusage-guide.mddoc2,740 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-footprinting
When your agent uses it
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identifying TF occupancy patterns within accessible regions, as TF binding protects DNA from Tn5 cutting.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,953 tokensWhen the skill is activated
Reference documents
537 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- TOBIAS Workflow
- TOBIAS Differential Footprinting
- Download JASPAR Motifs
- Prepare Input Files
- HINT-ATAC Alternative
- PIQ Footprinting
- Aggregate Footprint Plots
- Python: Custom Footprint Analysis
- Scan for Motifs
- Interpret Footprint Depth
- Quality Considerations
- Differential TF Activity
- TOBIAS Output Files
- Related Skills
Scripts executed separately
examples/run_tobias.sh
Files
SKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesSKILL.mdcore7,276 bytesexamples/run_tobias.shruns1,067 bytesusage-guide.mddoc2,312 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-motif-deviation
When your agent uses it
Analyze transcription factor motif accessibility variability using chromVAR. Use when identifying which TF motifs show variable accessibility across samples or conditions in ATAC-seq data.
What it loads into context
Frontmatter
54 tokensAlways available to the agent
SKILL.md
2,365 tokensWhen the skill is activated
Reference documents
530 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Packages
- Basic Workflow
- Get Motif Annotations
- Compute Deviations
- Interpreting Results
- Visualization
- Differential Motif Accessibility
- Working with Single-Cell ATAC-seq
- Background Peaks Strategy
- Export Results
- Complete Workflow
- Related Skills
Files
SKILL.mdcore9,126 bytesexamples/chromvar_analysis.Rasset2,972 bytesusage-guide.mddoc2,471 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-atac-seq-nucleosome-positioning
When your agent uses it
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing chromatin organization, identifying nucleosome-free regions at promoters, or characterizing nucleosome occupancy patterns from ATAC-seq fragment size distributions.
What it loads into context
Frontmatter
85 tokensAlways available to the agent
SKILL.md
2,502 tokensWhen the skill is activated
Reference documents
533 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Background
- ATACseqQC (R)
- NucleoATAC (Python)
- Fragment Analysis (Custom)
- DANPOS
- Complete Workflow
- Related Skills
Scripts executed separately
examples/nucleosome_analysis.R
Files
SKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesSKILL.mdcore9,100 bytesexamples/nucleosome_analysis.Rruns2,490 bytesusage-guide.mddoc2,211 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-basecalling
When your agent uses it
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.
What it loads into context
Frontmatter
80 tokensAlways available to the agent
SKILL.md
2,470 tokensWhen the skill is activated
Reference documents
617 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Dorado (Recommended)
- Guppy (Deprecated - Legacy Only)
- POD5 File Handling
- Quality Filtering
- Basecalling QC
- Model Selection Guide
- Complete Pipeline
- GPU Requirements
- Troubleshooting
- Related Skills
Scripts executed separately
examples/basecall_pipeline.shexamples/dorado_basecall.sh
Files
SKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesSKILL.mdcore8,155 bytesexamples/basecall_pipeline.shruns1,351 bytesexamples/dorado_basecall.shruns584 bytesusage-guide.mddoc2,304 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,878 tokensWhen the skill is activated
Reference documents
521 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Setup
- Rate Limits
- History Server
- Core Pattern: Batch Download
- Code Patterns
- Batch Size Guidelines
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/batch_by_ids.pyexamples/batch_fasta.pyexamples/robust_download.py
Files
SKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesSKILL.mdcore11,883 bytesexamples/batch_by_ids.pyruns2,390 bytesexamples/batch_fasta.pyruns1,755 bytesexamples/robust_download.pyruns2,893 bytesusage-guide.mddoc2,119 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-batch-processing
When your agent uses it
Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.
What it loads into context
Frontmatter
53 tokensAlways available to the agent
SKILL.md
2,203 tokensWhen the skill is activated
Reference documents
310 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Process Multiple Files
- Merge Files
- Split Files
- Batch Convert
- Parallel Processing
- Summary Statistics
- File Organization
- Common Patterns
- Related Skills
Scripts executed separately
examples/batch_process.py
Files
SKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesSKILL.mdcore8,827 bytesexamples/batch_process.pyruns1,573 bytesusage-guide.mddoc1,342 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,647 tokensWhen the skill is activated
Reference documents
848 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- bedGraph Format
- Create bedGraph from BAM
- Sort bedGraph
- Convert bedGraph to bigWig
- Convert bigWig to bedGraph
- Merge bedGraph Files
- Mathematical Operations
- Python with pyBigWig
- deepTools for Normalization
- Filtering and Subsetting
- Aggregate to Bins
- Quality Control
- Complete Pipeline
- Track Header for UCSC
- Related Skills
Scripts executed separately
examples/bam_to_bigwig.shexamples/bedgraph_operations.py
Files
SKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesSKILL.mdcore8,359 bytesexamples/bam_to_bigwig.shruns875 bytesexamples/bedgraph_operations.pyruns2,829 bytesusage-guide.mddoc3,179 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,700 tokensWhen the skill is activated
Reference documents
494 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Import
- BLAST Programs
- Core Function
- Common Databases
- Parsing Results
- Code Patterns
- Common Errors
- Timing Notes
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_blast.pyexamples/blastp_filtered.pyexamples/save_and_parse.py
Files
SKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesSKILL.mdcore10,141 bytesexamples/basic_blast.pyruns1,548 bytesexamples/blastp_filtered.pyruns1,395 bytesexamples/save_and_parse.pyruns2,283 bytesusage-guide.mddoc1,945 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-causal-genomics-colocalization-analysis
When your agent uses it
Test whether two traits share a causal variant at a genomic locus using Bayesian colocalization with coloc. Computes posterior probabilities for shared vs distinct causal variants between GWAS and eQTL signals. Use when determining if a GWAS signal and an eQTL share the same causal variant.
What it loads into context
Frontmatter
80 tokensAlways available to the agent
SKILL.md
2,570 tokensWhen the skill is activated
Reference documents
698 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Overview
- coloc.abf Analysis
- Prior Sensitivity
- Using P-values (No Beta/SE)
- SuSiE-Coloc (Multiple Causal Variants)
- HyPrColoc (Multi-Trait)
- Input Preparation
- Visualization
- LocusCompare Plot
- Decision Framework
- Related Skills
Files
SKILL.mdcore8,795 bytesexamples/coloc_analysis.Rasset2,251 bytesexamples/coloc_susie.Rasset2,236 bytesexamples/regional_plots.Rasset2,554 bytesusage-guide.mddoc2,816 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-causal-genomics-fine-mapping
When your agent uses it
Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
What it loads into context
Frontmatter
86 tokensAlways available to the agent
SKILL.md
2,686 tokensWhen the skill is activated
Reference documents
677 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Overview
- SuSiE (Sum of Single Effects)
- SuSiE with Summary Statistics (susie_rss)
- Choosing L (Number of Causal Variants)
- LD Reference Panel
- FINEMAP
- Functional Annotation with PolyFun
- Visualization
- Related Skills
Scripts executed separately
examples/finemap_pipeline.sh
Files
SKILL.mdcore9,236 bytesSKILL.mdcore9,236 bytesSKILL.mdcore9,236 bytesexamples/finemap_pipeline.shruns1,956 bytesexamples/pip_visualization.Rasset3,171 bytesexamples/susie_finemapping.Rasset2,330 bytesusage-guide.mddoc2,641 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-causal-genomics-mediation-analysis
When your agent uses it
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
2,547 tokensWhen the skill is activated
Reference documents
567 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Framework
- Basic Mediation with the mediation Package
- Interpreting Results
- eQTL Mediation
- Multi-Omics Mediation
- High-Dimensional Mediation (HDMA)
- Assumptions and Diagnostics
- Visualization
- Related Skills
Files
SKILL.mdcore9,762 bytesexamples/eqtl_mediation.Rasset3,304 bytesexamples/sensitivity_analysis.Rasset2,625 bytesusage-guide.mddoc2,572 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-causal-genomics-mendelian-randomization
When your agent uses it
Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.
What it loads into context
Frontmatter
87 tokensAlways available to the agent
SKILL.md
2,149 tokensWhen the skill is activated
Reference documents
700 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Concepts
- TwoSampleMR Workflow
- OpenGWAS Authentication
- Interpreting Results
- Instrument Strength
- Bidirectional MR
- Visualization
- Power Calculation
- Related Skills
Files
SKILL.mdcore8,724 bytesexamples/mr_visualization.Rasset2,373 bytesexamples/twosamplemr_analysis.Rasset3,425 bytesusage-guide.mddoc2,987 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-causal-genomics-pleiotropy-detection
When your agent uses it
Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.
What it loads into context
Frontmatter
91 tokensAlways available to the agent
SKILL.md
2,879 tokensWhen the skill is activated
Reference documents
678 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Overview
- MR-PRESSO
- MR-Egger Diagnostics
- Steiger Filtering
- Additional Sensitivity Methods
- Comprehensive Sensitivity Framework
- STROBE-MR Reporting
- Related Skills
Files
SKILL.mdcore10,861 bytesexamples/mr_presso_analysis.Rasset2,744 bytesexamples/sensitivity_analyses.Rasset3,961 bytesusage-guide.mddoc2,831 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-cfdna-preprocessing
When your agent uses it
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
What it loads into context
Frontmatter
74 tokensAlways available to the agent
SKILL.md
1,664 tokensWhen the skill is activated
Reference documents
458 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Pre-Analytical Considerations
- UMI-Aware Pipeline with fgbio
- Python Implementation
- Fragment Size Analysis
- Quality Thresholds
- Related Skills
Scripts executed separately
examples/preprocess_cfdna.py
Files
SKILL.mdcore6,421 bytesSKILL.mdcore6,421 bytesSKILL.mdcore6,421 bytesSKILL.mdcore6,421 bytesSKILL.mdcore6,421 bytesexamples/preprocess_cfdna.pyruns3,848 bytesusage-guide.mddoc1,943 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-differential-binding
When your agent uses it
Differential binding analysis using DiffBind. Compare ChIP-seq peaks between conditions with statistical rigor. Requires replicate samples. Outputs differentially bound regions with fold changes and p-values. Use when comparing ChIP-seq binding between conditions.
What it loads into context
Frontmatter
68 tokensAlways available to the agent
SKILL.md
1,945 tokensWhen the skill is activated
Reference documents
388 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Create Sample Sheet
- Load Data
- Count Reads in Peaks
- Normalize Data
- Set Up Contrast
- Run Differential Analysis
- View Results
- Filter Results
- Export Results
- Visualization
- Venn Diagram of Peaks
- Profile Plots
- Get Consensus Peaks
- Multi-Factor Design
- DiffBind 3.0 Notes
- Sample Sheet Columns
- Key Functions
- Related Skills
Files
SKILL.mdcore7,540 bytesexamples/diffbind_analysis.Rasset1,382 bytesusage-guide.mddoc1,825 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-motif-analysis
When your agent uses it
De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,907 tokensWhen the skill is activated
Reference documents
414 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Tool Comparison
- HOMER
- MEME Suite
- Motif Databases
- Python: Parse HOMER Results
- Python: Parse MEME Results
- Complete Workflows
- Visualization
- Quality Metrics
- Common Issues
- Related Skills
Scripts executed separately
examples/motif_analysis.sh
Files
SKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesSKILL.mdcore10,488 bytesexamples/motif_analysis.shruns1,512 bytesusage-guide.mddoc1,741 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-peak-annotation
When your agent uses it
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation plots and statistics. Use when annotating ChIP-seq peaks to genomic features.
What it loads into context
Frontmatter
87 tokensAlways available to the agent
SKILL.md
1,743 tokensWhen the skill is activated
Reference documents
431 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load Peaks and Annotations
- Annotate Peaks
- Custom Promoter Definition
- Extract Annotated Data Frame
- Get Genes with Peaks in Promoter
- Annotation Pie Chart
- Distance to TSS Plot
- Compare Multiple Peak Sets
- Venn Diagram of Peak Overlap
- Coverage Plot
- Profile Heatmap Around TSS
- Functional Enrichment of Peak Genes
- Seq2Gene - All Genes in Peak Regions
- Different Organisms
- Key Functions
- Annotation Categories
- Related Skills
Files
SKILL.mdcore6,383 bytesexamples/annotate_peaks.Rasset943 bytesusage-guide.mddoc1,803 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-peak-calling
When your agent uses it
ChIP-seq peak calling using MACS3 (or MACS2). Call narrow peaks for transcription factors or broad peaks for histone modifications. Supports input control, fragment size modeling, and various output formats including narrowPeak and broadPeak BED files. Use when calling peaks from ChIP-seq alignments.
What it loads into context
Frontmatter
86 tokensAlways available to the agent
SKILL.md
2,163 tokensWhen the skill is activated
Reference documents
477 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Peak Calling
- Without Input Control
- Narrow Peaks (TF, H3K4me3, H3K27ac)
- Broad Peaks (H3K36me3, H3K27me3, H3K9me3)
- Paired-End Data
- Multiple Replicates
- Custom Genome Size
- Common Genome Sizes
- Fixed Fragment Size
- Generate Signal Tracks
- Local Lambda for Broad Marks
- Cutoff Analysis
- Output Files
- narrowPeak Format
- Filter Peaks
- Key Parameters
- Related Skills
Scripts executed separately
examples/macs3_peak_calling.sh
Files
SKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesSKILL.mdcore8,165 bytesexamples/macs3_peak_calling.shruns998 bytesusage-guide.mddoc1,724 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-qc
When your agent uses it
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discovery Rate) for replicate concordance. Use to assess experiment quality before downstream analysis. Use when assessing ChIP-seq data quality metrics.
What it loads into context
Frontmatter
88 tokensAlways available to the agent
SKILL.md
3,289 tokensWhen the skill is activated
Reference documents
692 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- FRiP (Fraction of Reads in Peaks)
- Cross-Correlation Analysis (NSC/RSC)
- Library Complexity (NRF, PBC1, PBC2)
- IDR (Irreproducibility Discovery Rate)
- deepTools QC Metrics
- Complete QC Pipeline
- QC Summary Table
- Related Skills
Scripts executed separately
examples/calculate_frip.shexamples/chipseq_qc.pyexamples/run_idr.sh
Files
SKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesSKILL.mdcore10,961 bytesexamples/calculate_frip.shruns608 bytesexamples/chipseq_qc.pyruns1,572 bytesexamples/run_idr.shruns885 bytesusage-guide.mddoc2,867 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-super-enhancers
When your agent uses it
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions that cluster into large enhancer domains.
What it loads into context
Frontmatter
69 tokensAlways available to the agent
SKILL.md
2,363 tokensWhen the skill is activated
Reference documents
778 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Background
- ROSE (Rank Ordering of Super-Enhancers)
- Prepare Input Files
- Alternative: HOMER Super-Enhancers
- Alternative: SEanalysis
- Custom Hockey Stick Analysis (R)
- Calculate Enhancer Signal
- Downstream Analysis
- Complete Workflow
- Related Skills
Scripts executed separately
examples/analyze_super_enhancers.pyexamples/run_rose.sh
Files
SKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesSKILL.mdcore8,241 bytesexamples/analyze_super_enhancers.pyruns2,340 bytesexamples/run_rose.shruns1,085 bytesusage-guide.mddoc2,786 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-chipseq-visualization
When your agent uses it
Visualize ChIP-seq data using deepTools, Gviz, and ChIPseeker. Create heatmaps, profile plots, and genome browser tracks. Visualize signal around peaks, TSS, or custom regions. Use when visualizing ChIP-seq signal and peaks.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
2,183 tokensWhen the skill is activated
Reference documents
465 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- deepTools - Compute Matrix
- deepTools - Scale-Regions
- deepTools - Heatmap
- deepTools - Profile Plot
- Create BigWig from BAM
- ChIPseeker Profile Heatmap (R)
- Gviz - Genome Browser Tracks (R)
- Multiple Samples in Gviz
- EnrichedHeatmap (R)
- IGV Batch Screenshot
- Key Tools Comparison
- deepTools Key Commands
- Related Skills
Scripts executed separately
examples/deeptools_heatmap.sh
Files
SKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesexamples/chipseeker_profile.Rasset955 bytesexamples/deeptools_heatmap.shruns990 bytesusage-guide.mddoc1,943 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-clinvar-lookup
When your agent uses it
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
1,467 tokensWhen the skill is activated
Reference documents
461 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- REST API Queries
- Local ClinVar VCF
- Clinical Significance Categories
- Review Status Stars
- Parse ClinVar INFO Fields
- Batch Annotation with bcftools
- Related Skills
Scripts executed separately
examples/clinvar_query.py
Files
SKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesSKILL.mdcore5,717 bytesexamples/clinvar_query.pyruns2,965 bytesusage-guide.mddoc1,916 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-dbsnp-queries
When your agent uses it
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,277 tokensWhen the skill is activated
Reference documents
420 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Query rsID via myvariant.info
- Query via NCBI Entrez
- Map Coordinates to rsID
- Map rsID to Coordinates
- Batch rsID Lookup
- Parse dbSNP Annotations
- Variant Classes in dbSNP
- Query NCBI Variation Services API
- Related Skills
Scripts executed separately
examples/dbsnp_lookup.py
Files
SKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesSKILL.mdcore4,770 bytesexamples/dbsnp_lookup.pyruns2,830 bytesusage-guide.mddoc1,578 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-gnomad-frequencies
When your agent uses it
Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,713 tokensWhen the skill is activated
Reference documents
420 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- gnomAD REST API
- Query via myvariant.info
- Population-Specific Frequencies
- Filtering Thresholds
- Filter Variants by Frequency
- Batch Query with Local gnomAD
- Related Skills
Scripts executed separately
examples/gnomad_query.py
Files
SKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesSKILL.mdcore6,636 bytesexamples/gnomad_query.pyruns2,747 bytesusage-guide.mddoc1,744 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-hla-typing
When your agent uses it
Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.
What it loads into context
Frontmatter
77 tokensAlways available to the agent
SKILL.md
2,096 tokensWhen the skill is activated
Reference documents
558 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- OptiType (HLA Class I)
- HLA-HD (Full Resolution)
- arcasHLA (RNA-seq)
- HLA Nomenclature
- HLA and Pharmacogenomics
- Parse OptiType Results
- Class I vs Class II
- Tool Comparison
- Related Skills
Scripts executed separately
examples/optitype_workflow.sh
Files
SKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesSKILL.mdcore7,110 bytesexamples/optitype_workflow.shruns3,385 bytesusage-guide.mddoc1,875 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-myvariant-queries
When your agent uses it
Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
1,309 tokensWhen the skill is activated
Reference documents
425 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Initialize Client
- Query Single Variant
- Query Multiple Variants
- Search Variants
- Available Fields
- Extract Specific Annotations
- Batch Processing with DataFrame
- Rate Limiting
- Related Skills
Scripts executed separately
examples/query_myvariant.py
Files
SKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesSKILL.mdcore5,206 bytesexamples/query_myvariant.pyruns2,184 bytesusage-guide.mddoc1,748 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-pharmacogenomics
When your agent uses it
Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
2,100 tokensWhen the skill is activated
Reference documents
519 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- PharmGKB REST API
- Star Allele Interpretation
- Drug Interaction Lookup
- Common PGx Gene-Drug Pairs
- Batch PGx Annotation
- Related Skills
Scripts executed separately
examples/pharmgkb_query.py
Files
SKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesSKILL.mdcore7,727 bytesexamples/pharmgkb_query.pyruns5,283 bytesusage-guide.mddoc1,971 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-polygenic-risk
When your agent uses it
Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
2,216 tokensWhen the skill is activated
Reference documents
541 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- PRSice-2 Workflow
- GWAS Summary Statistics Format
- LDpred2 (R)
- PRS-CS
- Score Normalization
- Risk Stratification
- PGS Catalog Integration
- Validation Metrics
- Related Skills
Scripts executed separately
examples/prsice2_workflow.sh
Files
SKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesSKILL.mdcore7,761 bytesexamples/ldpred2_analysis.Rasset3,652 bytesexamples/prsice2_workflow.shruns2,746 bytesusage-guide.mddoc2,086 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-somatic-signatures
When your agent uses it
Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
2,100 tokensWhen the skill is activated
Reference documents
552 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- SigProfiler Workflow
- MutationalPatterns (R)
- COSMIC Signature Etiology
- Signature Categories
- Cosine Similarity
- Clinical Applications
- Related Skills
Scripts executed separately
examples/sigprofiler_analysis.py
Files
SKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesSKILL.mdcore8,608 bytesexamples/mutsig_fitting.Rasset4,208 bytesexamples/sigprofiler_analysis.pyruns6,243 bytesusage-guide.mddoc2,278 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-tumor-mutational-burden
When your agent uses it
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
2,427 tokensWhen the skill is activated
Reference documents
495 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- TMB Calculation from VCF (Ensembl VEP 111+)
- Panel-Specific TMB (Ensembl VEP 111+)
- TMB with Variant Filtering (Ensembl VEP 111+)
- Clinical TMB Thresholds (Ensembl VEP 111+)
- TMB by Variant Type (Ensembl VEP 111+)
- TMB vs MSI Comparison (Ensembl VEP 111+)
- Batch TMB Calculation
- Related Skills
Scripts executed separately
examples/tmb_calculation.py
Files
SKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesSKILL.mdcore9,274 bytesexamples/tmb_calculation.pyruns6,091 bytesusage-guide.mddoc1,847 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-clinical-databases-variant-prioritization
When your agent uses it
Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
1,991 tokensWhen the skill is activated
Reference documents
462 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Filtering Pipeline
- ACMG-Style Filtering
- Multi-Database Prioritization
- Inheritance-Based Filtering
- Output Priority Tiers
- Related Skills
Scripts executed separately
examples/prioritize_variants.py
Files
SKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesSKILL.mdcore7,840 bytesexamples/prioritize_variants.pyruns4,285 bytesusage-guide.mddoc2,035 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
445 tokensWhen the skill is activated
Reference documents
307 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Using ChIPseeker (R)
- Using BEDTools
- Python Annotation
- Related Skills
Files
SKILL.mdcore1,563 bytesSKILL.mdcore1,563 bytesSKILL.mdcore1,563 bytesexamples/annotate_peaks.Rasset381 bytesusage-guide.mddoc1,093 bytes
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View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
434 tokensWhen the skill is activated
Reference documents
300 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- STAR Alignment
- Bowtie2 Alternative
- Post-Alignment Processing
- Related Skills
Scripts executed separately
examples/align_clip.sh
Files
SKILL.mdcore1,559 bytesSKILL.mdcore1,559 bytesSKILL.mdcore1,559 bytesSKILL.mdcore1,559 bytesexamples/align_clip.shruns711 bytesusage-guide.mddoc1,113 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
374 tokensWhen the skill is activated
Reference documents
308 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- HOMER De Novo Motifs
- MEME-ChIP
- Known Motif Enrichment
- Related Skills
Scripts executed separately
examples/find_motifs.sh
Files
SKILL.mdcore1,372 bytesSKILL.mdcore1,372 bytesSKILL.mdcore1,372 bytesSKILL.mdcore1,372 bytesexamples/find_motifs.shruns440 bytesusage-guide.mddoc1,125 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,997 tokensWhen the skill is activated
Reference documents
467 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- CLIPper (Recommended)
- CLIPper Options
- PureCLIP (HMM-Based)
- Piranha
- PEAKachu (for PAR-CLIP)
- MACS3 for CLIP (Alternative)
- Strand-Specific Peak Calling
- Filter Peaks
- Merge Replicates
- Peak Metrics
- Quality Metrics
- Calculate FRiP
- Related Skills
Scripts executed separately
examples/call_peaks.sh
Files
SKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesSKILL.mdcore6,438 bytesexamples/call_peaks.shruns188 bytesusage-guide.mddoc1,698 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
990 tokensWhen the skill is activated
Reference documents
482 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- UMI Extraction (eCLIP/iCLIP)
- Adapter Trimming
- Two-Pass Trimming (eCLIP)
- PCR Duplicate Removal
- Python Preprocessing
- Quality Control
- Related Skills
Scripts executed separately
examples/preprocess_clip.sh
Files
SKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesSKILL.mdcore3,573 bytesexamples/preprocess_clip.shruns1,979 bytesusage-guide.mddoc1,775 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,822 tokensWhen the skill is activated
Reference documents
667 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Imports
- Basic Codon Counting
- Codon Adaptation Index (CAI)
- Synonymous Codon Usage
- Codon Tables
- Code Patterns
- Property Reference
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_analysis.pyexamples/codon_optimization.pyexamples/rscu_analysis.py
Files
SKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesSKILL.mdcore9,767 bytesexamples/basic_analysis.pyruns2,124 bytesexamples/codon_optimization.pyruns3,368 bytesexamples/rscu_analysis.pyruns2,786 bytesusage-guide.mddoc2,660 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,176 tokensWhen the skill is activated
Reference documents
526 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- PAML Ancestral Reconstruction
- IQ-TREE Ancestral Reconstruction
- Alternative State Analysis
- Ancestral Protein Resurrection
- Related Skills
Scripts executed separately
examples/ancestral_reconstruction.py
Files
SKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesSKILL.mdcore9,519 bytesexamples/ancestral_reconstruction.pyruns7,778 bytesusage-guide.mddoc2,329 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,767 tokensWhen the skill is activated
Reference documents
586 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- HGTector Workflow
- Compositional Analysis
- Phylogenetic Incongruence
- Genomic Island Detection
- Related Skills
Scripts executed separately
examples/hgt_detection.py
Files
SKILL.mdcore10,177 bytesSKILL.mdcore10,177 bytesSKILL.mdcore10,177 bytesSKILL.mdcore10,177 bytesexamples/hgt_detection.pyruns8,444 bytesusage-guide.mddoc2,433 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,215 tokensWhen the skill is activated
Reference documents
586 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- OrthoFinder Workflow
- Gene Trees and Reconciliation
- ProteinOrtho Alternative
- Functional Annotation Transfer
- Related Skills
Scripts executed separately
examples/ortholog_analysis.py
Files
SKILL.mdcore9,076 bytesSKILL.mdcore9,076 bytesSKILL.mdcore9,076 bytesSKILL.mdcore9,076 bytesexamples/ortholog_analysis.pyruns6,911 bytesusage-guide.mddoc2,283 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,742 tokensWhen the skill is activated
Reference documents
590 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- dN/dS Overview
- PAML Codeml Analysis
- Branch-Site Models
- HyPhy Alternative
- Related Skills
Scripts executed separately
examples/selection_analysis.py
Files
SKILL.mdcore10,272 bytesSKILL.mdcore10,272 bytesSKILL.mdcore10,272 bytesexamples/selection_analysis.pyruns7,328 bytesusage-guide.mddoc2,325 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,545 tokensWhen the skill is activated
Reference documents
586 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- MCScanX Workflow
- SyRI for Structural Variants
- JCVI Visualization
- Ks Analysis for Dating
- Related Skills
Scripts executed separately
examples/synteny_analysis.py
Files
SKILL.mdcore9,909 bytesSKILL.mdcore9,909 bytesSKILL.mdcore9,909 bytesSKILL.mdcore9,909 bytesexamples/synteny_analysis.pyruns8,415 bytesusage-guide.mddoc2,342 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-compressed-files
When your agent uses it
Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
2,146 tokensWhen the skill is activated
Reference documents
275 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Reading Compressed Files
- Writing Compressed Files
- BGZF: Indexable Compression
- Code Patterns
- Compression Comparison
- When to Use Each Format
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/compressed_io.py
Files
SKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesSKILL.mdcore8,002 bytesexamples/compressed_io.pyruns1,590 bytesusage-guide.mddoc1,140 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-consensus-sequences
When your agent uses it
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.
What it loads into context
Frontmatter
54 tokensAlways available to the agent
SKILL.md
2,366 tokensWhen the skill is activated
Reference documents
2,306 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Usage
- Haplotype Selection
- IUPAC Codes for Heterozygous Sites
- Missing Data Handling
- Region Selection
- Chain Files
- Sample-Specific Consensus
- Filtering Before Consensus
- Sequence Naming
- Common Workflows
- Verify Consensus
- Handling Overlapping Variants
- cyvcf2 Consensus (Simple Cases)
- Quick Reference
- Common Errors
- Related Skills
Scripts executed separately
examples/generate_consensus.sh
Files
SKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesSKILL.mdcore8,652 bytesexamples/generate_consensus.shruns1,098 bytesusage-guide.mddoc8,302 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-copy-number-cnv-annotation
When your agent uses it
Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis.
What it loads into context
Frontmatter
50 tokensAlways available to the agent
SKILL.md
2,475 tokensWhen the skill is activated
Reference documents
2,261 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Annotate with Gene Names (bedtools)
- CNVkit Gene Annotation
- Python: Comprehensive Annotation
- Annotate with Cancer Gene Census
- Annotate with ACMG/ClinVar
- GISTIC2 for Recurrent CNVs
- AnnotSV for Comprehensive Annotation
- R: Gene Enrichment of CNV Regions
- Interpret CNV States
- Output Report
- Related Skills
Scripts executed separately
examples/annotate_cnvs.py
Files
SKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesSKILL.mdcore8,975 bytesexamples/annotate_cnvs.pyruns1,681 bytesusage-guide.mddoc8,492 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-copy-number-cnv-visualization
When your agent uses it
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
2,927 tokensWhen the skill is activated
Reference documents
2,322 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- CNVkit Built-in Plots
- Python: Genome-wide Profile
- Python: Single Chromosome Plot
- Python: Cohort Heatmap
- R: ggplot2 Visualization
- Circos-style Plot
- GATK Plot Commands
- Related Skills
Scripts executed separately
examples/plot_cnv.py
Files
SKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesSKILL.mdcore10,203 bytesexamples/plot_cnv.pyruns1,881 bytesusage-guide.mddoc8,316 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-copy-number-cnvkit-analysis
When your agent uses it
Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
2,497 tokensWhen the skill is activated
Reference documents
2,227 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Workflow
- Build Reference from Normal Samples
- Flat Reference (No Matched Normal)
- WGS Mode
- bedGraph Input (Privacy-Preserving)
- Step-by-Step Pipeline
- Segmentation Options
- CNV Calling with Ploidy/Purity
- Export Results
- Visualization
- Key Output Files
- Python API
- Quality Control
- Key Parameters
- Related Skills
Scripts executed separately
examples/run_cnvkit.sh
Files
SKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesSKILL.mdcore9,485 bytesexamples/run_cnvkit.shruns1,359 bytesusage-guide.mddoc7,835 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-copy-number-gatk-cnv
When your agent uses it
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
2,265 tokensWhen the skill is activated
Reference documents
1,628 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Somatic CNV Workflow Overview
- Step 1: Preprocess Intervals
- Step 2: Collect Read Counts
- Step 3: Create Panel of Normals
- Step 4: Denoise Read Counts
- Step 5: Collect Allelic Counts
- Step 6: Model Segments
- Step 7: Call Copy Ratio Segments
- Plotting
- Germline CNV Workflow
- Complete Somatic Pipeline Script
- Key Output Files
- Related Skills
Scripts executed separately
examples/run_gatk_cnv.sh
Files
SKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesSKILL.mdcore8,248 bytesexamples/run_gatk_cnv.shruns1,232 bytesusage-guide.mddoc5,586 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-base-editing-analysis
When your agent uses it
Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying CRISPR base editor results, comparing ABE vs CBE efficiency, or assessing prime editing fidelity.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
915 tokensWhen the skill is activated
Reference documents
375 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- CRISPResso2 for Base Editing
- Key Metrics
- Base Editor Types
- Prime Editing Analysis
- Editing Window Analysis
- Quality Thresholds
- Related Skills
Scripts executed separately
examples/base_editing_analysis.sh
Files
SKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesSKILL.mdcore3,558 bytesexamples/base_editing_analysis.shruns4,119 bytesusage-guide.mddoc1,637 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-batch-correction
When your agent uses it
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
2,621 tokensWhen the skill is activated
Reference documents
683 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Median Normalization
- Size Factor Normalization
- Quantile Normalization
- Control-Based Normalization
- Batch Effect Removal with ComBat
- Batch-Aware Log-Fold Change
- Replicate Correlation Check
- Batch QC Metrics
- Visualization
- Related Skills
Scripts executed separately
examples/batch_correct.py
Files
SKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesSKILL.mdcore10,580 bytesexamples/batch_correct.pyruns6,799 bytesusage-guide.mddoc3,156 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-crispresso-editing
When your agent uses it
CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use when analyzing amplicon sequencing data from CRISPR editing experiments to assess editing efficiency.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
1,816 tokensWhen the skill is activated
Reference documents
621 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Analysis
- With HDR Template
- Batch Analysis
- Pool Analysis (Multiple Guides)
- WGS Analysis
- Parse Results in Python
- Key Output Files
- Quantify Specific Outcomes
- Base Editing Analysis
- Prime Editing Analysis
- Compare Samples
- Related Skills
Scripts executed separately
examples/crispresso_analysis.sh
Files
SKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesSKILL.mdcore6,565 bytesexamples/crispresso_analysis.shruns1,289 bytesusage-guide.mddoc2,535 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-hit-calling
When your agent uses it
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,539 tokensWhen the skill is activated
Reference documents
688 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- BAGEL2 Analysis
- DrugZ Analysis
- Custom Hit Calling in Python
- Robust Rank Aggregation (MAGeCK-style)
- Second-Best sgRNA Method
- Compare Methods
- Time-Course Analysis
- Visualize Results
- Related Skills
Scripts executed separately
examples/consensus_hits.py
Files
SKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesSKILL.mdcore9,118 bytesexamples/consensus_hits.pyruns1,348 bytesusage-guide.mddoc2,653 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-jacks-analysis
When your agent uses it
JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
2,531 tokensWhen the skill is activated
Reference documents
518 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Installation
- Input File Formats
- Basic JACKS Analysis
- Output Files
- Interpret Gene Results
- sgRNA Efficacy Analysis
- Visualization
- Multi-Screen Analysis
- Comparing JACKS vs MAGeCK
- Advanced Options
- Integration with Other Tools
- Related Skills
Scripts executed separately
examples/run_jacks.py
Files
SKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesSKILL.mdcore9,337 bytesexamples/run_jacks.pyruns4,712 bytesusage-guide.mddoc2,267 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-library-design
When your agent uses it
CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
3,699 tokensWhen the skill is activated
Reference documents
732 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- sgRNA Selection Criteria
- Library Composition
- Control Guide Design
- Off-Target Analysis
- Oligo Design for Cloning
- Pool Design for Synthesis
- Library QC
- Alternative PAM Systems
- Related Skills
Scripts executed separately
examples/design_library.py
Files
SKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesSKILL.mdcore14,237 bytesexamples/design_library.pyruns5,700 bytesusage-guide.mddoc2,792 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-mageck-analysis
When your agent uses it
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
1,812 tokensWhen the skill is activated
Reference documents
571 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Count sgRNAs from FASTQ
- Library File Format
- MAGeCK Test (RRA Algorithm)
- MAGeCK MLE (Maximum Likelihood)
- Interpret Results
- Visualize Results
- MAGeCK Pathway Analysis
- Time-Course Screens
- CRISPR Activation (CRISPRa) Screens
- MAGeCK-VISPR (Visualization)
- Related Skills
Scripts executed separately
examples/mageck_workflow.sh
Files
SKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesSKILL.mdcore6,621 bytesexamples/mageck_workflow.shruns1,321 bytesusage-guide.mddoc2,307 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-crispr-screens-screen-qc
When your agent uses it
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosing poor screen performance.
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
2,238 tokensWhen the skill is activated
Reference documents
664 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load Count Data
- Library Representation
- Read Distribution (Gini Index)
- Read Count Distribution
- Replicate Correlation
- Essential Gene Recovery
- sgRNA Performance
- Sample Normalization Check
- QC Summary Report
- Related Skills
Scripts executed separately
examples/screen_qc.py
Files
SKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesSKILL.mdcore8,388 bytesexamples/screen_qc.pyruns2,362 bytesusage-guide.mddoc2,838 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-ctdna-mutation-detection
When your agent uses it
Detects somatic mutations in circulating tumor DNA using variant callers optimized for low allele fractions with UMI-based error suppression. Reliably detects mutations at VAF above 0.5 percent using consensus-based approaches. Use when identifying tumor mutations from plasma DNA or tracking specific variants.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
1,831 tokensWhen the skill is activated
Reference documents
473 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Input Requirements
- VAF Detection Limits
- VarDict for High Sensitivity (Ensembl VEP 111+)
- Python Implementation
- UMI-VarCal for Best Specificity (Ensembl VEP 111+)
- Variant Annotation (Ensembl VEP 111+)
- Tracking Known Mutations
- Related Skills
Scripts executed separately
examples/detect_ctdna_mutations.py
Files
SKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesSKILL.mdcore6,907 bytesexamples/detect_ctdna_mutations.pyruns3,599 bytesusage-guide.mddoc1,934 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,984 tokensWhen the skill is activated
Reference documents
642 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Tool Options
- Circos (Original)
- pyCircos (Python)
- circlize (R)
- Common Use Cases
- Complete Workflow: Variant Summary
- Related Skills
Scripts executed separately
examples/circos_basic.Rexamples/circos_basic.py
Files
SKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesSKILL.mdcore9,505 bytesexamples/circos_basic.Rruns1,712 bytesexamples/circos_basic.pyruns1,885 bytesusage-guide.mddoc2,556 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,594 tokensWhen the skill is activated
Reference documents
607 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Palette Types
- viridis (Colorblind-Safe)
- RColorBrewer (R)
- matplotlib/seaborn (Python)
- Scientific Journal Palettes
- Custom Palettes
- Heatmap Colors
- Colorblind Simulation
- Recommended Palettes
- Transparency
- Extract Colors from Palette
- Related Skills
Files
SKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesSKILL.mdcore5,289 bytesexamples/palette_examples.Rasset2,622 bytesusage-guide.mddoc2,392 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,900 tokensWhen the skill is activated
Reference documents
602 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- pyGenomeTracks INI Configuration
- pyGenomeTracks Command
- pyGenomeTracks Python API
- Track Types
- IGV Batch Scripting
- IGV Batch Commands
- Gviz (R)
- Multi-Sample Comparison
- Publication Export
- Related Skills
Scripts executed separately
examples/generate_tracks.pyexamples/igv_batch.sh
Files
SKILL.mdcore6,449 bytesSKILL.mdcore6,449 bytesSKILL.mdcore6,449 bytesSKILL.mdcore6,449 bytesSKILL.mdcore6,449 bytesSKILL.mdcore6,449 bytesexamples/generate_tracks.pyruns4,086 bytesexamples/igv_batch.shruns2,726 bytesexamples/tracks.iniasset1,459 bytesusage-guide.mddoc2,394 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,737 tokensWhen the skill is activated
Reference documents
595 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- pyGenomeTracks (Python/CLI)
- pyGenomeTracks with Multiple Samples
- pyGenomeTracks Programmatic
- Gviz (R)
- Gviz with Multiple Samples
- Gviz Customization
- IGV.js (Web)
- Create BigWig from BAM
- Multi-Region Plot
- Related Skills
Files
SKILL.mdcore5,894 bytesSKILL.mdcore5,894 bytesSKILL.mdcore5,894 bytesSKILL.mdcore5,894 bytesSKILL.mdcore5,894 bytesexamples/tracks.iniasset988 bytesusage-guide.mddoc2,325 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,167 tokensWhen the skill is activated
Reference documents
550 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic Structure
- Common Geoms
- Aesthetic Mappings
- Publication Theme
- Color Palettes
- Volcano Plot
- MA Plot
- Boxplot with Points
- Faceting
- Labels and Text
- Multi-Panel Figures
- Saving Figures
- Axis Formatting
- Legend Customization
- Heatmap with pheatmap
- Related Skills
Files
SKILL.mdcore7,296 bytesexamples/publication_figures.Rasset3,555 bytesusage-guide.mddoc2,185 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,724 tokensWhen the skill is activated
Reference documents
567 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- pheatmap (R) - Quick Heatmaps
- pheatmap Customization
- ComplexHeatmap (R) - Advanced
- ComplexHeatmap with Annotations
- Multiple Heatmaps
- seaborn (Python)
- seaborn with Annotations
- Clustering Methods
- Extract Cluster Assignments
- Save Heatmaps
- Related Skills
Files
SKILL.mdcore6,148 bytesSKILL.mdcore6,148 bytesSKILL.mdcore6,148 bytesSKILL.mdcore6,148 bytesexamples/expression_heatmap.Rasset3,381 bytesusage-guide.mddoc2,368 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,604 tokensWhen the skill is activated
Reference documents
527 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- plotly (Python)
- Interactive Volcano Plot
- Interactive Heatmap
- plotly with Subplots
- plotly (R)
- Interactive MA Plot
- Linked Brushing
- bokeh (Python)
- bokeh with Widgets
- Save Interactive Plots
- Embed in Jupyter
- Related Skills
Scripts executed separately
examples/interactive_volcano.py
Files
SKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesSKILL.mdcore5,919 bytesexamples/interactive_volcano.pyruns2,265 bytesusage-guide.mddoc2,182 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,853 tokensWhen the skill is activated
Reference documents
696 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- patchwork Basics
- Panel Labels
- Layout Control
- Shared Legends
- Inset Plots
- cowplot Alternative
- Shared Axes
- Empty Spaces
- Titles and Captions
- Saving Multi-Panel Figures
- Complex Publication Figure
- matplotlib GridSpec (Python)
- matplotlib Panel Labels
- matplotlib Subfigures
- Publication Export
- Related Skills
Scripts executed separately
examples/multipanel_matplotlib.py
Files
SKILL.mdcore5,904 bytesSKILL.mdcore5,904 bytesSKILL.mdcore5,904 bytesSKILL.mdcore5,904 bytesSKILL.mdcore5,904 bytesexamples/multi_panel_figure.Rasset3,363 bytesexamples/multipanel_matplotlib.pyruns5,783 bytesusage-guide.mddoc2,616 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,510 tokensWhen the skill is activated
Reference documents
609 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Scope
- Volcano Plot (R)
- Volcano Plot (Python)
- MA Plot (R)
- PCA Plot (R)
- PCA Plot (Python)
- Dotplot for Enrichment (R)
- Boxplot with Statistics (R)
- UMAP/tSNE Plot (Python)
- Correlation Plot (R)
- Violin Plot with Split (R)
- Survival Curves (R)
- Related Skills
Files
SKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesSKILL.mdcore8,310 bytesexamples/omics_plots.Rasset2,782 bytesusage-guide.mddoc2,468 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,727 tokensWhen the skill is activated
Reference documents
527 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- UpSetR (R) - Basic Plot
- UpSetR Customization
- UpSetR with Queries
- UpSetR with Metadata Boxplots
- upsetplot (Python) - Basic
- upsetplot from DataFrame
- upsetplot Customization
- upsetplot with Metadata
- Save UpSet Plots
- Related Skills
Scripts executed separately
examples/upset_python.py
Files
SKILL.mdcore5,943 bytesSKILL.mdcore5,943 bytesSKILL.mdcore5,943 bytesSKILL.mdcore5,943 bytesSKILL.mdcore5,943 bytesSKILL.mdcore5,943 bytesexamples/upset_gene_sets.Rasset3,163 bytesexamples/upset_python.pyruns3,992 bytesusage-guide.mddoc2,196 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,117 tokensWhen the skill is activated
Reference documents
666 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- ggplot2 Basic Volcano
- ggplot2 with Gene Labels
- EnhancedVolcano (R)
- EnhancedVolcano with Custom Keyvals
- matplotlib Volcano (Python)
- matplotlib with Labels
- Threshold Customization
- Save Publication-Ready Volcano
- Related Skills
Scripts executed separately
examples/volcano_matplotlib.py
Files
SKILL.mdcore6,856 bytesSKILL.mdcore6,856 bytesSKILL.mdcore6,856 bytesSKILL.mdcore6,856 bytesexamples/volcano_ggplot.Rasset4,668 bytesexamples/volcano_matplotlib.pyruns5,823 bytesusage-guide.mddoc2,652 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-de-deseq2-basics
When your agent uses it
Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
2,758 tokensWhen the skill is activated
Reference documents
504 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Libraries
- Installation
- Creating DESeqDataSet
- Standard DESeq2 Workflow
- Design Formulas
- Specifying Contrasts
- Log Fold Change Shrinkage
- Setting Significance Thresholds
- Accessing DESeq2 Results
- Result Columns
- Normalization and Counts
- Multi-Factor Designs
- Interaction Models
- Likelihood Ratio Test
- Pre-Filtering Strategies
- Working with Existing Objects
- Exporting Results
- Common Errors
- Deprecated Features
- Quick Reference: Workflow Steps
- Related Skills
Files
SKILL.mdcore11,247 bytesexamples/basic_workflow.Rasset2,092 bytesexamples/batch_correction.Rasset1,280 bytesexamples/multi_condition.Rasset1,649 bytesusage-guide.mddoc2,158 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-de-edger-basics
When your agent uses it
Perform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
3,001 tokensWhen the skill is activated
Reference documents
506 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Libraries
- Installation
- Creating DGEList Object
- Standard edgeR Workflow (Quasi-Likelihood)
- Filtering Low-Expression Genes
- Normalization Methods
- Design Matrices
- Dispersion Estimation
- Quasi-Likelihood Testing
- Making Contrasts
- Accessing Results
- Result Columns
- Alternative: Exact Test (Classic edgeR)
- Alternative: glmLRT (Likelihood Ratio Test)
- Treat Test (Log Fold Change Threshold)
- Multi-Factor Designs
- Getting Normalized Counts
- Exporting Results
- Common Errors
- Deprecated/Changed Functions
- Quick Reference: Workflow Steps
- Choosing edgeR vs DESeq2
- Related Skills
Files
SKILL.mdcore11,575 bytesexamples/basic_workflow.Rasset1,344 bytesexamples/batch_correction.Rasset1,341 bytesexamples/contrasts.Rasset1,499 bytesusage-guide.mddoc2,163 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-de-results
When your agent uses it
Extract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.
What it loads into context
Frontmatter
69 tokensAlways available to the agent
SKILL.md
2,806 tokensWhen the skill is activated
Reference documents
480 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Libraries
- Extracting DESeq2 Results
- Extracting edgeR Results
- Filtering Significant Genes
- Ordering Results
- Summary Statistics
- Adding Gene Annotations
- Exporting Results
- Comparing Results Between Methods
- Multiple Testing Correction
- Handling NA Values
- Quick Reference: Result Columns
- Related Skills
Files
SKILL.mdcore10,502 bytesSKILL.mdcore10,502 bytesexamples/annotate_results.Rasset1,244 bytesexamples/export_excel.Rasset1,760 bytesexamples/filter_results.Rasset1,439 bytesusage-guide.mddoc1,860 bytes
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View the complete source on GitHubbio-de-visualization
When your agent uses it
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
3,343 tokensWhen the skill is activated
Reference documents
498 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Scope
- Required Libraries
- Installation
- MA Plot
- Volcano Plot
- PCA Plot
- Heatmaps
- Dispersion Plot
- Counts Plot for Individual Genes
- P-value Histogram
- Saving Plots
- Color Palettes
- Quick Reference: Common Plots
- Related Skills
Files
SKILL.mdcore12,115 bytesexamples/heatmap.Rasset1,335 bytesexamples/pca_plot.Rasset1,481 bytesexamples/volcano_plot.Rasset1,809 bytesusage-guide.mddoc2,122 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-differential-expression-batch-correction
When your agent uses it
Remove batch effects from RNA-seq data using ComBat, ComBat-Seq, limma removeBatchEffect, and SVA for unknown batch variables. Use when correcting batch effects in expression data.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,937 tokensWhen the skill is activated
Reference documents
484 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- ComBat-Seq (Count Data)
- ComBat (Normalized Data)
- limma removeBatchEffect
- DESeq2 Design Formula (Recommended for DE)
- Surrogate Variable Analysis (SVA)
- SVA with DESeq2
- Visualize Batch Effects
- Quantify Batch Effect
- Harmony (Single-Cell Integration)
- When NOT to Correct
- Related Skills
Files
SKILL.mdcore8,218 bytesexamples/batch_correction_workflow.Rasset2,363 bytesusage-guide.mddoc2,190 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-differential-expression-timeseries-de
When your agent uses it
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic expression patterns. Use when analyzing time-series or longitudinal expression data.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
2,690 tokensWhen the skill is activated
Reference documents
611 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Approaches
- limma with Splines
- maSigPro
- ImpulseDE2
- DESeq2 Likelihood Ratio Test
- Visualization
- Complete Workflow
- Related Skills
Scripts executed separately
examples/timeseries_limma.R
Files
SKILL.mdcore10,514 bytesexamples/timeseries_limma.Rruns2,860 bytesusage-guide.mddoc2,857 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-differential-splicing
When your agent uses it
Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
What it loads into context
Frontmatter
86 tokensAlways available to the agent
SKILL.md
1,575 tokensWhen the skill is activated
Reference documents
534 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Tool Comparison
- rMATS-turbo Analysis
- SUPPA2 Differential Analysis
- leafcutter Analysis
- Significance Thresholds
- Result Prioritization
- Related Skills
Scripts executed separately
examples/diff_splicing_leafcutter.Rexamples/diff_splicing_rmats.sh
Files
SKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesSKILL.mdcore6,015 bytesexamples/diff_splicing_leafcutter.Rruns2,815 bytesexamples/diff_splicing_rmats.shruns1,608 bytesusage-guide.mddoc2,338 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,876 tokensWhen the skill is activated
Reference documents
1,732 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why Remove Duplicates?
- Duplicate Marking Workflow
- samtools fixmate
- samtools markdup
- Duplicate Statistics
- pysam Python Alternative
- Alternative: From Aligner
- Quick Reference
- Duplicate FLAG
- Common Errors
- Related Skills
Scripts executed separately
examples/markdup_pipeline.sh
Files
SKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesSKILL.mdcore6,964 bytesexamples/markdup_pipeline.shruns672 bytesusage-guide.mddoc6,347 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,659 tokensWhen the skill is activated
Reference documents
555 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Setup
- Core Functions
- Parsing with Biopython
- Code Patterns
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/fetch_pubmed.pyexamples/fetch_sequences.pyexamples/fetch_summaries.py
Files
SKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesSKILL.mdcore9,657 bytesexamples/fetch_pubmed.pyruns1,467 bytesexamples/fetch_sequences.pyruns1,748 bytesexamples/fetch_summaries.pyruns1,565 bytesusage-guide.mddoc2,190 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,658 tokensWhen the skill is activated
Reference documents
526 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Setup
- Core Function
- Common Link Paths
- Code Patterns
- Link Commands
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_linking.pyexamples/chain_links.pyexamples/discover_links.py
Files
SKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesSKILL.mdcore9,926 bytesexamples/basic_linking.pyruns1,603 bytesexamples/chain_links.pyruns2,000 bytesexamples/discover_links.pyruns1,491 bytesusage-guide.mddoc2,107 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,457 tokensWhen the skill is activated
Reference documents
547 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Setup
- Core Functions
- Search Query Syntax
- Common Databases
- Code Patterns
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_search.pyexamples/database_info.pyexamples/global_query.py
Files
SKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesSKILL.mdcore9,218 bytesexamples/basic_search.pyruns1,632 bytesexamples/database_info.pyruns1,450 bytesexamples/global_query.pyruns1,272 bytesusage-guide.mddoc2,250 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-epidemiological-genomics-amr-surveillance
When your agent uses it
Detect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor resistance trends and identify emerging resistance patterns. Use when screening genomes for AMR genes or tracking resistance in surveillance programs.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,853 tokensWhen the skill is activated
Reference documents
339 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- AMRFinderPlus
- Parse AMRFinder Results
- ResFinder Alternative
- Track Resistance Trends
- Clinical Interpretation
- Surveillance Report
- Related Skills
Scripts executed separately
examples/amr_surveillance.py
Files
SKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesSKILL.mdcore7,581 bytesexamples/amr_surveillance.pyruns6,161 bytesusage-guide.mddoc1,475 bytes
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View the complete source on GitHubbio-epidemiological-genomics-pathogen-typing
When your agent uses it
Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
1,518 tokensWhen the skill is activated
Reference documents
343 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- MLST with mlst Tool
- Parse MLST Results
- Core Genome MLST (cgMLST)
- cgMLST Distance Analysis
- SNP-Based Typing
- Enterobase Integration
- Related Skills
Scripts executed separately
examples/mlst_typing.py
Files
SKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesSKILL.mdcore6,128 bytesexamples/mlst_typing.pyruns5,089 bytesusage-guide.mddoc1,451 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-epidemiological-genomics-phylodynamics
When your agent uses it
Construct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate divergence times, molecular clock rates, and ancestral states. Use when dating outbreak origins, estimating transmission rates, or building time-calibrated trees.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
1,732 tokensWhen the skill is activated
Reference documents
381 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- TreeTime Basic Usage
- TreeTime CLI
- Date File Format
- Interpret Clock Results
- Skyline Plot (Population Dynamics)
- BEAST2 Integration
- Related Skills
Scripts executed separately
examples/treetime_analysis.py
Files
SKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesexamples/treetime_analysis.pyruns4,570 bytesusage-guide.mddoc1,657 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-epidemiological-genomics-transmission-inference
When your agent uses it
Infer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction algorithms. Estimate who-infected-whom from genomic and epidemiological data. Use when investigating outbreak transmission chains or identifying superspreaders.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,826 tokensWhen the skill is activated
Reference documents
345 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- TransPhylo in R
- Prepare Data
- Interpret Results
- Python Alternative: outbreaker2 Wrapper
- Network Visualization
- Superspreader Analysis
- Related Skills
Scripts executed separately
examples/transmission_inference.py
Files
SKILL.mdcore7,809 bytesSKILL.mdcore7,809 bytesSKILL.mdcore7,809 bytesSKILL.mdcore7,809 bytesSKILL.mdcore7,809 bytesexamples/transmission_inference.pyruns6,081 bytesusage-guide.mddoc1,532 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-epidemiological-genomics-variant-surveillance
When your agent uses it
Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
What it loads into context
Frontmatter
74 tokensAlways available to the agent
SKILL.md
2,008 tokensWhen the skill is activated
Reference documents
352 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Nextclade CLI
- Pangolin for SARS-CoV-2
- Parse Nextclade Results
- Track Variants of Concern
- Mutation Analysis
- Surveillance Report
- Related Skills
Scripts executed separately
examples/variant_surveillance.py
Files
SKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesSKILL.mdcore7,955 bytesexamples/variant_surveillance.pyruns5,517 bytesusage-guide.mddoc1,512 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
694 tokensWhen the skill is activated
Reference documents
408 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- exomePeak2 Differential Analysis
- QNB for Differential Methylation
- Visualization
- Related Skills
Files
SKILL.mdcore2,347 bytesexamples/differential_m6a.Rasset2,063 bytesusage-guide.mddoc1,600 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
617 tokensWhen the skill is activated
Reference documents
452 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- exomePeak2 (Recommended)
- MACS3 Alternative
- MeTPeak
- Peak Filtering
- Related Skills
Scripts executed separately
examples/macs3_peaks.sh
Files
SKILL.mdcore2,018 bytesSKILL.mdcore2,018 bytesSKILL.mdcore2,018 bytesexamples/exomepeak2_peaks.Rasset967 bytesexamples/macs3_peaks.shruns858 bytesusage-guide.mddoc1,566 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
641 tokensWhen the skill is activated
Reference documents
432 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Data Preparation
- Run m6Anet
- CLI Workflow
- Interpret Results
- Related Skills
Scripts executed separately
examples/m6anet_workflow.py
Files
SKILL.mdcore2,287 bytesSKILL.mdcore2,287 bytesSKILL.mdcore2,287 bytesSKILL.mdcore2,287 bytesSKILL.mdcore2,287 bytesSKILL.mdcore2,287 bytesexamples/m6anet_workflow.pyruns3,115 bytesusage-guide.mddoc1,629 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
564 tokensWhen the skill is activated
Reference documents
396 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Alignment with STAR
- QC Metrics
- IP/Input Correlation
- Related Skills
Scripts executed separately
examples/align_merip.shexamples/merip_qc.py
Files
SKILL.mdcore2,077 bytesSKILL.mdcore2,077 bytesSKILL.mdcore2,077 bytesSKILL.mdcore2,077 bytesexamples/align_merip.shruns885 bytesexamples/merip_qc.pyruns2,840 bytesusage-guide.mddoc1,460 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
633 tokensWhen the skill is activated
Reference documents
480 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Metagene Plots with Guitar
- Custom Metagene with deepTools
- Browser Tracks
- Heatmaps
- Related Skills
Scripts executed separately
examples/deeptools_metagene.sh
Files
SKILL.mdcore2,210 bytesSKILL.mdcore2,210 bytesSKILL.mdcore2,210 bytesexamples/deeptools_metagene.shruns1,192 bytesexamples/guitar_metagene.Rasset1,088 bytesusage-guide.mddoc1,774 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
718 tokensWhen the skill is activated
Reference documents
489 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Principle
- Design Rules
- Balanced Design Example
- Sample Assignment
- Detecting Batch Effects
- Correction Methods
- Documenting Design
- Related Skills
Files
SKILL.mdcore2,985 bytesexamples/batch_design.Rasset5,104 bytesusage-guide.mddoc2,076 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
752 tokensWhen the skill is activated
Reference documents
524 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- The Problem
- Common Methods
- Method Selection Guide
- Python Equivalent
- Interpreting Results
- Related Skills
Files
SKILL.mdcore2,867 bytesSKILL.mdcore2,867 bytesexamples/multiple_testing_correction.Rasset4,653 bytesusage-guide.mddoc2,049 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
702 tokensWhen the skill is activated
Reference documents
578 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Concept
- RNA-seq Power Analysis
- CV Guidelines
- ATAC-seq Power (ssizeRNA)
- Quick Reference
- Related Skills
Files
SKILL.mdcore2,550 bytesexamples/rnaseq_power.Rasset3,626 bytesusage-guide.mddoc2,197 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
727 tokensWhen the skill is activated
Reference documents
525 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- RNA-seq Sample Size
- DESeq2-based Estimation
- Single-cell Sample Size
- Sample Size by Assay Type
- Budget Optimization
- Related Skills
Files
SKILL.mdcore2,674 bytesexamples/sample_size_estimation.Rasset3,905 bytesusage-guide.mddoc2,101 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,551 tokensWhen the skill is activated
Reference documents
1,425 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic CSV/TSV Loading
- featureCounts Output
- Salmon Quant Files
- kallisto Abundance Files
- 10X Genomics Sparse Matrix
- AnnData H5AD Files
- RDS Files (from R)
- Combine Multiple Files
- Filter Low-Count Genes
- Handle Gene ID Versions
- Save Count Matrix
- R Loading Equivalents
- Related Skills
Scripts executed separately
examples/load_counts.py
Files
SKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesSKILL.mdcore5,681 bytesexamples/load_counts.pyruns2,141 bytesusage-guide.mddoc5,612 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,040 tokensWhen the skill is activated
Reference documents
1,830 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Python: mygene
- Python: pyensembl
- Python: gseapy
- R: biomaRt
- R: org.db Packages
- Apply Mapping to Count Matrix
- R Equivalent
- Handle Unmapped IDs
- Common ID Types
- Related Skills
Scripts executed separately
examples/map_gene_ids.py
Files
SKILL.mdcore7,069 bytesSKILL.mdcore7,069 bytesSKILL.mdcore7,069 bytesSKILL.mdcore7,069 bytesSKILL.mdcore7,069 bytesSKILL.mdcore7,069 bytesexamples/map_gene_ids.pyruns2,046 bytesusage-guide.mddoc6,874 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,788 tokensWhen the skill is activated
Reference documents
1,701 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Load Sample Metadata
- Basic Join
- Handle Sample Name Mismatches
- Flexible Sample Name Matching
- Add Gene Annotations
- R: Create DESeq2 Data
- R: Create edgeR DGEList
- Create AnnData with Metadata
- Validate Metadata
- Merge Multiple Metadata Files
- Related Skills
Scripts executed separately
examples/join_metadata.py
Files
SKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesSKILL.mdcore7,549 bytesexamples/join_metadata.pyruns2,025 bytesusage-guide.mddoc7,199 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,688 tokensWhen the skill is activated
Reference documents
1,562 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Check Sparsity
- Convert Dense to Sparse
- Convert Sparse to Dense
- Memory Comparison
- Save/Load Sparse Matrices
- AnnData with Sparse Matrices
- Sparse Operations
- Subsetting Sparse Matrices
- Normalization on Sparse
- 10X Matrix Format
- Related Skills
Scripts executed separately
examples/sparse_operations.py
Files
SKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesSKILL.mdcore6,326 bytesexamples/sparse_operations.pyruns2,260 bytesusage-guide.mddoc5,895 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-fastq-quality
When your agent uses it
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
What it loads into context
Frontmatter
52 tokensAlways available to the agent
SKILL.md
2,339 tokensWhen the skill is activated
Reference documents
347 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Accessing Quality Scores
- Quality Score Basics
- Code Patterns
- FASTQ Format Variants
- Quality Score Conversion
- Common Errors
- Related Skills
Scripts executed separately
examples/fastq_quality.py
Files
SKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesSKILL.mdcore8,750 bytesexamples/fastq_quality.pyruns2,073 bytesusage-guide.mddoc1,338 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-filter-sequences
When your agent uses it
Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.
What it loads into context
Frontmatter
58 tokensAlways available to the agent
SKILL.md
2,063 tokensWhen the skill is activated
Reference documents
294 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Core Pattern
- Filter by Length
- Filter by ID
- Filter by GC Content
- Filter by Sequence Content
- Filter by Description
- Combine Multiple Filters
- Sample Sequences
- Split by Criteria
- Common Errors
- Related Skills
Scripts executed separately
examples/filter_seqs.py
Files
SKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesSKILL.mdcore7,614 bytesexamples/filter_seqs.pyruns1,975 bytesusage-guide.mddoc1,221 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-bead-normalization
When your agent uses it
Bead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
2,484 tokensWhen the skill is activated
Reference documents
614 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- CyTOF EQ Bead Normalization
- Calculate Normalization Factors
- Apply Normalization
- Time-Based Drift Correction
- Batch Normalization with CytoNorm
- Quantile Normalization
- CATALYST-Based Normalization
- Visualization
- Export Normalized Data
- Related Skills
Files
SKILL.mdcore10,257 bytesexamples/bead_normalize.Rasset5,299 bytesusage-guide.mddoc2,543 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-clustering-phenotyping
When your agent uses it
Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
1,807 tokensWhen the skill is activated
Reference documents
547 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- FlowSOM Clustering
- CATALYST Workflow (Full Pipeline)
- Phenograph Clustering
- Dimensionality Reduction
- Cluster Annotation
- Cluster Merging
- Abundance Analysis (per sample)
- Marker Expression Summary
- Export Results
- Choosing Number of Clusters
- Batch Integration
- Related Skills
Files
SKILL.mdcore7,037 bytesexamples/cluster_cytof.Rasset1,050 bytesusage-guide.mddoc2,174 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-compensation-transformation
When your agent uses it
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
1,386 tokensWhen the skill is activated
Reference documents
462 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load Compensation Matrix
- Apply Compensation
- Calculate Compensation from Controls
- Transformation: Biexponential (Logicle)
- Transformation: Arcsinh (CyTOF)
- Transformation: Log
- View Before/After Compensation
- Complete Preprocessing Pipeline
- CATALYST Preprocessing (CyTOF)
- Panel File Format (CATALYST)
- Save Preprocessed Data
- Related Skills
Files
SKILL.mdcore5,489 bytesexamples/compensate_transform.Rasset1,282 bytesusage-guide.mddoc2,001 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-cytometry-qc
When your agent uses it
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.
What it loads into context
Frontmatter
69 tokensAlways available to the agent
SKILL.md
2,984 tokensWhen the skill is activated
Reference documents
708 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Automated QC with flowAI
- Flow Rate Stability
- Signal Drift Detection
- Margin Events Removal
- Dead Cell Exclusion
- CyTOF-Specific QC
- Batch QC Summary
- Visualization
- QC Report Generation
- Related Skills
Files
SKILL.mdcore11,171 bytesexamples/run_qc.Rasset6,229 bytesusage-guide.mddoc2,726 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-differential-analysis
When your agent uses it
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.
What it loads into context
Frontmatter
59 tokensAlways available to the agent
SKILL.md
1,562 tokensWhen the skill is activated
Reference documents
536 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Differential Abundance (DA)
- Differential State (DS)
- Visualization
- Manual Statistical Testing
- Mixed Effects Models
- CITRUS (Automated Discovery)
- Volcano Plot
- Export Results
- Multiple Comparisons
- Related Skills
Files
SKILL.mdcore5,951 bytesexamples/differential_abundance.Rasset1,007 bytesusage-guide.mddoc2,344 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-doublet-detection
When your agent uses it
Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection methods. Use when filtering out cell aggregates before clustering or quantitative analysis.
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
2,285 tokensWhen the skill is activated
Reference documents
598 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- FSC-A vs FSC-H Gating (Standard Method)
- Automated Singlet Gating with flowDensity
- flowAI Quality Control
- FSC-A/FSC-W Method (Width Parameter)
- Ratio-Based Doublet Detection
- SSC-Based Doublet Detection
- CyTOF Doublet Detection
- CATALYST Workflow with Doublet Removal
- Batch Processing
- Visualization
- Related Skills
Files
SKILL.mdcore7,846 bytesexamples/detect_doublets.Rasset4,155 bytesusage-guide.mddoc2,343 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-fcs-handling
When your agent uses it
Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,356 tokensWhen the skill is activated
Reference documents
543 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load FCS Files
- Load Multiple Files
- Access Expression Data
- Channel Metadata
- Rename Channels
- Subsetting Data
- Merge flowSets
- Write FCS Files
- Sample Metadata
- Basic Visualization
- Check Data Quality
- Convert to Data Frame
- Related Skills
Files
SKILL.mdcore5,084 bytesexamples/load_fcs.Rasset974 bytesusage-guide.mddoc2,145 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-flow-cytometry-gating-analysis
When your agent uses it
Manual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.
What it loads into context
Frontmatter
56 tokensAlways available to the agent
SKILL.md
1,284 tokensWhen the skill is activated
Reference documents
558 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Manual Rectangular Gates
- Polygon Gates
- Gating Hierarchy (flowWorkspace)
- Automated Gating: flowDensity
- Automated Gating: openCyto
- Quadrant Gates
- Boolean Gates
- Extract Gated Populations
- Visualization
- Export Gating Strategy
- Related Skills
Files
SKILL.mdcore4,655 bytesexamples/gating_workflow.Rasset1,268 bytesusage-guide.mddoc2,254 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-format-conversion
When your agent uses it
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
1,483 tokensWhen the skill is activated
Reference documents
255 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Core Function
- Common Conversions
- Code Patterns
- Format Compatibility Matrix
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/convert_format.py
Files
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No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-fragment-analysis
When your agent uses it
Analyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome positioning patterns, fragment ratios, and DELFI-style fragmentation profiles for cancer detection. Use when leveraging fragment patterns for tumor detection or tissue-of-origin analysis.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,506 tokensWhen the skill is activated
Reference documents
411 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Tool Selection
- Fragment Size Metrics
- FinaleToolkit Analysis
- Griffin Nucleosome Profiling
- Genome-Wide Fragmentation Profile
- Interpretation
- Related Skills
Scripts executed separately
examples/fragment_analysis.py
Files
SKILL.mdcore6,527 bytesSKILL.mdcore6,527 bytesSKILL.mdcore6,527 bytesSKILL.mdcore6,527 bytesSKILL.mdcore6,527 bytesSKILL.mdcore6,527 bytesexamples/fragment_analysis.pyruns4,249 bytesusage-guide.mddoc1,847 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-gatk-variant-calling
When your agent uses it
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.
What it loads into context
Frontmatter
80 tokensAlways available to the agent
SKILL.md
3,280 tokensWhen the skill is activated
Reference documents
895 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Prerequisites
- Single-Sample Calling
- GVCF Workflow (Recommended for Cohorts)
- Variant Quality Score Recalibration (VQSR)
- Hard Filtering (When VQSR Not Suitable)
- Base Quality Score Recalibration (BQSR)
- Parallel Processing
- CNN Score Variant Filter (Deep Learning)
- Complete Single-Sample Pipeline
- Key Annotations
- Resource Files
- Related Skills
Scripts executed separately
examples/joint_calling.shexamples/single_sample.sh
Files
SKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesSKILL.mdcore11,263 bytesexamples/joint_calling.shruns824 bytesexamples/single_sample.shruns1,087 bytesusage-guide.mddoc3,338 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,289 tokensWhen the skill is activated
Reference documents
517 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Polishing Strategies
- Recommended Workflows
- Pilon (Illumina Polishing)
- medaka (ONT Polishing)
- Racon (Long-Read Polishing)
- Complete Polishing Workflow
- NextPolish (Combined Approach)
- Quality Assessment
- Related Skills
Scripts executed separately
examples/polish_assembly.sh
Files
SKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesSKILL.mdcore7,394 bytesexamples/polish_assembly.shruns1,003 bytesusage-guide.mddoc2,150 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,206 tokensWhen the skill is activated
Reference documents
498 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Key Metrics
- QUAST
- BUSCO
- Complete QC Workflow
- Compare Assemblies
- Python: Parse QUAST Output
- Python: Parse BUSCO Output
- MetaQUAST (Metagenomes)
- Troubleshooting
- Related Skills
Scripts executed separately
examples/run_qc.sh
Files
SKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesSKILL.mdcore7,643 bytesexamples/run_qc.shruns949 bytesusage-guide.mddoc2,028 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,871 tokensWhen the skill is activated
Reference documents
547 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- CheckM2 (Recommended)
- Interpret CheckM2 Results
- CheckM (Original)
- CheckM Plots
- GTDB-Tk Taxonomic Classification
- GTDB-Tk De Novo Workflow
- GUNC Chimerism Detection
- GUNC Interpretation
- Comprehensive QC Pipeline
- Filter by Quality Standards
- Remove Contamination
- Detect Foreign Contigs
- Decontaminate with BlobTools
- Related Skills
Scripts executed separately
examples/mag_qc_pipeline.sh
Files
SKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesSKILL.mdcore6,519 bytesexamples/mag_qc_pipeline.shruns2,139 bytesusage-guide.mddoc2,168 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,462 tokensWhen the skill is activated
Reference documents
585 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic Assembly
- Trio-Binned Phasing
- Hi-C Phasing
- Key Parameters
- Purge Duplicates
- Ultra-Long ONT Integration
- Assembly Stats
- Memory and Runtime
- Python Wrapper
- Troubleshooting
- Related Skills
Scripts executed separately
examples/hifi_assembly_workflow.sh
Files
SKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesSKILL.mdcore4,923 bytesexamples/hifi_assembly_workflow.shruns1,434 bytesusage-guide.mddoc2,206 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,946 tokensWhen the skill is activated
Reference documents
541 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Tool Comparison
- Flye
- Canu
- Wtdbg2 (Fast Draft)
- Complete Workflows
- Quality Expectations
- Troubleshooting
- Related Skills
Scripts executed separately
examples/flye_assembly.sh
Files
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No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,797 tokensWhen the skill is activated
Reference documents
610 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- metaFlye (Long Reads)
- metaSPAdes (Short Reads)
- Hybrid Assembly
- Key Parameters
- Binning Workflow
- SemiBin2 (Deep Learning Binning)
- Quality Assessment
- Circular Genome Detection
- Python Pipeline
- Expected Outputs
- Troubleshooting
- Related Skills
Scripts executed separately
examples/metagenome_workflow.sh
Files
SKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesSKILL.mdcore6,422 bytesexamples/metagenome_workflow.shruns1,844 bytesusage-guide.mddoc2,292 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,666 tokensWhen the skill is activated
Reference documents
584 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Hi-C Data Preprocessing
- YaHS Scaffolding (Recommended)
- YaHS with Error Correction
- 3D-DNA Pipeline
- SALSA2 Scaffolding
- Generate Contact Map
- Visualize with HiGlass
- Manual Curation (Juicebox)
- Post-Scaffolding Gap Filling
- Validate Scaffolding
- Check Telomeres
- Rename to Chromosomes
- Related Skills
Scripts executed separately
examples/yahs_scaffolding.sh
Files
SKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesSKILL.mdcore5,619 bytesexamples/yahs_scaffolding.shruns1,505 bytesusage-guide.mddoc2,271 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,022 tokensWhen the skill is activated
Reference documents
516 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- SPAdes Overview
- Basic Usage
- Assembly Modes
- Key Options
- Multiple Libraries
- K-mer Selection
- Output Files
- Memory and Performance
- Complete Workflows
- Alternative Assemblers
- Troubleshooting
- Related Skills
Scripts executed separately
examples/bacterial_assembly.sh
Files
SKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesSKILL.mdcore6,581 bytesexamples/bacterial_assembly.shruns947 bytesusage-guide.mddoc2,022 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-genome-engineering-base-editing-design
When your agent uses it
Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
2,360 tokensWhen the skill is activated
Reference documents
418 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Base Editor Types
- Find Editable Positions
- Editing Efficiency by Position
- Bystander Edit Prediction
- Dual Base Editor Design
- Sequence Context Effects
- Related Skills
Scripts executed separately
examples/base_editing_design.py
Files
SKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesSKILL.mdcore9,103 bytesexamples/base_editing_design.pyruns6,207 bytesusage-guide.mddoc1,655 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-genome-engineering-grna-design
When your agent uses it
Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models. Use when designing sgRNAs for gene knockout, activation, or repression experiments.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
1,836 tokensWhen the skill is activated
Reference documents
380 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Find PAM Sites
- Score On-Target Activity
- CRISPRscan Scoring
- Design Workflow
- Cas12a Guide Design
- Related Skills
Scripts executed separately
examples/grna_design.py
Files
SKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesSKILL.mdcore7,119 bytesexamples/grna_design.pyruns4,160 bytesusage-guide.mddoc1,538 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-genome-engineering-hdr-template-design
When your agent uses it
Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement.
What it loads into context
Frontmatter
79 tokensAlways available to the agent
SKILL.md
2,343 tokensWhen the skill is activated
Reference documents
431 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Template Types
- ssODN Design
- Asymmetric Arm Design
- dsDNA Donor Design
- Common Insertions
- PAM Mutation to Prevent Re-cutting
- Related Skills
Scripts executed separately
examples/hdr_template_design.py
Files
SKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesSKILL.mdcore8,865 bytesexamples/hdr_template_design.pyruns6,673 bytesusage-guide.mddoc1,696 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-genome-engineering-off-target-prediction
When your agent uses it
Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,137 tokensWhen the skill is activated
Reference documents
438 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Cas-OFFinder (CLI)
- Cas-OFFinder Input Preparation
- Parse Cas-OFFinder Output
- CFD Score Calculation
- Aggregate Off-Target Score
- CRISPOR-style Analysis
- Related Skills
Scripts executed separately
examples/off_target_analysis.py
Files
SKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesSKILL.mdcore7,842 bytesexamples/off_target_analysis.pyruns5,047 bytesusage-guide.mddoc1,821 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-genome-engineering-prime-editing-design
When your agent uses it
Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations.
What it loads into context
Frontmatter
73 tokensAlways available to the agent
SKILL.md
2,448 tokensWhen the skill is activated
Reference documents
459 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- pegRNA Structure
- Design pegRNA for Point Mutation
- PBS Length Optimization
- RT Template Design
- PE3 Nicking Guide Design
- Complete pegRNA Assembly
- Related Skills
Scripts executed separately
examples/prime_editing_design.py
Files
SKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesSKILL.mdcore9,638 bytesexamples/prime_editing_design.pyruns6,664 bytesusage-guide.mddoc1,718 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,441 tokensWhen the skill is activated
Reference documents
759 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- BED Format Columns
- Coordinate System
- Create BED Files
- Sort BED Files
- Validate BED Files
- Read BED Files
- Filter BED Files
- Convert Formats
- Interval Arithmetic Basics
- Make Windows - Create Genomic Intervals
- Common BED Extensions
- Cleanup Temp Files
- Related Skills
Scripts executed separately
examples/create_bed.pyexamples/validate_bed.sh
Files
SKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesSKILL.mdcore8,282 bytesexamples/create_bed.pyruns2,112 bytesexamples/validate_bed.shruns1,618 bytesusage-guide.mddoc2,974 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,515 tokensWhen the skill is activated
Reference documents
826 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why BigWig?
- Convert bedGraph to bigWig (CLI)
- Read BigWig with pyBigWig (Python)
- Create BigWig with pyBigWig
- deepTools for BigWig Operations
- Convert BigWig to bedGraph
- Common Patterns
- Related Skills
Scripts executed separately
examples/bedgraph_to_bigwig.shexamples/pybigwig_demo.py
Files
SKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesSKILL.mdcore8,476 bytesexamples/bedgraph_to_bigwig.shruns1,988 bytesexamples/pybigwig_demo.pyruns2,893 bytesusage-guide.mddoc3,195 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,202 tokensWhen the skill is activated
Reference documents
830 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- genomecov - Genome-wide Coverage
- coverage - Coverage per Feature
- multicov - Counts Across Multiple BAMs
- Calculate Coverage Statistics
- Common Patterns
- bedGraph Format
- Key Parameters
- Related Skills
Scripts executed separately
examples/bedgraph_from_bam.shexamples/coverage_analysis.py
Files
SKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesSKILL.mdcore7,824 bytesexamples/bedgraph_from_bam.shruns2,359 bytesexamples/coverage_analysis.pyruns3,211 bytesusage-guide.mddoc3,282 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,520 tokensWhen the skill is activated
Reference documents
832 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Format Comparison
- GTF Format
- GFF3 Format
- Parse GTF with gtfparse (Python)
- Parse GFF with gffutils (Python)
- Convert Formats with gffread (CLI)
- Extract Regions with bedtools
- Python: GTF to BED Conversion
- Validate GTF/GFF
- Common Attributes
- Memory-Efficient Processing
- Related Skills
Scripts executed separately
examples/gffread_convert.shexamples/parse_gtf.py
Files
SKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesSKILL.mdcore8,581 bytesexamples/gffread_convert.shruns1,885 bytesexamples/parse_gtf.pyruns3,139 bytesusage-guide.mddoc3,159 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
3,306 tokensWhen the skill is activated
Reference documents
758 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Intersect - Find Overlapping Regions
- Subtract - Remove Overlapping Regions
- Merge - Combine Overlapping/Adjacent Intervals
- Complement - Get Uncovered Regions
- Cluster - Group Overlapping Intervals
- Multiinter - Find Multi-way Overlaps
- Jaccard - Similarity Metric
- Fisher's Exact Test
- Shuffle - Random Permutation
- Map - Transfer Values Between Files
- Groupby - Aggregate by Columns
- Common Patterns
- Key Parameters
- Related Skills
Scripts executed separately
examples/intersect_examples.shexamples/interval_operations.py
Files
SKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesSKILL.mdcore11,798 bytesexamples/intersect_examples.shruns1,036 bytesexamples/interval_operations.pyruns3,040 bytesusage-guide.mddoc3,305 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,513 tokensWhen the skill is activated
Reference documents
829 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Closest - Find Nearest Feature
- Window - Find Features Within Distance
- Slop - Extend Interval Boundaries
- Flank - Get Flanking Regions
- Shift - Move Intervals
- Common Patterns
- Genome File Format
- Key Parameters
- Related Skills
Scripts executed separately
examples/create_promoters.shexamples/proximity_analysis.py
Files
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No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,805 tokensWhen the skill is activated
Reference documents
540 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Setup
- GEO Database Types
- Searching GEO
- Fetching GEO Information
- Code Patterns
- Download Options
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/geo_from_pubmed.pyexamples/geo_to_sra.pyexamples/search_geo.py
Files
SKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesSKILL.mdcore10,230 bytesexamples/geo_from_pubmed.pyruns1,757 bytesexamples/geo_to_sra.pyruns2,567 bytesexamples/search_geo.pyruns2,046 bytesusage-guide.mddoc2,151 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-compartment-analysis
When your agent uses it
Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
2,164 tokensWhen the skill is activated
Reference documents
263 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Compute Compartment Eigenvectors
- Use GC Content for Phasing
- Extract Compartment Calls
- Compartment Strength (Saddle Plot)
- Plot Saddle
- Compartment Strength Score
- Plot Eigenvector Track
- Export Compartment Calls
- Compare Compartments Between Samples
- Correlate with Gene Expression
- Related Skills
Scripts executed separately
examples/call_compartments.py
Files
SKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesSKILL.mdcore7,852 bytesexamples/call_compartments.pyruns1,420 bytesusage-guide.mddoc1,160 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-contact-pairs
When your agent uses it
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
1,822 tokensWhen the skill is activated
Reference documents
270 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Pairtools Workflow Overview
- Parse Alignments to Pairs
- Sort Pairs
- Remove Duplicates
- View Pairs File
- Filter by Pair Type
- Filter by Distance
- Filter by MAPQ
- Generate Statistics
- Split by Pair Type
- Merge Pairs Files
- Generate Fragment Pairs (Restriction Sites)
- Convert to Different Formats
- Create Cooler from Pairs
- Python: Parse Pairs File
- Full Processing Pipeline
- Related Skills
Scripts executed separately
examples/process_pairs.sh
Files
SKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesSKILL.mdcore6,443 bytesexamples/process_pairs.shruns913 bytesusage-guide.mddoc1,088 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-hic-data-io
When your agent uses it
Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,800 tokensWhen the skill is activated
Reference documents
278 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Load a Cooler File
- Load Multi-Resolution Cooler (.mcool)
- Access Bin Information
- Access Pixel (Contact) Information
- Extract Contact Matrix
- Extract Submatrix (Two Regions)
- Convert from .hic to Cooler
- Convert from Text Formats
- Create Cooler from Matrix
- Merge Cooler Files
- Coarsen Resolution
- Export to Other Formats
- Dump to Pairs Format
- Access Metadata
- List Cooler Contents
- Related Skills
Scripts executed separately
examples/load_cooler.py
Files
SKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesSKILL.mdcore6,654 bytesexamples/load_cooler.pyruns770 bytesusage-guide.mddoc1,162 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-hic-differential
When your agent uses it
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
2,970 tokensWhen the skill is activated
Reference documents
256 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Load Two Conditions
- Compute Log2 Fold Change
- Plot Differential Contact Map
- Split View Comparison
- Depth Normalization
- Statistical Testing (Per-Pixel)
- FDR Correction
- Differential at Distance Bins
- Compare Compartment Changes
- Compare TAD Boundaries
- Differential Loop Analysis
- Export Differential Results
- Related Skills
Scripts executed separately
examples/compare_hic.py
Files
SKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesSKILL.mdcore10,599 bytesexamples/compare_hic.pyruns1,652 bytesusage-guide.mddoc1,226 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-hic-visualization
When your agent uses it
Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
2,699 tokensWhen the skill is activated
Reference documents
300 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Basic Contact Matrix Plot
- Triangle (Upper Triangle) Plot
- Plot with TADs
- Plot with Loops
- Compare Two Matrices
- Split View (Upper/Lower Triangle)
- Virtual 4C
- Multi-Track Figure
- Using HiCExplorer Visualization
- Cooltools Pileup Plot
- Related Skills
Scripts executed separately
examples/plot_hic.py
Files
SKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesSKILL.mdcore8,877 bytesexamples/plot_hic.pyruns981 bytesusage-guide.mddoc1,186 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-loop-calling
When your agent uses it
Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,365 tokensWhen the skill is activated
Reference documents
284 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Call Loops with cooltools (Dot Calling)
- Using chromosight (CLI)
- Parse chromosight Output
- Using HiCExplorer hicDetectLoops
- Loop Statistics
- Filter Loops by Score
- Annotate Loops with Features
- Compare Loops Between Conditions
- Aggregate Peak Analysis (APA)
- Using cooltools pileup for APA
- Export Loops
- Loops at Promoter-Enhancer Pairs
- Related Skills
Scripts executed separately
examples/call_loops.py
Files
SKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesSKILL.mdcore8,477 bytesexamples/call_loops.pyruns1,077 bytesusage-guide.mddoc1,105 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-matrix-operations
When your agent uses it
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
1,835 tokensWhen the skill is activated
Reference documents
228 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Matrix Balancing (ICE)
- Balance with CLI
- Access Balanced vs Raw Matrix
- Compute Expected Values
- Observed/Expected Matrix
- Using cooltools for O/E
- Log Transform
- Distance Decay Normalization
- Aggregate Multiple Replicates
- Smooth Matrix
- Downsample/Coarsen Matrix
- Correlation Matrix
- Save Modified Matrix
- Related Skills
Scripts executed separately
examples/balance_matrix.py
Files
SKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesSKILL.mdcore7,264 bytesexamples/balance_matrix.pyruns941 bytesusage-guide.mddoc999 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-hi-c-analysis-tad-detection
When your agent uses it
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
1,942 tokensWhen the skill is activated
Reference documents
309 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Compute Insulation Score
- Call TAD Boundaries
- Extract TAD Regions
- Using HiCExplorer (CLI)
- Using HiCExplorer in Python
- TAD Statistics
- Plot Insulation Score
- Compare TAD Boundaries Between Conditions
- Hierarchical TADs
- Export TADs
- Related Skills
Scripts executed separately
examples/call_tads.py
Files
SKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesSKILL.mdcore7,141 bytesexamples/call_tads.pyruns1,740 bytesusage-guide.mddoc1,269 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-cell-segmentation
When your agent uses it
Cell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear and whole-cell segmentation. Use when extracting single-cell data from IMC or MIBI images after preprocessing.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,704 tokensWhen the skill is activated
Reference documents
435 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Cellpose Segmentation
- Whole-Cell Segmentation with Cellpose
- Mesmer (DeepCell)
- steinbock Segmentation
- Extract Single-Cell Data
- Quality Control
- Expand Nuclei to Cells
- Save Results
- Related Skills
Scripts executed separately
examples/segment_cells.py
Files
SKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesSKILL.mdcore6,724 bytesexamples/segment_cells.pyruns1,327 bytesusage-guide.mddoc1,947 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-data-preprocessing
When your agent uses it
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
What it loads into context
Frontmatter
77 tokensAlways available to the agent
SKILL.md
1,985 tokensWhen the skill is activated
Reference documents
412 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load MCD Files with steinbock
- Panel File Format
- Python-Based Loading
- Hot Pixel Removal
- Spillover Correction
- Estimate Spillover from Single-Stain Controls
- Image Normalization
- steinbock Preprocessing Pipeline
- Visualize with napari
- Create AnnData Object
- Batch Processing
- Related Skills
Scripts executed separately
examples/preprocess_imc.py
Files
SKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesSKILL.mdcore7,848 bytesexamples/preprocess_imc.pyruns1,267 bytesusage-guide.mddoc1,740 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-interactive-annotation
When your agent uses it
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
2,491 tokensWhen the skill is activated
Reference documents
413 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Napari-Based Annotation
- Marker-Guided Annotation
- Training Data Generation
- Semi-Automated Annotation
- Annotation Validation
- Napari Plugin Interface
- Batch Annotation Workflow
- Related Skills
Scripts executed separately
examples/napari_annotation.py
Files
SKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesSKILL.mdcore10,620 bytesexamples/napari_annotation.pyruns4,118 bytesusage-guide.mddoc1,943 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-phenotyping
When your agent uses it
Cell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.
What it loads into context
Frontmatter
74 tokensAlways available to the agent
SKILL.md
1,876 tokensWhen the skill is activated
Reference documents
456 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load Single-Cell Data
- Data Transformation
- Clustering-Based Phenotyping
- Manual Gating
- Cluster Annotation
- SOM-Based Clustering (FlowSOM-Style)
- Automated Annotation
- Visualize Phenotypes
- Cell Type Frequencies
- Save Results
- Related Skills
Scripts executed separately
examples/phenotype_cells.py
Files
SKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesSKILL.mdcore6,906 bytesexamples/phenotype_cells.pyruns1,677 bytesusage-guide.mddoc1,975 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-quality-metrics
When your agent uses it
Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.
What it loads into context
Frontmatter
59 tokensAlways available to the agent
SKILL.md
2,656 tokensWhen the skill is activated
Reference documents
424 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Signal-to-Noise Ratio
- Channel Correlation
- Tissue Integrity
- Acquisition QC
- Dynamic Range
- Segmentation Quality Metrics
- Batch QC Summary
- Visualization
- Related Skills
Scripts executed separately
examples/run_qc.py
Files
SKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesSKILL.mdcore10,630 bytesexamples/run_qc.pyruns6,118 bytesusage-guide.mddoc1,936 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-imaging-mass-cytometry-spatial-analysis
When your agent uses it
Spatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction testing. Use when analyzing spatial relationships between cell types, testing for neighborhood enrichment, or identifying cell-cell interaction patterns in imaging mass cytometry data.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
1,962 tokensWhen the skill is activated
Reference documents
398 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Build Spatial Graph
- Neighborhood Enrichment
- Co-occurrence Analysis
- Ripley's Statistics
- Cell-Cell Interaction
- Custom Neighborhood Analysis
- Spatial Clustering
- Interaction Hotspots
- Visualize Spatial Patterns
- Statistical Testing
- Export Results
- Related Skills
Scripts executed separately
examples/spatial_analysis.py
Files
SKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesSKILL.mdcore7,661 bytesexamples/spatial_analysis.pyruns1,504 bytesusage-guide.mddoc1,956 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-immunoinformatics-epitope-prediction
When your agent uses it
Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
2,048 tokensWhen the skill is activated
Reference documents
359 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- B-Cell Epitope Prediction
- T-Cell Epitope Prediction
- Linear vs Conformational Epitopes
- Combine Multiple Predictions
- Epitope Mapping from Experimental Data
- Related Skills
Scripts executed separately
examples/epitope_prediction.py
Files
SKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesSKILL.mdcore8,406 bytesexamples/epitope_prediction.pyruns5,313 bytesusage-guide.mddoc1,407 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-immunoinformatics-immunogenicity-scoring
When your agent uses it
Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.
What it loads into context
Frontmatter
84 tokensAlways available to the agent
SKILL.md
2,229 tokensWhen the skill is activated
Reference documents
334 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Multi-Factor Scoring
- Processing Prediction
- Self-Similarity Assessment
- Hydrophobicity at Position 2
- Rank Epitopes
- Compare Candidates
- Related Skills
Scripts executed separately
examples/immunogenicity_scoring.py
Files
SKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesSKILL.mdcore8,985 bytesexamples/immunogenicity_scoring.pyruns5,639 bytesusage-guide.mddoc1,406 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-immunoinformatics-mhc-binding-prediction
When your agent uses it
Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
2,136 tokensWhen the skill is activated
Reference documents
385 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- MHCflurry Setup
- MHCflurry Python API
- Interpret Binding Predictions
- Batch Prediction
- Scan Protein Sequence
- MHC Class II Prediction
- Common HLA Alleles
- Related Skills
Scripts executed separately
examples/mhc_binding.py
Files
SKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesSKILL.mdcore8,168 bytesexamples/mhc_binding.pyruns5,165 bytesusage-guide.mddoc1,480 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-immunoinformatics-neoantigen-prediction
When your agent uses it
Identify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides that bind patient HLA and may elicit T-cell responses. Use when identifying vaccine targets or checkpoint inhibitor response biomarkers from tumor sequencing data.
What it loads into context
Frontmatter
79 tokensAlways available to the agent
SKILL.md
2,439 tokensWhen the skill is activated
Reference documents
385 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- pVACtools Pipeline (Ensembl VEP 111+)
- pVACseq Workflow (Ensembl VEP 111+)
- VCF Annotation Requirements (Ensembl VEP 111+)
- Parse pVACseq Results
- Prioritize Neoantigens (Ensembl VEP 111+)
- Alternative: Manual Neoantigen Pipeline (Ensembl VEP 111+)
- Neoantigen Quality Metrics (Ensembl VEP 111+)
- Related Skills
Scripts executed separately
examples/neoantigen_prediction.py
Files
SKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesSKILL.mdcore9,445 bytesexamples/neoantigen_prediction.pyruns5,399 bytesusage-guide.mddoc1,528 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-immunoinformatics-tcr-epitope-binding
When your agent uses it
Predict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to their cognate epitopes or predict TCR targets. Use when analyzing TCR repertoire specificity or identifying antigen-reactive T-cells.
What it loads into context
Frontmatter
84 tokensAlways available to the agent
SKILL.md
2,150 tokensWhen the skill is activated
Reference documents
379 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- ERGO-II Model
- TCR Input Format
- Predict TCR-Epitope Binding
- Match TCRs to Known Epitopes
- TCR Clustering
- Analyze Repertoire Specificity
- Related Skills
Scripts executed separately
examples/tcr_epitope.py
Files
SKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesSKILL.mdcore8,308 bytesexamples/tcr_epitope.pyruns6,526 bytesusage-guide.mddoc1,501 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-isoform-switching
When your agent uses it
Analyzes isoform switching events and functional consequences using IsoformSwitchAnalyzeR. Predicts protein domain changes, NMD sensitivity, ORF alterations, and coding potential shifts between conditions. Use when investigating how splicing changes affect protein function.
What it loads into context
Frontmatter
73 tokensAlways available to the agent
SKILL.md
1,342 tokensWhen the skill is activated
Reference documents
532 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- IsoformSwitchAnalyzeR Workflow
- Functional Annotation
- Consequence Analysis
- Visualization
- Significance Thresholds
- Consequence Types
- Related Skills
Scripts executed separately
examples/isoform_switch_analysis.R
Files
SKILL.mdcore5,833 bytesexamples/isoform_switch_analysis.Rruns4,997 bytesusage-guide.mddoc2,390 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,255 tokensWhen the skill is activated
Reference documents
689 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Pipeline Overview
- Step 0: Pre-Analytical QC
- Step 1: cfDNA Preprocessing with UMI Consensus
- Step 2: Fragment QC Checkpoint
- Step 3a: Tumor Fraction Estimation (sWGS)
- Step 3b: Mutation Detection (Targeted Panel)
- Step 4: CHIP Filtering
- Step 5: Fragmentomics Analysis (Optional)
- Step 6: Longitudinal Tracking
- Complete Pipeline Script
- Related Skills
Scripts executed separately
examples/liquid_biopsy_pipeline.py
Files
SKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesSKILL.mdcore8,596 bytesexamples/liquid_biopsy_pipeline.pyruns5,317 bytesusage-guide.mddoc2,668 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,871 tokensWhen the skill is activated
Reference documents
588 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Installation
- BLAST+ Programs
- Creating BLAST Databases
- Running BLAST Searches
- Code Patterns
- Prebuilt Databases
- Common Errors
- Local vs Remote BLAST
- Decision Tree
- Related Skills
Scripts executed separately
examples/blast_wrapper.pyexamples/create_database.shexamples/reciprocal_best.shexamples/run_blast.sh
Files
SKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesSKILL.mdcore9,674 bytesexamples/blast_wrapper.pyruns3,574 bytesexamples/create_database.shruns563 bytesexamples/reciprocal_best.shruns1,231 bytesexamples/run_blast.shruns660 bytesusage-guide.mddoc2,297 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-long-read-sequencing-clair3-variants
When your agent uses it
Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
2,077 tokensWhen the skill is activated
Reference documents
605 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Usage
- Platform-Specific Models
- Key Parameters
- Region-Specific Calling
- gVCF Output
- Phased Variant Calling
- Quality Filtering
- Python Wrapper
- Comparison with Other Callers
- Troubleshooting
- Docker Usage
- Related Skills
Scripts executed separately
examples/clair3_workflow.sh
Files
SKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesSKILL.mdcore7,389 bytesexamples/clair3_workflow.shruns1,796 bytesusage-guide.mddoc2,382 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-long-read-sequencing-isoseq-analysis
When your agent uses it
Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants.
What it loads into context
Frontmatter
55 tokensAlways available to the agent
SKILL.md
2,415 tokensWhen the skill is activated
Reference documents
313 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- IsoSeq3 Pipeline Overview
- CCS Generation
- Primer Removal with Lima
- Primer File Format
- Refine Full-Length Reads
- Cluster Into Isoforms
- Align to Reference
- Collapse Redundant Isoforms
- SQANTI3 Quality Control
- SQANTI3 Categories
- SQANTI3 Filtering
- Quantification with Pigeon
- TAMA for Annotation Merge
- Python Processing
- Differential Isoform Usage
- Quality Metrics
- Troubleshooting
- Docker/Singularity
- Related Skills
Scripts executed separately
examples/isoseq3_workflow.shexamples/sqanti3_qc.sh
Files
SKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesSKILL.mdcore8,911 bytesexamples/isoseq3_workflow.shruns1,419 bytesexamples/sqanti3_qc.shruns1,538 bytesusage-guide.mddoc1,188 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-long-read-sequencing-nanopore-methylation
When your agent uses it
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
What it loads into context
Frontmatter
68 tokensAlways available to the agent
SKILL.md
816 tokensWhen the skill is activated
Reference documents
396 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Modern Workflow (modkit)
- Basecalling with Methylation
- Region-Specific Analysis
- Sample Summary
- Differential Methylation
- Quality Considerations
- Related Skills
Scripts executed separately
examples/modkit_methylation.sh
Files
SKILL.mdcore3,018 bytesSKILL.mdcore3,018 bytesSKILL.mdcore3,018 bytesSKILL.mdcore3,018 bytesSKILL.mdcore3,018 bytesSKILL.mdcore3,018 bytesexamples/modkit_methylation.shruns4,144 bytesusage-guide.mddoc1,662 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-longitudinal-monitoring
When your agent uses it
Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or detecting molecular relapse before clinical progression.
What it loads into context
Frontmatter
67 tokensAlways available to the agent
SKILL.md
2,024 tokensWhen the skill is activated
Reference documents
350 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Key Metrics
- Tracking Tumor Fraction
- Mutation Tracking
- Relapse Detection
- Visualization
- Clinical Integration
- Related Skills
Scripts executed separately
examples/longitudinal_monitoring.py
Files
SKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesSKILL.mdcore8,648 bytesexamples/longitudinal_monitoring.pyruns4,204 bytesusage-guide.mddoc1,734 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-longread-alignment
When your agent uses it
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,430 tokensWhen the skill is activated
Reference documents
537 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Oxford Nanopore Alignment
- PacBio HiFi Alignment
- PacBio CLR Alignment
- Pre-Build Index for Multiple Runs
- Common Options
- Splice-Aware Alignment (RNA)
- With Junction BED (Known Splice Sites)
- Assembly to Reference Alignment
- Output PAF (Faster, No BAM)
- Keep Secondary and Supplementary
- Filter Alignments
- Multiple FASTQ Files
- Output Statistics
- Convert PAF to BED
- Key Presets
- Key Parameters
- Output Formats
- Related Skills
Scripts executed separately
examples/minimap2_align.sh
Files
SKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesSKILL.mdcore5,277 bytesexamples/minimap2_align.shruns601 bytesusage-guide.mddoc2,050 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-longread-medaka
When your agent uses it
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
1,420 tokensWhen the skill is activated
Reference documents
547 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Consensus Polishing
- Variant Calling (Haploid)
- Step-by-Step Workflow
- List Available Models
- Common Models
- Choose Model Based on Basecaller
- Polish Region Only
- Multiple Rounds of Polishing
- Call Variants from Existing BAM
- Filter VCF Output
- Output Files
- Key Parameters
- GPU Acceleration
- Related Skills
Scripts executed separately
examples/medaka_polish.shexamples/medaka_variant.sh
Files
SKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesSKILL.mdcore5,070 bytesexamples/medaka_polish.shruns670 bytesexamples/medaka_variant.shruns883 bytesusage-guide.mddoc2,090 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-longread-qc
When your agent uses it
Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,642 tokensWhen the skill is activated
Reference documents
524 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- NanoPlot - Visualization
- NanoPlot - Common Options
- NanoStat - Statistics Only
- chopper - Filter Reads
- chopper - Common Options
- NanoFilt - Alternative Filter
- Porechop - Adapter Trimming
- Generate Summary Statistics
- PycoQC - From Basecalling
- Calculate N50
- Parse FASTQ Quality in Python
- NanoPlot Output Files
- Key Parameters - NanoPlot
- Key Parameters - chopper
- Quality Thresholds
- Related Skills
Scripts executed separately
examples/qc_workflow.sh
Files
SKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesSKILL.mdcore6,091 bytesexamples/qc_workflow.shruns1,252 bytesusage-guide.mddoc2,176 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-longread-structural-variants
When your agent uses it
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
1,551 tokensWhen the skill is activated
Reference documents
515 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Sniffles2 - Basic SV Calling
- Sniffles2 - Common Options
- Sniffles2 - Population Calling
- cuteSV - Alternative Caller
- cuteSV - ONT Optimized
- cuteSV - PacBio HiFi Optimized
- SVIM - Another Alternative
- pbsv - PacBio Specific
- Filter SV Calls
- Merge Multiple Callers
- Annotate SVs
- SV Types
- Key Parameters - Sniffles2
- Key Parameters - cuteSV
- Coverage Guidelines
- Related Skills
Scripts executed separately
examples/sv_calling.sh
Files
SKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesSKILL.mdcore5,697 bytesexamples/sv_calling.shruns1,489 bytesusage-guide.mddoc2,153 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,232 tokensWhen the skill is activated
Reference documents
555 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- scVI Reference Mapping (scArches)
- scANVI for Label Transfer
- Prediction Confidence
- Joint Embedding Visualization
- Pre-trained Reference Atlases
- Training Parameters
- Related Skills
Scripts executed separately
examples/scarches_annotation.py
Files
SKILL.mdcore4,758 bytesSKILL.mdcore4,758 bytesSKILL.mdcore4,758 bytesSKILL.mdcore4,758 bytesSKILL.mdcore4,758 bytesSKILL.mdcore4,758 bytesexamples/scarches_annotation.pyruns2,927 bytesusage-guide.mddoc2,404 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,255 tokensWhen the skill is activated
Reference documents
569 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Boruta All-Relevant Selection
- mRMR (Minimum Redundancy Maximum Relevance)
- LASSO Feature Selection
- Univariate Filtering (Pre-filter)
- Combined Pipeline
- Method Comparison
- Stability Selection
- Related Skills
Scripts executed separately
examples/boruta_feature_selection.pyexamples/lasso_biomarker.py
Files
SKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesSKILL.mdcore5,058 bytesexamples/boruta_feature_selection.pyruns2,258 bytesexamples/lasso_biomarker.pyruns2,510 bytesusage-guide.mddoc2,386 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,230 tokensWhen the skill is activated
Reference documents
536 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why Nested CV Matters
- Nested Cross-Validation
- Stratified K-Fold
- Repeated Stratified K-Fold
- Leave-One-Out (Small Datasets)
- Group-Aware Splits
- CV Strategy Selection
- Avoiding Data Leakage
- Related Skills
Scripts executed separately
examples/nested_cv_biomarker.py
Files
SKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesSKILL.mdcore4,745 bytesexamples/nested_cv_biomarker.pyruns2,532 bytesusage-guide.mddoc2,393 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,052 tokensWhen the skill is activated
Reference documents
555 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Workflow
- XGBoost Classifier
- Logistic Regression with Regularization
- ROC Curve Visualization
- Multi-class Classification
- Feature Importance from Trees
- Preprocessing Guidelines
- Related Skills
Scripts executed separately
examples/logistic_regression.pyexamples/rf_xgboost_classifier.py
Files
SKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesSKILL.mdcore4,248 bytesexamples/logistic_regression.pyruns2,003 bytesexamples/rf_xgboost_classifier.pyruns2,600 bytesusage-guide.mddoc2,449 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,156 tokensWhen the skill is activated
Reference documents
563 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- SHAP TreeExplainer (v0.47+ API)
- Summary Plot (Global Feature Importance)
- Force Plot (Individual Prediction)
- SHAP for XGBoost
- LIME (Local Interpretable Model-agnostic Explanations)
- Extract Top Features from SHAP
- Dependence Plot (Feature Interactions)
- Multi-class SHAP
- Related Skills
Scripts executed separately
examples/lime_explanation.pyexamples/shap_omics_classifier.py
Files
SKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesSKILL.mdcore4,537 bytesexamples/lime_explanation.pyruns2,141 bytesexamples/shap_omics_classifier.pyruns2,288 bytesusage-guide.mddoc2,344 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,312 tokensWhen the skill is activated
Reference documents
616 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Kaplan-Meier Curves
- Compare Groups with Log-Rank Test
- Cox Proportional Hazards Regression
- Multivariate Cox Model
- Predict Risk Scores
- Check Proportional Hazards Assumption
- Survival at Specific Time
- Feature Selection for Survival
- Related Skills
Scripts executed separately
examples/cox_regression.pyexamples/kaplan_meier.py
Files
SKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesSKILL.mdcore4,806 bytesexamples/cox_regression.pyruns2,829 bytesexamples/kaplan_meier.pyruns2,036 bytesusage-guide.mddoc2,657 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-lipidomics
When your agent uses it
Specialized lipidomics analysis for lipid identification, quantification, and pathway interpretation. Covers LC-MS lipidomics with LipidSearch, MS-DIAL, and LipidMaps annotation. Use when analyzing lipid classes, chain composition, or lipid-specific pathways.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,902 tokensWhen the skill is activated
Reference documents
710 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- R Workflow with lipidr
- Lipid Annotation
- Normalization
- Differential Analysis
- Enrichment Analysis
- Python Workflow with LipidFinder
- MS-DIAL Lipidomics
- Lipid Class Visualization
- Pathway Mapping
- Saturation Analysis
- Export Results
- Related Skills
Files
SKILL.mdcore7,307 bytesSKILL.mdcore7,307 bytesexamples/lipidomics_workflow.Rasset5,190 bytesusage-guide.mddoc2,842 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-metabolite-annotation
When your agent uses it
Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
1,857 tokensWhen the skill is activated
Reference documents
645 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Database Matching by m/z
- MS/MS Spectral Matching
- SIRIUS + CSI:FingerID
- MetFrag In Silico Fragmentation
- RT Prediction for Validation
- Confidence Levels (MSI)
- CAMERA Adduct Annotation
- Batch Annotation Pipeline
- Export Annotated Results
- Related Skills
Scripts executed separately
examples/annotate_features.py
Files
SKILL.mdcore7,284 bytesSKILL.mdcore7,284 bytesSKILL.mdcore7,284 bytesSKILL.mdcore7,284 bytesexamples/annotate_features.pyruns1,865 bytesusage-guide.mddoc2,565 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-msdial-preprocessing
When your agent uses it
MS-DIAL-based metabolomics preprocessing as alternative to XCMS. Covers peak detection, alignment, annotation, and export for downstream analysis. Use when processing MS-DIAL output files for R/Python analysis or when preferring GUI-based preprocessing.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,385 tokensWhen the skill is activated
Reference documents
722 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- MS-DIAL GUI Workflow
- Export MS-DIAL Results to R
- Filter MS-DIAL Results
- MS-DIAL Data to XCMS-Like Format
- MS-DIAL Batch Processing (Console Mode)
- Parameter File Example
- Python Processing of MS-DIAL Output
- MS-DIAL Annotation Levels
- Compare MS-DIAL vs XCMS Results
- Export for MetaboAnalyst
- Normalization Options
- Related Skills
Files
SKILL.mdcore9,327 bytesSKILL.mdcore9,327 bytesSKILL.mdcore9,327 bytesexamples/process_msdial_output.Rasset5,048 bytesusage-guide.mddoc2,963 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-normalization-qc
When your agent uses it
Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
2,233 tokensWhen the skill is activated
Reference documents
582 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load and Inspect Data
- QC-Based Normalization (QC-RSC)
- Total Ion Current (TIC) Normalization
- Probabilistic Quotient Normalization (PQN)
- Batch Correction (ComBat)
- Missing Value Handling
- Data Transformation
- QC Assessment
- Quality Report
- Related Skills
Files
SKILL.mdcore9,092 bytesexamples/normalize_data.Rasset1,336 bytesusage-guide.mddoc2,382 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-pathway-mapping
When your agent uses it
Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
1,838 tokensWhen the skill is activated
Reference documents
635 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- KEGG Pathway Enrichment
- Quantitative Enrichment Analysis (QEA)
- Topology-Based Analysis
- Reactome Pathways
- KEGG Mapper (Direct API)
- Pathway Visualization
- Network-Based Analysis
- Metabolite Set Enrichment
- Combine with Gene Expression
- Export Results
- Related Skills
Files
SKILL.mdcore6,589 bytesexamples/pathway_analysis.Rasset1,301 bytesusage-guide.mddoc2,732 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-statistical-analysis
When your agent uses it
Statistical analysis for metabolomics data. Covers univariate testing, multivariate methods (PCA, PLS-DA), and biomarker discovery. Use when identifying differentially abundant metabolites or building classification models.
What it loads into context
Frontmatter
64 tokensAlways available to the agent
SKILL.md
2,265 tokensWhen the skill is activated
Reference documents
686 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Univariate Analysis
- Fold Change Calculation
- Volcano Plot
- PCA
- PLS-DA
- sPLS-DA (Sparse)
- OPLS-DA (Orthogonal PLS-DA)
- Random Forest
- ROC Analysis
- Heatmap
- Related Skills
Files
SKILL.mdcore8,676 bytesexamples/metabolomics_stats.Rasset1,593 bytesusage-guide.mddoc2,715 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-targeted-analysis
When your agent uses it
Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves and internal standards.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
2,786 tokensWhen the skill is activated
Reference documents
740 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Skyline Data Export Processing
- Standard Curve Fitting
- Calculate Concentrations
- Internal Standard Normalization
- Method Validation Metrics
- Limit of Detection/Quantification
- Multi-Compound Analysis
- Python Workflow
- Quality Control
- Export Results
- Related Skills
Files
SKILL.mdcore9,931 bytesSKILL.mdcore9,931 bytesexamples/targeted_quantification.Rasset4,597 bytesusage-guide.mddoc3,064 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metabolomics-xcms-preprocessing
When your agent uses it
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
2,052 tokensWhen the skill is activated
Reference documents
573 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Load Raw Data
- Define Sample Groups
- Peak Detection (Centroided)
- Peak Detection (Profile Data)
- Retention Time Alignment
- Peak Correspondence (Grouping)
- Gap Filling
- Extract Feature Table
- Quality Control
- CAMERA Annotation (Isotopes/Adducts)
- Export for MetaboAnalyst
- Related Skills
Files
SKILL.mdcore7,994 bytesexamples/xcms_workflow.Rasset1,729 bytesusage-guide.mddoc2,379 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-abundance
When your agent uses it
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates. Use when accurate species-level abundances are needed from Kraken2 classification output.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
1,581 tokensWhen the skill is activated
Reference documents
541 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Abundance Estimation
- Full Workflow with Kraken2
- Different Taxonomic Levels
- Build Bracken Database
- Output Format
- Filter Low-Abundance Taxa
- Combine Multiple Samples
- Parse Bracken Output in Python
- Convert to Relative Abundance
- Create Abundance Matrix
- Key Parameters
- Taxonomic Levels
- Read Length Options
- Related Skills
Scripts executed separately
examples/bracken_abundance.sh
Files
SKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesSKILL.mdcore5,892 bytesexamples/bracken_abundance.shruns875 bytesusage-guide.mddoc2,299 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-amr-detection
When your agent uses it
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
What it loads into context
Frontmatter
70 tokensAlways available to the agent
SKILL.md
1,958 tokensWhen the skill is activated
Reference documents
628 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Tool Comparison
- AMRFinderPlus (NCBI)
- ResFinder
- CARD/RGI
- ABRicate (Quick Screening)
- Metagenome AMR Profiling
- Complete Workflow
- Summarize Results
- Related Skills
Scripts executed separately
examples/batch_amr_screening.pyexamples/run_amrfinder.sh
Files
SKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesSKILL.mdcore7,217 bytesexamples/batch_amr_screening.pyruns2,060 bytesexamples/run_amrfinder.shruns814 bytesusage-guide.mddoc2,626 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-functional-profiling
When your agent uses it
Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
What it loads into context
Frontmatter
59 tokensAlways available to the agent
SKILL.md
1,988 tokensWhen the skill is activated
Reference documents
660 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- HUMAnN3 Workflow
- Output Format
- Batch Processing
- Normalization
- Regroup Gene Families
- Stratification
- Quality Control
- Differential Analysis
- Visualization
- Related Skills
Scripts executed separately
examples/humann_workflow.sh
Files
SKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesSKILL.mdcore7,529 bytesexamples/humann_workflow.shruns1,174 bytesusage-guide.mddoc2,622 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-kraken
When your agent uses it
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when performing initial taxonomic classification of shotgun metagenomic reads before abundance estimation with Bracken.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
1,513 tokensWhen the skill is activated
Reference documents
538 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Classification
- Paired-End Reads
- Common Options
- Memory-Efficient Mode
- Report Only (No Per-Read Output)
- Classified/Unclassified Output
- Build Custom Database
- Add Custom Sequences
- Inspect Database
- Report Format
- Parse Kraken Output in Python
- Filter Report by Rank
- Key Parameters
- Database Libraries
- Related Skills
Scripts executed separately
examples/kraken2_classify.sh
Files
SKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesSKILL.mdcore5,819 bytesexamples/kraken2_classify.shruns1,149 bytesusage-guide.mddoc2,220 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-metaphlan
When your agent uses it
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
What it loads into context
Frontmatter
77 tokensAlways available to the agent
SKILL.md
1,722 tokensWhen the skill is activated
Reference documents
630 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Profiling
- Paired-End Reads
- Save Mapping Output for Reuse
- Long-Read Support (MetaPhlAn 4+)
- Common Options
- Install Database
- Analysis Types
- Multiple Samples
- Filter by Taxonomic Level
- Output Format
- Parse Output in Python
- Extract SGBs (Strain-level)
- Sample Metadata in Output
- Key Parameters
- Analysis Types (-t)
- Related Skills
Scripts executed separately
examples/metaphlan_profile.sh
Files
SKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesSKILL.mdcore6,301 bytesexamples/metaphlan_profile.shruns863 bytesusage-guide.mddoc2,589 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-strain-tracking
When your agent uses it
Track bacterial strains using MASH, sourmash, fastANI, and inStrain. Compare genomes, detect contamination, and monitor strain-level variation. Use when needing sub-species resolution for outbreak tracking, transmission analysis, or within-host strain dynamics.
What it loads into context
Frontmatter
74 tokensAlways available to the agent
SKILL.md
2,044 tokensWhen the skill is activated
Reference documents
657 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Tool Comparison
- MASH
- sourmash
- fastANI
- inStrain
- Complete Workflow: Outbreak Tracking
- Python Analysis
- Related Skills
Scripts executed separately
examples/mash_comparison.shexamples/sourmash_gather.py
Files
SKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesSKILL.mdcore7,682 bytesexamples/mash_comparison.shruns1,058 bytesexamples/sourmash_gather.pyruns2,089 bytesusage-guide.mddoc2,648 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-metagenomics-visualization
When your agent uses it
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses. Use when creating publication-quality figures from MetaPhlAn, Bracken, or other taxonomic profiling output.
What it loads into context
Frontmatter
85 tokensAlways available to the agent
SKILL.md
1,933 tokensWhen the skill is activated
Reference documents
576 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Python - Stacked Bar Plot
- Python - Heatmap
- Python - PCA
- R - phyloseq Setup
- R - Stacked Bar Plot
- R - Ordination (PCoA)
- R - Alpha Diversity
- R - Beta Diversity (PERMANOVA)
- Krona Chart
- Key Packages
- Related Skills
Scripts executed separately
examples/visualization_python.py
Files
SKILL.mdcore7,089 bytesSKILL.mdcore7,089 bytesSKILL.mdcore7,089 bytesSKILL.mdcore7,089 bytesSKILL.mdcore7,089 bytesexamples/visualization_phyloseq.Rasset2,166 bytesexamples/visualization_python.pyruns2,053 bytesusage-guide.mddoc2,337 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-methylation-based-detection
When your agent uses it
Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease.
What it loads into context
Frontmatter
86 tokensAlways available to the agent
SKILL.md
1,717 tokensWhen the skill is activated
Reference documents
429 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Methods Overview
- MethylDackel Pipeline
- Python Implementation
- DMR Detection
- Tissue Deconvolution
- MCED Panel Analysis
- cfMeDIP-seq Analysis
- Related Skills
Scripts executed separately
examples/cfdna_methylation.py
Files
SKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesSKILL.mdcore6,986 bytesexamples/cfdna_methylation.pyruns2,822 bytesusage-guide.mddoc1,838 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-methylation-bismark-alignment
When your agent uses it
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
What it loads into context
Frontmatter
79 tokensAlways available to the agent
SKILL.md
1,499 tokensWhen the skill is activated
Reference documents
541 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Prepare Genome Index
- Basic Single-End Alignment
- Paired-End Alignment
- Common Options
- RRBS Mode
- PBAT Libraries
- Non-Directional Libraries
- With Quality/Adapter Trimming (Pre-alignment)
- Multicore Processing
- Output Files
- Sort and Index BAM
- Deduplicate (Optional)
- Check Alignment Statistics
- Genome Preparation with HISAT2 (Recommended for Large Genomes)
- Key Parameters
- Library Types
- Related Skills
Scripts executed separately
examples/bismark_basic.sh
Files
SKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesSKILL.mdcore5,493 bytesexamples/bismark_basic.shruns684 bytesusage-guide.mddoc2,220 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-methylation-calling
When your agent uses it
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
1,558 tokensWhen the skill is activated
Reference documents
532 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Extraction
- Paired-End Extraction
- Common Options
- CpG Context Only
- Genome-Wide Cytosine Report
- Strand-Specific Output
- Avoid Double-Counting Overlapping Reads
- Generate Coverage File
- Convert to BigWig for Visualization
- M-Bias Plot
- Ignore End Bias
- Output Files
- Parse Output in Python
- Key Parameters
- Output Formats
- Related Skills
Scripts executed separately
examples/extract_methylation.sh
Files
SKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesSKILL.mdcore5,997 bytesexamples/extract_methylation.shruns539 bytesusage-guide.mddoc2,167 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-methylation-dmr-detection
When your agent uses it
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
1,615 tokensWhen the skill is activated
Reference documents
740 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- methylKit Tile-Based DMRs
- bsseq BSmooth DMRs
- DMRcate Method
- Annotate DMRs with Genes
- Annotate with genomation
- Visualize DMR
- Merge Adjacent DMRs
- Export DMRs
- DMR Comparison Across Methods
- Key Parameters
- Related Skills
Files
SKILL.mdcore5,901 bytesexamples/dmr_methylkit.Rasset2,329 bytesusage-guide.mddoc2,961 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-methylation-methylkit
When your agent uses it
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,654 tokensWhen the skill is activated
Reference documents
620 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Read Bismark Coverage Files
- Read Bismark cytosine Report
- Basic Statistics
- Filter by Coverage
- Normalize Coverage
- Merge Samples (Unite)
- Visualize Samples
- Differential Methylation (Single CpGs)
- Tile-Based Analysis (Regions)
- Export Results
- Annotate with Genomic Features
- Reorganize for Multi-Group Comparison
- Pool Replicates
- Key Functions
- Key Parameters for calculateDiffMeth
- Related Skills
Files
SKILL.mdcore6,150 bytesexamples/methylkit_analysis.Rasset1,793 bytesusage-guide.mddoc2,629 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-amplicon-processing
When your agent uses it
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.
What it loads into context
Frontmatter
91 tokensAlways available to the agent
SKILL.md
1,164 tokensWhen the skill is activated
Reference documents
622 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Complete DADA2 Workflow
- Quality Filtering and Trimming
- Error Rate Learning
- Sample Inference (Denoising)
- Merge Paired Reads
- Construct Sequence Table
- Remove Chimeras
- Track Reads Through Pipeline
- ITS-Specific Processing
- Related Skills
Files
SKILL.mdcore4,380 bytesexamples/dada2_workflow.Rasset2,542 bytesusage-guide.mddoc2,436 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-differential-abundance
When your agent uses it
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
1,364 tokensWhen the skill is activated
Reference documents
565 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- The Compositionality Problem
- ALDEx2 (Recommended)
- ANCOM-BC2 (Recommended)
- MaAsLin2
- DESeq2 (with caution)
- Visualization
- Method Comparison
- Related Skills
Files
SKILL.mdcore4,984 bytesexamples/aldex2_analysis.Rasset3,072 bytesusage-guide.mddoc2,305 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-diversity-analysis
When your agent uses it
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
1,523 tokensWhen the skill is activated
Reference documents
708 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Create phyloseq Object
- Alpha Diversity
- Alpha Diversity Plots
- Faith's Phylogenetic Diversity
- Rarefaction Curves
- Rarefaction
- Beta Diversity
- PERMANOVA
- Beta Dispersion
- NMDS Ordination
- Distance Metrics Comparison
- Related Skills
Files
SKILL.mdcore5,640 bytesexamples/diversity_analysis.Rasset2,763 bytesusage-guide.mddoc3,085 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-functional-prediction
When your agent uses it
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun metagenomics sequencing.
What it loads into context
Frontmatter
81 tokensAlways available to the agent
SKILL.md
1,325 tokensWhen the skill is activated
Reference documents
634 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Prepare Input Files
- Run PICRUSt2 Pipeline
- Step-by-Step Pipeline
- Quality Control: NSTI
- Analyze Pathway Output
- Add Pathway Descriptions
- KEGG Module Analysis
- Limitations
- Related Skills
Scripts executed separately
examples/run_picrust2.sh
Files
SKILL.mdcore4,752 bytesSKILL.mdcore4,752 bytesSKILL.mdcore4,752 bytesSKILL.mdcore4,752 bytesSKILL.mdcore4,752 bytesexamples/run_picrust2.shruns1,996 bytesusage-guide.mddoc2,554 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-qiime2-workflow
When your agent uses it
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.
What it loads into context
Frontmatter
84 tokensAlways available to the agent
SKILL.md
1,761 tokensWhen the skill is activated
Reference documents
729 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Import Data
- Denoise with DADA2
- Alternative: Deblur Denoising
- Taxonomy Assignment
- Phylogenetic Tree
- Diversity Analysis
- Differential Abundance (ANCOM)
- Export to R/Python
- Manifest File Format
- Metadata File Format
- Related Skills
Scripts executed separately
examples/qiime2_16s.sh
Files
SKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesSKILL.mdcore6,220 bytesexamples/qiime2_16s.shruns2,750 bytesusage-guide.mddoc2,729 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-microbiome-taxonomy-assignment
When your agent uses it
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.
What it loads into context
Frontmatter
80 tokensAlways available to the agent
SKILL.md
1,499 tokensWhen the skill is activated
Reference documents
600 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- DADA2 Naive Bayes Classifier
- GTDB for 16S
- UNITE for ITS (Fungi)
- QIIME2 Feature Classifier
- VSEARCH Exact Matching
- RDP Classifier
- IDTAXA (DECIPHER) - Often More Accurate
- Confidence Filtering
- Combine into phyloseq
- Database Comparison
- Related Skills
Files
SKILL.mdcore5,333 bytesSKILL.mdcore5,333 bytesSKILL.mdcore5,333 bytesexamples/assign_silva.Rasset1,565 bytesusage-guide.mddoc2,353 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-molecular-descriptors
When your agent uses it
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.
What it loads into context
Frontmatter
80 tokensAlways available to the agent
SKILL.md
1,642 tokensWhen the skill is activated
Reference documents
445 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Morgan Fingerprints (ECFP)
- MACCS Keys
- Lipinski Properties
- QED Drug-Likeness
- Complete Descriptor Set
- 3D Conformer Descriptors
- Batch Descriptor Calculation
- Related Skills
Scripts executed separately
examples/calculate_descriptors.py
Files
SKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesSKILL.mdcore6,344 bytesexamples/calculate_descriptors.pyruns4,514 bytesusage-guide.mddoc1,858 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-molecular-io
When your agent uses it
Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.
What it loads into context
Frontmatter
88 tokensAlways available to the agent
SKILL.md
1,465 tokensWhen the skill is activated
Reference documents
440 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Supported Formats
- Reading Molecules
- Writing Molecules
- Structure Standardization
- Open Babel Conversion
- Molecular Drawing
- Related Skills
Scripts executed separately
examples/molecule_io.py
Files
SKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesSKILL.mdcore5,841 bytesexamples/molecule_io.pyruns4,729 bytesusage-guide.mddoc1,977 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,616 tokensWhen the skill is activated
Reference documents
566 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Imports
- Core Methods
- Code Patterns
- Bio.motifs Module
- Reading Motif Files
- Common Motif Patterns
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_search.pyexamples/motif_files.pyexamples/pwm_search.pyexamples/regex_search.py
Files
SKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesSKILL.mdcore9,495 bytesexamples/basic_search.pyruns1,729 bytesexamples/motif_files.pyruns2,278 bytesexamples/pwm_search.pyruns2,453 bytesexamples/regex_search.pyruns1,893 bytesusage-guide.mddoc2,267 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-multi-omics-data-harmonization
When your agent uses it
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.
What it loads into context
Frontmatter
67 tokensAlways available to the agent
SKILL.md
1,954 tokensWhen the skill is activated
Reference documents
599 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- MultiAssayExperiment Structure
- Normalization Per Assay
- Cross-Omics Batch Correction
- Feature Alignment (Gene-Level)
- Missing Value Handling
- Sample Matching and Subsetting
- Scale and Center
- Export Harmonized Data
- Related Skills
Files
SKILL.mdcore7,477 bytesexamples/harmonize_data.Rasset1,944 bytesusage-guide.mddoc2,580 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-multi-omics-mixomics-analysis
When your agent uses it
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate between groups.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
2,041 tokensWhen the skill is activated
Reference documents
599 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Setup and Data Preparation
- Pairwise Integration: sPLS
- DIABLO: Multi-Block Discriminant Analysis
- DIABLO Visualization
- Extract Selected Features
- MINT: Multi-Study Integration
- Unsupervised: sPCA and sPLS-DA Single Omics
- Model Performance and Validation
- Related Skills
Files
SKILL.mdcore7,739 bytesexamples/diablo_workflow.Rasset1,372 bytesusage-guide.mddoc2,448 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-multi-omics-mofa-integration
When your agent uses it
Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.
What it loads into context
Frontmatter
83 tokensAlways available to the agent
SKILL.md
1,900 tokensWhen the skill is activated
Reference documents
530 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Prepare Multi-Omics Data
- Create and Train MOFA Model
- Analyze Factors
- Visualize Results
- Factor Interpretation
- Add Sample Metadata
- Multi-Group MOFA
- MOFA+ for Single-Cell
- Export Results
- Related Skills
Files
SKILL.mdcore7,632 bytesexamples/mofa_workflow.Rasset2,079 bytesusage-guide.mddoc2,239 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-multi-omics-similarity-network
When your agent uses it
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,935 tokensWhen the skill is activated
Reference documents
498 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic SNF Workflow
- Cluster Patients
- Visualize Network
- Normalized Mutual Information
- Feature Ranking with SNF
- Survival Analysis with Clusters
- Parameter Tuning
- Integration with Clinical Features
- Related Skills
Files
SKILL.mdcore7,485 bytesexamples/snf_clustering.Rasset1,363 bytesusage-guide.mddoc2,229 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-orchestrator
When your agent uses it
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
What it loads into context
Frontmatter
146 tokensAlways available to the agent
SKILL.md
1,314 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Routing Table
- Decision Process
- File Type Detection
- Report Template
- Multi-Skill Chaining Example
- Safety Rules
- Example Queries
Scripts executed separately
orchestrator.py
Files
SKILL.mdcore5,129 bytesSKILL.mdcore5,129 bytesSKILL.mdcore5,129 bytesorchestrator.pyruns14,905 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-paired-end-fastq
When your agent uses it
Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.
What it loads into context
Frontmatter
67 tokensAlways available to the agent
SKILL.md
3,030 tokensWhen the skill is activated
Reference documents
420 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Paired File Naming Conventions
- Iterate Pairs Together
- Filter Pairs Together
- Interleave Pairs
- Deinterleave
- Paired Statistics
- Find Paired Files
- Compressed Paired Files
- Common Errors
- Related Skills
Scripts executed separately
examples/paired_end_io.py
Files
SKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesSKILL.mdcore10,246 bytesexamples/paired_end_io.pyruns2,280 bytesusage-guide.mddoc1,569 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-enrichment-visualization
When your agent uses it
Visualize enrichment results using enrichplot package functions. Use when creating publication-quality figures from clusterProfiler results. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2, ridgeplot, and treeplot.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,873 tokensWhen the skill is activated
Reference documents
727 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Scope
- Setup
- Dot Plot
- Bar Plot
- Gene-Concept Network (cnetplot)
- Enrichment Map (emapplot)
- Tree Plot
- Upset Plot
- GSEA-Specific Plots
- GO-Specific Plot (goplot)
- Heatplot
- Compare Multiple Analyses
- Customize ggplot2 Elements
- Save Plots
- Visualization Summary
- Related Skills
Files
SKILL.mdcore7,002 bytesSKILL.mdcore7,002 bytesexamples/visualization_gsea.Rasset1,709 bytesexamples/visualization_ora.Rasset1,235 bytesusage-guide.mddoc3,108 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-go-enrichment
When your agent uses it
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression or other analyses. Supports all three ontologies (BP, MF, CC), multiple ID types, and customizable statistical thresholds.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,746 tokensWhen the skill is activated
Reference documents
599 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Pattern
- Prepare Gene List from DE Results
- ID Conversion with bitr
- With Background Universe
- All Three Ontologies
- Make Results Readable
- Extract and Export Results
- Simplify Redundant Terms
- Different Organisms
- Group GO Terms by Ancestor
- Key Parameters
- Related Skills
Files
SKILL.mdcore6,597 bytesexamples/go_all_ontologies.Rasset1,163 bytesexamples/go_enrichment_basic.Rasset832 bytesusage-guide.mddoc2,618 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-gsea
When your agent uses it
Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.
What it loads into context
Frontmatter
65 tokensAlways available to the agent
SKILL.md
1,893 tokensWhen the skill is activated
Reference documents
750 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Concept
- Prepare Ranked Gene List
- Convert Gene IDs for GSEA
- Alternative Ranking Statistics
- GSEA with GO
- GSEA with KEGG
- GSEA with Custom Gene Sets
- MSigDB Gene Sets
- Understanding Results
- Interpreting NES (Normalized Enrichment Score)
- Key Parameters
- Export Results
- Notes
- Related Skills
Files
SKILL.mdcore7,220 bytesexamples/gsea_go.Rasset1,345 bytesexamples/gsea_msigdb.Rasset1,454 bytesusage-guide.mddoc3,091 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-kegg-pathways
When your agent uses it
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
What it loads into context
Frontmatter
69 tokensAlways available to the agent
SKILL.md
1,815 tokensWhen the skill is activated
Reference documents
618 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Pattern
- Prepare Gene List
- KEGG ID Conversion
- Run KEGG Pathway Enrichment
- Make Results Readable
- KEGG Module Enrichment
- Common Organism Codes
- With Background Universe
- Extract and Export Results
- Browse KEGG Pathways
- Key Parameters
- Compare Multiple Gene Lists
- Notes
- Related Skills
Files
SKILL.mdcore6,789 bytesexamples/kegg_enrichment.Rasset851 bytesexamples/kegg_module.Rasset1,198 bytesusage-guide.mddoc2,572 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-reactome
When your agent uses it
Reactome pathway enrichment using ReactomePA package. Use when analyzing gene lists against Reactome's curated peer-reviewed pathway database. Performs over-representation analysis and GSEA with visualization and pathway hierarchy exploration.
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
1,596 tokensWhen the skill is activated
Reference documents
623 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Pattern - Over-Representation Analysis
- Prepare Gene List from DE Results
- GSEA on Reactome Pathways
- With Background Universe
- Visualization
- View Pathway in Browser
- Export Results
- Different Organisms
- Compare Clusters
- Key Parameters
- Supported Organisms
- Related Skills
Files
SKILL.mdcore6,289 bytesexamples/reactome_gsea.Rasset925 bytesexamples/reactome_ora.Rasset902 bytesusage-guide.mddoc2,675 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pathway-wikipathways
When your agent uses it
WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
1,817 tokensWhen the skill is activated
Reference documents
694 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Core Pattern - Over-Representation Analysis
- Prepare Gene List
- GSEA on WikiPathways
- With Background Universe
- Make Results Readable
- Visualization
- Using rWikiPathways Directly
- Custom GMT-Based Analysis
- Different Organisms
- Compare Clusters
- Export Results
- Key Parameters
- Common Organisms
- WikiPathways vs Other Databases
- Related Skills
Files
SKILL.mdcore6,912 bytesSKILL.mdcore6,912 bytesSKILL.mdcore6,912 bytesexamples/wikipathways_explore.Rasset598 bytesexamples/wikipathways_ora.Rasset924 bytesusage-guide.mddoc2,934 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pdb-geometric-analysis
When your agent uses it
Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).
What it loads into context
Frontmatter
68 tokensAlways available to the agent
SKILL.md
3,573 tokensWhen the skill is activated
Reference documents
578 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Distance Between Atoms
- Distance Matrix
- Angle Between Three Atoms
- Dihedral Angles
- Ramachandran Angles for All Residues
- Finding Neighbor Atoms
- Finding Residue Contacts
- Contact Levels
- Superimposing Structures
- Calculating RMSD
- CEAligner for Dissimilar Structures
- Center of Mass
- Radius of Gyration
- Finding Surface Residues
- Vector Operations
- Chi Angles (Sidechain Dihedrals)
- Solvent Accessible Surface Area (SASA)
- SASA with Custom Parameters
- Identifying Buried vs Exposed Residues
- Related Skills
Scripts executed separately
examples/find_contacts.pyexamples/measure_distance.pyexamples/superimpose.py
Files
SKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesSKILL.mdcore12,685 bytesexamples/find_contacts.pyruns861 bytesexamples/measure_distance.pyruns885 bytesexamples/superimpose.pyruns900 bytesusage-guide.mddoc2,426 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pdb-structure-io
When your agent uses it
Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.
What it loads into context
Frontmatter
69 tokensAlways available to the agent
SKILL.md
2,141 tokensWhen the skill is activated
Reference documents
510 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Supported Formats
- Parsing PDB Files
- Parsing mmCIF Files
- Parsing MMTF Files
- Parsing BinaryCIF Files
- Downloading from RCSB PDB
- Batch Downloading
- Writing PDB Files
- Writing mmCIF Files
- Selective Output with Select Class
- Select Class Methods
- Extracting Header Information
- mmCIF Metadata with MMCIF2Dict
- Quick Structure Inspection
- Format Conversion
- Writing PQR Files
- Handling Parser Warnings
- Related Skills
Scripts executed separately
examples/download_structure.pyexamples/extract_chain.pyexamples/parse_pdb.py
Files
SKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesSKILL.mdcore7,698 bytesexamples/download_structure.pyruns469 bytesexamples/extract_chain.pyruns552 bytesexamples/parse_pdb.pyruns658 bytesusage-guide.mddoc2,044 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pdb-structure-modification
When your agent uses it
Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.
What it loads into context
Frontmatter
62 tokensAlways available to the agent
SKILL.md
3,303 tokensWhen the skill is activated
Reference documents
513 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- Transforming Coordinates
- Rotation Around Axis
- Applying Transformation Matrix
- Center Structure at Origin
- Removing Atoms
- Removing Residues
- Removing a Chain
- Modifying B-factors
- Modifying Occupancy
- Renumbering Residues
- Changing Chain ID
- Building Structure from Scratch
- Using StructureBuilder
- Adding a Residue to Existing Chain
- Copying a Chain
- Extract and Save Specific Residues
- Merge Two Structures
- Related Skills
Scripts executed separately
examples/modify_bfactor.pyexamples/remove_water.pyexamples/transform_coords.py
Files
SKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesSKILL.mdcore11,130 bytesexamples/modify_bfactor.pyruns716 bytesexamples/remove_water.pyruns657 bytesexamples/transform_coords.pyruns704 bytesusage-guide.mddoc2,096 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-pdb-structure-navigation
When your agent uses it
Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
2,406 tokensWhen the skill is activated
Reference documents
510 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Imports
- SMCRA Hierarchy
- Accessing Hierarchy Levels
- Iterating Over Structure
- Residue Identification
- Atom Properties
- Getting Full Identifiers
- Checking for Children
- Getting Parent Entity
- Extracting Polypeptide Sequences
- Using CaPPBuilder for Broken Chains
- Converting Residue Names
- Using Selection.unfold_entities
- Handling Disordered Atoms
- Handling Disordered Residues
- Finding Specific Atoms
- Filtering by Residue Type
- Counting Entities
- Working with NMR Ensembles
- Related Skills
Scripts executed separately
examples/extract_sequence.pyexamples/find_ligands.pyexamples/iterate_structure.py
Files
SKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesSKILL.mdcore9,049 bytesexamples/extract_sequence.pyruns459 bytesexamples/find_ligands.pyruns593 bytesexamples/iterate_structure.pyruns861 bytesusage-guide.mddoc2,044 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,549 tokensWhen the skill is activated
Reference documents
1,669 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Beagle Imputation
- Beagle with Options
- Impute Per Chromosome
- IMPUTE5 (Alternative)
- Minimac4 (Michigan Imputation Server)
- Input Preparation
- Extract Imputation Quality
- Output Formats
- Using Dosages for GWAS
- Quality Thresholds
- Key Parameters
- Imputation Servers
- Related Skills
Scripts executed separately
examples/run_beagle_imputation.sh
Files
SKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesexamples/run_beagle_imputation.shruns578 bytesusage-guide.mddoc5,538 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,392 tokensWhen the skill is activated
Reference documents
1,360 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Beagle 5.4 Phasing (Recommended)
- Beagle Options
- Phase Per Chromosome
- SHAPEIT5 Phasing (for Large Datasets)
- SHAPEIT5 with Reference Panel
- Beagle with Reference Panel
- Input Preparation
- Check Phasing Results
- Genetic Maps
- Key Parameters
- Memory Requirements
- Phasing Accuracy Metrics
- Related Skills
Scripts executed separately
examples/run_shapeit.sh
Files
SKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesSKILL.mdcore4,811 bytesexamples/run_shapeit.shruns565 bytesusage-guide.mddoc4,724 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,514 tokensWhen the skill is activated
Reference documents
2,152 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Extract INFO Scores
- Filter by INFO Score
- INFO Score Distribution
- Summarize Imputation Quality
- Check Concordance with Typed Variants
- Python: Comprehensive QC Report
- Compare Multiple Imputation Runs
- Hardy-Weinberg Filter
- Final QC Pipeline
- Quality Thresholds by Application
- Related Skills
Scripts executed separately
examples/imputation_qc.py
Files
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SKILL.md
1,608 tokensWhen the skill is activated
Reference documents
1,749 tokensLoaded on request
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The playbook
- 1000 Genomes Phase 3 (GRCh38)
- Subset by Population
- Convert to Beagle Format
- Convert to IMPUTE5 Format
- HRC Reference Panel
- TOPMed Reference Panel
- Genetic Maps
- Check Reference Panel
- Lift Over Reference Panel
- Align Study to Reference
- Filter Reference Panel
- Merge Custom Panel with 1000G
- Reference Panel Comparison
- Related Skills
Scripts executed separately
examples/download_reference.sh
Files
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SKILL.md
2,226 tokensWhen the skill is activated
Reference documents
558 tokensLoaded on request
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The playbook
- Required Import
- Distance Matrix from Alignment
- Available Distance Models
- Building Trees with Distance Methods
- Pairwise Distances Between Taxa
- Creating Distance Matrix Manually
- Parsimony Tree Construction
- Bootstrap Analysis
- Consensus Tree Methods
- Tree Depths and Total Length
- Comparing Tree Distances
- Complete Pipeline: Alignment to Bootstrapped Tree
- Quick Reference: Distance Models
- Related Skills
Scripts executed separately
examples/bootstrap_consensus.pyexamples/build_nj_tree.pyexamples/pairwise_tree_distances.py
Files
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0 tokensAlways available to the agent
SKILL.md
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Reference documents
763 tokensLoaded on request
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The playbook
- IQ-TREE2 Basic Usage
- IQ-TREE2 Output Files
- Model Selection
- Common DNA Substitution Models
- Ultrafast Bootstrap
- Interpreting Bootstrap Values
- Partitioned Analysis
- RAxML-ng Basic Usage
- RAxML-ng Model Specification
- RAxML-ng Output Files
- RAxML-ng Advanced Options
- Comparing IQ-TREE2 vs RAxML-ng
- Large Dataset Strategies
- Tree Topology Tests
- Constrained Analysis
- Complete Workflow Example
- Resuming Interrupted Runs
- Reproducibility
- Related Skills
Scripts executed separately
examples/iqtree_basic.shexamples/partitioned_analysis.shexamples/raxml_analysis.sh
Files
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SKILL.md
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The playbook
- Required Import
- Supported Formats
- Reading Trees
- Writing Trees
- Serialize to String
- Format Conversion
- Quick Tree Inspection
- Accessing Tree Structure
- Tree from Newick String Patterns
- Working with PhyloXML Metadata
- Handling Multiple Trees
- Iterating Over Large Tree Files
- Common Newick Format Variations
- Error Handling
- Format-Specific Notes
- Related Skills
Scripts executed separately
examples/convert_formats.pyexamples/parse_multiple_trees.pyexamples/read_newick.py
Files
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0 tokensAlways available to the agent
SKILL.md
2,519 tokensWhen the skill is activated
Reference documents
569 tokensLoaded on request
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The playbook
- Required Import
- Rooting Trees
- Ladderizing
- Pruning Trees
- Collapsing Clades
- Extracting Subtrees
- Tree Traversal
- Finding Clades
- Getting Path Between Nodes
- Checking Tree Properties
- Modifying Branch Lengths
- Renaming Taxa
- Counting Nodes
- Tree Depths
- Splitting Clades
- Generating Random Trees
- Quick Reference: Tree Methods
- Related Skills
Scripts executed separately
examples/common_ancestor.pyexamples/prune_taxa.pyexamples/root_tree.py
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,831 tokensWhen the skill is activated
Reference documents
546 tokensLoaded on request
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The playbook
- Required Import
- ASCII Tree Display
- Basic Tree Drawing
- Customizing Tree Appearance
- Label Customization
- Branch Labels (Bootstrap, Lengths)
- Coloring Trees
- Highlighting Clades
- Multiple Output Formats
- Figure Size and Layout
- Phylo.draw() Parameters
- Pre-Processing for Better Visualization
- Side-by-Side Tree Comparison
- Hide Axis and Frame
- Deprecated Functions
- Common Issues
- Related Skills
Scripts executed separately
examples/ascii_tree.pyexamples/basic_tree_plot.pyexamples/labeled_tree.py
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,449 tokensWhen the skill is activated
Reference documents
2,272 tokensLoaded on request
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The playbook
- What is Pileup?
- samtools mpileup
- Output Format
- Quality Filtering Options
- Variant Calling Pipeline
- pysam Python Alternative
- Pileup Options Summary
- Quick Reference
- Common Errors
- Related Skills
Scripts executed separately
examples/allele_counts.py
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,193 tokensWhen the skill is activated
Reference documents
971 tokensLoaded on request
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The playbook
- PLINK 2.0 Association Testing
- Covariate Files
- GLM Options
- Output Format
- Population Stratification Control
- Result Filtering
- Visualization
- Genomic Inflation
- Related Skills
Scripts executed separately
examples/gwas_pipeline.sh
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,894 tokensWhen the skill is activated
Reference documents
922 tokensLoaded on request
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The playbook
- PLINK LD Calculations
- LD Pruning
- scikit-allel LD
- Haplotype Blocks
- LD Matrix Visualization
- LD-based Clumping (GWAS)
- vcftools LD
- Complete Workflow
- Related Skills
Scripts executed separately
examples/ld_analysis.sh
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,464 tokensWhen the skill is activated
Reference documents
1,094 tokensLoaded on request
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The playbook
- File Formats
- Format Conversion
- Quality Control Filtering
- Sample and Variant Selection
- Allele Frequency
- Missing Data Statistics
- Sex Check
- Sample Information
- Merging Datasets
- Variant Information
- PLINK 2.0 vs 1.9 Summary
- Related Skills
Scripts executed separately
examples/qc_pipeline.sh
Files
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What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,614 tokensWhen the skill is activated
Reference documents
989 tokensLoaded on request
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The playbook
- Principal Component Analysis (PCA)
- LD Pruning (Before Admixture)
- ADMIXTURE Analysis
- FlashPCA2 (Fast PCA for Large Datasets)
- MDS (Alternative to PCA)
- Kinship/Relatedness
- Complete Workflow
- Related Skills
Scripts executed separately
examples/structure_analysis.sh
Files
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What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,068 tokensWhen the skill is activated
Reference documents
895 tokensLoaded on request
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The playbook
- Installation
- Reading VCF Files
- Genotype Arrays
- Allele Counts and Frequencies
- Haplotype Arrays
- PCA
- Diversity Statistics
- Site Frequency Spectrum
- Windowed Statistics
- Sample Subsetting
- Filter Variants
- Complete Workflow Example
- Related Skills
Scripts executed separately
examples/basic_analysis.py
Files
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Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,989 tokensWhen the skill is activated
Reference documents
847 tokensLoaded on request
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The playbook
- Fst - Population Differentiation
- Tajima's D - Departures from Neutrality
- iHS - Integrated Haplotype Score
- XP-EHH - Cross-Population Extended Haplotype Homozygosity
- NSL - Number of Segregating Sites by Length
- Garud's H Statistics
- Composite Selection Score
- Complete Selection Scan
- Related Skills
Scripts executed separately
examples/selection_scan.py
Files
SKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesSKILL.mdcore6,394 bytesexamples/selection_scan.pyruns2,932 bytesusage-guide.mddoc3,627 bytes
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View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,521 tokensWhen the skill is activated
Reference documents
554 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Imports
- Sequence Preparation (p3helpers)
- Basic Primer Design
- Extract Primer Results
- Target a Specific Region
- Primers Must Span a Region
- Exclude Regions
- Constrain Primer Positions
- Design for Sequencing
- Full Parameter Control
- Load Sequence from FASTA
- Calculate Tm Directly
- Calculate Hairpin and Dimer Tm
- Format Results as DataFrame
- Common Global Arguments
- Related Skills
Scripts executed separately
examples/primer_design.py
Files
SKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesSKILL.mdcore8,586 bytesexamples/primer_design.pyruns2,104 bytesusage-guide.mddoc2,114 bytes
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What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
3,332 tokensWhen the skill is activated
Reference documents
507 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Imports
- Check Hairpin Formation
- Check Self-Dimer (Homodimer)
- Check Primer-Primer Dimer (Heterodimer)
- Complete Primer Validation
- Validate Primer Pair
- Calculate End Stability (Native Function)
- Quick Tm-Only Checks (Lightweight)
- Fast Batch Screening with Tm-Only Functions
- Check Specificity (3' End)
- Batch Validation
- Thermodynamic Parameters Under Different Conditions
- Validation Thresholds
- Related Skills
Scripts executed separately
examples/validate_primers.py
Files
SKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesSKILL.mdcore10,572 bytesexamples/validate_primers.pyruns1,913 bytesusage-guide.mddoc1,958 bytes
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What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,441 tokensWhen the skill is activated
Reference documents
561 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Imports
- Design Primers with TaqMan Probe
- Extract Probe Results
- qPCR-Optimized Parameters
- TaqMan Probe Constraints
- SYBR Green Primers (No Probe)
- Design for Exon-Spanning (Avoid Genomic DNA)
- Multiplex Primer Design
- Validate Tm Calculations
- Format qPCR Results
- qPCR Design Guidelines
- Related Skills
Scripts executed separately
examples/qpcr_design.py
Files
SKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesSKILL.mdcore8,150 bytesexamples/qpcr_design.pyruns1,803 bytesusage-guide.mddoc2,118 bytes
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View the complete source on GitHubbio-proteomics-data-import
When your agent uses it
Load and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant proteinGroups.txt. Use when starting a proteomics analysis with raw or processed MS data. Handles contaminant filtering and missing value assessment.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,104 tokensWhen the skill is activated
Reference documents
499 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Loading mzML/mzXML Files with pyOpenMS
- Loading MaxQuant Output
- Loading Spectronaut/DIA-NN Output
- R: Loading with MSnbase
- Missing Value Assessment
- Related Skills
Scripts executed separately
examples/load_maxquant.py
Files
SKILL.mdcore4,648 bytesSKILL.mdcore4,648 bytesSKILL.mdcore4,648 bytesSKILL.mdcore4,648 bytesSKILL.mdcore4,648 bytesexamples/load_maxquant.pyruns1,539 bytesusage-guide.mddoc2,105 bytes
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View the complete source on GitHubbio-proteomics-dia-analysis
When your agent uses it
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
1,835 tokensWhen the skill is activated
Reference documents
640 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- DIA-NN Library-Free Analysis
- DIA-NN with Spectral Library
- DIA-NN Output Files
- Load DIA-NN Results in R
- Load DIA-NN Results in Python
- MSFragger-DIA Analysis
- Spectronaut Export Processing
- DIA Quality Metrics
- Match Between Runs
- DIA vs DDA Comparison
- Related Skills
Scripts executed separately
examples/diann_analysis.sh
Files
SKILL.mdcore7,362 bytesSKILL.mdcore7,362 bytesSKILL.mdcore7,362 bytesSKILL.mdcore7,362 bytesSKILL.mdcore7,362 bytesSKILL.mdcore7,362 bytesexamples/diann_analysis.shruns1,142 bytesusage-guide.mddoc2,785 bytes
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View the complete source on GitHubbio-proteomics-differential-abundance
When your agent uses it
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.
What it loads into context
Frontmatter
58 tokensAlways available to the agent
SKILL.md
1,238 tokensWhen the skill is activated
Reference documents
571 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- MSstats Group Comparison (R stats (base)+)
- limma for Proteomics (R stats (base)+)
- QFeatures/proDA (Modern Alternative)
- Python: scipy/statsmodels
- Visualization (R stats (base)+)
- Related Skills
Files
SKILL.mdcore4,882 bytesSKILL.mdcore4,882 bytesexamples/limma_analysis.Rasset1,226 bytesusage-guide.mddoc2,574 bytes
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View the complete source on GitHubbio-proteomics-peptide-identification
When your agent uses it
Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
946 tokensWhen the skill is activated
Reference documents
582 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Database Search with pyOpenMS
- Working with Search Results (idXML)
- FDR Estimation (Target-Decoy)
- R: Search Result Processing
- Spectral Library Search
- Related Skills
Scripts executed separately
examples/fdr_filtering.py
Files
SKILL.mdcore3,933 bytesSKILL.mdcore3,933 bytesSKILL.mdcore3,933 bytesSKILL.mdcore3,933 bytesSKILL.mdcore3,933 bytesexamples/fdr_filtering.pyruns1,310 bytesusage-guide.mddoc2,366 bytes
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View the complete source on GitHubbio-proteomics-protein-inference
When your agent uses it
Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and protein-level FDR control using parsimony and probabilistic approaches.
What it loads into context
Frontmatter
60 tokensAlways available to the agent
SKILL.md
1,344 tokensWhen the skill is activated
Reference documents
590 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- The Protein Inference Problem
- Parsimony Principle
- Protein Groups
- pyOpenMS Protein Inference
- R: Protein Inference with ProteinInference
- Protein-Level FDR
- Related Skills
Scripts executed separately
examples/protein_groups.py
Files
SKILL.mdcore5,760 bytesSKILL.mdcore5,760 bytesSKILL.mdcore5,760 bytesSKILL.mdcore5,760 bytesSKILL.mdcore5,760 bytesSKILL.mdcore5,760 bytesexamples/protein_groups.pyruns2,140 bytesusage-guide.mddoc2,702 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-proteomics-proteomics-qc
When your agent uses it
Quality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis. Covers sample metrics, missing value patterns, replicate correlation, batch effects, and intensity distributions.
What it loads into context
Frontmatter
61 tokensAlways available to the agent
SKILL.md
1,780 tokensWhen the skill is activated
Reference documents
612 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Sample Quality Metrics
- Replicate Correlation
- Missing Value Patterns
- Batch Effect Detection with PCA
- R: QC with limma
- Coefficient of Variation
- Digestion Efficiency
- QC Report Summary
- Related Skills
Scripts executed separately
examples/qc_analysis.py
Files
SKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesexamples/qc_analysis.pyruns3,609 bytesusage-guide.mddoc2,745 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-proteomics-ptm-analysis
When your agent uses it
Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.
What it loads into context
Frontmatter
68 tokensAlways available to the agent
SKILL.md
1,293 tokensWhen the skill is activated
Reference documents
671 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Common PTMs and Mass Shifts
- Processing MaxQuant PTM Output
- Site Localization Scoring
- Motif Analysis
- R: Site-Level Quantification with MSstatsPTM
- Related Skills
Scripts executed separately
examples/phospho_analysis.py
Files
SKILL.mdcore4,909 bytesSKILL.mdcore4,909 bytesSKILL.mdcore4,909 bytesSKILL.mdcore4,909 bytesSKILL.mdcore4,909 bytesexamples/phospho_analysis.pyruns1,948 bytesusage-guide.mddoc2,764 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-proteomics-quantification
When your agent uses it
Protein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ), and metabolic labeling (SILAC) approaches. Use when extracting protein abundances from MS data for differential analysis.
What it loads into context
Frontmatter
75 tokensAlways available to the agent
SKILL.md
1,229 tokensWhen the skill is activated
Reference documents
541 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Label-Free Quantification (LFQ)
- TMT/iTRAQ Quantification
- SILAC Quantification
- MSstats Workflow (R)
- Related Skills
Scripts executed separately
examples/lfq_normalization.py
Files
SKILL.mdcore4,686 bytesSKILL.mdcore4,686 bytesSKILL.mdcore4,686 bytesSKILL.mdcore4,686 bytesSKILL.mdcore4,686 bytesexamples/lfq_normalization.pyruns1,842 bytesusage-guide.mddoc2,393 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-proteomics-spectral-libraries
When your agent uses it
Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.
What it loads into context
Frontmatter
66 tokensAlways available to the agent
SKILL.md
1,923 tokensWhen the skill is activated
Reference documents
651 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Build Library from DDA Data
- Predicted Libraries
- Library Formats
- Library QC
- Merge Libraries
- iRT Calibration
- Related Skills
Scripts executed separately
examples/build_library.py
Files
SKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesSKILL.mdcore7,300 bytesexamples/build_library.pyruns2,052 bytesusage-guide.mddoc2,748 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-reaction-enumeration
When your agent uses it
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with product validation. Use when creating combinatorial libraries or enumerating products from synthetic routes.
What it loads into context
Frontmatter
63 tokensAlways available to the agent
SKILL.md
1,933 tokensWhen the skill is activated
Reference documents
399 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Reaction SMARTS Basics
- Common Reaction SMARTS
- Combinatorial Library Enumeration
- Multi-Step Synthesis
- Product Validation
- Reaction Templates
- Related Skills
Scripts executed separately
examples/enumerate_reactions.py
Files
SKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesSKILL.mdcore7,734 bytesexamples/enumerate_reactions.pyruns4,323 bytesusage-guide.mddoc1,816 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,522 tokensWhen the skill is activated
Reference documents
893 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Build Index
- Basic Alignment
- Alignment Modes
- Sensitivity Presets
- ChIP-seq Alignment
- ATAC-seq Alignment
- Fragment Size Options
- Read Group and Output Options
- Multi-mapping Reads
- Output Unmapped Reads
- Key Parameters
- Alignment Statistics
- Related Skills
Scripts executed separately
examples/align_bowtie2.sh
Files
SKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesSKILL.mdcore4,730 bytesexamples/align_bowtie2.shruns609 bytesusage-guide.mddoc3,102 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,385 tokensWhen the skill is activated
Reference documents
875 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Build Index
- Basic Alignment
- Alignment with Read Groups
- Direct to Sorted BAM
- Mark Duplicates Pipeline
- Common Options
- Key Parameters
- Output Filters
- Split Read Alignment
- Memory Requirements
- BWA-MEM (Alternative)
- BWA-MEM vs BWA-MEM2
- Related Skills
Scripts executed separately
examples/align_bwa.sh
Files
SKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesSKILL.mdcore4,439 bytesexamples/align_bwa.shruns668 bytesusage-guide.mddoc3,170 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,671 tokensWhen the skill is activated
Reference documents
1,058 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Build Index
- Basic Alignment
- Direct to Sorted BAM
- Stranded Libraries
- Novel Splice Junction Discovery
- Two-Pass Alignment (Manual)
- Read Group Information
- Downstream Quantification
- Key Parameters
- For StringTie/Cufflinks
- Alignment Summary
- Memory Comparison
- Related Skills
Scripts executed separately
examples/align_hisat2.sh
Files
SKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesSKILL.mdcore5,163 bytesexamples/align_hisat2.shruns517 bytesusage-guide.mddoc3,797 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,505 tokensWhen the skill is activated
Reference documents
996 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Generate Genome Index
- Index with Specific Read Length
- Basic Alignment
- Single-End Alignment
- Two-Pass Mode
- Quantification Mode
- ENCODE Options
- Fusion Detection
- Output Files
- Memory Requirements
- Shared Memory Mode
- Key Parameters
- Related Skills
Scripts executed separately
examples/align_star.sh
Files
SKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesSKILL.mdcore5,377 bytesexamples/align_star.shruns749 bytesusage-guide.mddoc3,703 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-adapter-trimming
When your agent uses it
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
What it loads into context
Frontmatter
74 tokensAlways available to the agent
SKILL.md
1,889 tokensWhen the skill is activated
Reference documents
564 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Common Adapter Sequences
- Cutadapt
- Trimmomatic
- Performance
- Verify Trimming
- Related Skills
Scripts executed separately
examples/trim_adapters.sh
Files
SKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesSKILL.mdcore5,976 bytesexamples/trim_adapters.shruns1,189 bytesusage-guide.mddoc2,342 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-contamination-screening
When your agent uses it
Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.
What it loads into context
Frontmatter
72 tokensAlways available to the agent
SKILL.md
1,682 tokensWhen the skill is activated
Reference documents
590 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- FastQ Screen Overview
- Basic Usage
- Configuration File
- Screening Options
- Output Options
- Filter Codes
- Output Files
- Interpreting Results
- MultiQC Integration
- Custom Database Setup
- Example Workflows
- Related Skills
Scripts executed separately
examples/screen_samples.sh
Files
SKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesSKILL.mdcore6,372 bytesexamples/screen_samples.shruns1,335 bytesusage-guide.mddoc2,553 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-fastp-workflow
When your agent uses it
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.
What it loads into context
Frontmatter
78 tokensAlways available to the agent
SKILL.md
2,151 tokensWhen the skill is activated
Reference documents
546 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Basic Usage
- Adapter Trimming
- Quality Filtering
- Quality Trimming
- Length Filtering
- Poly-X Trimming
- N Base Handling
- Deduplication
- Base Correction (Paired-End Only)
- Paired-End Merge
- UMI Processing
- Complete Workflow Example
- Output Files
- JSON Report Structure
- Performance
- Related Skills
Scripts executed separately
examples/fastp_pipeline.sh
Files
SKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesSKILL.mdcore6,890 bytesexamples/fastp_pipeline.shruns1,559 bytesusage-guide.mddoc2,303 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-quality-filtering
When your agent uses it
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard reads below thresholds. Use when reads have poor quality tails or require minimum quality for downstream analysis.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
1,904 tokensWhen the skill is activated
Reference documents
597 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Trimmomatic Quality Operations
- fastp Quality Filtering
- Cutadapt Quality Trimming
- Combined Adapter + Quality Trimming
- Poly-G Trimming (NovaSeq/NextSeq)
- Quality Thresholds
- Related Skills
Scripts executed separately
examples/quality_filter.sh
Files
SKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesSKILL.mdcore6,178 bytesexamples/quality_filter.shruns1,352 bytesusage-guide.mddoc2,579 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-quality-reports
When your agent uses it
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
1,303 tokensWhen the skill is activated
Reference documents
525 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- FastQC - Single Sample Reports
- MultiQC - Aggregate Reports
- Batch Processing
- Interpretation Guide
- Configuration
- Related Skills
Scripts executed separately
examples/run_qc_pipeline.sh
Files
SKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesSKILL.mdcore5,304 bytesexamples/run_qc_pipeline.shruns1,014 bytesusage-guide.mddoc2,263 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-qc-umi-processing
When your agent uses it
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.
What it loads into context
Frontmatter
82 tokensAlways available to the agent
SKILL.md
2,883 tokensWhen the skill is activated
Reference documents
595 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- UMI Workflow Overview
- Extract UMIs from Reads
- Quality Filtering During Extraction
- Deduplication
- UMI Counting
- Group UMIs Without Deduplication
- Complete Workflows
- Statistics and QC
- Performance Tips
- Alternative: fastp UMI Handling
- Related Skills
Scripts executed separately
examples/umi_workflow.sh
Files
SKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesSKILL.mdcore9,702 bytesexamples/umi_workflow.shruns1,762 bytesusage-guide.mddoc2,301 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-read-sequences
When your agent uses it
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.
What it loads into context
Frontmatter
76 tokensAlways available to the agent
SKILL.md
2,788 tokensWhen the skill is activated
Reference documents
452 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- Required Import
- Core Functions
- High-Performance Parsing
- Common Formats
- Specialized Formats
- Alignment Formats (Read-Only)
- SeqRecord Object Attributes
- Code Patterns
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_parsing.pyexamples/fastq_quality.pyexamples/genbank_features.pyexamples/random_access.py
Files
SKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesSKILL.mdcore10,588 bytesexamples/basic_parsing.pyruns932 bytesexamples/fastq_quality.pyruns939 bytesexamples/genbank_features.pyruns855 bytesexamples/random_access.pyruns1,018 bytesexamples/sample.fastaasset277 bytesexamples/sample.fastqasset418 bytesexamples/sample.gbasset1,245 bytesexamples/single.fastaasset106 bytestests.jsonasset2,694 bytesusage-guide.mddoc1,800 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,983 tokensWhen the skill is activated
Reference documents
2,014 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- samtools faidx - Index Reference FASTA
- samtools dict - Create Sequence Dictionary
- samtools consensus - Generate Consensus
- pysam Python Alternative
- Reference Preparation Workflow
- Common Operations
- Quick Reference
- Related Skills
Scripts executed separately
examples/prepare_reference.sh
Files
SKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesSKILL.mdcore7,308 bytesexamples/prepare_reference.shruns737 bytesusage-guide.mddoc7,678 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
630 tokensWhen the skill is activated
Reference documents
467 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic Usage
- Supported Tools
- Configuration
- Custom Data
- Python API
- Related Skills
Scripts executed separately
examples/multiqc_pipeline.sh
Files
SKILL.mdcore2,415 bytesSKILL.mdcore2,415 bytesSKILL.mdcore2,415 bytesSKILL.mdcore2,415 bytesexamples/multiqc_pipeline.shruns3,465 bytesusage-guide.mddoc1,998 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
872 tokensWhen the skill is activated
Reference documents
512 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Python (matplotlib)
- R (ggplot2)
- Journal Requirements
- Multi-panel Figures
- Color Considerations
- Related Skills
Scripts executed separately
examples/publication_figures.py
Files
SKILL.mdcore3,140 bytesSKILL.mdcore3,140 bytesSKILL.mdcore3,140 bytesexamples/publication_figures.pyruns6,037 bytesusage-guide.mddoc2,092 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
586 tokensWhen the skill is activated
Reference documents
442 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Parameterized Notebooks
- Creating Parameterized Templates
- Batch Processing
- Converting to HTML/PDF
- Best Practices
- Related Skills
Scripts executed separately
examples/papermill_batch.py
Files
SKILL.mdcore2,386 bytesSKILL.mdcore2,386 bytesSKILL.mdcore2,386 bytesSKILL.mdcore2,386 bytesSKILL.mdcore2,386 bytesSKILL.mdcore2,386 bytesexamples/papermill_batch.pyruns4,212 bytesusage-guide.mddoc1,973 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,256 tokensWhen the skill is activated
Reference documents
668 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic Document
- Python Document
- R Document
- Multiple Formats
- Parameters
- Tabsets
- Callouts
- Cross-References
- Code Cell Options
- Inline Code
- Presentations
- Quarto Projects
- Bibliography
- Freeze Computations
- Include Files
- Diagrams with Mermaid
- Multi-Language Document
- Related Skills
Files
SKILL.mdcore4,414 bytesSKILL.mdcore4,414 bytesSKILL.mdcore4,414 bytesSKILL.mdcore4,414 bytesexamples/basic_report.qmdasset1,302 bytesexamples/scrnaseq_report.qmdasset2,568 bytesusage-guide.mddoc2,720 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,514 tokensWhen the skill is activated
Reference documents
621 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Basic Document Structure
- Setup Chunk
- Code Chunk Options
- Parameterized Reports
- Tables
- Figures
- Inline Code
- Child Documents
- PDF Output
- HTML with Tabs
- Caching Long Computations
- Custom CSS
- Complete Report Template
- Related Skills
Files
SKILL.mdcore5,217 bytesexamples/rnaseq_report_template.Rmdasset4,169 bytesusage-guide.mddoc2,656 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,079 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- What This Skill Does
- Inputs
- Quick CLI Usage
- Workflow
- QC Expectations
- Related Assets
Scripts executed separately
scripts/biomarker_signature_studio.py
Files
SKILL.mdcore4,561 bytesSKILL.mdcore4,561 bytesSKILL.mdcore4,561 bytesexamples/configs/biomarker_studio_template.yamlasset715 bytesscripts/biomarker_signature_studio.pyruns20,692 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
2,642 tokensWhen the skill is activated
Reference documents
1,142 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Find Enzymes by Cut Frequency
- Find Non-Cutters for Insert
- Find Compatible Enzyme Pairs
- Filter by Overhang Type
- Filter by Recognition Site Length
- Find Enzymes with Specific Overhang
- Find Unique Cutters in Multiple Sequences
- Select Enzymes for Directional Cloning
- Check Commercial Availability
- Find Isoschizomers
- Check Methylation Sensitivity
- Type IIS Enzymes for Golden Gate Cloning
- Enzyme Properties Reference
- Related Skills
Scripts executed separately
examples/cloning_strategy.pyexamples/golden_gate_check.pyexamples/select_enzymes.py
Files
SKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesSKILL.mdcore9,705 bytesexamples/cloning_strategy.pyruns2,054 bytesexamples/golden_gate_check.pyruns1,667 bytesexamples/select_enzymes.pyruns1,851 bytesusage-guide.mddoc4,296 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,961 tokensWhen the skill is activated
Reference documents
1,076 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Get Fragment Sizes
- Linear vs Circular Digestion
- Get Fragment Sequences
- Double Digest
- Calculate Fragment Sizes from Positions
- Simulate Gel Pattern
- Detailed Fragment Report
- Compare Expected vs Observed Fragments
- Fragment with Sequence Context
- Notes
- Related Skills
Scripts executed separately
examples/gel_simulation.pyexamples/predict_fragments.py
Files
SKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesSKILL.mdcore7,497 bytesexamples/gel_simulation.pyruns1,739 bytesexamples/predict_fragments.pyruns1,612 bytesusage-guide.mddoc3,973 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,662 tokensWhen the skill is activated
Reference documents
858 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Create Basic Restriction Map
- Output Formats
- Calculate Distances Between Sites
- Create Detailed Restriction Map
- Text-Based Map Visualization
- Map with GenBank Features
- Export Map to File
- Circular Map Coordinates
- Related Skills
Scripts executed separately
examples/create_map.pyexamples/plasmid_map.py
Files
SKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesSKILL.mdcore6,384 bytesexamples/create_map.pyruns1,551 bytesexamples/plasmid_map.pyruns2,282 bytesusage-guide.mddoc3,467 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,483 tokensWhen the skill is activated
Reference documents
811 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Pattern
- Search with Single Enzyme
- Search with Multiple Enzymes
- Use Built-in Enzyme Collections
- Linear vs Circular DNA
- Filter Results
- Get Enzyme Information
- Common Cloning Enzymes
- Access Enzymes by Name
- Search Multiple Sequences
- Notes
- Related Skills
Scripts executed separately
examples/circular_plasmid.pyexamples/find_sites.py
Files
SKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesSKILL.mdcore5,496 bytesexamples/circular_plasmid.pyruns1,576 bytesexamples/find_sites.pyruns1,285 bytesusage-guide.mddoc3,219 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
1,718 tokensWhen the skill is activated
Reference documents
628 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Required Import
- Core Methods
- Base Pairing Rules
- Code Patterns
- Common Use Cases
- Common Errors
- Decision Tree
- Related Skills
Scripts executed separately
examples/basic_operations.pyexamples/palindrome_check.pyexamples/primer_design.py
Files
SKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesSKILL.mdcore6,298 bytesexamples/basic_operations.pyruns1,494 bytesexamples/palindrome_check.pyruns1,543 bytesexamples/primer_design.pyruns1,938 bytesusage-guide.mddoc2,539 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-ribo-seq-orf-detection
When your agent uses it
Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated regions beyond annotated coding sequences or quantifying ORF-level translation.
What it loads into context
Frontmatter
71 tokensAlways available to the agent
SKILL.md
2,329 tokensWhen the skill is activated
Reference documents
444 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Version Compatibility
- RiboCode Workflow
- One-Step RiboCode
- RiboCode Output
- Parse RiboCode Results
- Alternative: RibORF
- Manual ORF Detection
- uORF Analysis
- ORF Categories
- ORFquant for ORF Quantification
- Related Skills
Scripts executed separately
examples/detect_orfs.sh
Files
SKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesSKILL.mdcore8,734 bytesexamples/detect_orfs.shruns1,763 bytesusage-guide.mddoc1,745 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubSkills included
- adaptyv
- adhd-daily-planner
- aeon
- agent-browser
- ai-analyzer
- alphafold
- alphafold-database
- anndata
- arboreto
- arxiv-search
- benchling-integration
- bgpt-paper-search
- bindcraft
- binder-design
- binding-characterization
- bindingdb-database
- bio-admet-prediction
- bio-alignment-io
- bio-alignment-msa-parsing
- bio-alignment-msa-statistics
- bio-alignment-pairwise
- bio-atac-seq-atac-peak-calling
- bio-atac-seq-atac-qc
- bio-atac-seq-differential-accessibility
- bio-atac-seq-footprinting
- bio-atac-seq-motif-deviation
- bio-atac-seq-nucleosome-positioning
- bio-basecalling
- bio-batch-processing
- bio-causal-genomics-colocalization-analysis
- bio-causal-genomics-fine-mapping
- bio-causal-genomics-mediation-analysis
- bio-causal-genomics-mendelian-randomization
- bio-causal-genomics-pleiotropy-detection
- bio-cfdna-preprocessing
- bio-chipseq-differential-binding
- bio-chipseq-motif-analysis
- bio-chipseq-peak-annotation
- bio-chipseq-peak-calling
- bio-chipseq-qc
- bio-chipseq-super-enhancers
- bio-chipseq-visualization
- bio-clinical-databases-clinvar-lookup
- bio-clinical-databases-dbsnp-queries
- bio-clinical-databases-gnomad-frequencies
- bio-clinical-databases-hla-typing
- bio-clinical-databases-myvariant-queries
- bio-clinical-databases-pharmacogenomics
- bio-clinical-databases-polygenic-risk
- bio-clinical-databases-somatic-signatures
- bio-clinical-databases-tumor-mutational-burden
- bio-clinical-databases-variant-prioritization
- bio-compressed-files
- bio-consensus-sequences
- bio-copy-number-cnv-annotation
- bio-copy-number-cnv-visualization
- bio-copy-number-cnvkit-analysis
- bio-copy-number-gatk-cnv
- bio-crispr-screens-base-editing-analysis
- bio-crispr-screens-batch-correction
- bio-crispr-screens-crispresso-editing
- bio-crispr-screens-hit-calling
- bio-crispr-screens-jacks-analysis
- bio-crispr-screens-library-design
- bio-crispr-screens-mageck-analysis
- bio-crispr-screens-screen-qc
- bio-ctdna-mutation-detection
- bio-de-deseq2-basics
- bio-de-edger-basics
- bio-de-results
- bio-de-visualization
- bio-differential-expression-batch-correction
- bio-differential-expression-timeseries-de
- bio-differential-splicing
- bio-epidemiological-genomics-amr-surveillance
- bio-epidemiological-genomics-pathogen-typing
- bio-epidemiological-genomics-phylodynamics
- bio-epidemiological-genomics-transmission-inference
- bio-epidemiological-genomics-variant-surveillance
- bio-fastq-quality
- bio-filter-sequences
- bio-flow-cytometry-bead-normalization
- bio-flow-cytometry-clustering-phenotyping
- bio-flow-cytometry-compensation-transformation
- bio-flow-cytometry-cytometry-qc
- bio-flow-cytometry-differential-analysis
- bio-flow-cytometry-doublet-detection
- bio-flow-cytometry-fcs-handling
- bio-flow-cytometry-gating-analysis
- bio-format-conversion
- bio-fragment-analysis
- bio-gatk-variant-calling
- bio-genome-engineering-base-editing-design
- bio-genome-engineering-grna-design
- bio-genome-engineering-hdr-template-design
- bio-genome-engineering-off-target-prediction
- bio-genome-engineering-prime-editing-design
- bio-hi-c-analysis-compartment-analysis
- bio-hi-c-analysis-contact-pairs
- bio-hi-c-analysis-hic-data-io
- bio-hi-c-analysis-hic-differential
- bio-hi-c-analysis-hic-visualization
- bio-hi-c-analysis-loop-calling
- bio-hi-c-analysis-matrix-operations
- bio-hi-c-analysis-tad-detection
- bio-imaging-mass-cytometry-cell-segmentation
- bio-imaging-mass-cytometry-data-preprocessing
- bio-imaging-mass-cytometry-interactive-annotation
- bio-imaging-mass-cytometry-phenotyping
- bio-imaging-mass-cytometry-quality-metrics
- bio-imaging-mass-cytometry-spatial-analysis
- bio-immunoinformatics-epitope-prediction
- bio-immunoinformatics-immunogenicity-scoring
- bio-immunoinformatics-mhc-binding-prediction
- bio-immunoinformatics-neoantigen-prediction
- bio-immunoinformatics-tcr-epitope-binding
- bio-isoform-switching
- bio-long-read-sequencing-clair3-variants
- bio-long-read-sequencing-isoseq-analysis
- bio-long-read-sequencing-nanopore-methylation
- bio-longitudinal-monitoring
- bio-longread-alignment
- bio-longread-medaka
- bio-longread-qc
- bio-longread-structural-variants
- bio-metabolomics-lipidomics
- bio-metabolomics-metabolite-annotation
- bio-metabolomics-msdial-preprocessing
- bio-metabolomics-normalization-qc
- bio-metabolomics-pathway-mapping
- bio-metabolomics-statistical-analysis
- bio-metabolomics-targeted-analysis
- bio-metabolomics-xcms-preprocessing
- bio-metagenomics-abundance
- bio-metagenomics-amr-detection
- bio-metagenomics-functional-profiling
- bio-metagenomics-kraken
- bio-metagenomics-metaphlan
- bio-metagenomics-strain-tracking
- bio-metagenomics-visualization
- bio-methylation-based-detection
- bio-methylation-bismark-alignment
- bio-methylation-calling
- bio-methylation-dmr-detection
- bio-methylation-methylkit
- bio-microbiome-amplicon-processing
- bio-microbiome-differential-abundance
- bio-microbiome-diversity-analysis
- bio-microbiome-functional-prediction
- bio-microbiome-qiime2-workflow
- bio-microbiome-taxonomy-assignment
- bio-molecular-descriptors
- bio-molecular-io
- bio-multi-omics-data-harmonization
- bio-multi-omics-mixomics-analysis
- bio-multi-omics-mofa-integration
- bio-multi-omics-similarity-network
- bio-orchestrator
- bio-paired-end-fastq
- bio-pathway-enrichment-visualization
- bio-pathway-go-enrichment
- bio-pathway-gsea
- bio-pathway-kegg-pathways
- bio-pathway-reactome
- bio-pathway-wikipathways
- bio-pdb-geometric-analysis
- bio-pdb-structure-io
- bio-pdb-structure-modification
- bio-pdb-structure-navigation
- bio-proteomics-data-import
- bio-proteomics-dia-analysis
- bio-proteomics-differential-abundance
- bio-proteomics-peptide-identification
- bio-proteomics-protein-inference
- bio-proteomics-proteomics-qc
- bio-proteomics-ptm-analysis
- bio-proteomics-quantification
- bio-proteomics-spectral-libraries
- bio-reaction-enumeration
- bio-read-qc-adapter-trimming
- bio-read-qc-contamination-screening
- bio-read-qc-fastp-workflow
- bio-read-qc-quality-filtering
- bio-read-qc-quality-reports
- bio-read-qc-umi-processing
- bio-read-sequences
- bio-ribo-seq-orf-detection
Showing 300 of 897 skills. See GitHub for the complete repository.
Repository facts
- License
- No license detected
- Created
- Mar 8, 2026
- Last pushed
- Jul 21, 2026
- Forks
- 422
- Open issues
- 9
- Project activity
- Slowing
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Before you install
Network or broad shellAutomated signals, not a guarantee
Checked Nov 2, 2026
Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.
Show 9,687 notes
skills/aav-vector-design-agent/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/adaptyv/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/adaptyv/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/adaptyv/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/aeon/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzed
- 46 broad permissionsin 46 files: adhd-daily-planner/SKILL.md:1 bgpt-paper-search/SKILL.md:1 citation-management/SKILL.md:1 and 43 more
- 130 dangerous shell commandsin 73 files: biomcp-server/repo/docs/troubleshooting.md:29 cellagent-annotation/repo/CellTypeAgent/get_selection.py:161 biomni-general-agent/repo/biomni_env/install_cli_tools.sh:27 and 70 more
- 17,405 network referencesin 1,508 files: biomcp-server/repo/uv.lock:12 biomcp-server/repo/tests/data/myvariant/variants_full_braf_v600e.json:8 biomcp-server/repo/tests/data/myvariant/variants_full_braf_v600e.txt:11 and 1,505 more
- 760 obfuscation signalsin 59 files: MAGE/repo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynb:121 mage-antibody-generator/repo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynb:121 MAGE/repo/Data cleaning/final_processing/detagging_script_24-03-04.ipynb:121 and 56 more
- No instruction overrides
- 1,472 executable scriptsin 1,469 files: skills/pharmgx-reporter/pharmgx_reporter.py:1 agentd-drug-discovery/agent_d.py:1 MAGE/repo/Data cleaning/CoVAbDab/covabdab_gen_curation_allBinders_allVariants_v2_24-03-12.ipynb:1 and 1,466 more
- 2,049 references to secretsin 354 files: biomcp-server/repo/docs/tutorials/nci-prompts.md:34 biomcp-server/repo/src/biomcp/individual_tools.py:675 biomcp-server/repo/docs/how-to-guides/06-search-nci-organizations-and-interventions.md:24 and 351 more
- No requests to vote in Hot
Show all 21,862 signals by file
skills/adaptyv/SKILL.md
- Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 30
[Credential-related source omitted] - Network accessline 52
[Credential-related source omitted] - Access to secretsline 52
[Credential-related source omitted] - Network accessline 53
base_url = "https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws" - Access to secretsline 56
[Credential-related source omitted] - Network accessline 60
# Submit experiment response = requests.post( - Network accessline 61
response = requests.post( - Network accessline 65
"sequences": ">protein1\nMKVLWALLGLLGAA...", "experiment_type": "binding", "webhook_url": "https://your-webhook.com/callback" - Network accessline 66
"experiment_type": "binding", "webhook_url": "https://your-webhook.com/callback" } - Network accessline 67
"webhook_url": "https://your-webhook.com/callback"
skills/adaptyv/reference/api_reference.md
- Network accessline 6
https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws - Access to secretsline 14
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 41
"experiment_type": "binding|expression|thermostability|enzyme_activity", "target_id": "optional_target_identifier", "webhook_url": "https://your-webhook.com/callback", - Network accessline 42
"target_id": "optional_target_identifier", "webhook_url": "https://your-webhook.com/callback", "metadata": { - Network accessline 43
"webhook_url": "https://your-webhook.com/callback", - Network accessline 145
], "download_urls": { "raw_data": "https://...", - Network accessline 146
"download_urls": { "raw_data": "https://...", "analysis_package": "https://...", - Network accessline 147
"raw_data": "https://...", - Network accessline 148
"analysis_package": "https://...", - Network accessline 149
"report": "https://..." - Network accessline 305
For API issues or questions: - Email: support@adaptyvbio.com - Documentation updates: https://docs.adaptyvbio.com - Network accessline 306
- Email: support@adaptyvbio.com - Documentation updates: https://docs.adaptyvbio.com - Report bugs with experiment IDs and request details - Network accessline 307
- Documentation updates: https://docs.adaptyvbio.com
skills/adaptyv/reference/examples.md
- Network accessline 15
[Credential-related source omitted] - Access to secretsline 16
[Credential-related source omitted] - Network accessline 17
BASE_URL = "https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws" - Access to secretsline 21
[Credential-related source omitted] - Network accessline 26
"""Verify API connection and credentials""" try: response = requests.get(f"{BASE_URL}/organization/credits", headers=HEADERS) - Network accessline 27
try: response = requests.get(f"{BASE_URL}/organization/credits", headers=HEADERS) response.raise_for_status() - Network accessline 28
response = requests.get(f"{BASE_URL}/organization/credits", headers=HEADERS) - Access to secretsline 42
[Credential-related source omitted] - Network accessline 79
response = requests.post( - Network accessline 129
response = requests.post( - Network accessline 185
response = requests.post( - Network accessline 200
# Example webhook_url = "https://your-server.com/adaptyv-webhook" - Network accessline 201
webhook_url = "https://your-server.com/adaptyv-webhook" - Network accessline 221
response = requests.get( - Network accessline 263
response = requests.get( - Network accessline 337
# Get results response = requests.get( - Network accessline 338
response = requests.get( - Network accessline 479
response = requests.get( - Network accessline 528
response = requests.post( - Network accessline 775
for attempt in range(max_retries): try: response = requests.request(method, url, **kwargs) - Network accessline 776
try: response = requests.request(method, url, **kwargs) response.raise_for_status() - Network accessline 777
response = requests.request(method, url, **kwargs)
skills/adaptyv/reference/experiments.md
skills/adaptyv/reference/protein_optimization.md
- Network accessline 75
def predict_solubility_netsolp(sequence): """Predict protein solubility using NetSolP web service""" url = "https://services.healthtech.dtu.dk/services/NetSolP-1.0/api/predict" - Network accessline 77
url = "https://services.healthtech.dtu.dk/services/NetSolP-1.0/api/predict" - Network accessline 84
response = requests.post(url, data=data) - Network accessline 597
# Submit to Adaptyv import requests response = requests.post( - Network accessline 598
import requests response = requests.post( "https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws/experiments", - Network accessline 599
response = requests.post( - Network accessline 600
"https://kq5jp7qj7wdqklhsxmovkzn4l40obksv.lambda-url.eu-central-1.on.aws/experiments", - Access to secretsline 601
[Credential-related source omitted]
skills/adhd-daily-planner/SKILL.md
- Broad permissionsline 1
Read, Edit, Write, Bash, Glob, Grep, WebFetch, WebSearch, Task
skills/aeon/SKILL.md
- Network accessline 368
- Documentation: https://www.aeon-toolkit.org/ - Network accessline 369
- GitHub: https://github.com/aeon-toolkit/aeon - Network accessline 370
- Examples: https://www.aeon-toolkit.org/en/stable/examples.html - Network accessline 371
- API Reference: https://www.aeon-toolkit.org/en/stable/api_reference.html
skills/aeon/references/networks.md
- Access to secretsline 182
[Credential-related source omitted]
skills/agent-browser/SKILL.md
- Network accessline 107
# Login once agent-browser open https://app.example.com/login - Network accessline 108
agent-browser open https://app.example.com/login - Network accessline 116
# Later: load saved state agent-browser state load auth.json agent-browser open https://app.example.com/dashboard - Network accessline 118
agent-browser open https://app.example.com/dashboard - Access to secretsline 124
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 126
[Credential-related source omitted] - Dangerous shell operationline 134
agent-browser eval "document.title" # Run JavaScript - Network accessline 140
agent-browser open https://example.com/form - Network accessline 154
agent-browser open https://example.com/products
skills/agentd-drug-discovery/README.md
- Network accessline 97
- AgentD: https://github.com/hoon-ock/AgentD
skills/agentd-drug-discovery/agent_d.py
- Executable scriptline 1
Executable file
skills/alphafold-database/SKILL.md
- Network accessline 56
# Get prediction metadata for a UniProt accession uniprot_id = "P00520" api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" - Network accessline 57
uniprot_id = "P00520" api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" response = requests.get(api_url) - Network accessline 58
api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" response = requests.get(api_url) prediction_data = response.json() - Network accessline 59
response = requests.get(api_url) - Network accessline 74
def get_uniprot_ids(query, query_type='PDB_ID'): """Query UniProt to get accession IDs""" url = 'https://www.uniprot.org/uploadlists/' - Network accessline 75
"""Query UniProt to get accession IDs""" url = 'https://www.uniprot.org/uploadlists/' params = { - Network accessline 76
url = 'https://www.uniprot.org/uploadlists/' - Network accessline 82
} data = urllib.parse.urlencode(params).encode('ascii') with urllib.request.urlopen(urllib.request.Request(url, data)) as response: - Network accessline 83
data = urllib.parse.urlencode(params).encode('ascii') with urllib.request.urlopen(urllib.request.Request(url, data)) as response: return response.read().decode('utf-8').splitlines() - Network accessline 84
with urllib.request.urlopen(urllib.request.Request(url, data)) as response: - Network accessline 109
# Model coordinates (mmCIF) model_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.cif" response = requests.get(model_url) - Network accessline 110
model_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.cif" response = requests.get(model_url) with open(f"{alphafold_id}.cif", "w") as f: - Network accessline 111
response = requests.get(model_url) - Network accessline 115
# Confidence scores (JSON) confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_{version}.json" response = requests.get(confidence_url) - Network accessline 116
confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_{version}.json" response = requests.get(confidence_url) confidence_data = response.json() - Network accessline 117
response = requests.get(confidence_url) - Network accessline 120
# Predicted Aligned Error (JSON) pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_{version}.json" response = requests.get(pae_url) - Network accessline 121
pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_{version}.json" response = requests.get(pae_url) pae_data = response.json() - Network accessline 122
response = requests.get(pae_url) - Network accessline 129
# Download as PDB format instead of mmCIF pdb_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.pdb" - Network accessline 130
pdb_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.pdb" response = requests.get(pdb_url) with open(f"{alphafold_id}.pdb", "wb") as f: - Network accessline 131
response = requests.get(pdb_url) - Network accessline 146
# Load confidence scores alphafold_id = "AF-P00520-F1" confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" - Network accessline 147
alphafold_id = "AF-P00520-F1" confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" confidence = requests.get(confidence_url).json() - Network accessline 148
confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" - Network accessline 149
confidence = requests.get(confidence_url).json() - Network accessline 172
# Load PAE matrix pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_v4.json" pae = requests.get(pae_url).json() - Network accessline 173
pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_v4.json" - Network accessline 174
pae = requests.get(pae_url).json() - Network accessline 331
# Get confidence data alphafold_id = pred['entryId'] conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" - Network accessline 332
alphafold_id = pred['entryId'] conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" conf_data = requests.get(conf_url).json() - Network accessline 333
conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" - Network accessline 334
conf_data = requests.get(conf_url).json() - Network accessline 381
# Query via 3D-Beacons uniprot_id = "P00520" url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" - Network accessline 382
uniprot_id = "P00520" url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" response = requests.get(url) - Network accessline 383
url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" response = requests.get(url) data = response.json() - Network accessline 384
response = requests.get(url) - Network accessline 492
- **AlphaFold DB Website:** https://alphafold.ebi.ac.uk/ - Network accessline 493
- **API Documentation:** https://alphafold.ebi.ac.uk/api-docs - Network accessline 494
- **Google Cloud Dataset:** https://cloud.google.com/blog/products/ai-machine-learning/alphafold-protein-structure-database - Network accessline 495
- **3D-Beacons API:** https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/ - Network accessline 496
- **AlphaFold Papers:** - Nature (2021): https://doi.org/10.1038/s41586-021-03819-2 - Nucleic Acids Research (2024): https://doi.org/10.1093/nar/gkad1011 - Network accessline 497
- Nature (2021): https://doi.org/10.1038/s41586-021-03819-2 - Network accessline 498
- Nucleic Acids Research (2024): https://doi.org/10.1093/nar/gkad1011 - Network accessline 499
- **Biopython Documentation:** https://biopython.org/docs/dev/api/Bio.PDB.alphafold_db.html - Network accessline 500
- **GitHub Repository:** https://github.com/google-deepmind/alphafold
skills/alphafold-database/references/api_reference.md
- Network accessline 23
https://alphafold.ebi.ac.uk/api/ - Network accessline 39
curl https://alphafold.ebi.ac.uk/api/prediction/P00520 - Network accessline 57
"latestVersion": 4, "allVersions": [1, 2, 3, 4], "cifUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.cif", - Network accessline 58
"allVersions": [1, 2, 3, 4], "cifUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.cif", "bcifUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.bcif", - Network accessline 59
"cifUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.cif", - Network accessline 60
"bcifUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.bcif", - Network accessline 61
"pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.pdb", - Network accessline 62
"paeImageUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-predicted_aligned_error_v4.png", - Network accessline 63
"paeDocUrl": "https://alphafold.ebi.ac.uk/files/AF-P00520-F1-predicted_aligned_error_v4.json" - Network accessline 89
**Endpoint:** `https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json` - Network accessline 95
uniprot_id = "P00520" url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" response = requests.get(url) - Network accessline 96
url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" response = requests.get(url) data = response.json() - Network accessline 97
response = requests.get(url) - Network accessline 117
https://alphafold.ebi.ac.uk/files/{alphafold_id}-{file_type}_{version}.{extension} - Network accessline 132
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.cif - Network accessline 141
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.bcif - Network accessline 150
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-model_v4.pdb - Network accessline 161
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-confidence_v4.json - Network accessline 179
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-predicted_aligned_error_v4.json - Network accessline 197
https://alphafold.ebi.ac.uk/files/AF-P00520-F1-predicted_aligned_error_v4.png - Network accessline 303
# Or install Google Cloud SDK curl https://sdk.cloud.google.com | bash - Dangerous shell operationline 304
curl https://sdk.cloud.google.com | bash - Network accessline 304
curl https://sdk.cloud.google.com | bash - Network accessline 406
- **AlphaFold GitHub:** https://github.com/google-deepmind/alphafold - Network accessline 407
- **Google Cloud Documentation:** https://cloud.google.com/datasets/alphafold - Network accessline 408
- **3D-Beacons Documentation:** https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/docs - Network accessline 409
- **Biopython Tutorial:** https://biopython.org/wiki/AlphaFold
skills/alphafold/SKILL.md
- Network accessline 47
git clone https://github.com/deepmind/alphafold.git
skills/anndata/SKILL.md
- Network accessline 391
- **Official documentation**: https://anndata.readthedocs.io/ - Network accessline 392
- **Scanpy tutorials**: https://scanpy.readthedocs.io/ - Network accessline 393
- **Scverse ecosystem**: https://scverse.org/ - Network accessline 394
- **GitHub repository**: https://github.com/scverse/anndata
skills/anndata/references/io_operations.md
- Network accessline 82
# Access Zarr from URL store = fsspec.get_mapper('https://example.com/data.zarr') - Network accessline 83
store = fsspec.get_mapper('https://example.com/data.zarr') - Network accessline 287
# Read directly from URL (for h5ad files) url = 'https://example.com/data.h5ad' - Network accessline 288
url = 'https://example.com/data.h5ad' - Network accessline 291
# For other formats, download first import urllib.request urllib.request.urlretrieve(url, 'local_file.h5ad') - Network accessline 292
import urllib.request urllib.request.urlretrieve(url, 'local_file.h5ad') adata = ad.read_h5ad('local_file.h5ad') - Network accessline 293
urllib.request.urlretrieve(url, 'local_file.h5ad')
skills/antibody-design-agent/MAGE/README.md
- Network accessline 65
- https://github.com/IGlab-VUMC/MAGE_ab_generation
skills/antibody-design-agent/MAGE/repo/Data cleaning/CoVAbDab/covabdab_gen_curation_allBinders_allVariants_v2_24-03-12.ipynb
- Executable scriptline 1
Executable file - Network accessline 342
"source": [ "### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", - Network accessline 343
"### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", "wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY - Network accessline 344
"# https://www.rcsb.org/structure/6m0j\n", - Possible obfuscationline 345
"wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'" - Network accessline 363
" 'SARS-CoV2_WT':wt_rbd}\n", "\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Network accessline 364
"\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", "cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQ - Network accessline 365
"# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Possible obfuscationline 366
"cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLG - Network accessline 371
"ant_dict['SARS-CoV2_Omicron-BA1.1'] = variant_rbd_list['Omicron_BA.1.1__BA.1_add[R346K]__EPI_ISL_10000001']\n", "\n", "# https://www.rcsb.org/structure/8ASY\n", - Network accessline 372
"\n", "# https://www.rcsb.org/structure/8ASY\n", "ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQ - Network accessline 373
"# https://www.rcsb.org/structure/8ASY\n", - Network accessline 374
"ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKKSLL - Possible obfuscationline 374
"ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKKSLL - Network accessline 375
"\n", "# https://www.uniprot.org/uniprotkb/A0A6G6A1M4/entry\n", "ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLG - Network accessline 376
"# https://www.uniprot.org/uniprotkb/A0A6G6A1M4/entry\n", - Network accessline 377
"ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLGVYYHNNNKTWVENEFRVYSSANNCTFEYISQPFLMDLEGKQGNFKNLREFVFKNVDGYFKIYSKHTPIDLVR - Possible obfuscationline 377
"ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLGVYYHNNNKTWVENEFRVYSSANNCTFEYISQPFLMDLEGKQGNFKNLREFVFKNVDGYFKIYSKHTPIDLVR - Network accessline 378
"\n", "# https://www.uniprot.org/uniprotkb/A0A6B9WHD3/entry#sequences\n", "ant_dict['RaTG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF - Network accessline 379
"# https://www.uniprot.org/uniprotkb/A0A6B9WHD3/entry#sequences\n", - Possible obfuscationline 380
"ant_dict['RaTG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLP - Possible obfuscationline 381
"ant_dict['RatG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLP - Possible obfuscationline 863
"sars_cov2_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGF
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/10618/10618_antigen_alignment_v1_24-03-06.ipynb
- Executable scriptline 1
Executable file - Network accessline 122
"antigen_dict = dict(zip(antigen_seqs['LSS_name'], antigen_seqs['Seq']))\n", "\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Network accessline 123
"\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", "cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQ - Network accessline 124
"# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Possible obfuscationline 125
"cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLG - Network accessline 126
"antigen_dict['SARS-1.LSS'] = cov1_spike\n", "\n", "# https://www.rcsb.org/structure/8IOU\n", - Network accessline 127
"\n", "# https://www.rcsb.org/structure/8IOU\n", "xbb1_spike = 'LLMGCVAETGSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQ - Network accessline 128
"# https://www.rcsb.org/structure/8IOU\n", - Possible obfuscationline 129
"xbb1_spike = 'LLMGCVAETGSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLP - Network accessline 130
"antigen_dict['XBB.1.LSS'] = xbb1_spike\n", "\n", "# https://www.rcsb.org/structure/8I4G\n", - Network accessline 131
"\n", "# https://www.rcsb.org/structure/8I4G\n", "bq11_spike = 'QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF - Network accessline 132
"# https://www.rcsb.org/structure/8I4G\n", - Possible obfuscationline 133
"bq11_spike = 'QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLA - Possible obfuscationline 137
"oc43_spike = 'VIGDLKCPLDSRTGSLNNIDTGPPSISTATVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGTDKLSTLWFKPPFLSDFINGIFAKVKNTKVFKDGVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGVNKLQGLLEVSVCQYNMCEYPHTICHPKLGNHFKELWHMDTGVVSCLYKRNFTYDVNATYLYFHFYQEGGTFYAYFTDTGVVTK - Possible obfuscationline 140
"hku1_spike = 'VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVM
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/10618/AA_10618_LLM-clean_24-03-06.ipynb
- Executable scriptline 1
Executable file
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/SAbDab/SAbDab_final_clean_v1_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 355
"source": [ "Should probably remove leucine repeats here as well: \\\n", "https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." - Network accessline 356
"Should probably remove leucine repeats here as well: \\\n", "https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." ] - Network accessline 357
"https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." - Possible obfuscationline 368
"'MQPTGREGSRALSRRYLRRLLLLLLLLLLRQPVTRAETTPGAPRALSTLGSPSLFTTPGVPSALTTPGLTTPGTPKTLDLRGRAQALMRSFPLVDGHNDLPQVLRQRYKNVLQDVNLRNFSHGQTSLDRLRDGLVGAQFWSASVSCQSQDQTAVRLALEQIDLIHRMCASYSELELVTSAEGLNSSQKLACLIGVEGGHSLDSSLSVLRSFYVLGVRYLTLTFTCSTPWAESSTKFRH
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 114
"HAtag = 'YPYDVPDYA'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 115
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 116
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Possible obfuscationline 121
"# ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW - Network accessline 212
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 213
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " X_ant.loc[tagged_dfs[flagtag].index] = tagged_dfs[flagtag]\n" - Network accessline 214
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Possible obfuscationline 314
"DLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF - Possible obfuscationline 317
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 320
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 323
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 326
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 329
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 332
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 335
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 338
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 341
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 344
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 347
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 350
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 380
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 383
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 386
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 389
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 392
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 395
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 398
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 401
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 404
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 407
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 410
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 413
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 416
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 419
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 422
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 425
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 428
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 431
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 434
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 437
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 440
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 443
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 446
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 449
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 452
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 455
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 458
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 461
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 464
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 467
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 470
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 473
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 476
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 479
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 482
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 485
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 488
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 491
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 494
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 497
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 500
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 503
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 506
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSCMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 509
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 512
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 515
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 518
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 521
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 524
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 527
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 530
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 533
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 536
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 539
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 542
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 545
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 548
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 551
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 554
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 557
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 560
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 563
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 566
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 569
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 572
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 575
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 578
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGA - Possible obfuscationline 581
"SQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTP - Possible obfuscationline 584
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 587
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 590
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 593
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 596
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 599
"VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSG - Possible obfuscationline 602
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 605
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 652
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 655
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 1334
"long attachment for: SDKICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENKHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLATASSWSYIVETSSSNNGTCYPGDFINYEELREQLSSVSSFEKFEIFPKTSSWPNHETNKGVTAACPHAGTNSFYKNLIWLVKKENSYPKINISYTNNRGKEVLVLWAIHHPPTSTDQQSLYQNANSYVFVGSSRYSRKFEPEIATR - Possible obfuscationline 1335
"long attachment for: SDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSVAGWILGNPECESLFSKESWSYIAETPKPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTAACSHNGKSSFYKNLLWLTEKNGLYPNLSKSYVNNKEKEVLVLWGVHHPSNIGDQRAIYHTENAYVSVVSSHYSRRFTPEIAKR - Possible obfuscationline 1337
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1338
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1339
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1340
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1341
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1342
"long attachment for: GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITASGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH - Possible obfuscationline 1343
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSLPEPEWTYPRLSCPGSTFQKALLISPHRFGEIKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEA - Possible obfuscationline 1344
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1345
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1357
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1358
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1359
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1360
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1361
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1362
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1363
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1364
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1365
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1366
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1367
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1368
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1369
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1370
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1371
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1372
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1373
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1374
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1375
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1376
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1377
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1378
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1379
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1380
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1381
"long attachment for: TQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGI - Possible obfuscationline 1438
"long attachment for: QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCA - Possible obfuscationline 1449
"long attachment for: YKDDDDAMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGENLYFQGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTK - Possible obfuscationline 1466
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1467
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1468
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1469
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1470
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1471
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1472
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1473
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1474
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1475
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1476
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1477
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1478
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1483
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1484
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1485
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1486
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1487
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1488
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1489
"long attachment for: CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESECGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1536
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1537
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1538
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1539
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1599
"long attachment for: MDERLSLLRSPPPPSARHRAHPPQRPASSGGAHTLVNHGYAEPAAGRELPPDMTVVPGDHLLEPEVADGGGAPPQGGCGGGGCDRYEPLPPSLPAAGEQDCCGERVVINISGLRFETQLKTLCQFPETLLGDPKRRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLREEERPLPRRDFQR - Network accessline 1602
], "source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", - Network accessline 1603
"source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", "X_ant = X_ant.apply(lambda x: find_and_replace_ - Network accessline 1604
"# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/atlas_antigen_alignment_v1_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 174
], "source": [ "# Downloaded from plasmid here: https://www.addgene.org/154754/\n", - Network accessline 175
"source": [ "# Downloaded from plasmid here: https://www.addgene.org/154754/\n", "hexapro = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDP - Network accessline 176
"# Downloaded from plasmid here: https://www.addgene.org/154754/\n", - Possible obfuscationline 177
"hexapro = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVD
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/published_LIBRA-seq_concatenation_24-05-31.ipynb
- Executable scriptline 1
Executable file - Network accessline 402
"metadata": {}, "source": [ "By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need - Network accessline 403
"source": [ "By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need fasta inputs" ] - Network accessline 404
"By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need fasta inputs"
skills/antibody-design-agent/MAGE/repo/Data cleaning/Other_notebooks/signalP/detagging_nonSAbDab_24-03-12.ipynb
- Executable scriptline 1
Executable file - Network accessline 504
"flagtag = 'DYKDDDDK'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 505
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 506
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/PlAbDab/ebola_Bornholdt_24-03-07.ipynb
- Executable scriptline 1
Executable file - Network accessline 35
], "source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Network accessline 36
"source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", "gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFF - Network accessline 37
"# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Possible obfuscationline 38
"gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYL - Network accessline 41
"gpTM = gp[:650]\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Network accessline 42
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", "sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRL - Network accessline 43
"# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Possible obfuscationline 44
"sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY
skills/antibody-design-agent/MAGE/repo/Data cleaning/PlAbDab/ebola_EhrHardt_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 47
"source": [ "# Q1PDC7| VGP_MABVR Envelope glycoprotein OS=Lake Victoria marburgvirus (strain Ravn-87) \n", "# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", - Network accessline 48
"# Q1PDC7| VGP_MABVR Envelope glycoprotein OS=Lake Victoria marburgvirus (strain Ravn-87) \n", "# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", "# gp = \"MKTIYFLISLILIQSIKTLPVLEIASNSQPQDVDSVCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAF - Network accessline 49
"# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", - Possible obfuscationline 50
"# gp = \"MKTIYFLISLILIQSIKTLPVLEIASNSQPQDVDSVCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAFRTGVPPKNVEYTEGEEAKTCYNISVTDPSGKSLLLDPPSNIRDYPKCKTVHHIQGQNPHAQGIALHLWGAFFLYDRVASTTMYRGKVFTEGNIAAMIVNKTVHRMIFSRQGQGYRHMNLTSTNKYWTSSNETQRNDTGCFGILQEYNSTNNQTCPPSL - Network accessline 52
"\n", "# Q05320|VGP_EBOZM Envelope glycoprotein OS=Zaire ebolavirus (strain Mayinga-76)\n", "# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", - Network accessline 53
"# Q05320|VGP_EBOZM Envelope glycoprotein OS=Zaire ebolavirus (strain Mayinga-76)\n", "# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", "\n", - Network accessline 54
"# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", - Possible obfuscationline 56
"gp = \"MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY - Network accessline 129
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 130
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " hc_df['clone'] = hc_df['clone'].apply(lambda x: x.split('clone')[1].split(' - Network accessline 131
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 135
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 136
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " lc_df['clone'] = lc_df['clone'].apply(lambda x: x.split('clone')[1].split(' - Network accessline 137
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/PlAbDab/gilman_RSV_24-01-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 121
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 122
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df.dropna(inplace=True)\n", - Network accessline 123
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 127
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 128
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['GenBank Accession Number (VH)'] = seq_df['GenBank Accession Number - Network accessline 129
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 133
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 134
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['GenBank Accession Number (VL)'] = seq_df['GenBank Accession Number - Network accessline 135
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 163
"source": [ "# sp|P03420|FUS_HRSVA Fusion glycoprotein F0 OS=Human respiratory syncytial virus A (strain A2) OX=11259 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", - Network accessline 164
"# sp|P03420|FUS_HRSVA Fusion glycoprotein F0 OS=Human respiratory syncytial virus A (strain A2) OX=11259 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", "rsvAf = 'MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSK - Network accessline 165
"# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", - Possible obfuscationline 166
"rsvAf = 'MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRL - Network accessline 167
"\n", "# sp|P13843|FUS_HRSV1 Fusion glycoprotein F0 OS=Human respiratory syncytial virus B (strain 18537) OX=11251 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", - Network accessline 168
"# sp|P13843|FUS_HRSV1 Fusion glycoprotein F0 OS=Human respiratory syncytial virus B (strain 18537) OX=11251 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", "rsvBf = 'MELLIHRSSAIFLTLAVNALYLTSSQNITEEFYQSTCSA - Network accessline 169
"# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", - Possible obfuscationline 170
"rsvBf = 'MELLIHRSSAIFLTLAVNALYLTSSQNITEEFYQSTCSAVSRGYFSALRTGWYTSVITIELSNIKETKCNGTDTKVKLIKQELDKYKNAVTELQLLMQNTPAANNRARREAPQYMNYTINTTKNLNVSISKKRKRRFLGFLLGVGSAIASGIAVSKVLHLEGEVNKIKNALLSTNKAVVSLSNGVSVLTSKVLDLKNYINNRLLPIVNQQSCRISNIETVIEFQQMNSRL
skills/antibody-design-agent/MAGE/repo/Data cleaning/PlAbDab/hcv_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 16
"source": [ "This is from Weber et al.\n", "https://doi.org/10.1016/j.immuni.2021.12.003\n", - Network accessline 17
"This is from Weber et al.\n", "https://doi.org/10.1016/j.immuni.2021.12.003\n", "\n", - Network accessline 18
"https://doi.org/10.1016/j.immuni.2021.12.003\n", - Network accessline 41
"source": [ "# Took E1/E2 from here:\n", "# https://www.ncbi.nlm.nih.gov/protein/1479555230\n", - Network accessline 42
"# Took E1/E2 from here:\n", "# https://www.ncbi.nlm.nih.gov/protein/1479555230\n", "# Was linked in paper\n", - Network accessline 43
"# https://www.ncbi.nlm.nih.gov/protein/1479555230\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/crowe_ebola/crowe_ebola_processing_24-03-07.ipynb
- Executable scriptline 1
Executable file - Network accessline 28
"outputs": [], "source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", - Network accessline 29
"source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", "ebov_gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHK - Network accessline 30
"# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", - Possible obfuscationline 31
"ebov_gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTN - Network accessline 34
"len(ebov_gp)\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", - Network accessline 35
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", "bdbv_gp = 'MVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTG - Network accessline 36
"# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", - Possible obfuscationline 37
"bdbv_gp = 'MVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTN - Network accessline 39
"len(bdbv_gp)\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", - Network accessline 40
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", "sudv_gp = 'MGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTG - Network accessline 41
"# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", - Possible obfuscationline 42
"sudv_gp = 'MGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFFLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQ - Network accessline 44
"len(sudv_gp)\n", "\n", "# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", - Network accessline 45
"\n", "# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", "sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGD - Network accessline 46
"# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", - Possible obfuscationline 47
"sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY - Network accessline 70
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 71
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " binding_df['sGP'] = supp_table[['sGP ELISA1', 'sGP ELISA2']].mean(axis=1)\n - Network accessline 72
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/denovo_absci/denovo_trastuzamab_24-02-29.ipynb
- Executable scriptline 1
Executable file - Network accessline 6
"source": [ "# Unlocking denovo antibody design\n", "* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", - Network accessline 7
"# Unlocking denovo antibody design\n", "* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", "\n", - Network accessline 8
"* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", - Network accessline 9
"\n", "References for Trastuzamab:\n", "* https://www.genome.jp/entry/D03257\n", - Network accessline 10
"References for Trastuzamab:\n", "* https://www.genome.jp/entry/D03257\n", "* https://www.rcsb.org/structure/5xhg\n", - Network accessline 11
"* https://www.genome.jp/entry/D03257\n", - Network accessline 12
"* https://www.rcsb.org/structure/5xhg\n", - Possible obfuscationline 33
"trast_hc = 'EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH - Possible obfuscationline 34
"trast_lc = 'DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC'\n", - Possible obfuscationline 35
"her2 = 'TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCL - Network accessline 181
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 182
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['antigen_seq'] = her2\n", - Network accessline 183
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 187
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 188
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['antigen_name'] = 'HER2'\n", - Network accessline 189
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 193
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 194
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['source'] = 'Absci_denovo'\n" - Network accessline 195
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/final_processing/detagging_script_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 114
"HAtag = 'YPYDVPDYA'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 115
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 116
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Possible obfuscationline 121
"# ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW - Network accessline 212
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 213
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " X_ant.loc[tagged_dfs[flagtag].index] = tagged_dfs[flagtag]\n" - Network accessline 214
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Possible obfuscationline 314
"DLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF - Possible obfuscationline 317
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 320
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 323
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 326
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 329
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 332
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 335
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 338
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 341
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 344
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 347
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 350
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 380
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 383
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 386
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 389
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 392
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 395
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 398
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 401
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 404
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 407
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 410
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 413
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 416
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 419
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 422
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 425
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 428
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 431
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 434
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 437
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 440
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 443
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 446
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 449
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 452
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 455
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 458
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 461
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 464
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 467
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 470
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 473
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 476
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 479
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 482
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 485
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 488
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 491
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 494
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 497
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 500
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 503
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 506
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSCMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 509
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 512
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 515
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 518
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 521
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 524
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 527
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 530
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 533
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 536
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 539
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 542
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 545
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 548
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 551
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 554
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 557
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 560
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 563
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 566
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 569
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 572
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 575
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 578
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGA - Possible obfuscationline 581
"SQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTP - Possible obfuscationline 584
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 587
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 590
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 593
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 596
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 599
"VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSG - Possible obfuscationline 602
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 605
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 652
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 655
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 1236
"long attachment for: SDKICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENKHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLATASSWSYIVETSSSNNGTCYPGDFINYEELREQLSSVSSFEKFEIFPKTSSWPNHETNKGVTAACPHAGTNSFYKNLIWLVKKENSYPKINISYTNNRGKEVLVLWAIHHPPTSTDQQSLYQNANSYVFVGSSRYSRKFEPEIATR - Possible obfuscationline 1237
"long attachment for: SDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSVAGWILGNPECESLFSKESWSYIAETPKPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTAACSHNGKSSFYKNLLWLTEKNGLYPNLSKSYVNNKEKEVLVLWGVHHPSNIGDQRAIYHTENAYVSVVSSHYSRRFTPEIAKR - Possible obfuscationline 1239
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1240
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1241
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1242
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1243
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1244
"long attachment for: GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITASGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH - Possible obfuscationline 1245
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSLPEPEWTYPRLSCPGSTFQKALLISPHRFGEIKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEA - Possible obfuscationline 1246
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1247
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1259
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1260
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1261
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1262
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1263
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1264
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1265
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1266
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1267
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1268
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1269
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1270
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1271
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1272
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1273
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1274
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1275
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1276
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1277
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1278
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1279
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1280
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1281
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1282
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1283
"long attachment for: TQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGI - Possible obfuscationline 1336
"long attachment for: QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCA - Possible obfuscationline 1339
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1340
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1341
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1342
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Network accessline 1350
], "source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", - Network accessline 1351
"source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", "X_ant = X_ant.apply(lambda x: find_and_replace_ - Network accessline 1352
"# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/final_processing/final_concat_v2_24-03-12.ipynb
- Executable scriptline 1
Executable file
skills/antibody-design-agent/MAGE/repo/Data cleaning/flu_LLM_paper/wang_preprint_flu_cleaning_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 284
], "source": [ "# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", - Network accessline 285
"source": [ "# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", "# I am sourcing antibodies from certain references contained here. The annotations in 'Binds to' are not sufficient for our model since we need antige - Network accessline 286
"# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", - Network accessline 427
"source": [ "# Joyce et al. Group 1 - top group with 440 binding to HA:Unk for Group 1,2\n", "# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416 - Network accessline 428
"# Joyce et al. Group 1 - top group with 440 binding to HA:Unk for Group 1,2\n", "# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416308510%3Fshowall - Network accessline 429
"# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416308510%3Fshowall%3Dtrue#secsectitle0080\n", - Possible obfuscationline 436
"h3n2_HA = 'QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSS - Possible obfuscationline 534
"bris = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGKIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGPYKIGTSGSCPNITNGNGFFATMAWAVPKNDKNKTATNPLTIEVPYICTEGEDQITVWGFHSDDETQMAKLYGDSKPQKFTSS - Possible obfuscationline 537
"phuk = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEKIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKIGFFATMAWAVPKDNYKNATNPLTVEVPYICTEGEDQITVWGFHSDNKTQMKSLYGDSNPQKFTSSA - Possible obfuscationline 540
"mala = \"MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGNIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGSYKIGTSGSCPNVTNGNGFFATMAWAVPKNDNNKTATNSLTIEVPYICTEGEDQITVWGFHSDNEAQMAKLYGDSKPQKFTS - Possible obfuscationline 543
"flor = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKSGFFATMAWAVPKDNNKNATNPLTVEVPYICTEGEDQITVWGFHSDDKTQMKNLYGDSNPQKFTSSA - Possible obfuscationline 546
"yama = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTKTRGKLCPNCLNCTDLDVALGRPMCMGTIPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTHNVINAERAPGGPYRLGTSGSCPNVTSRNGFFATMAWAVPRDNKTATNPLTVEVPYICTKGEDQITVWGFHSDDKTQMKNLYGDSNPQKFTSSAN - Possible obfuscationline 549
"lee = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTRSHFANLKGTQTRGKLCPNCFNCTDLDVALGRPKCMGNIPSAKVSILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTSNVINAETAPGGPYKVGTSGSCPNVANRNGFFNTMAWVIPKDNNKTAINPVTVEVPYICSEGEDQITVWGFHSDDKTQMERLYGDSNPQKFTSSAN - Network accessline 580
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 581
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " liu_df['antigen_seq'] = liu_meta['Sorted Population']\n" - Network accessline 582
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 612
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 613
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " liu_df['antigen_seq'] = liu_df['antigen_seq'].map(ant_map)\n" - Network accessline 614
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 694
"outputs": [], "source": [ "#https://www.rcsb.org/structure/3LZG\n", - Network accessline 695
"source": [ "#https://www.rcsb.org/structure/3LZG\n", "cal09 = 'MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWL - Network accessline 696
"#https://www.rcsb.org/structure/3LZG\n", - Possible obfuscationline 697
"cal09 = 'MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPE - Network accessline 748
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 749
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " andrews_df['Ab'] = andrews_df.index\n" - Network accessline 750
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 770
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 771
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " andrews_df['Ab'] = andrews_df['Ab'].apply(lambda x: x[-4:len(x)])\n" - Network accessline 772
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/antibody-design-agent/MAGE/repo/Data cleaning/zurbuchen/zurbuchen_data_23-03-08.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 89
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAkQAAAGwCAYAAABIC3rIAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAArC0lEQVR4nO3de1iVdb7//9eSk8DISjFOiadC89RBLAJnRieV3MWwu2rGZj - Possible obfuscationline 295
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAjsAAAGxCAYAAACEFXd4AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAAuD0lEQVR4nO3dfXBUVZ7G8ach0EmAIBDIixASJBBeFBjQjKACAsF3XVaHWU - Network accessline 521
"## Seqs from CoVAbDab notebook\n", "\n", "### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", - Network accessline 522
"\n", "### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", "b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK - Network accessline 523
"### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", - Network accessline 524
"b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLP - Possible obfuscationline 524
"b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLP - Network accessline 525
"\n", "### Spike B.1.617.2 (delta) https://www.rcsb.org/structure/7tov\n", "b16172 = 'MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYH - Network accessline 526
"### Spike B.1.617.2 (delta) https://www.rcsb.org/structure/7tov\n", - Possible obfuscationline 527
"b16172 = 'MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Network accessline 528
"\n", "### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", - Network accessline 529
"### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", "wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY - Network accessline 530
"# https://www.rcsb.org/structure/6m0j\n", - Possible obfuscationline 531
"wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Network accessline 532
"\n", "### SARS-2_WT RBD\n", "# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", - Network accessline 533
"### SARS-2_WT RBD\n", "# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", "wt_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE - Network accessline 534
"# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", - Possible obfuscationline 535
"wt_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLV - Possible obfuscationline 560
"RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF - Possible obfuscationline 561
"MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQ - Possible obfuscationline 562
"MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTL - Possible obfuscationline 563
"MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQ
skills/antibody-design-agent/MAGE/repo/Fine_tuning/full_model_training_24-03-12.py
skills/antibody-design-agent/MAGE/repo/Fine_tuning/selected_abs_Figure_2-3_24-06-10.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 140
"rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Possible obfuscationline 274
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAXkAAAEvCAYAAACg1LHXAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABjU0lEQVR4nO3deTxU6x8H8M+xbyE77RQhaUPaiLRqEapbUioltG/aS9q3W0 - Possible obfuscationline 323
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAO0AAAG/CAYAAAC0fFDHAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABUlElEQVR4nO3de1xM+f8H8FdXKSlKF0pbMYNEbRGVW7RarRVrXZbcldvGyq - Possible obfuscationline 377
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeUAAAFACAYAAACC4WQ/AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAADJ8ElEQVR4nOydd3gUVdfAfzNb0ntIIYUQaiAU6R0pAtJEQQVBRJFXxYKvBS - Possible obfuscationline 458
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeQAAAFOCAYAAABXKW5xAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABWiUlEQVR4nO3deVxN+f8H8NcpXUX7JhlbRWmxL2ULDRMKKctgjH3Ivm+NMU - Possible obfuscationline 550
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeYAAAFOCAYAAABT3L5MAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABlyklEQVR4nO3dd1gUV/s38O+w0hRRqgpiIhgWBUQWwY5RfsaGRiP2rrGD3V
skills/antibody-design-agent/MAGE/repo/LICENSE
skills/antibody-design-agent/MAGE/repo/Output_analysis/figure1_plots_24-06-10.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 118
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAe0AAAGBCAYAAABLgunaAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAACIvElEQVR4nO3dd1gUV/s38O+CLkWkCIiCiIgIiguKoqKIRDAQZcWaiAVsqN - Possible obfuscationline 183
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAWUAAADtCAYAAABnEWS6AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAA8sUlEQVR4nO3deVQT1/s/8HfAsCgCssim4o4VUFwBkSq4o7ZKqUpbccUVRE - Possible obfuscationline 245
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAYAAAAGACAYAAACkx7W/AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAA+XklEQVR4nO3deVgTV9sG8DsgiCibsinuKKCIKAoWawtCrfqKW5G6ixvWBX - Possible obfuscationline 312
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAdMAAAF9CAYAAABf6IIzAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAADG/UlEQVR4nOzdd3gU1dfA8e9sy6ZtekIqJPTeqwhIEamKgOIPxAYWLFjwFX - Possible obfuscationline 375
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAbUAAAF/CAYAAADO2VcPAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAEAAElEQVR4nOy9d3xc9ZW//9wyVaPeLUu2LPduYxsbjAHTa0ICCaRAAiGFbM - Possible obfuscationline 425
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAX8AAAFOCAYAAABuYh1vAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABe6UlEQVR4nO3deVwT19oH8F8ICYsYdhdQFFFQAQWrCFpBRatWqAv01latrd - Possible obfuscationline 470
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAX8AAAFOCAYAAABuYh1vAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABkvUlEQVR4nO3dd1xV9f/A8de9l3sZIlMExZELEgRHDhy5K03JXZaafnNkki
skills/antibody-design-agent/MAGE/repo/Output_analysis/output_filtering_annotation.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 45
"RBD_seq = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'" - Network accessline 142
"source": [ "Fasta output for humanness analysis:\n", "https://biophi.dichlab.org/humanization/humanness/" - Network accessline 143
"Fasta output for humanness analysis:\n", "https://biophi.dichlab.org/humanization/humanness/" ] - Network accessline 144
"https://biophi.dichlab.org/humanization/humanness/"
skills/antibody-design-agent/MAGE/repo/Output_analysis/selected_abs_Figure_2-3_24-06-10.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 140
"rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Possible obfuscationline 265
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAXkAAAEvCAYAAACg1LHXAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABjU0lEQVR4nO3deTxU6x8H8M+xbyE77RQhaUPaiLRqEapbUioltG/aS9q3W0 - Possible obfuscationline 314
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAO0AAAG/CAYAAAC0fFDHAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABUlElEQVR4nO3de1xM+f8H8FdXKSlKF0pbMYNEbRGVW7RarRVrXZbcldvGyq - Possible obfuscationline 368
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeUAAAFACAYAAACC4WQ/AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAADJ8ElEQVR4nOydd3gUVdfAfzNb0ntIIYUQaiAU6R0pAtJEQQVBRJFXxYKvBS - Possible obfuscationline 449
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeQAAAFOCAYAAABXKW5xAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABWiUlEQVR4nO3deVxN+f8H8NcpXUX7JhlbRWmxL2ULDRMKKctgjH3Ivm+NMU - Possible obfuscationline 541
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeYAAAFOCAYAAABT3L5MAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABlyklEQVR4nO3dd1gUV/s38O+w0hRRqgpiIhgWBUQWwY5RfsaGRiP2rrGD3V
skills/antibody-design-agent/MAGE/repo/Output_analysis/selection_pipeline_24-03-16.ipynb
skills/antibody-design-agent/MAGE/repo/README.md
- Network accessline 18
This repository contains Python scripts to accompany Wasdin et al., including antibody generation and follow-up analyses presented in the manuscript. All analyses were initially ran in Linux Red Hat 8.4, but have also been tested in Ubuntu - Network accessline 32
The Progen2 repository must cloned from: https://github.com/enijkamp/progen2 - Network accessline 33
https://github.com/enijkamp/progen2 - Network accessline 59
- Example: python generate_antibodies.py --n=1 --output=MAGE_antibodies.csv - This was tested on an Nvidia A6000 and took ~15 seconds to generate one antibody sequence against RBD. - To annotate and analyze output sequences without installi - Network accessline 61
- To annotate and analyze output sequences without installing the follow-up analyses libraries listed above, generated sequences can be uploaded to the IMGT Domain Gap Align webserver: https://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.
skills/antibody-design-agent/MAGE/repo/generate_antibodies.py
- Executable scriptline 1
Executable file - Possible obfuscationline 44
rbd_prompt = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'
skills/arboreto/references/distributed_computing.md
skills/arboreto/scripts/basic_grn_inference.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/arxiv-search/SKILL.md
- Network accessline 30
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 31
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 52
1. **Ask the user for their API key:** "To search arXiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 53
"To search arXiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 64
User: Search arXiv for transformer architecture papers → Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai" - Network accessline 65
→ Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai" → User: "val_abc123..." - Network accessline 66
→ Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai" - Network accessline 91
{ "title": "Article Title", "url": "https://arxiv.org/abs/...", - Network accessline 92
"title": "Article Title", "url": "https://arxiv.org/abs/...", "content": "Full article text with figures...", - Network accessline 93
"url": "https://arxiv.org/abs/...", - Network accessline 95
"source": "arxiv", "relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] - Network accessline 96
"relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] } - Network accessline 97
"images": ["https://example.com/figure1.jpg"] - Network accessline 167
- Base URL: `https://api.valyu.ai/v1` - Network accessline 179
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 190
[Credential-related source omitted] - Network accessline 224
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/arxiv-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/arxiv-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/bayesian-optimizer/bayesian_optimization.py
- Executable scriptline 1
Executable file
skills/bayesian-optimizer/stats_essentials.py
- Executable scriptline 1
Executable file
skills/benchling-integration/SKILL.md
- Network accessline 43
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 44
url="https://your-tenant.benchling.com", - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Network accessline 56
) benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 57
benchling = Benchling( url="https://your-tenant.benchling.com", auth_method=auth_method - Network accessline 58
url="https://your-tenant.benchling.com", - Network accessline 331
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 332
url="https://your-tenant.benchling.com", - Access to secretsline 333
[Credential-related source omitted] - Network accessline 470
- **Official Documentation:** https://docs.benchling.com - Network accessline 471
- **Python SDK Reference:** https://benchling.com/sdk-docs/ - Network accessline 472
- **API Reference:** https://benchling.com/api/reference
skills/benchling-integration/references/api_endpoints.md
- Network accessline 7
https://{tenant}.benchling.com/api/v2 - Network accessline 24
[Credential-related source omitted] - Access to secretsline 24
[Credential-related source omitted] - Network accessline 25
https://your-tenant.benchling.com/api/v2/dna-sequences \ - Access to secretsline 26
[Credential-related source omitted] - Network accessline 31
[Credential-related source omitted] - Access to secretsline 31
[Credential-related source omitted] - Network accessline 32
https://your-tenant.benchling.com/api/v2/dna-sequences \ - Access to secretsline 33
[Credential-related source omitted] - Network accessline 79
curl -X GET \ - Network accessline 80
"https://your-tenant.benchling.com/api/v2/dna-sequences?pageSize=50&nextToken=abc123" - Network accessline 791
curl -X GET \ - Network accessline 792
"https://tenant.benchling.com/api/v2/dna-sequences?name=plasmid&folderId=fld_abc&archived=false" - Network accessline 816
async function fetchSequence(id) { try { const response = await fetch( - Network accessline 817
try { const response = await fetch( `https://tenant.benchling.com/api/v2/dna-sequences/${id}`, - Network accessline 818
const response = await fetch( - Network accessline 819
`https://tenant.benchling.com/api/v2/dna-sequences/${id}`, - Network accessline 856
do { const url = new URL('https://tenant.benchling.com/api/v2/dna-sequences'); - Network accessline 857
const url = new URL('https://tenant.benchling.com/api/v2/dna-sequences'); - Network accessline 863
const response = await fetch(url, { - Network accessline 881
- **API Documentation:** https://benchling.com/api/reference - Network accessline 882
- **Interactive API Explorer:** https://your-tenant.benchling.com/api/reference (requires authentication) - Network accessline 883
- **Changelog:** https://docs.benchling.com/changelog
skills/benchling-integration/references/authentication.md
- Network accessline 28
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 29
url="https://your-tenant.benchling.com", - Network accessline 36
curl -X GET \ - Network accessline 37
https://your-tenant.benchling.com/api/v2/dna-sequences \ - Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Access to secretsline 83
[Credential-related source omitted] - Network accessline 86
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 87
url="https://your-tenant.benchling.com", - Network accessline 96
# Get access token curl -X POST \ - Network accessline 97
[Credential-related source omitted] - Access to secretsline 97
[Credential-related source omitted] - Network accessline 98
https://your-tenant.benchling.com/api/v2/token \ - Access to secretsline 102
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Network accessline 111
# Use access token curl -X GET \ - Network accessline 112
curl -X GET \ - Network accessline 113
https://your-tenant.benchling.com/api/v2/dna-sequences \ - Network accessline 147
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 148
url="https://your-tenant.benchling.com", - Network accessline 155
curl -X GET \ - Network accessline 156
https://your-tenant.benchling.com/api/v2/dna-sequences \ - Access to secretsline 181
[Credential-related source omitted] - Access to secretsline 184
[Credential-related source omitted] - Access to secretsline 185
[Credential-related source omitted] - Network accessline 290
# Test API key curl -X GET \ - Network accessline 291
[Credential-related source omitted] - Access to secretsline 291
[Credential-related source omitted] - Network accessline 292
https://your-tenant.benchling.com/api/v2/users/me \ - Access to secretsline 293
[Credential-related source omitted] - Network accessline 296
# Test OAuth token curl -X GET \ - Network accessline 297
curl -X GET \ - Network accessline 298
https://your-tenant.benchling.com/api/v2/users/me \ - Network accessline 310
try: benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 311
benchling = Benchling( url="https://your-tenant.benchling.com", auth_method=ApiKeyAuth("your_api_key") - Network accessline 312
url="https://your-tenant.benchling.com", - Access to secretsline 313
[Credential-related source omitted] - Network accessline 330
tenants = { "production": { "url": "https://prod.benchling.com", - Network accessline 331
[Credential-related source omitted] - Network accessline 332
"url": "https://prod.benchling.com", - Access to secretsline 333
[Credential-related source omitted] - Network accessline 334
}, "staging": { "url": "https://staging.benchling.com", - Network accessline 335
[Credential-related source omitted] - Network accessline 336
"url": "https://staging.benchling.com", - Access to secretsline 337
[Credential-related source omitted] - Access to secretsline 346
[Credential-related source omitted] - Network accessline 362
# Custom httpx client with certificate verification custom_client = httpx.Client( - Network accessline 363
custom_client = httpx.Client( - Network accessline 368
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 369
url="https://your-tenant.benchling.com", - Access to secretsline 370
[Credential-related source omitted] - Network accessline 377
- **Official Authentication Docs:** https://docs.benchling.com/docs/authentication - Network accessline 378
- **Developer Console:** https://your-tenant.benchling.com/developer - Network accessline 379
- **SDK Documentation:** https://benchling.com/sdk-docs/
skills/benchling-integration/references/sdk_reference.md
- Network accessline 29
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 30
url="https://your-tenant.benchling.com", - Access to secretsline 31
[Credential-related source omitted] - Network accessline 571
benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 572
url="https://your-tenant.benchling.com", - Access to secretsline 573
[Credential-related source omitted] - Network accessline 577
# Disable retries benchling = Benchling( url="https://your-tenant.benchling.com", - Network accessline 578
benchling = Benchling( url="https://your-tenant.benchling.com", auth_method=ApiKeyAuth("your_api_key"), - Network accessline 579
url="https://your-tenant.benchling.com", - Access to secretsline 580
[Credential-related source omitted] - Network accessline 771
- **SDK Source:** https://github.com/benchling/benchling-sdk - Network accessline 772
- **SDK Docs:** https://benchling.com/sdk-docs/ - Network accessline 773
- **API Reference:** https://benchling.com/api/reference - Network accessline 774
- **Common Examples:** https://docs.benchling.com/docs/common-sdk-interactions-and-examples
skills/bgpt-paper-search/SKILL.md
- Broad permissionsline 1
Bash - Network accessline 6
metadata: skill-author: BGPT website: https://bgpt.pro/mcp - Network accessline 7
skill-author: BGPT website: https://bgpt.pro/mcp github: https://github.com/connerlambden/bgpt-mcp - Network accessline 8
website: https://bgpt.pro/mcp - Network accessline 9
github: https://github.com/connerlambden/bgpt-mcp - Network accessline 40
"bgpt": { "command": "npx", "args": ["mcp-remote", "https://bgpt.pro/mcp/sse"] - Network accessline 41
"command": "npx", "args": ["mcp-remote", "https://bgpt.pro/mcp/sse"] } - Network accessline 42
"args": ["mcp-remote", "https://bgpt.pro/mcp/sse"] - Network accessline 72
- **Free tier**: 50 searches per network, no API key required - **Paid**: $0.01 per result with an API key from [bgpt.pro/mcp](https://bgpt.pro/mcp) - Network accessline 73
- **Paid**: $0.01 per result with an API key from [bgpt.pro/mcp](https://bgpt.pro/mcp)
skills/bindcraft/SKILL.md
- Network accessline 16
tags: [structure-design, sequence-design, binder, pipeline] proteinbase_slug: bindcraft proteinbase_url: https://proteinbase.com/design-methods/bindcraft - Network accessline 17
proteinbase_slug: bindcraft proteinbase_url: https://proteinbase.com/design-methods/bindcraft biomodals_script: modal_bindcraft.py - Network accessline 18
proteinbase_url: https://proteinbase.com/design-methods/bindcraft - Network accessline 52
git clone https://github.com/martinpacesa/BindCraft.git
skills/binder-design/references/tool-comparison.md
skills/binding-characterization/SKILL.md
- Network accessline 215
### Platform comparisons - [BLI vs SPR Comparison - Sartorius](https://www.sartorius.hr/en/news/blog/bli-vs-spr-choosing-the-ideal-method-for-analyzing-biomolecular-interactions/) - Network accessline 216
- [BLI vs SPR Comparison - Sartorius](https://www.sartorius.hr/en/news/blog/bli-vs-spr-choosing-the-ideal-method-for-analyzing-biomolecular-interactions/) - Network accessline 217
- [BLI vs SPR - Nicoya](https://nicoyalife.com/blog/biolayer-interferometry-vs-surface-plasmon-resonance/) - Network accessline 219
### SPR protocols - [SPR Guidelines - van der Merwe, Oxford](https://www.path.ox.ac.uk/wp-content/uploads/2023/09/SPR-guidelines-1.pdf) - Network accessline 220
- [SPR Guidelines - van der Merwe, Oxford](https://www.path.ox.ac.uk/wp-content/uploads/2023/09/SPR-guidelines-1.pdf) - Network accessline 221
- [SPR Experiment Guide - Duke DHVI](https://dhvi.duke.edu/sites/default/files/2022-08/SPR%20Experiment%20Guide%20v1.3.pdf) - Network accessline 223
### Troubleshooting - [4 Ways to Reduce NSB in SPR - Nicoya](https://nicoyalife.com/blog/4-ways-reduce-non-specific-binding-spr/) - Network accessline 224
- [4 Ways to Reduce NSB in SPR - Nicoya](https://nicoyalife.com/blog/4-ways-reduce-non-specific-binding-spr/) - Network accessline 225
- [3 Ways to Limit Mass Transfer Effects - Nicoya](https://nicoyalife.com/blog/3-ways-to-limit-mass-transfer-effects/) - Network accessline 226
- [Suppressing NSB in BLI - ACS Omega](https://pubs.acs.org/doi/10.1021/acsomega.1c05659) - Network accessline 228
### Regeneration - [SPR Regeneration - SPRpages](https://www.sprpages.nl/kinetics/regeneration) - Network accessline 229
- [SPR Regeneration - SPRpages](https://www.sprpages.nl/kinetics/regeneration) - Network accessline 230
- [Mastering Regeneration - Nicoya](https://nicoyalife.com/blog/regeneration-buffer-spr-experiment/) - Network accessline 232
### Mass transport - [Mass Transport Limitation in SPR - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4134667/) - Network accessline 233
- [Mass Transport Limitation in SPR - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4134667/) - Network accessline 234
- [Mass-Transfer Kinetics - SPRpages](https://www.sprpages.nl/data-fitting/kinetic-models/mass-transfer)
skills/bindingdb-database/SKILL.md
- Network accessline 13
BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains over 3 million binding data records for ~1.4 million compounds tested against ~9,200 protein targets, curated fro - Network accessline 15
**Key resources:** - BindingDB website: https://www.bindingdb.org/ - Network accessline 16
- BindingDB website: https://www.bindingdb.org/ - REST API: https://www.bindingdb.org/axis2/services/BDBService - Downloads: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 17
- REST API: https://www.bindingdb.org/axis2/services/BDBService - Downloads: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - GitHub: https://github.com/drugilsberg/bindingdb - Network accessline 18
- Downloads: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 19
- GitHub: https://github.com/drugilsberg/bindingdb - Network accessline 37
Base URL: `https://www.bindingdb.org/axis2/services/BDBService` - Network accessline 42
BASE_URL = "https://www.bindingdb.org/axis2/services/BDBService" - Network accessline 45
"""Query the BindingDB REST API.""" url = f"{BASE_URL}/{method}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 46
url = f"{BASE_URL}/{method}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) response.raise_for_status() - Network accessline 47
response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 117
""" Load BindingDB TSV file. Download from: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 118
Load BindingDB TSV file. Download from: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp """ - Network accessline 119
Download from: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 328
- **BindingDB website**: https://www.bindingdb.org/ - **Data downloads**: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 329
- **Data downloads**: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp - Network accessline 330
- **API documentation**: https://www.bindingdb.org/bind/BindingDBRESTfulAPI.jsp - Network accessline 332
- **Related resources**: ChEMBL (https://www.ebi.ac.uk/chembl/), PubChem BioAssay
skills/bindingdb-database/references/affinity_queries.md
- Network accessline 42
REST API query for BindingDB affinities by UniProt target ID. """ url = "https://www.bindingdb.org/axis2/services/BDBService/getLigandsByUniprotID" - Network accessline 43
""" url = "https://www.bindingdb.org/axis2/services/BDBService/getLigandsByUniprotID" params = { - Network accessline 44
url = "https://www.bindingdb.org/axis2/services/BDBService/getLigandsByUniprotID" - Network accessline 49
"response": "json" } response = requests.get(url, params=params) - Network accessline 50
} response = requests.get(url, params=params) return response.json() - Network accessline 51
response = requests.get(url, params=params) - Network accessline 72
def query_by_pubchem_cid(pubchem_cid): """Get all binding data for a specific compound by PubChem CID.""" url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByCID" - Network accessline 73
"""Get all binding data for a specific compound by PubChem CID.""" url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByCID" params = {"cid": pubchem_cid, "response": "json"} - Network accessline 74
url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByCID" params = {"cid": pubchem_cid, "response": "json"} response = requests.get(url, params=params) - Network accessline 75
params = {"cid": pubchem_cid, "response": "json"} response = requests.get(url, params=params) return response.json() - Network accessline 76
response = requests.get(url, params=params) - Network accessline 86
def query_by_target_name(target_name, affinity_cutoff=100): """Query BindingDB by target name.""" url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByTarget" - Network accessline 87
"""Query BindingDB by target name.""" url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByTarget" params = { - Network accessline 88
url = "https://www.bindingdb.org/axis2/services/BDBService/getAffinitiesByTarget" - Network accessline 92
"response": "json" } response = requests.get(url, params=params) - Network accessline 93
} response = requests.get(url, params=params) return response.json() - Network accessline 94
response = requests.get(url, params=params)
skills/bio-admet-prediction/SKILL.md
skills/bio-admet-prediction/examples/predict_admet.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 15
def predict_admetlab(smiles_list, api_url='https://admetlab3.scbdd.com/api/predict'): - Network accessline 22
payload = {'smiles': smiles_list} response = requests.post(api_url, json=payload, timeout=60) - Network accessline 23
response = requests.post(api_url, json=payload, timeout=60)
skills/bio-alignment-files-bam-statistics/examples/qc_report.py
- Executable scriptline 1
Executable file
skills/bio-alignment-filtering/SKILL.md
- Network accessline 239
with pysam.AlignmentFile('input.bam', 'rb') as infile: with pysam.AlignmentFile('region.bam', 'wb', header=infile.header) as outfile: for read in infile.fetch('chr1', 1000000, 2000000): - Network accessline 240
with pysam.AlignmentFile('region.bam', 'wb', header=infile.header) as outfile: for read in infile.fetch('chr1', 1000000, 2000000): outfile.write(read) - Network accessline 241
for read in infile.fetch('chr1', 1000000, 2000000): - Network accessline 262
with pysam.AlignmentFile('targets.bam', 'wb', header=infile.header) as outfile: for chrom, start, end in regions: for read in infile.fetch(chrom, start, end): - Network accessline 263
for chrom, start, end in regions: for read in infile.fetch(chrom, start, end): outfile.write(read) - Network accessline 264
for read in infile.fetch(chrom, start, end):
skills/bio-alignment-filtering/examples/filter_bam.py
- Executable scriptline 1
Executable file - Network accessline 23
chrom, coords = region.split(':') start, end = map(int, coords.split('-')) iterator = infile.fetch(chrom, start, end) - Network accessline 24
start, end = map(int, coords.split('-')) iterator = infile.fetch(chrom, start, end) else: - Network accessline 25
iterator = infile.fetch(chrom, start, end)
skills/bio-alignment-indexing/SKILL.md
- Network accessline 115
with pysam.AlignmentFile('input.bam', 'rb') as bam: # fetch() requires index - Network accessline 116
# fetch() requires index - Network accessline 117
for read in bam.fetch('chr1', 1000000, 2000000): - Network accessline 140
with pysam.AlignmentFile('input.bam', 'rb') as bam: for chrom, start, end in regions: count = sum(1 for _ in bam.fetch(chrom, start, end)) - Network accessline 141
for chrom, start, end in regions: count = sum(1 for _ in bam.fetch(chrom, start, end)) print(f'{chrom}:{start}-{end}: {count} reads') - Network accessline 142
count = sum(1 for _ in bam.fetch(chrom, start, end)) - Network accessline 155
with pysam.AlignmentFile('input.bam', 'rb') as bam: for read in bam.fetch('chr1', 1000000, 1000001): - Network accessline 156
for read in bam.fetch('chr1', 1000000, 1000001): - Network accessline 216
with pysam.FastaFile('reference.fa') as ref: seq = ref.fetch('chr1', 1000, 2000) - Network accessline 217
seq = ref.fetch('chr1', 1000, 2000) - Network accessline 225
| Create BAI | `samtools index file.bam` | `pysam.index('file.bam')` | | Create CSI | `samtools index -c file.bam` | `pysam.index('file.bam', csi=True)` | | Fetch region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` - Network accessline 226
| Create CSI | `samtools index -c file.bam` | `pysam.index('file.bam', csi=True)` | | Fetch region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` | | Count in region | `samtools view -c file.bam chr1:1-1000` | `bam.co - Network accessline 227
| Fetch region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` |
skills/bio-alignment-indexing/examples/fetch_regions.py
- Executable scriptline 1
Executable file - Network accessline 31
with pysam.AlignmentFile(bam_path, 'rb') as bam: count = 0 for read in bam.fetch(chrom, start - 1, end): # Convert to 0-based - Network accessline 32
count = 0 for read in bam.fetch(chrom, start - 1, end): # Convert to 0-based count += 1 - Network accessline 33
for read in bam.fetch(chrom, start - 1, end): # Convert to 0-based
skills/bio-alignment-indexing/usage-guide.md
- Network accessline 140
with pysam.AlignmentFile('input.bam', 'rb') as bam: for read in bam.fetch('chr1', 1000000, 2000000): - Network accessline 141
for read in bam.fetch('chr1', 1000000, 2000000): - Network accessline 163
with pysam.FastaFile('reference.fa') as ref: seq = ref.fetch('chr1', 999, 2000) # 0-based coordinates - Network accessline 164
seq = ref.fetch('chr1', 999, 2000) # 0-based coordinates - Network accessline 199
- Rebuild the index after any BAM modification - Use CSI format for genomes with very large chromosomes - Check that index exists before using fetch() in pysam - Network accessline 200
- Use CSI format for genomes with very large chromosomes - Check that index exists before using fetch() in pysam - Multi-threading (`-@ 8`) significantly speeds up large file indexing - Network accessline 201
- Check that index exists before using fetch() in pysam
skills/bio-alignment-io/examples/batch_convert.py
- Executable scriptline 1
Executable file
skills/bio-alignment-io/examples/convert_formats.py
- Executable scriptline 1
Executable file
skills/bio-alignment-io/examples/read_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-io/examples/slice_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-parsing/examples/analyze_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-parsing/examples/clean_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-parsing/examples/consensus_sequence.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-parsing/examples/find_conserved.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-parsing/examples/gap_analysis.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-statistics/examples/conservation_profile.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-statistics/examples/entropy_analysis.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-statistics/examples/gap_statistics.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-statistics/examples/identity_matrix.py
- Executable scriptline 1
Executable file
skills/bio-alignment-msa-statistics/examples/substitution_counts.py
- Executable scriptline 1
Executable file
skills/bio-alignment-pairwise/examples/alignment_from_file.py
- Executable scriptline 1
Executable file
skills/bio-alignment-pairwise/examples/global_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-pairwise/examples/local_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-pairwise/examples/protein_alignment.py
- Executable scriptline 1
Executable file
skills/bio-alignment-sorting/examples/sort_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-alignment-validation/SKILL.md
- Network accessline 67
sizes = [] bam = pysam.AlignmentFile(bam_file, 'rb') for i, read in enumerate(bam.fetch()): - Network accessline 68
bam = pysam.AlignmentFile(bam_file, 'rb') for i, read in enumerate(bam.fetch()): if i >= max_reads: - Network accessline 69
for i, read in enumerate(bam.fetch()): - Network accessline 304
proper = 0 paired = 0 for i, read in enumerate(self.bam.fetch()): - Network accessline 305
paired = 0 for i, read in enumerate(self.bam.fetch()): if i >= sample_size: - Network accessline 306
for i, read in enumerate(self.bam.fetch()): - Network accessline 315
def mapq_distribution(self, sample_size=100000): mapqs = [] for i, read in enumerate(self.bam.fetch()): - Network accessline 316
mapqs = [] for i, read in enumerate(self.bam.fetch()): if i >= sample_size: - Network accessline 317
for i, read in enumerate(self.bam.fetch()): - Network accessline 325
forward = 0 reverse = 0 for i, read in enumerate(self.bam.fetch()): - Network accessline 326
reverse = 0 for i, read in enumerate(self.bam.fetch()): if i >= sample_size: - Network accessline 327
for i, read in enumerate(self.bam.fetch()):
skills/bio-alignment-validation/examples/validate_alignment.py
skills/bio-alignment-validation/examples/validate_alignment.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-alignment-validation/usage-guide.md
- Network accessline 196
sizes = [] with pysam.AlignmentFile(bam_file, 'rb') as bam: for i, read in enumerate(bam.fetch()): - Network accessline 197
with pysam.AlignmentFile(bam_file, 'rb') as bam: for i, read in enumerate(bam.fetch()): if i >= max_reads: - Network accessline 198
for i, read in enumerate(bam.fetch()): - Network accessline 226
def proper_pair_rate(self, sample_size=100000): proper, paired = 0, 0 for i, read in enumerate(self.bam.fetch()): - Network accessline 227
proper, paired = 0, 0 for i, read in enumerate(self.bam.fetch()): if i >= sample_size: - Network accessline 228
for i, read in enumerate(self.bam.fetch()): - Network accessline 237
def strand_balance(self, sample_size=100000): forward, reverse = 0, 0 for i, read in enumerate(self.bam.fetch()): - Network accessline 238
forward, reverse = 0, 0 for i, read in enumerate(self.bam.fetch()): if i >= sample_size: - Network accessline 239
for i, read in enumerate(self.bam.fetch()):
skills/bio-atac-seq-atac-peak-calling/examples/call_atac_peaks.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-atac-seq-atac-qc/SKILL.md
skills/bio-atac-seq-atac-qc/examples/atac_qc_metrics.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-atac-seq-differential-accessibility/examples/diff_accessibility.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-atac-seq-footprinting/SKILL.md
skills/bio-atac-seq-footprinting/examples/run_tobias.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-atac-seq-nucleosome-positioning/SKILL.md
skills/bio-atac-seq-nucleosome-positioning/examples/nucleosome_analysis.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-basecalling/examples/basecall_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-basecalling/examples/dorado_basecall.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-basecalling/usage-guide.md
- Network accessline 8
# Dorado (from ONT community) # Download from https://github.com/nanoporetech/dorado - Network accessline 9
# Download from https://github.com/nanoporetech/dorado - Network accessline 85
## Resources - [Dorado GitHub](https://github.com/nanoporetech/dorado) - Network accessline 86
- [Dorado GitHub](https://github.com/nanoporetech/dorado) - Network accessline 87
- [ONT Community](https://community.nanoporetech.com/)
skills/bio-batch-downloads/SKILL.md
- Access to secretsline 36
[Credential-related source omitted] - Network accessline 46
Get an API key at: https://www.ncbi.nlm.nih.gov/account/settings/ - Access to secretsline 122
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 173
[Credential-related source omitted] - Access to secretsline 208
[Credential-related source omitted] - Access to secretsline 275
[Credential-related source omitted]
skills/bio-batch-downloads/examples/batch_by_ids.py
skills/bio-batch-downloads/examples/batch_fasta.py
skills/bio-batch-downloads/examples/robust_download.py
skills/bio-batch-downloads/usage-guide.md
skills/bio-batch-processing/examples/batch_process.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-bedgraph-handling/SKILL.md
- Dangerous shell operationline 316
rm ${NAME}.bedgraph ${NAME}.sorted.bedgraph ${NAME}.clipped.bedgraph
skills/bio-bedgraph-handling/examples/bam_to_bigwig.sh
skills/bio-bedgraph-handling/examples/bedgraph_operations.py
- Executable scriptline 1
Executable file
skills/bio-bedgraph-handling/usage-guide.md
- Network accessline 97
## Resources - [bedGraph Format](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) - Network accessline 98
- [bedGraph Format](https://genome.ucsc.edu/goldenPath/help/bedgraph.html) - Network accessline 99
- [bedtools genomecov](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html) - Network accessline 100
- [UCSC Tools](http://hgdownload.soe.ucsc.edu/admin/exe/)
skills/bio-blast-searches/examples/basic_blast.py
- Executable scriptline 1
Executable file
skills/bio-blast-searches/examples/blastp_filtered.py
- Executable scriptline 1
Executable file
skills/bio-blast-searches/examples/save_and_parse.py
- Executable scriptline 1
Executable file
skills/bio-causal-genomics-fine-mapping/SKILL.md
skills/bio-causal-genomics-fine-mapping/examples/finemap_pipeline.sh
- Executable scriptline 1
#!/usr/bin/env bash
skills/bio-causal-genomics-fine-mapping/usage-guide.md
skills/bio-causal-genomics-mendelian-randomization/SKILL.md
- Network accessline 98
OpenGWAS (ieugwasr) requires authentication. The auth system has changed multiple times. Refer to the ieugwasr README for current instructions: https://github.com/MRCIEU/ieugwasr - Network accessline 100
https://github.com/MRCIEU/ieugwasr - Network accessline 208
# MR power depends on: sample size, variance explained by instruments, effect size # Use mRnd web tool: https://shiny.cnsgenomics.com/mRnd/ - Network accessline 209
# Use mRnd web tool: https://shiny.cnsgenomics.com/mRnd/
skills/bio-cfdna-preprocessing/SKILL.md
- Network accessline 169
for read in bam.fetch():
skills/bio-cfdna-preprocessing/examples/preprocess_cfdna.py
skills/bio-chipseq-motif-analysis/SKILL.md
- Network accessline 230
# Download JASPAR motifs wget https://jaspar.genereg.net/download/data/2024/CORE/JASPAR2024_CORE_vertebrates_non-redundant_pfms_meme.txt - Network accessline 231
wget https://jaspar.genereg.net/download/data/2024/CORE/JASPAR2024_CORE_vertebrates_non-redundant_pfms_meme.txt - Network accessline 240
# Download HOCOMOCO wget https://hocomoco11.autosome.org/final_bundle/hocomoco11/core/HUMAN/mono/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme - Network accessline 241
wget https://hocomoco11.autosome.org/final_bundle/hocomoco11/core/HUMAN/mono/HOCOMOCOv11_core_HUMAN_mono_meme_format.meme
skills/bio-chipseq-motif-analysis/examples/motif_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-chipseq-peak-calling/examples/macs3_peak_calling.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-chipseq-qc/examples/calculate_frip.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-chipseq-qc/examples/chipseq_qc.py
skills/bio-chipseq-qc/examples/run_idr.sh
skills/bio-chipseq-super-enhancers/SKILL.md
- Network accessline 39
git clone https://github.com/stjude/ROSE.git
skills/bio-chipseq-super-enhancers/examples/analyze_super_enhancers.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-chipseq-super-enhancers/examples/run_rose.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-chipseq-super-enhancers/usage-guide.md
- Network accessline 10
# ROSE (standard method) git clone https://github.com/stjude/ROSE.git - Network accessline 11
git clone https://github.com/stjude/ROSE.git - Network accessline 111
- [ROSE paper](https://www.cell.com/cell/fulltext/S0092-8674(13)00392-9) - Network accessline 112
- [Super-enhancer review](https://www.nature.com/articles/nrg.2016.167)
skills/bio-chipseq-visualization/examples/deeptools_heatmap.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-clinical-databases-clinvar-lookup/SKILL.md
- Network accessline 27
**"Look up this variant in ClinVar"** → Query ClinVar database for clinical significance, review status, and disease associations. - Python: `requests.get()` against NCBI E-utilities (requests) - Network accessline 28
- Python: `requests.get()` against NCBI E-utilities (requests) - Network accessline 36
def query_clinvar_by_id(variation_id): '''Query ClinVar by variation ID''' url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' - Network accessline 37
'''Query ClinVar by variation ID''' url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' params = { - Network accessline 38
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' - Network accessline 42
'retmode': 'json' } response = requests.get(url, params=params) - Network accessline 43
} response = requests.get(url, params=params) return response.json() - Network accessline 44
response = requests.get(url, params=params) - Network accessline 53
def search_clinvar_gene(gene_symbol, pathogenic_only=False): '''Search ClinVar for variants in a gene''' url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' - Network accessline 55
url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' - Network accessline 65
'retmode': 'json' } response = requests.get(url, params=params) - Network accessline 66
} response = requests.get(url, params=params) return response.json() - Network accessline 67
response = requests.get(url, params=params) - Network accessline 74
def search_clinvar_hgvs(hgvs): '''Search ClinVar by HGVS notation''' url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' - Network accessline 75
'''Search ClinVar by HGVS notation''' url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' params = { - Network accessline 76
url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' - Network accessline 80
'retmode': 'json' } response = requests.get(url, params=params) - Network accessline 81
} response = requests.get(url, params=params) return response.json() - Network accessline 82
response = requests.get(url, params=params) - Network accessline 95
# GRCh38 wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 96
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 97
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 99
# GRCh37 wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz - Network accessline 100
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz
skills/bio-clinical-databases-clinvar-lookup/examples/clinvar_query.py
- Executable scriptline 1
Executable file - Network accessline 9
url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' params = {'db': 'clinvar', 'term': term, 'retmax': retmax, 'retmode': 'json'} response = requests.get(url, params=params) - Network accessline 10
params = {'db': 'clinvar', 'term': term, 'retmax': retmax, 'retmode': 'json'} response = requests.get(url, params=params) data = response.json() - Network accessline 11
response = requests.get(url, params=params) - Network accessline 17
if not ids: return [] url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' - Network accessline 18
return [] url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' params = {'db': 'clinvar', 'id': ','.join(ids), 'retmode': 'json'} - Network accessline 19
url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' params = {'db': 'clinvar', 'id': ','.join(ids), 'retmode': 'json'} response = requests.get(url, params=params) - Network accessline 20
params = {'db': 'clinvar', 'id': ','.join(ids), 'retmode': 'json'} response = requests.get(url, params=params) data = response.json() - Network accessline 21
response = requests.get(url, params=params)
skills/bio-clinical-databases-clinvar-lookup/usage-guide.md
- Network accessline 12
# For local ClinVar queries wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 13
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 14
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
skills/bio-clinical-databases-dbsnp-queries/SKILL.md
- Network accessline 158
def query_spdi(rsid): '''Query NCBI Variation Services for SPDI notation''' url = f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid[2:]}' - Network accessline 159
'''Query NCBI Variation Services for SPDI notation''' url = f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid[2:]}' response = requests.get(url) - Network accessline 160
url = f'https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid[2:]}' response = requests.get(url) if response.ok: - Network accessline 161
response = requests.get(url)
skills/bio-clinical-databases-dbsnp-queries/examples/dbsnp_lookup.py
- Executable scriptline 1
Executable file
skills/bio-clinical-databases-gnomad-frequencies/SKILL.md
- Network accessline 26
**"Check how common this variant is in the population"** → Query gnomAD for allele frequency, allele count, and homozygote count. - Python: GraphQL via `requests.post()` (requests) - Network accessline 27
- Python: GraphQL via `requests.post()` (requests) - Network accessline 38
dataset options: gnomad_r4, gnomad_r3, gnomad_r2_1 ''' url = 'https://gnomad.broadinstitute.org/api' - Network accessline 40
url = 'https://gnomad.broadinstitute.org/api' - Network accessline 64
response = requests.post(url, json={'query': query, 'variables': variables})
skills/bio-clinical-databases-gnomad-frequencies/examples/gnomad_query.py
- Executable scriptline 1
Executable file
skills/bio-clinical-databases-hla-typing/examples/optitype_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-clinical-databases-hla-typing/usage-guide.md
skills/bio-clinical-databases-myvariant-queries/examples/query_myvariant.py
- Executable scriptline 1
Executable file
skills/bio-clinical-databases-pharmacogenomics/SKILL.md
- Network accessline 26
**"Find pharmacogenomic annotations for this gene"** → Query PharmGKB for clinical annotations linking genes to drug response. - Python: `requests.get()` against PharmGKB API (requests) - Network accessline 27
- Python: `requests.get()` against PharmGKB API (requests) - Network accessline 34
def get_pharmgkb_annotations(gene_symbol): '''Get PharmGKB clinical annotations for a gene''' url = f'https://api.pharmgkb.org/v1/data/clinicalAnnotation' - Network accessline 35
'''Get PharmGKB clinical annotations for a gene''' url = f'https://api.pharmgkb.org/v1/data/clinicalAnnotation' params = {'view': 'base', 'location.genes.symbol': gene_symbol} - Network accessline 36
url = f'https://api.pharmgkb.org/v1/data/clinicalAnnotation' params = {'view': 'base', 'location.genes.symbol': gene_symbol} response = requests.get(url, params=params) - Network accessline 37
params = {'view': 'base', 'location.genes.symbol': gene_symbol} response = requests.get(url, params=params) return response.json()['data'] - Network accessline 38
response = requests.get(url, params=params) - Network accessline 49
def get_drug_annotations(drug_name): '''Get pharmacogenomic annotations for a drug''' url = 'https://api.pharmgkb.org/v1/data/clinicalAnnotation' - Network accessline 50
'''Get pharmacogenomic annotations for a drug''' url = 'https://api.pharmgkb.org/v1/data/clinicalAnnotation' params = {'view': 'base', 'chemicals.name': drug_name} - Network accessline 51
url = 'https://api.pharmgkb.org/v1/data/clinicalAnnotation' params = {'view': 'base', 'chemicals.name': drug_name} response = requests.get(url, params=params) - Network accessline 52
params = {'view': 'base', 'chemicals.name': drug_name} response = requests.get(url, params=params) return response.json()['data'] - Network accessline 53
response = requests.get(url, params=params) - Network accessline 62
def get_cpic_guidelines(gene_symbol): '''Get CPIC dosing guidelines for a gene''' url = 'https://api.pharmgkb.org/v1/data/guideline' - Network accessline 63
'''Get CPIC dosing guidelines for a gene''' url = 'https://api.pharmgkb.org/v1/data/guideline' params = {'view': 'base', 'relatedGenes.symbol': gene_symbol, 'source': 'CPIC'} - Network accessline 64
url = 'https://api.pharmgkb.org/v1/data/guideline' params = {'view': 'base', 'relatedGenes.symbol': gene_symbol, 'source': 'CPIC'} response = requests.get(url, params=params) - Network accessline 65
params = {'view': 'base', 'relatedGenes.symbol': gene_symbol, 'source': 'CPIC'} response = requests.get(url, params=params) return response.json()['data'] - Network accessline 66
response = requests.get(url, params=params) - Network accessline 159
def check_pgx_interaction(drug, gene, variant): '''Check for pharmacogenomic drug-gene-variant interaction''' url = 'https://api.pharmgkb.org/v1/data/variantAnnotation' - Network accessline 160
'''Check for pharmacogenomic drug-gene-variant interaction''' url = 'https://api.pharmgkb.org/v1/data/variantAnnotation' params = { - Network accessline 161
url = 'https://api.pharmgkb.org/v1/data/variantAnnotation' - Network accessline 164
'location.genes.symbol': gene } response = requests.get(url, params=params) - Network accessline 165
} response = requests.get(url, params=params) annotations = response.json().get('data', []) - Network accessline 166
response = requests.get(url, params=params)
skills/bio-clinical-databases-pharmacogenomics/examples/pharmgkb_query.py
- Executable scriptline 1
Executable file - Network accessline 13
url = 'https://api.pharmgkb.org/v1/data/clinicalAnnotation' params = {'view': 'base', 'location.genes.symbol': gene_symbol} response = requests.get(url, params=params) - Network accessline 14
params = {'view': 'base', 'location.genes.symbol': gene_symbol} response = requests.get(url, params=params) if response.status_code == 200: - Network accessline 15
response = requests.get(url, params=params) - Network accessline 22
url = 'https://api.pharmgkb.org/v1/data/guideline' params = {'view': 'base', 'relatedGenes.symbol': gene_symbol, 'source': 'CPIC'} response = requests.get(url, params=params) - Network accessline 23
params = {'view': 'base', 'relatedGenes.symbol': gene_symbol, 'source': 'CPIC'} response = requests.get(url, params=params) if response.status_code == 200: - Network accessline 24
response = requests.get(url, params=params) - Network accessline 29
# --- Star Allele Activity Scores --- # Based on CPIC Clinical Pharmacogenetics Implementation Consortium guidelines # https://cpicpgx.org/ - Network accessline 31
# https://cpicpgx.org/
skills/bio-clinical-databases-polygenic-risk/SKILL.md
- Network accessline 238
''' import requests url = f'https://www.pgscatalog.org/rest/score/{pgs_id}' - Network accessline 239
import requests url = f'https://www.pgscatalog.org/rest/score/{pgs_id}' response = requests.get(url) - Network accessline 240
url = f'https://www.pgscatalog.org/rest/score/{pgs_id}' response = requests.get(url) score_info = response.json() - Network accessline 241
response = requests.get(url) - Network accessline 244
# Download scoring file ftp_url = score_info['ftp_scoring_file'] # Use wget or requests to download - Network accessline 246
# Use wget or requests to download
skills/bio-clinical-databases-polygenic-risk/examples/prsice2_workflow.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 9
# # Example data: # - Download GWAS from GWAS Catalog: https://www.ebi.ac.uk/gwas/ - Network accessline 10
# Example data: # - Download GWAS from GWAS Catalog: https://www.ebi.ac.uk/gwas/ # - Download 1000 Genomes for testing: https://www.internationalgenome.org/ - Network accessline 11
# - Download GWAS from GWAS Catalog: https://www.ebi.ac.uk/gwas/ - Network accessline 12
# - Download 1000 Genomes for testing: https://www.internationalgenome.org/
skills/bio-clinical-databases-polygenic-risk/usage-guide.md
- Network accessline 10
# PRSice-2 wget https://github.com/choishingwan/PRSice/releases/download/2.3.5/PRSice_linux.zip - Network accessline 11
wget https://github.com/choishingwan/PRSice/releases/download/2.3.5/PRSice_linux.zip - Network accessline 14
# PRS-CS git clone https://github.com/getian107/PRScs.git - Network accessline 15
git clone https://github.com/getian107/PRScs.git
skills/bio-clinical-databases-somatic-signatures/examples/mutsig_fitting.R
skills/bio-clinical-databases-somatic-signatures/examples/sigprofiler_analysis.py
- Executable scriptline 1
Executable file - Network accessline 10
# --- ALTERNATIVE: Use public data --- # Download TCGA VCFs from GDC portal: # https://portal.gdc.cancer.gov/ - Network accessline 11
# Download TCGA VCFs from GDC portal: # https://portal.gdc.cancer.gov/ # Or use PCAWG signatures: https://dcc.icgc.org/releases/PCAWG - Network accessline 12
# https://portal.gdc.cancer.gov/ - Network accessline 13
# Or use PCAWG signatures: https://dcc.icgc.org/releases/PCAWG
skills/bio-clinical-databases-tumor-mutational-burden/examples/tmb_calculation.py
- Executable scriptline 1
Executable file
skills/bio-clinical-databases-variant-prioritization/examples/prioritize_variants.py
- Executable scriptline 1
Executable file
skills/bio-clip-seq-clip-alignment/examples/align_clip.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-clip-seq-clip-motif-analysis/examples/find_motifs.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-clip-seq-clip-peak-calling/examples/call_peaks.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-clip-seq-clip-preprocessing/examples/preprocess_clip.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-codon-usage/SKILL.md
- Network accessline 314
| CAI | 0-1 | Higher = better adapted to host | | RSCU | 0-N | 1.0 = no bias, >1 = overused, <1 = underused | | Nc | 20-61 | Lower = more biased | - Network accessline 315
| RSCU | 0-N | 1.0 = no bias, >1 = overused, <1 = underused | | Nc | 20-61 | Lower = more biased | | GC3 | 0-100% | GC at wobble position | - Network accessline 316
| Nc | 20-61 | Lower = more biased | - Network accessline 338
│ └── Use GC123() ├── Measure overall bias? │ └── Calculate Nc (effective number of codons) - Network accessline 339
├── Measure overall bias? │ └── Calculate Nc (effective number of codons) └── Optimize for expression? - Network accessline 340
│ └── Calculate Nc (effective number of codons)
skills/bio-codon-usage/examples/basic_analysis.py
- Executable scriptline 1
Executable file
skills/bio-codon-usage/examples/codon_optimization.py
- Executable scriptline 1
Executable file
skills/bio-codon-usage/examples/rscu_analysis.py
- Executable scriptline 1
Executable file
skills/bio-codon-usage/usage-guide.md
- Network accessline 78
### Nc (Effective Number of Codons)
skills/bio-comparative-genomics-ancestral-reconstruction/examples/ancestral_reconstruction.py
- Executable scriptline 1
Executable file
skills/bio-comparative-genomics-hgt-detection/examples/hgt_detection.py
- Executable scriptline 1
Executable file
skills/bio-comparative-genomics-ortholog-inference/examples/ortholog_analysis.py
- Executable scriptline 1
Executable file
skills/bio-comparative-genomics-positive-selection/examples/selection_analysis.py
- Executable scriptline 1
Executable file
skills/bio-comparative-genomics-synteny-analysis/examples/synteny_analysis.py
- Executable scriptline 1
Executable file
skills/bio-comparative-genomics-synteny-analysis/usage-guide.md
skills/bio-compressed-files/examples/compressed_io.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-consensus-sequences/examples/generate_consensus.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-consensus-sequences/usage-guide.md
- Network accessline 358
- [bcftools consensus documentation](http://www.htslib.org/doc/bcftools.html#consensus)
skills/bio-copy-number-cnv-annotation/SKILL.md
- Network accessline 151
for rec in vcf.fetch(chrom, row['start'], row['end']):
skills/bio-copy-number-cnv-annotation/examples/annotate_cnvs.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-copy-number-cnv-visualization/examples/plot_cnv.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-copy-number-cnvkit-analysis/examples/run_cnvkit.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-copy-number-gatk-cnv/examples/run_gatk_cnv.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-crispr-screens-base-editing-analysis/examples/base_editing_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-crispr-screens-batch-correction/examples/batch_correct.py
- Executable scriptline 1
Executable file
skills/bio-crispr-screens-crispresso-editing/examples/crispresso_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-crispr-screens-crispresso-editing/usage-guide.md
skills/bio-crispr-screens-hit-calling/examples/consensus_hits.py
- Executable scriptline 1
Executable file
skills/bio-crispr-screens-jacks-analysis/SKILL.md
skills/bio-crispr-screens-jacks-analysis/examples/run_jacks.py
skills/bio-crispr-screens-jacks-analysis/usage-guide.md
- Network accessline 10
pip install jacks # or from source: git clone https://github.com/felicityallen/JACKS.git - Network accessline 11
# or from source: git clone https://github.com/felicityallen/JACKS.git cd JACKS && pip install -e . - Network accessline 12
git clone https://github.com/felicityallen/JACKS.git
skills/bio-crispr-screens-library-design/examples/design_library.py
- Executable scriptline 1
Executable file
skills/bio-crispr-screens-mageck-analysis/examples/mageck_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-crispr-screens-mageck-analysis/usage-guide.md
skills/bio-crispr-screens-screen-qc/examples/screen_qc.py
- Executable scriptline 1
Executable file
skills/bio-crispr-screens-screen-qc/usage-guide.md
skills/bio-ctdna-mutation-detection/examples/detect_ctdna_mutations.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-data-visualization-circos-plots/SKILL.md
skills/bio-data-visualization-circos-plots/examples/circos_basic.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-data-visualization-circos-plots/examples/circos_basic.py
- Executable scriptline 1
Executable file
skills/bio-data-visualization-genome-browser-tracks/examples/generate_tracks.py
- Executable scriptline 1
Executable file - Network accessline 16
# --- ALTERNATIVE: Use real data --- # Download example files from ENCODE: # wget https://www.encodeproject.org/files/ENCFF000ABC/@@download/ENCFF000ABC.bigWig - Network accessline 17
# Download example files from ENCODE: # wget https://www.encodeproject.org/files/ENCFF000ABC/@@download/ENCFF000ABC.bigWig # wget https://www.encodeproject.org/files/ENCFF000XYZ/@@download/ENCFF000XYZ.bed - Network accessline 18
# wget https://www.encodeproject.org/files/ENCFF000ABC/@@download/ENCFF000ABC.bigWig - Network accessline 19
# wget https://www.encodeproject.org/files/ENCFF000XYZ/@@download/ENCFF000XYZ.bed
skills/bio-data-visualization-genome-browser-tracks/examples/igv_batch.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-data-visualization-genome-browser-tracks/examples/tracks.ini
- Network accessline 11
# ChIP-seq coverage track # For realistic data, replace with your bigWig file: # wget https://www.encodeproject.org/files/ENCFF123ABC/@@download/ENCFF123ABC.bigWig - Network accessline 12
# For realistic data, replace with your bigWig file: # wget https://www.encodeproject.org/files/ENCFF123ABC/@@download/ENCFF123ABC.bigWig [chip_coverage] - Network accessline 13
# wget https://www.encodeproject.org/files/ENCFF123ABC/@@download/ENCFF123ABC.bigWig
skills/bio-data-visualization-genome-browser-tracks/usage-guide.md
skills/bio-data-visualization-genome-tracks/SKILL.md
- Network accessline 179
<html> <head> <script src="https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.min.js"></script> - Network accessline 180
<head> <script src="https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.min.js"></script> </head> - Network accessline 181
<script src="https://cdn.jsdelivr.net/npm/igv@3.0.0/dist/igv.min.js"></script>
skills/bio-data-visualization-interactive-visualization/examples/interactive_volcano.py
- Executable scriptline 1
Executable file
skills/bio-data-visualization-multipanel-figures/examples/multipanel_matplotlib.py
- Executable scriptline 1
Executable file
skills/bio-data-visualization-upset-plots/examples/upset_python.py
- Executable scriptline 1
Executable file
skills/bio-data-visualization-volcano-customization/examples/volcano_matplotlib.py
- Executable scriptline 1
Executable file
skills/bio-differential-expression-timeseries-de/examples/timeseries_limma.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-differential-splicing/examples/diff_splicing_leafcutter.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-differential-splicing/examples/diff_splicing_rmats.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-duplicate-handling/examples/markdup_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-entrez-fetch/SKILL.md
- Access to secretsline 35
[Credential-related source omitted]
skills/bio-entrez-fetch/examples/fetch_pubmed.py
- Executable scriptline 1
Executable file
skills/bio-entrez-fetch/examples/fetch_sequences.py
- Executable scriptline 1
Executable file
skills/bio-entrez-fetch/examples/fetch_summaries.py
- Executable scriptline 1
Executable file
skills/bio-entrez-link/SKILL.md
- Access to secretsline 35
[Credential-related source omitted]
skills/bio-entrez-link/examples/basic_linking.py
- Executable scriptline 1
Executable file
skills/bio-entrez-link/examples/chain_links.py
- Executable scriptline 1
Executable file
skills/bio-entrez-link/examples/discover_links.py
- Executable scriptline 1
Executable file
skills/bio-entrez-search/SKILL.md
- Access to secretsline 35
[Credential-related source omitted]
skills/bio-entrez-search/examples/basic_search.py
- Executable scriptline 1
Executable file
skills/bio-entrez-search/examples/database_info.py
- Executable scriptline 1
Executable file
skills/bio-entrez-search/examples/global_query.py
- Executable scriptline 1
Executable file
skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md
skills/bio-epidemiological-genomics-amr-surveillance/examples/amr_surveillance.py
- Executable scriptline 1
Executable file
skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md
- Network accessline 187
''' # Note: Requires API token url = f'https://enterobase.warwick.ac.uk/api/v2.0/{organism}/sts/{st}' - Network accessline 189
url = f'https://enterobase.warwick.ac.uk/api/v2.0/{organism}/sts/{st}' - Network accessline 191
[Credential-related source omitted] - Network accessline 192
[Credential-related source omitted]
skills/bio-epidemiological-genomics-pathogen-typing/examples/mlst_typing.py
- Executable scriptline 1
Executable file
skills/bio-epidemiological-genomics-phylodynamics/SKILL.md
skills/bio-epidemiological-genomics-phylodynamics/examples/treetime_analysis.py
- Executable scriptline 1
Executable file
skills/bio-epidemiological-genomics-transmission-inference/examples/transmission_inference.py
- Executable scriptline 1
Executable file
skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md
- Network accessline 31
# Or download binary curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o nextclade - Network accessline 32
curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o nextclade
skills/bio-epidemiological-genomics-variant-surveillance/examples/variant_surveillance.py
- Executable scriptline 1
Executable file
skills/bio-epitranscriptomics-m6a-peak-calling/examples/macs3_peaks.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md
- Network accessline 27
Documentation: https://m6anet.readthedocs.io/
skills/bio-epitranscriptomics-m6anet-analysis/examples/m6anet_workflow.py
- Executable scriptline 1
Executable file
skills/bio-epitranscriptomics-merip-preprocessing/examples/align_merip.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-epitranscriptomics-merip-preprocessing/examples/merip_qc.py
- Executable scriptline 1
Executable file
skills/bio-epitranscriptomics-modification-visualization/examples/deeptools_metagene.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-expression-matrix-counts-ingest/examples/load_counts.py
- Executable scriptline 1
Executable file
skills/bio-expression-matrix-gene-id-mapping/examples/map_gene_ids.py
- Executable scriptline 1
Executable file
skills/bio-expression-matrix-metadata-joins/examples/join_metadata.py
- Executable scriptline 1
Executable file
skills/bio-expression-matrix-sparse-handling/examples/sparse_operations.py
- Executable scriptline 1
Executable file
skills/bio-fastq-quality/examples/fastq_quality.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-filter-sequences/examples/filter_seqs.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-flow-cytometry-compensation-transformation/examples/compensate_transform.R
skills/bio-flow-cytometry-fcs-handling/examples/load_fcs.R
- Network accessline 4
# Public flow cytometry data sources: # - FlowRepository: https://flowrepository.org (FR-FCM-ZZPH for CyTOF) - Network accessline 5
# - FlowRepository: https://flowrepository.org (FR-FCM-ZZPH for CyTOF) - Network accessline 6
# - ImmPort: https://www.immport.org (immunology FCS files) - Network accessline 7
# - Cytobank: https://community.cytobank.org (public experiments)
skills/bio-flow-cytometry-fcs-handling/usage-guide.md
skills/bio-format-conversion/examples/convert_format.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-fragment-analysis/SKILL.md
skills/bio-fragment-analysis/examples/fragment_analysis.py
skills/bio-gatk-variant-calling/examples/joint_calling.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-gatk-variant-calling/examples/single_sample.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-gatk-variant-calling/usage-guide.md
skills/bio-genome-assembly-assembly-polishing/examples/polish_assembly.sh
skills/bio-genome-assembly-assembly-qc/examples/run_qc.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-assembly-contamination-detection/examples/mag_qc_pipeline.sh
skills/bio-genome-assembly-hifi-assembly/examples/hifi_assembly_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-assembly-long-read-assembly/examples/flye_assembly.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-assembly-metagenome-assembly/examples/metagenome_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-assembly-scaffolding/examples/yahs_scaffolding.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-assembly-scaffolding/usage-guide.md
- Network accessline 26
# 3D-DNA git clone https://github.com/aidenlab/3d-dna.git - Network accessline 27
git clone https://github.com/aidenlab/3d-dna.git - Network accessline 32
# Juicer tools wget https://github.com/aidenlab/juicer/releases/download/v2.0/juicer_tools.2.0.jar - Network accessline 33
wget https://github.com/aidenlab/juicer/releases/download/v2.0/juicer_tools.2.0.jar
skills/bio-genome-assembly-short-read-assembly/examples/bacterial_assembly.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-engineering-base-editing-design/examples/base_editing_design.py
- Executable scriptline 1
Executable file
skills/bio-genome-engineering-grna-design/examples/grna_design.py
- Executable scriptline 1
Executable file - Network accessline 7
# Rule Set 2 position-weight matrix (simplified from Doench et al. 2016) # Position 0 = PAM-distal, Position 19 = PAM-proximal # Full model available at: https://github.com/MicrosoftResearch/Azimuth - Network accessline 9
# Full model available at: https://github.com/MicrosoftResearch/Azimuth - Possible obfuscationline 113
target_seq = 'ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGA'
skills/bio-genome-engineering-hdr-template-design/examples/hdr_template_design.py
- Executable scriptline 1
Executable file
skills/bio-genome-engineering-off-target-prediction/examples/off_target_analysis.py
- Executable scriptline 1
Executable file
skills/bio-genome-engineering-off-target-prediction/usage-guide.md
- Network accessline 10
# Cas-OFFinder (download binary from http://www.rgenome.net/cas-offinder/) - Network accessline 11
# Or compile from source: git clone https://github.com/nickloman/cas-offinder cd cas-offinder && cmake . && make - Network accessline 12
git clone https://github.com/nickloman/cas-offinder
skills/bio-genome-engineering-prime-editing-design/examples/prime_editing_design.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-bed-file-basics/examples/create_bed.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-bed-file-basics/examples/validate_bed.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-intervals-bed-file-basics/usage-guide.md
- Network accessline 89
## Resources - [UCSC BED Format Specification](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - Network accessline 90
- [UCSC BED Format Specification](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - Network accessline 91
- [bedtools Documentation](https://bedtools.readthedocs.io/) - Network accessline 92
- [pybedtools Documentation](https://daler.github.io/pybedtools/)
skills/bio-genome-intervals-bigwig-tracks/SKILL.md
- Network accessline 44
# Or download directly wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig - Network accessline 45
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig - Network accessline 69
# Download from UCSC wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes - Network accessline 70
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes - Dangerous shell operationline 89
rm coverage.bedGraph coverage.sorted.bedGraph
skills/bio-genome-intervals-bigwig-tracks/examples/bedgraph_to_bigwig.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 19
echo "" echo "Create from FASTA: cut -f1,2 reference.fa.fai > chrom.sizes" echo "Download hg38: wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" - Network accessline 20
echo "Create from FASTA: cut -f1,2 reference.fa.fai > chrom.sizes" echo "Download hg38: wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" exit 1 - Network accessline 21
echo "Download hg38: wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes" - Dangerous shell operationline 71
rm -f "$SORTED_FILE"
skills/bio-genome-intervals-bigwig-tracks/examples/pybigwig_demo.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-bigwig-tracks/usage-guide.md
- Network accessline 84
## Resources - [pyBigWig GitHub](https://github.com/deeptools/pyBigWig) - Network accessline 85
- [pyBigWig GitHub](https://github.com/deeptools/pyBigWig) - Network accessline 86
- [UCSC Tools](http://hgdownload.soe.ucsc.edu/admin/exe/) - Network accessline 87
- [deepTools Documentation](https://deeptools.readthedocs.io/) - Network accessline 88
- [bigWig Format](https://genome.ucsc.edu/goldenPath/help/bigWig.html)
skills/bio-genome-intervals-coverage-analysis/examples/bedgraph_from_bam.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-genome-intervals-coverage-analysis/examples/coverage_analysis.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-coverage-analysis/usage-guide.md
- Network accessline 90
## Resources - [bedtools genomecov](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html) - Network accessline 91
- [bedtools genomecov](https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html) - Network accessline 92
- [bedtools coverage](https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html) - Network accessline 93
- [bedGraph format](https://genome.ucsc.edu/goldenPath/help/bedgraph.html)
skills/bio-genome-intervals-gtf-gff-handling/examples/gffread_convert.sh
skills/bio-genome-intervals-gtf-gff-handling/examples/parse_gtf.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-gtf-gff-handling/usage-guide.md
- Network accessline 84
## Resources - [GENCODE](https://www.gencodegenes.org/) - Human/mouse annotations - Network accessline 85
- [GENCODE](https://www.gencodegenes.org/) - Human/mouse annotations - Network accessline 86
- [Ensembl FTP](https://ftp.ensembl.org/) - Multi-species annotations - Network accessline 87
- [gffread documentation](http://ccb.jhu.edu/software/stringtie/gff.shtml) - Network accessline 88
- [gtfparse GitHub](https://github.com/openvax/gtfparse) - Network accessline 89
- [gffutils documentation](https://daler.github.io/gffutils/)
skills/bio-genome-intervals-interval-arithmetic/examples/intersect_examples.sh
skills/bio-genome-intervals-interval-arithmetic/examples/interval_operations.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-interval-arithmetic/usage-guide.md
- Network accessline 82
## Resources - [bedtools intersect](https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html) - Network accessline 83
- [bedtools intersect](https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html) - Network accessline 84
- [bedtools merge](https://bedtools.readthedocs.io/en/latest/content/tools/merge.html) - Network accessline 85
- [pybedtools tutorial](https://daler.github.io/pybedtools/topical-intersections.html)
skills/bio-genome-intervals-proximity-operations/SKILL.md
skills/bio-genome-intervals-proximity-operations/examples/create_promoters.sh
skills/bio-genome-intervals-proximity-operations/examples/proximity_analysis.py
- Executable scriptline 1
Executable file
skills/bio-genome-intervals-proximity-operations/usage-guide.md
- Network accessline 82
## Resources - [bedtools closest](https://bedtools.readthedocs.io/en/latest/content/tools/closest.html) - Network accessline 83
- [bedtools closest](https://bedtools.readthedocs.io/en/latest/content/tools/closest.html) - Network accessline 84
- [bedtools window](https://bedtools.readthedocs.io/en/latest/content/tools/window.html) - Network accessline 85
- [bedtools slop](https://bedtools.readthedocs.io/en/latest/content/tools/slop.html) - Network accessline 86
- [bedtools flank](https://bedtools.readthedocs.io/en/latest/content/tools/flank.html)
skills/bio-geo-data/SKILL.md
- Access to secretsline 35
[Credential-related source omitted] - Network accessline 321
# Download entire GSE wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/ - Network accessline 322
wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/ - Network accessline 324
# Download specific file types wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/*counts*.txt.gz - Network accessline 325
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/*counts*.txt.gz - Network accessline 335
'''Download series matrix file''' gse_prefix = gse[:len(gse)-3] + 'nnn' url = f'https://ftp.ncbi.nlm.nih.gov/geo/series/{gse_prefix}/{gse}/matrix/{gse}_series_matrix.txt.gz' - Network accessline 337
url = f'https://ftp.ncbi.nlm.nih.gov/geo/series/{gse_prefix}/{gse}/matrix/{gse}_series_matrix.txt.gz' - Network accessline 339
filename = f'{gse}_series_matrix.txt.gz' urllib.request.urlretrieve(url, filename) - Network accessline 340
urllib.request.urlretrieve(url, filename)
skills/bio-geo-data/examples/geo_from_pubmed.py
- Executable scriptline 1
Executable file
skills/bio-geo-data/examples/geo_to_sra.py
- Executable scriptline 1
Executable file
skills/bio-geo-data/examples/search_geo.py
- Executable scriptline 1
Executable file
skills/bio-hi-c-analysis-compartment-analysis/examples/call_compartments.py
- Executable scriptline 1
Executable file
skills/bio-hi-c-analysis-contact-pairs/examples/process_pairs.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-hi-c-analysis-hic-data-io/SKILL.md
- Network accessline 68
# Get bins for a chromosome chr1_bins = clr.bins().fetch('chr1') - Network accessline 69
chr1_bins = clr.bins().fetch('chr1') - Network accessline 81
# Get contacts for a region region_pixels = clr.pixels().fetch('chr1:0-10000000') - Network accessline 82
region_pixels = clr.pixels().fetch('chr1:0-10000000') - Network accessline 88
# Get matrix for a chromosome matrix = clr.matrix(balance=True).fetch('chr1') - Network accessline 89
matrix = clr.matrix(balance=True).fetch('chr1') - Network accessline 92
# Get matrix for a region region_matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 93
region_matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 95
# Get raw (unbalanced) matrix raw_matrix = clr.matrix(balance=False).fetch('chr1') - Network accessline 96
raw_matrix = clr.matrix(balance=False).fetch('chr1') - Network accessline 98
# Sparse matrix for memory efficiency from scipy import sparse sparse_matrix = clr.matrix(balance=True, sparse=True).fetch('chr1') - Network accessline 100
sparse_matrix = clr.matrix(balance=True, sparse=True).fetch('chr1') - Network accessline 107
region1 = 'chr1:50000000-60000000' region2 = 'chr1:70000000-80000000' submatrix = clr.matrix(balance=True).fetch(region1, region2) - Network accessline 108
region2 = 'chr1:70000000-80000000' submatrix = clr.matrix(balance=True).fetch(region1, region2) print(f'Submatrix shape: {submatrix.shape}') - Network accessline 109
submatrix = clr.matrix(balance=True).fetch(region1, region2) - Network accessline 112
# Inter-chromosomal contacts inter_matrix = clr.matrix(balance=True).fetch('chr1', 'chr2') - Network accessline 113
inter_matrix = clr.matrix(balance=True).fetch('chr1', 'chr2') - Network accessline 207
# Export matrix to numpy matrix = clr.matrix(balance=True).fetch('chr1') - Network accessline 208
matrix = clr.matrix(balance=True).fetch('chr1')
skills/bio-hi-c-analysis-hic-data-io/examples/load_cooler.py
skills/bio-hi-c-analysis-hic-differential/SKILL.md
- Network accessline 52
def log2_fold_change(clr1, clr2, region, pseudocount=1): '''Compute log2(condition2/condition1) for a region''' mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 53
'''Compute log2(condition2/condition1) for a region''' mat1 = clr1.matrix(balance=True).fetch(region) mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 54
mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 55
mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 73
# Condition 1 mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 74
mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 79
# Condition 2 mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 80
mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 109
mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 110
mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 130
mat1_norm = clr1.matrix(balance=True).fetch(region) * scale1 - Network accessline 131
mat2_norm = clr2.matrix(balance=True).fetch(region) * scale2 - Network accessline 167
# Example with replicates rep1_cond1 = [clr.matrix(balance=True).fetch(region) for clr in condition1_reps] - Network accessline 168
rep1_cond1 = [clr.matrix(balance=True).fetch(region) for clr in condition1_reps] - Network accessline 169
rep1_cond2 = [clr.matrix(balance=True).fetch(region) for clr in condition2_reps]
skills/bio-hi-c-analysis-hic-differential/examples/compare_hic.py
skills/bio-hi-c-analysis-hic-visualization/SKILL.md
- Network accessline 44
# Get matrix for a region matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 45
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 75
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 87
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 109
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 136
region = 'chr1:50000000-60000000' mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 137
mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 138
mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 166
mat1 = clr1.matrix(balance=True).fetch(region) - Network accessline 167
mat2 = clr2.matrix(balance=True).fetch(region) - Network accessline 192
# Get contacts from this bin to all others on same chromosome matrix = clr.matrix(balance=True).fetch(viewpoint_chrom) - Network accessline 193
matrix = clr.matrix(balance=True).fetch(viewpoint_chrom) - Network accessline 196
# Create coordinates bins = clr.bins().fetch(viewpoint_chrom) - Network accessline 197
bins = clr.bins().fetch(viewpoint_chrom) - Network accessline 219
# Hi-C matrix (triangle) ax1 = fig.add_axes([0.1, 0.5, 0.8, 0.4]) matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') - Network accessline 220
ax1 = fig.add_axes([0.1, 0.5, 0.8, 0.4]) matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000') plot_triangle(matrix, ax1, vmin=0.001, vmax=0.1) - Network accessline 221
matrix = clr.matrix(balance=True).fetch('chr1:50000000-60000000')
skills/bio-hi-c-analysis-hic-visualization/examples/plot_hic.py
skills/bio-hi-c-analysis-loop-calling/SKILL.md
- Network accessline 190
try: # Get region around loop snippet = clr.matrix(balance=True).fetch( - Network accessline 191
# Get region around loop snippet = clr.matrix(balance=True).fetch( f"{loop['chrom1']}:{loop['start1']-window}-{loop['end1']+window}", - Network accessline 192
snippet = clr.matrix(balance=True).fetch(
skills/bio-hi-c-analysis-loop-calling/examples/call_loops.py
- Executable scriptline 1
Executable file
skills/bio-hi-c-analysis-matrix-operations/SKILL.md
- Network accessline 62
# Balanced (normalized) matrix balanced = clr.matrix(balance=True).fetch('chr1') - Network accessline 63
balanced = clr.matrix(balance=True).fetch('chr1') - Network accessline 65
# Raw (count) matrix raw = clr.matrix(balance=False).fetch('chr1') - Network accessline 66
raw = clr.matrix(balance=False).fetch('chr1') - Network accessline 99
# Get O/E matrix for a region def get_oe_matrix(clr, region, expected_df): matrix = clr.matrix(balance=True).fetch(region) - Network accessline 100
def get_oe_matrix(clr, region, expected_df): matrix = clr.matrix(balance=True).fetch(region) n = matrix.shape[0] - Network accessline 101
matrix = clr.matrix(balance=True).fetch(region) - Network accessline 189
for f in files: clr = cooler.Cooler(f) m = clr.matrix(balance=False).fetch('chr1') - Network accessline 190
clr = cooler.Cooler(f) m = clr.matrix(balance=False).fetch('chr1') matrices.append(m) - Network accessline 191
m = clr.matrix(balance=False).fetch('chr1')
skills/bio-hi-c-analysis-matrix-operations/examples/balance_matrix.py
skills/bio-hi-c-analysis-tad-detection/examples/call_tads.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-cell-segmentation/examples/segment_cells.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-data-preprocessing/examples/preprocess_imc.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-interactive-annotation/examples/napari_annotation.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-phenotyping/examples/phenotype_cells.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-quality-metrics/examples/run_qc.py
- Executable scriptline 1
Executable file
skills/bio-imaging-mass-cytometry-spatial-analysis/examples/spatial_analysis.py
- Executable scriptline 1
Executable file
skills/bio-immunoinformatics-epitope-prediction/SKILL.md
- Network accessline 46
Threshold: >0.5 predicted as epitope (default) ''' url = 'http://tools-cluster-interface.iedb.org/tools_api/bcell/' - Network accessline 48
url = 'http://tools-cluster-interface.iedb.org/tools_api/bcell/' - Network accessline 55
response = requests.post(url, data=params) - Network accessline 127
- netmhciipan ''' url = 'http://tools-cluster-interface.iedb.org/tools_api/mhci/' - Network accessline 129
url = 'http://tools-cluster-interface.iedb.org/tools_api/mhci/' - Network accessline 140
response = requests.post(url, data=params) - Network accessline 183
print('For conformational epitopes:') print('- DiscoTope: http://tools.iedb.org/discotope/') - Network accessline 184
print('- DiscoTope: http://tools.iedb.org/discotope/') - Network accessline 185
print('- ElliPro: http://tools.iedb.org/ellipro/')
skills/bio-immunoinformatics-epitope-prediction/examples/epitope_prediction.py
skills/bio-immunoinformatics-immunogenicity-scoring/examples/immunogenicity_scoring.py
- Executable scriptline 1
Executable file
skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md
skills/bio-immunoinformatics-mhc-binding-prediction/examples/mhc_binding.py
- Executable scriptline 1
Executable file
skills/bio-immunoinformatics-neoantigen-prediction/examples/neoantigen_prediction.py
- Executable scriptline 1
Executable file
skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md
- Network accessline 26
# ERGO-II uses deep learning to predict TCR-epitope binding # GitHub: https://github.com/IdoSpringer/ERGO-II - Network accessline 27
# GitHub: https://github.com/IdoSpringer/ERGO-II - Network accessline 40
''' print('ERGO-II setup:') print('1. Clone: git clone https://github.com/IdoSpringer/ERGO-II') - Network accessline 41
print('ERGO-II setup:') print('1. Clone: git clone https://github.com/IdoSpringer/ERGO-II') print('2. Install: pip install torch pandas scikit-learn') - Network accessline 42
print('1. Clone: git clone https://github.com/IdoSpringer/ERGO-II') print('2. Install: pip install torch pandas scikit-learn') print('3. Download models from repository') - Network accessline 125
VDJdb is a curated database of TCR-epitope pairs. Download from: https://vdjdb.cdr3.net/ - Network accessline 126
Download from: https://vdjdb.cdr3.net/
skills/bio-immunoinformatics-tcr-epitope-binding/examples/tcr_epitope.py
- Executable scriptline 1
Executable file
skills/bio-immunoinformatics-tcr-epitope-binding/usage-guide.md
skills/bio-isoform-switching/examples/isoform_switch_analysis.R
- Executable scriptline 1
#!/usr/bin/env Rscript - Network accessline 59
cat(sprintf('Sequences written to: %s\n', output_dir)) cat('Run external tools:\n') cat(' - CPC2: http://cpc2.gao-lab.org/\n') - Network accessline 60
cat('Run external tools:\n') cat(' - CPC2: http://cpc2.gao-lab.org/\n') cat(' - Pfam: https://www.ebi.ac.uk/Tools/hmmer/\n') - Network accessline 61
cat(' - CPC2: http://cpc2.gao-lab.org/\n') - Network accessline 62
cat(' - Pfam: https://www.ebi.ac.uk/Tools/hmmer/\n') - Network accessline 63
cat(' - SignalP: https://services.healthtech.dtu.dk/service.php?SignalP\n') - Network accessline 64
cat(' - IUPred2A: https://iupred2a.elte.hu/\n')
skills/bio-isoform-switching/usage-guide.md
- Network accessline 14
# External tools for functional annotation: # - CPC2: http://cpc2.gao-lab.org/ - Network accessline 15
# - CPC2: http://cpc2.gao-lab.org/ - Network accessline 16
# - Pfam: https://www.ebi.ac.uk/Tools/hmmer/ - Network accessline 17
# - SignalP: https://services.healthtech.dtu.dk/service.php?SignalP - Network accessline 18
# - IUPred2A: https://iupred2a.elte.hu/
skills/bio-liquid-biopsy-pipeline/SKILL.md
- Network accessline 123
for read in bam.fetch():
skills/bio-liquid-biopsy-pipeline/examples/liquid_biopsy_pipeline.py
- Executable scriptline 1
Executable file - Network accessline 84
bam = pysam.AlignmentFile(bam_path, 'rb') sizes = [] for read in bam.fetch(): - Network accessline 85
sizes = [] for read in bam.fetch(): if read.is_proper_pair and not read.is_secondary and 0 < read.template_length <= 400: - Network accessline 86
for read in bam.fetch():
skills/bio-local-blast/SKILL.md
skills/bio-local-blast/examples/blast_wrapper.py
- Executable scriptline 1
Executable file
skills/bio-local-blast/examples/create_database.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-local-blast/examples/reciprocal_best.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-local-blast/examples/run_blast.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-local-blast/usage-guide.md
- Dangerous shell operationline 29
sudo apt install ncbi-blast+
skills/bio-long-read-sequencing-clair3-variants/SKILL.md
- Access to secretsline 168
[Credential-related source omitted]
skills/bio-long-read-sequencing-clair3-variants/examples/clair3_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-long-read-sequencing-clair3-variants/usage-guide.md
skills/bio-long-read-sequencing-isoseq-analysis/examples/isoseq3_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-long-read-sequencing-isoseq-analysis/examples/sqanti3_qc.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-long-read-sequencing-nanopore-methylation/examples/modkit_methylation.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-long-read-sequencing-nanopore-methylation/usage-guide.md
- Network accessline 10
# modkit (ONT tool) # Download from https://github.com/nanoporetech/modkit - Network accessline 11
# Download from https://github.com/nanoporetech/modkit - Network accessline 13
# Dorado basecaller with methylation models # Download from https://github.com/nanoporetech/dorado - Network accessline 14
# Download from https://github.com/nanoporetech/dorado
skills/bio-longitudinal-monitoring/examples/longitudinal_monitoring.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-longread-alignment/examples/minimap2_align.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-longread-alignment/usage-guide.md
skills/bio-longread-medaka/SKILL.md
- Network accessline 45
Note: Diploid variant calling has been deprecated in medaka v2.0. For diploid samples, use [Clair3](https://github.com/HKU-BAL/Clair3) instead.
skills/bio-longread-medaka/examples/medaka_polish.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-longread-medaka/examples/medaka_variant.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-longread-medaka/usage-guide.md
skills/bio-longread-qc/examples/qc_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-longread-qc/usage-guide.md
skills/bio-longread-structural-variants/examples/sv_calling.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-longread-structural-variants/usage-guide.md
skills/bio-machine-learning-atlas-mapping/examples/scarches_annotation.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-biomarker-discovery/examples/boruta_feature_selection.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-biomarker-discovery/examples/lasso_biomarker.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-model-validation/examples/nested_cv_biomarker.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-omics-classifiers/examples/logistic_regression.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-omics-classifiers/examples/rf_xgboost_classifier.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-prediction-explanation/examples/lime_explanation.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-prediction-explanation/examples/shap_omics_classifier.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-survival-analysis/examples/cox_regression.py
- Executable scriptline 1
Executable file
skills/bio-machine-learning-survival-analysis/examples/kaplan_meier.py
- Executable scriptline 1
Executable file
skills/bio-metabolomics-lipidomics/SKILL.md
- Network accessline 131
url = f'https://www.lipidmaps.org/rest/compound/lm_id/{mz}'
skills/bio-metabolomics-metabolite-annotation/examples/annotate_features.py
skills/bio-metabolomics-metabolite-annotation/usage-guide.md
skills/bio-metabolomics-msdial-preprocessing/usage-guide.md
- Network accessline 10
# Download MS-DIAL # https://systemsomicslab.github.io/compms/msdial/main.html - Network accessline 11
# https://systemsomicslab.github.io/compms/msdial/main.html - Network accessline 13
# For data conversion # ProteoWizard: https://proteowizard.sourceforge.io/ - Network accessline 14
# ProteoWizard: https://proteowizard.sourceforge.io/
skills/bio-metabolomics-pathway-mapping/usage-guide.md
- Network accessline 17
# Web tool: https://www.metaboanalyst.ca/
skills/bio-metabolomics-targeted-analysis/usage-guide.md
skills/bio-metabolomics-xcms-preprocessing/usage-guide.md
skills/bio-metagenomics-abundance/examples/bracken_abundance.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-abundance/usage-guide.md
skills/bio-metagenomics-amr-detection/SKILL.md
skills/bio-metagenomics-amr-detection/examples/batch_amr_screening.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-metagenomics-amr-detection/examples/run_amrfinder.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-amr-detection/usage-guide.md
- Network accessline 77
## Resources - [AMRFinderPlus wiki](https://github.com/ncbi/amr/wiki) - Network accessline 78
- [AMRFinderPlus wiki](https://github.com/ncbi/amr/wiki) - Network accessline 79
- [CARD database](https://card.mcmaster.ca/) - Network accessline 80
- [ResFinder web server](https://cge.food.dtu.dk/services/ResFinder/)
skills/bio-metagenomics-functional-profiling/examples/humann_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-functional-profiling/usage-guide.md
skills/bio-metagenomics-kraken/examples/kraken2_classify.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-kraken/usage-guide.md
- Network accessline 10
# Download pre-built database wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20230605.tar.gz - Network accessline 11
wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20230605.tar.gz - Network accessline 60
## Resources - [Kraken2 GitHub](https://github.com/DerrickWood/kraken2) - Network accessline 61
- [Kraken2 GitHub](https://github.com/DerrickWood/kraken2) - Network accessline 62
- [Pre-built Databases](https://benlangmead.github.io/aws-indexes/k2)
skills/bio-metagenomics-metaphlan/examples/metaphlan_profile.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-metaphlan/usage-guide.md
skills/bio-metagenomics-strain-tracking/examples/mash_comparison.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-metagenomics-strain-tracking/examples/sourmash_gather.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-metagenomics-strain-tracking/usage-guide.md
- Network accessline 76
## Resources - [MASH documentation](https://mash.readthedocs.io/) - Network accessline 77
- [MASH documentation](https://mash.readthedocs.io/) - Network accessline 78
- [sourmash documentation](https://sourmash.readthedocs.io/) - Network accessline 79
- [inStrain tutorial](https://instrain.readthedocs.io/) - Network accessline 80
- [fastANI paper](https://doi.org/10.1038/s41467-018-07641-9)
skills/bio-metagenomics-visualization/examples/visualization_python.py
- Executable scriptline 1
Executable file
skills/bio-metagenomics-visualization/usage-guide.md
skills/bio-methylation-based-detection/examples/cfdna_methylation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-methylation-bismark-alignment/examples/bismark_basic.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-methylation-calling/examples/extract_methylation.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-microbiome-differential-abundance/examples/aldex2_analysis.R
- Network accessline 8
# - Bioconductor: microbiomeDataSets package (curated phyloseq objects) # - curatedMetagenomicData package (1000s of samples) # - HMP: https://hmpdacc.org (Human Microbiome Project) - Network accessline 9
# - curatedMetagenomicData package (1000s of samples) # - HMP: https://hmpdacc.org (Human Microbiome Project) # - Example: data('GlobalPatterns', package = 'phyloseq') - Network accessline 10
# - HMP: https://hmpdacc.org (Human Microbiome Project)
skills/bio-microbiome-diversity-analysis/examples/diversity_analysis.R
- Network accessline 7
# Public microbiome datasets: # - Qiita: https://qiita.ucsd.edu (16S/metagenomics studies) - Network accessline 8
# - Qiita: https://qiita.ucsd.edu (16S/metagenomics studies) - Network accessline 9
# - Earth Microbiome Project: https://earthmicrobiome.org/data-and-code - Network accessline 10
# - HMP: https://hmpdacc.org (Human Microbiome Project) - Network accessline 11
# - Bioconductor: microbiomeDataSets package with curated phyloseq objects # - MicrobiomeDB: https://microbiomedb.org # Example: data('GlobalPatterns', package = 'phyloseq') for built-in demo - Network accessline 12
# - MicrobiomeDB: https://microbiomedb.org
skills/bio-microbiome-functional-prediction/examples/run_picrust2.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-microbiome-qiime2-workflow/SKILL.md
skills/bio-microbiome-qiime2-workflow/examples/qiime2_16s.sh
skills/bio-microbiome-qiime2-workflow/usage-guide.md
skills/bio-microbiome-taxonomy-assignment/SKILL.md
skills/bio-microbiome-taxonomy-assignment/examples/assign_silva.R
skills/bio-microbiome-taxonomy-assignment/usage-guide.md
skills/bio-molecular-descriptors/examples/calculate_descriptors.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-molecular-io/examples/molecule_io.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-motif-search/examples/basic_search.py
- Executable scriptline 1
Executable file
skills/bio-motif-search/examples/motif_files.py
- Executable scriptline 1
Executable file
skills/bio-motif-search/examples/pwm_search.py
- Executable scriptline 1
Executable file
skills/bio-motif-search/examples/regex_search.py
- Executable scriptline 1
Executable file
skills/bio-multi-omics-mixomics-analysis/usage-guide.md
skills/bio-multi-omics-mofa-integration/examples/mofa_workflow.R
skills/bio-multi-omics-mofa-integration/usage-guide.md
skills/bio-multi-omics-similarity-network/usage-guide.md
skills/bio-orchestrator/SKILL.md
skills/bio-orchestrator/orchestrator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-paired-end-fastq/examples/paired_end_io.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-pdb-geometric-analysis/examples/find_contacts.py
- Executable scriptline 1
Executable file
skills/bio-pdb-geometric-analysis/examples/measure_distance.py
- Executable scriptline 1
Executable file
skills/bio-pdb-geometric-analysis/examples/superimpose.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-io/examples/download_structure.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-io/examples/extract_chain.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-io/examples/parse_pdb.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-modification/examples/modify_bfactor.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-modification/examples/remove_water.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-modification/examples/transform_coords.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-navigation/examples/extract_sequence.py
- Executable scriptline 1
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skills/bio-pdb-structure-navigation/examples/find_ligands.py
- Executable scriptline 1
Executable file
skills/bio-pdb-structure-navigation/examples/iterate_structure.py
- Executable scriptline 1
Executable file
skills/bio-phasing-imputation-genotype-imputation/examples/run_beagle_imputation.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-phasing-imputation-genotype-imputation/usage-guide.md
- Network accessline 21
# Beagle (download jar) wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 22
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 30
# Genetic maps wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 31
wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 34
# Reference panel (e.g., 1000 Genomes) # Download from http://ftp.1000genomes.ebi.ac.uk/ - Network accessline 35
# Download from http://ftp.1000genomes.ebi.ac.uk/
skills/bio-phasing-imputation-haplotype-phasing/SKILL.md
- Network accessline 30
# Download Beagle 5.4 wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 31
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 151
# Download genetic maps (GRCh38) wget https://faculty.washington.edu/browning/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 152
wget https://faculty.washington.edu/browning/beagle/genetic_maps/plink.GRCh38.map.zip
skills/bio-phasing-imputation-haplotype-phasing/examples/run_shapeit.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-phasing-imputation-haplotype-phasing/usage-guide.md
- Network accessline 21
# Beagle (download jar) wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 22
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar - Network accessline 30
# Genetic maps (required for phasing) wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 31
wget https://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/plink.GRCh38.map.zip
skills/bio-phasing-imputation-imputation-qc/examples/imputation_qc.py
- Executable scriptline 1
Executable file
skills/bio-phasing-imputation-reference-panels/SKILL.md
- Network accessline 30
# Download from IGSR BASE_URL="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased" - Network accessline 31
BASE_URL="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased" - Network accessline 33
for chr in {1..22}; do wget ${BASE_URL}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz - Network accessline 34
wget ${BASE_URL}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz - Network accessline 35
wget ${BASE_URL}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz.tbi - Network accessline 42
# Download sample info wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/1000G_2504_high_coverage.sequence.index - Network accessline 43
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/1000G_2504_high_coverage.sequence.index - Network accessline 104
# Beagle format (GRCh38) - from Browning lab wget https://faculty.washington.edu/browning/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 105
wget https://faculty.washington.edu/browning/beagle/genetic_maps/plink.GRCh38.map.zip - Network accessline 108
# SHAPEIT5 format (recommended for SHAPEIT5) wget https://github.com/odelaneau/shapeit5/raw/main/maps/genetic_maps.b38.tar.gz - Network accessline 109
wget https://github.com/odelaneau/shapeit5/raw/main/maps/genetic_maps.b38.tar.gz
skills/bio-phasing-imputation-reference-panels/examples/download_reference.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 18
for chr in {1..22}; do wget -P $OUTPUT_DIR \ - Network accessline 19
wget -P $OUTPUT_DIR \ - Network accessline 20
"http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz" - Network accessline 24
"HRC") echo "HRC panel requires application - see http://www.haplotype-reference-consortium.org/" - Network accessline 25
echo "HRC panel requires application - see http://www.haplotype-reference-consortium.org/" - Network accessline 28
"TOPMed") echo "TOPMed requires dbGaP access - see https://topmed.nhlbi.nih.gov/" - Network accessline 29
echo "TOPMed requires dbGaP access - see https://topmed.nhlbi.nih.gov/"
skills/bio-phasing-imputation-reference-panels/usage-guide.md
- Network accessline 27
# wget for downloading panels - Network accessline 96
# Download high-coverage data FTP="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased" - Network accessline 97
FTP="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased" - Network accessline 99
for chr in {1..22}; do echo "Downloading chromosome $chr..." wget -P $BASE_DIR ${FTP}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz - Network accessline 100
echo "Downloading chromosome $chr..." wget -P $BASE_DIR ${FTP}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz wget -P $BASE_DIR ${FTP}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2 - Network accessline 101
wget -P $BASE_DIR ${FTP}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz - Network accessline 102
wget -P $BASE_DIR ${FTP}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz.tbi - Network accessline 105
# Download sample information wget -P $BASE_DIR http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt - Network accessline 106
wget -P $BASE_DIR http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt - Network accessline 156
# GRCh37 to GRCh38 using Picard wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz - Network accessline 157
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz - Network accessline 179
# Upload to https://imputationserver.sph.umich.edu - Network accessline 185
# Same preparation, upload to: # https://imputation.biodatacatalyst.nhlbi.nih.gov - Network accessline 186
# https://imputation.biodatacatalyst.nhlbi.nih.gov
skills/bio-phylo-distance-calculations/examples/bootstrap_consensus.py
- Executable scriptline 1
Executable file
skills/bio-phylo-distance-calculations/examples/build_nj_tree.py
- Executable scriptline 1
Executable file
skills/bio-phylo-distance-calculations/examples/pairwise_tree_distances.py
- Executable scriptline 1
Executable file
skills/bio-phylo-modern-tree-inference/examples/iqtree_basic.sh
skills/bio-phylo-modern-tree-inference/examples/partitioned_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-phylo-modern-tree-inference/examples/raxml_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-phylo-modern-tree-inference/usage-guide.md
skills/bio-phylo-tree-io/examples/convert_formats.py
- Executable scriptline 1
Executable file
skills/bio-phylo-tree-io/examples/parse_multiple_trees.py
- Executable scriptline 1
Executable file
skills/bio-phylo-tree-io/examples/read_newick.py
- Executable scriptline 1
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skills/bio-phylo-tree-manipulation/examples/common_ancestor.py
- Executable scriptline 1
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skills/bio-phylo-tree-manipulation/examples/prune_taxa.py
- Executable scriptline 1
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skills/bio-phylo-tree-manipulation/examples/root_tree.py
- Executable scriptline 1
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skills/bio-phylo-tree-visualization/examples/ascii_tree.py
- Executable scriptline 1
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skills/bio-phylo-tree-visualization/examples/basic_tree_plot.py
- Executable scriptline 1
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skills/bio-phylo-tree-visualization/examples/labeled_tree.py
- Executable scriptline 1
Executable file
skills/bio-pileup-generation/SKILL.md
- Network accessline 251
for pileup_column in bam.pileup(chrom, start, end, truncate=True): pos = pileup_column.pos ref_base = ref.fetch(chrom, pos, pos + 1) - Network accessline 252
pos = pileup_column.pos ref_base = ref.fetch(chrom, pos, pos + 1) depth = pileup_column.n - Network accessline 253
ref_base = ref.fetch(chrom, pos, pos + 1)
skills/bio-pileup-generation/examples/allele_counts.py
- Executable scriptline 1
Executable file
skills/bio-pileup-generation/usage-guide.md
- Network accessline 201
for pileup_column in bam.pileup(chrom, start, end, truncate=True, min_base_quality=20): pos = pileup_column.pos ref_base = ref.fetch(chrom, pos, pos + 1).upper() - Network accessline 202
pos = pileup_column.pos ref_base = ref.fetch(chrom, pos, pos + 1).upper() alleles = Counter() - Network accessline 203
ref_base = ref.fetch(chrom, pos, pos + 1).upper()
skills/bio-population-genetics-association-testing/examples/gwas_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-population-genetics-association-testing/usage-guide.md
skills/bio-population-genetics-linkage-disequilibrium/examples/ld_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-population-genetics-linkage-disequilibrium/usage-guide.md
skills/bio-population-genetics-plink-basics/examples/qc_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-population-genetics-plink-basics/usage-guide.md
skills/bio-population-genetics-population-structure/SKILL.md
skills/bio-population-genetics-population-structure/examples/structure_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-population-genetics-population-structure/usage-guide.md
skills/bio-population-genetics-scikit-allel-analysis/examples/basic_analysis.py
- Executable scriptline 1
Executable file
skills/bio-population-genetics-scikit-allel-analysis/usage-guide.md
- Network accessline 29
**Note**: scikit-allel is in maintenance mode. For new projects, consider [sgkit](https://github.com/sgkit-dev/sgkit) for long-term support. - Network accessline 122
- [scikit-allel Documentation](https://scikit-allel.readthedocs.io/) - Network accessline 123
- [scikit-allel GitHub](https://github.com/cggh/scikit-allel) - Network accessline 124
- [sgkit (successor)](https://github.com/sgkit-dev/sgkit)
skills/bio-population-genetics-selection-statistics/examples/selection_scan.py
- Executable scriptline 1
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skills/bio-population-genetics-selection-statistics/usage-guide.md
skills/bio-primer-design-primer-basics/examples/primer_design.py
- Executable scriptline 1
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skills/bio-primer-design-primer-validation/examples/validate_primers.py
- Executable scriptline 1
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skills/bio-primer-design-qpcr-primers/examples/qpcr_design.py
- Executable scriptline 1
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skills/bio-proteomics-data-import/examples/load_maxquant.py
- Executable scriptline 1
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skills/bio-proteomics-dia-analysis/examples/diann_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-proteomics-peptide-identification/examples/fdr_filtering.py
- Executable scriptline 1
Executable file
skills/bio-proteomics-protein-inference/examples/protein_groups.py
- Executable scriptline 1
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skills/bio-proteomics-proteomics-qc/examples/qc_analysis.py
- Executable scriptline 1
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skills/bio-proteomics-ptm-analysis/examples/phospho_analysis.py
- Executable scriptline 1
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skills/bio-proteomics-quantification/examples/lfq_normalization.py
- Executable scriptline 1
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skills/bio-proteomics-spectral-libraries/SKILL.md
skills/bio-proteomics-spectral-libraries/examples/build_library.py
- Executable scriptline 1
Executable file
skills/bio-reaction-enumeration/examples/enumerate_reactions.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-read-alignment-bowtie2-alignment/examples/align_bowtie2.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-alignment-bwa-alignment/examples/align_bwa.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-alignment-hisat2-alignment/examples/align_hisat2.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-alignment-star-alignment/examples/align_star.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-adapter-trimming/examples/trim_adapters.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-adapter-trimming/usage-guide.md
- Network accessline 62
## Resources - [Cutadapt Documentation](https://cutadapt.readthedocs.io/) - Network accessline 63
- [Cutadapt Documentation](https://cutadapt.readthedocs.io/) - Network accessline 64
- [Trimmomatic Manual](http://www.usadellab.org/cms/?page=trimmomatic) - Network accessline 65
- [Illumina Adapter Sequences](https://support.illumina.com/downloads/illumina-adapter-sequences-document-1000000002694.html)
skills/bio-read-qc-contamination-screening/examples/screen_samples.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-contamination-screening/usage-guide.md
- Network accessline 72
## Resources - [FastQ Screen Documentation](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) - Network accessline 73
- [FastQ Screen Documentation](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/) - Network accessline 74
- [Pre-built Databases](https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_v0.15.3.tar.gz)
skills/bio-read-qc-fastp-workflow/examples/fastp_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-fastp-workflow/usage-guide.md
skills/bio-read-qc-quality-filtering/examples/quality_filter.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-quality-filtering/usage-guide.md
- Network accessline 74
## Resources - [Trimmomatic Manual](http://www.usadellab.org/cms/?page=trimmomatic) - Network accessline 75
- [Trimmomatic Manual](http://www.usadellab.org/cms/?page=trimmomatic) - Network accessline 76
- [fastp Documentation](https://github.com/OpenGene/fastp) - Network accessline 77
- [Quality Score Tutorial](https://www.drive5.com/usearch/manual/quality_score.html)
skills/bio-read-qc-quality-reports/examples/run_qc_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-quality-reports/usage-guide.md
- Network accessline 60
## Resources - [FastQC Documentation](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - Network accessline 61
- [FastQC Documentation](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - Network accessline 62
- [MultiQC Documentation](https://multiqc.info/) - Network accessline 63
- [FastQC Example Reports](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/good_sequence_short_fastqc.html)
skills/bio-read-qc-umi-processing/examples/umi_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-read-qc-umi-processing/usage-guide.md
skills/bio-read-sequences/examples/basic_parsing.py
- Executable scriptline 1
Executable file
skills/bio-read-sequences/examples/fastq_quality.py
- Executable scriptline 1
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skills/bio-read-sequences/examples/genbank_features.py
- Executable scriptline 1
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skills/bio-read-sequences/examples/random_access.py
- Executable scriptline 1
Executable file
skills/bio-reference-operations/SKILL.md
- Network accessline 136
with pysam.FastaFile('reference.fa') as ref: seq = ref.fetch('chr1', 999, 2000) # 0-based - Network accessline 137
seq = ref.fetch('chr1', 999, 2000) # 0-based - Network accessline 151
with pysam.FastaFile('reference.fa') as ref: for chrom in ref.references: seq = ref.fetch(chrom) - Network accessline 152
for chrom in ref.references: seq = ref.fetch(chrom) print(f'>{chrom}') - Network accessline 153
seq = ref.fetch(chrom)
skills/bio-reference-operations/examples/prepare_reference.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-reference-operations/usage-guide.md
- Network accessline 142
with pysam.FastaFile('reference.fa') as ref: seq = ref.fetch('chr1', 999, 2000) # 0-based, half-open - Network accessline 143
seq = ref.fetch('chr1', 999, 2000) # 0-based, half-open - Network accessline 163
with pysam.FastaFile('reference.fa') as ref: for chrom, start, end in regions: seq = ref.fetch(chrom, start, end) - Network accessline 164
for chrom, start, end in regions: seq = ref.fetch(chrom, start, end) print(f'>{chrom}:{start+1}-{end}') - Network accessline 165
seq = ref.fetch(chrom, start, end) - Network accessline 201
consensus = simple_consensus(bam_path, chrom, start, end) with pysam.FastaFile(ref_path) as ref: reference = ref.fetch(chrom, start, end) - Network accessline 202
with pysam.FastaFile(ref_path) as ref: reference = ref.fetch(chrom, start, end) differences = [] - Network accessline 203
reference = ref.fetch(chrom, start, end)
skills/bio-reporting-automated-qc-reports/examples/multiqc_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-reporting-figure-export/examples/publication_figures.py
- Executable scriptline 1
Executable file
skills/bio-reporting-jupyter-reports/examples/papermill_batch.py
- Executable scriptline 1
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skills/bio-reporting-quarto-reports/usage-guide.md
- Network accessline 21
# Install Quarto - download from https://quarto.org/docs/download/
skills/bio-research-tools-biomarker-signature-studio/scripts/biomarker_signature_studio.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-restriction-enzyme-selection/examples/cloning_strategy.py
- Executable scriptline 1
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skills/bio-restriction-enzyme-selection/examples/golden_gate_check.py
- Executable scriptline 1
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skills/bio-restriction-enzyme-selection/examples/select_enzymes.py
- Executable scriptline 1
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skills/bio-restriction-fragment-analysis/examples/gel_simulation.py
- Executable scriptline 1
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skills/bio-restriction-fragment-analysis/examples/predict_fragments.py
- Executable scriptline 1
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skills/bio-restriction-mapping/examples/create_map.py
- Executable scriptline 1
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skills/bio-restriction-mapping/examples/plasmid_map.py
- Executable scriptline 1
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skills/bio-restriction-sites/examples/circular_plasmid.py
- Executable scriptline 1
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skills/bio-restriction-sites/examples/find_sites.py
- Executable scriptline 1
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skills/bio-reverse-complement/examples/basic_operations.py
- Executable scriptline 1
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skills/bio-reverse-complement/examples/palindrome_check.py
- Executable scriptline 1
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skills/bio-reverse-complement/examples/primer_design.py
- Executable scriptline 1
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skills/bio-ribo-seq-orf-detection/examples/detect_orfs.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-ribo-seq-riboseq-preprocessing/examples/preprocess_riboseq.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-ribo-seq-ribosome-periodicity/examples/periodicity_analysis.py
- Executable scriptline 1
Executable file
skills/bio-ribo-seq-ribosome-stalling/examples/detect_stalling.py
- Executable scriptline 1
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skills/bio-ribo-seq-translation-efficiency/examples/calculate_te.py
- Executable scriptline 1
Executable file
skills/bio-rna-quantification-alignment-free-quant/examples/kallisto_quant.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-rna-quantification-alignment-free-quant/examples/salmon_quant.sh
skills/bio-rna-quantification-alignment-free-quant/usage-guide.md
- Network accessline 61
# Human wget https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz - Network accessline 62
wget https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz - Network accessline 64
# Mouse wget https://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz - Network accessline 65
wget https://ftp.ensembl.org/pub/release-110/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz - Network accessline 70
# Human wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz - Network accessline 71
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.transcripts.fa.gz - Network accessline 76
# Get genome and transcriptome wget genome.fa.gz - Network accessline 77
wget genome.fa.gz - Network accessline 78
wget transcripts.fa.gz
skills/bio-rna-quantification-count-matrix-qc/examples/qc_analysis.py
- Executable scriptline 1
Executable file
skills/bio-rna-quantification-featurecounts-counting/examples/count_genes.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-rna-quantification-featurecounts-counting/examples/process_counts.py
- Executable scriptline 1
Executable file
skills/bio-rna-quantification-featurecounts-counting/usage-guide.md
- Dangerous shell operationline 25
sudo apt install subread - Network accessline 27
# From source wget https://sourceforge.net/projects/subread/files/subread-2.0.6/subread-2.0.6-Linux-x86_64.tar.gz - Network accessline 28
wget https://sourceforge.net/projects/subread/files/subread-2.0.6/subread-2.0.6-Linux-x86_64.tar.gz
skills/bio-rnaseq-qc/SKILL.md
- Network accessline 280
for i, read in enumerate(bam.fetch()):
skills/bio-rnaseq-qc/examples/check_rrna.sh
skills/bio-rnaseq-qc/examples/rnaseq_qc.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-rnaseq-qc/usage-guide.md
- Network accessline 70
## Resources - [RSeQC Documentation](http://rseqc.sourceforge.net/) - Network accessline 71
- [RSeQC Documentation](http://rseqc.sourceforge.net/) - Network accessline 72
- [SortMeRNA GitHub](https://github.com/biocore/sortmerna) - Network accessline 73
- [Picard RNA Metrics](https://broadinstitute.github.io/picard/)
skills/bio-sam-bam-basics/SKILL.md
- Network accessline 206
with pysam.AlignmentFile('input.bam', 'rb') as bam: for read in bam.fetch('chr1', 1000, 2000): - Network accessline 207
for read in bam.fetch('chr1', 1000, 2000): - Network accessline 232
| View header | `samtools view -H file.bam` | `bam.header` | | Count reads | `samtools view -c file.bam` | `sum(1 for _ in bam)` | | Get region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` | - Network accessline 233
| Count reads | `samtools view -c file.bam` | `sum(1 for _ in bam)` | | Get region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` | | BAM to SAM | `samtools view -h -o out.sam in.bam` | Open with 'w' mode | - Network accessline 234
| Get region | `samtools view file.bam chr1:1-1000` | `bam.fetch('chr1', 0, 1000)` |
skills/bio-sam-bam-basics/examples/convert_formats.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-sam-bam-basics/examples/view_bam.py
- Executable scriptline 1
Executable file
skills/bio-sam-bam-basics/usage-guide.md
skills/bio-sashimi-plots/examples/plot_sashimi.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-seq-objects/examples/basic_seq.py
- Executable scriptline 1
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skills/bio-seq-objects/examples/seqrecord_annotations.py
- Executable scriptline 1
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skills/bio-sequence-properties/examples/advanced_analysis.py
- Executable scriptline 1
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skills/bio-sequence-properties/examples/dna_properties.py
- Executable scriptline 1
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skills/bio-sequence-properties/examples/gc_analysis.py
- Executable scriptline 1
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skills/bio-sequence-properties/examples/protein_properties.py
- Executable scriptline 1
Executable file - Possible obfuscationline 14
protein_seq = 'MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGMKNGKKIELKDLVSGFLAEKQGSPTFFGYMKFLSNSEIVVLPNNVAPNVRYIIQQYGFYHHVGTWNNNSHAKIGLIILYLNKEKTLFNNNVQNKRTSHLL
skills/bio-sequence-similarity/SKILL.md
skills/bio-sequence-similarity/examples/find_orthologs.py
- Executable scriptline 1
Executable file
skills/bio-sequence-similarity/examples/psiblast_search.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-sequence-slicing/examples/basic_slicing.py
- Executable scriptline 1
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skills/bio-sequence-slicing/examples/chunking.py
- Executable scriptline 1
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skills/bio-sequence-slicing/examples/concatenation.py
- Executable scriptline 1
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skills/bio-sequence-statistics/examples/seq_stats.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-similarity-searching/examples/similarity_search.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-single-cell-batch-integration/examples/harmony_integration.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-single-cell-batch-integration/examples/harmony_integration.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-single-cell-cell-annotation/examples/celltypist_annotation.py
- Executable scriptline 1
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skills/bio-single-cell-cell-communication/examples/liana_analysis.py
- Executable scriptline 1
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skills/bio-single-cell-clustering/examples/cluster_scanpy.py
- Executable scriptline 1
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skills/bio-single-cell-data-io/examples/load_10x_scanpy.py
- Executable scriptline 1
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skills/bio-single-cell-doublet-detection/examples/scrublet_detection.py
- Executable scriptline 1
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skills/bio-single-cell-lineage-tracing/examples/cassiopeia_reconstruction.py
- Executable scriptline 1
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skills/bio-single-cell-lineage-tracing/examples/cospar_dynamics.py
- Executable scriptline 1
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skills/bio-single-cell-markers-annotation/examples/find_markers_scanpy.py
- Executable scriptline 1
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skills/bio-single-cell-metabolite-communication/examples/metabolite_communication.py
- Executable scriptline 1
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skills/bio-single-cell-multimodal-integration/examples/cite_seq_analysis.py
- Executable scriptline 1
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skills/bio-single-cell-perturb-seq/examples/pertpy_analysis.py
- Executable scriptline 1
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skills/bio-single-cell-preprocessing/examples/preprocess_scanpy.py
- Executable scriptline 1
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skills/bio-single-cell-scatac-analysis/examples/scatac_workflow.py
- Executable scriptline 1
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skills/bio-single-cell-splicing/examples/sc_splicing_brie2.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-single-cell-splicing/usage-guide.md
skills/bio-single-cell-trajectory-inference/examples/scvelo_velocity.py
- Executable scriptline 1
Executable file
skills/bio-small-rna-seq-mirdeep2-analysis/SKILL.md
skills/bio-small-rna-seq-mirdeep2-analysis/examples/mirdeep2_workflow.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 12
if [ ! -f "$MIRBASE_DIR/mature.fa" ]; then echo "Downloading miRBase..." wget -q -O $MIRBASE_DIR/mature.fa https://www.mirbase.org/download/mature.fa - Network accessline 13
echo "Downloading miRBase..." wget -q -O $MIRBASE_DIR/mature.fa https://www.mirbase.org/download/mature.fa wget -q -O $MIRBASE_DIR/hairpin.fa https://www.mirbase.org/download/hairpin.fa - Network accessline 14
wget -q -O $MIRBASE_DIR/mature.fa https://www.mirbase.org/download/mature.fa - Network accessline 15
wget -q -O $MIRBASE_DIR/hairpin.fa https://www.mirbase.org/download/hairpin.fa
skills/bio-small-rna-seq-mirdeep2-analysis/usage-guide.md
skills/bio-small-rna-seq-mirge3-analysis/examples/mirge3_quantify.py
- Executable scriptline 1
Executable file
skills/bio-small-rna-seq-smrna-preprocessing/examples/preprocess_smrna.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-small-rna-seq-target-prediction/SKILL.md
- Network accessline 75
''' # TargetScan provides downloadable files # For human: https://www.targetscan.org/vert_80/vert_80_data_download/ - Network accessline 76
# TargetScan provides downloadable files # For human: https://www.targetscan.org/vert_80/vert_80_data_download/ targetscan_file = 'Predicted_Targets_Context_Scores.txt' - Network accessline 77
# For human: https://www.targetscan.org/vert_80/vert_80_data_download/ - Network accessline 92
Score > 80 indicates high confidence ''' # Download from http://mirdb.org/download.html - Network accessline 93
''' # Download from http://mirdb.org/download.html mirdb_file = 'miRDB_v6.0_prediction_result.txt' - Network accessline 94
# Download from http://mirdb.org/download.html - Network accessline 141
def get_validated_targets(mirna): '''Get experimentally validated targets from miRTarBase''' # Download from https://mirtarbase.cuhk.edu.cn/ - Network accessline 142
'''Get experimentally validated targets from miRTarBase''' # Download from https://mirtarbase.cuhk.edu.cn/ mirtarbase_file = 'miRTarBase_MTI.xlsx' - Network accessline 143
# Download from https://mirtarbase.cuhk.edu.cn/
skills/bio-small-rna-seq-target-prediction/examples/predict_targets.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-image-analysis/examples/extract_features.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-communication/examples/ligrec_analysis.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-data-io/examples/load_visium.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-deconvolution/examples/deconvolve_spatial.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-domains/examples/detect_domains.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-multiomics/examples/spatialdata_workflow.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-multiomics/examples/squidpy_highres.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-neighbors/examples/build_spatial_graph.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-preprocessing/examples/preprocess_spatial.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-proteomics/examples/spatial_proteomics_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-spatial-transcriptomics-spatial-statistics/examples/spatial_autocorr.py
- Executable scriptline 1
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skills/bio-spatial-transcriptomics-spatial-visualization/examples/spatial_plot.py
- Executable scriptline 1
Executable file
skills/bio-splicing-pipeline/examples/splicing_pipeline.sh
skills/bio-splicing-qc/SKILL.md
- Network accessline 142
for read in bam.fetch():
skills/bio-splicing-qc/examples/splicing_qc.py
skills/bio-splicing-quantification/examples/quantify_splicing.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-sra-data/SKILL.md
skills/bio-sra-data/examples/download_batch.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-sra-data/examples/download_single.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-sra-data/examples/find_sra_runs.py
- Executable scriptline 1
Executable file
skills/bio-sra-data/examples/prefetch_large.sh
skills/bio-sra-data/usage-guide.md
- Dangerous shell operationline 29
sudo apt install sra-toolkit
skills/bio-structural-biology-alphafold-predictions/SKILL.md
- Network accessline 20
**"Get the AlphaFold predicted structure for my protein"** → Download pre-computed AlphaFold structures by UniProt ID and assess prediction quality via per-residue pLDDT confidence scores. - Python: `requests.get(f'https://alphafold.ebi.ac. - Network accessline 21
- Python: `requests.get(f'https://alphafold.ebi.ac.uk/files/AF-{uniprot}-F1-model_v4.pdb')` - Network accessline 36
def download_alphafold(uniprot_id, output_dir='.'): '''Download AlphaFold structure for UniProt accession''' base_url = 'https://alphafold.ebi.ac.uk/files' - Network accessline 37
'''Download AlphaFold structure for UniProt accession''' base_url = 'https://alphafold.ebi.ac.uk/files' pdb_url = f'{base_url}/AF-{uniprot_id}-F1-model_v4.pdb' - Network accessline 38
base_url = 'https://alphafold.ebi.ac.uk/files' - Network accessline 42
response = requests.get(pdb_url) - Network accessline 56
def check_alphafold_exists(uniprot_id): '''Check if AlphaFold prediction exists''' url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' - Network accessline 57
'''Check if AlphaFold prediction exists''' url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' response = requests.get(url) - Network accessline 58
url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' response = requests.get(url) return response.status_code == 200 - Network accessline 59
response = requests.get(url) - Network accessline 69
def get_alphafold_info(uniprot_id): '''Get AlphaFold prediction metadata''' url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' - Network accessline 70
'''Get AlphaFold prediction metadata''' url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' response = requests.get(url) - Network accessline 71
url = f'https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}' response = requests.get(url) if response.status_code == 200: - Network accessline 72
response = requests.get(url) - Network accessline 94
def download_pae(uniprot_id, output_dir='.'): '''Download PAE (predicted aligned error) matrix''' url = f'https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-predicted_aligned_error_v4.json' - Network accessline 95
'''Download PAE (predicted aligned error) matrix''' url = f'https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-predicted_aligned_error_v4.json' response = requests.get(url) - Network accessline 96
url = f'https://alphafold.ebi.ac.uk/files/AF-{uniprot_id}-F1-predicted_aligned_error_v4.json' response = requests.get(url) if response.status_code == 200: - Network accessline 97
response = requests.get(url)
skills/bio-structural-biology-alphafold-predictions/examples/download_alphafold.py
- Executable scriptline 1
Executable file - Network accessline 6
def download_alphafold(uniprot_id, output_dir='.'): os.makedirs(output_dir, exist_ok=True) base_url = 'https://alphafold.ebi.ac.uk/files' - Network accessline 8
base_url = 'https://alphafold.ebi.ac.uk/files' - Network accessline 10
pdb_url = f'{base_url}/AF-{uniprot_id}-F1-model_v4.pdb' response = requests.get(pdb_url) - Network accessline 11
response = requests.get(pdb_url)
skills/bio-structural-biology-alphafold-predictions/usage-guide.md
- Network accessline 60
**Direct download URLs:** - Structure: `https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-model_v4.pdb` - Network accessline 61
- Structure: `https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-model_v4.pdb` - Network accessline 62
- mmCIF: `https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-model_v4.cif` - Network accessline 63
- PAE: `https://alphafold.ebi.ac.uk/files/AF-{UNIPROT_ID}-F1-predicted_aligned_error_v4.json` - Network accessline 65
**API endpoint:** `https://alphafold.ebi.ac.uk/api/prediction/{UNIPROT_ID}`
skills/bio-structural-biology-modern-structure-prediction/SKILL.md
- Network accessline 49
def predict_esmfold(sequence): '''Predict structure using ESMFold API''' url = 'https://api.esmatlas.com/foldSequence/v1/pdb/' - Network accessline 50
'''Predict structure using ESMFold API''' url = 'https://api.esmatlas.com/foldSequence/v1/pdb/' response = requests.post(url, data=sequence, timeout=300) - Network accessline 51
url = 'https://api.esmatlas.com/foldSequence/v1/pdb/' response = requests.post(url, data=sequence, timeout=300) if response.status_code == 200: - Network accessline 52
response = requests.post(url, data=sequence, timeout=300)
skills/bio-structural-biology-modern-structure-prediction/examples/compare_predictions.py
- Executable scriptline 1
Executable file
skills/bio-structural-biology-modern-structure-prediction/examples/esmfold_api.py
skills/bio-substructure-search/examples/substructure_search.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-systems-biology-context-specific-models/SKILL.md
skills/bio-systems-biology-context-specific-models/examples/context_specific.py
- Executable scriptline 1
Executable file
skills/bio-systems-biology-flux-balance-analysis/SKILL.md
- Network accessline 40
# BiGG models available at: http://bigg.ucsd.edu/models
skills/bio-systems-biology-flux-balance-analysis/examples/fba_analysis.py
skills/bio-systems-biology-gene-essentiality/examples/gene_essentiality.py
- Executable scriptline 1
Executable file
skills/bio-systems-biology-metabolic-reconstruction/SKILL.md
skills/bio-systems-biology-metabolic-reconstruction/examples/model_reconstruction.py
- Executable scriptline 1
Executable file
skills/bio-systems-biology-metabolic-reconstruction/usage-guide.md
skills/bio-systems-biology-model-curation/examples/model_curation.py
- Executable scriptline 1
Executable file
skills/bio-tcr-bcr-analysis-immcantation-analysis/usage-guide.md
skills/bio-tcr-bcr-analysis-mixcr-analysis/examples/mixcr_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-tcr-bcr-analysis-mixcr-analysis/usage-guide.md
skills/bio-tcr-bcr-analysis-repertoire-visualization/examples/repertoire_plots.py
- Executable scriptline 1
Executable file
skills/bio-tcr-bcr-analysis-scirpy-analysis/examples/scirpy_integration.py
- Executable scriptline 1
Executable file
skills/bio-tcr-bcr-analysis-vdjtools-analysis/examples/diversity_analysis.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-tcr-bcr-analysis-vdjtools-analysis/usage-guide.md
skills/bio-transcription-translation/examples/basic_conversion.py
- Executable scriptline 1
Executable file
skills/bio-transcription-translation/examples/codon_tables.py
- Executable scriptline 1
Executable file
skills/bio-transcription-translation/examples/orf_finding.py
- Executable scriptline 1
Executable file
skills/bio-tumor-fraction-estimation/examples/estimate_tumor_fraction.R
- Executable scriptline 1
#!/usr/bin/env Rscript
skills/bio-uniprot-access/SKILL.md
- Network accessline 36
def fetch_uniprot(accession, format='fasta'): '''Fetch UniProt entry. Formats: fasta, json, txt, xml, gff''' url = f'https://rest.uniprot.org/uniprotkb/{accession}.{format}' - Network accessline 37
'''Fetch UniProt entry. Formats: fasta, json, txt, xml, gff''' url = f'https://rest.uniprot.org/uniprotkb/{accession}.{format}' response = requests.get(url) - Network accessline 38
url = f'https://rest.uniprot.org/uniprotkb/{accession}.{format}' response = requests.get(url) response.raise_for_status() - Network accessline 39
response = requests.get(url) - Network accessline 50
def search_uniprot(query, format='json', size=25): '''Search UniProt with query syntax''' url = 'https://rest.uniprot.org/uniprotkb/search' - Network accessline 51
'''Search UniProt with query syntax''' url = 'https://rest.uniprot.org/uniprotkb/search' params = {'query': query, 'format': format, 'size': size} - Network accessline 52
url = 'https://rest.uniprot.org/uniprotkb/search' params = {'query': query, 'format': format, 'size': size} response = requests.get(url, params=params) - Network accessline 53
params = {'query': query, 'format': format, 'size': size} response = requests.get(url, params=params) response.raise_for_status() - Network accessline 54
response = requests.get(url, params=params) - Network accessline 89
def batch_fetch(accessions, format='fasta'): '''Fetch multiple entries''' url = 'https://rest.uniprot.org/uniprotkb/accessions' - Network accessline 90
'''Fetch multiple entries''' url = 'https://rest.uniprot.org/uniprotkb/accessions' params = {'accessions': ','.join(accessions), 'format': format} - Network accessline 91
url = 'https://rest.uniprot.org/uniprotkb/accessions' params = {'accessions': ','.join(accessions), 'format': format} response = requests.get(url, params=params) - Network accessline 92
params = {'accessions': ','.join(accessions), 'format': format} response = requests.get(url, params=params) return response.text - Network accessline 93
response = requests.get(url, params=params) - Network accessline 103
def search_all(query, format='tsv', fields=None): '''Stream all results for large queries''' url = 'https://rest.uniprot.org/uniprotkb/stream' - Network accessline 104
'''Stream all results for large queries''' url = 'https://rest.uniprot.org/uniprotkb/stream' params = {'query': query, 'format': format} - Network accessline 105
url = 'https://rest.uniprot.org/uniprotkb/stream' - Network accessline 107
if fields: params['fields'] = ','.join(fields) response = requests.get(url, params=params, stream=True) - Network accessline 108
params['fields'] = ','.join(fields) response = requests.get(url, params=params, stream=True) return response.text - Network accessline 109
response = requests.get(url, params=params, stream=True) - Network accessline 124
def map_ids(ids, from_db, to_db): '''Map IDs between databases''' url = 'https://rest.uniprot.org/idmapping/run' - Network accessline 125
'''Map IDs between databases''' url = 'https://rest.uniprot.org/idmapping/run' response = requests.post(url, data={'ids': ','.join(ids), 'from': from_db, 'to': to_db}) - Network accessline 126
url = 'https://rest.uniprot.org/idmapping/run' response = requests.post(url, data={'ids': ','.join(ids), 'from': from_db, 'to': to_db}) job_id = response.json()['jobId'] - Network accessline 127
response = requests.post(url, data={'ids': ','.join(ids), 'from': from_db, 'to': to_db}) - Network accessline 130
# Poll for results while True: status = requests.get(f'https://rest.uniprot.org/idmapping/status/{job_id}') - Network accessline 131
while True: status = requests.get(f'https://rest.uniprot.org/idmapping/status/{job_id}') if 'results' in status.json() or 'failedIds' in status.json(): - Network accessline 132
status = requests.get(f'https://rest.uniprot.org/idmapping/status/{job_id}') - Network accessline 137
results = requests.get(f'https://rest.uniprot.org/idmapping/results/{job_id}') - Network accessline 194
url = 'https://rest.uniprot.org/uniprotkb/search' params = {'query': query, 'format': 'tsv', 'fields': ','.join(fields), 'size': 500} response = requests.get(url, params=params) - Network accessline 195
params = {'query': query, 'format': 'tsv', 'fields': ','.join(fields), 'size': 500} response = requests.get(url, params=params) return pd.read_csv(StringIO(response.text), sep='\t') - Network accessline 196
response = requests.get(url, params=params)
skills/bio-uniprot-access/examples/uniprot_query.py
- Executable scriptline 1
Executable file - Network accessline 15
def search_uniprot(query, fields, size=500): url = 'https://rest.uniprot.org/uniprotkb/search' - Network accessline 16
url = 'https://rest.uniprot.org/uniprotkb/search' params = {'query': query, 'format': 'tsv', 'fields': ','.join(fields), 'size': size} response = requests.get(url, params=params) - Network accessline 17
params = {'query': query, 'format': 'tsv', 'fields': ','.join(fields), 'size': size} response = requests.get(url, params=params) response.raise_for_status() - Network accessline 18
response = requests.get(url, params=params)
skills/bio-variant-annotation/SKILL.md
- Network accessline 273
# Download from https://annovar.openbioinformatics.org/ (registration required)
skills/bio-variant-annotation/examples/annotate_vcf.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-annotation/usage-guide.md
- Network accessline 258
# Download wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz - Network accessline 259
wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz - Network accessline 260
wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz.tbi - Network accessline 271
# Download chromosome 1 wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz - Network accessline 272
wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz - Network accessline 273
wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi - Network accessline 285
# Download wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 286
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 287
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 388
- [bcftools annotate documentation](http://www.htslib.org/doc/bcftools.html#annotate) - Network accessline 389
- [bcftools csq documentation](http://www.htslib.org/doc/bcftools.html#csq)
skills/bio-variant-calling-clinical-interpretation/SKILL.md
- Network accessline 55
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 56
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 120
git clone https://github.com/WGLab/InterVar.git cd InterVar # Download databases per documentation
skills/bio-variant-calling-clinical-interpretation/examples/clinical_filter.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-variant-calling-clinical-interpretation/usage-guide.md
- Network accessline 13
# ClinVar database wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 14
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 124
- [ACMG guidelines](https://www.acmg.net/ACMG/Medical-Genetics-Practice-Resources/) - Network accessline 125
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/)
skills/bio-variant-calling-deepvariant/examples/run_deepvariant.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-calling-deepvariant/usage-guide.md
skills/bio-variant-calling-filtering-best-practices/examples/filter_variants.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-calling-joint-calling/examples/joint_calling_gatk.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-calling-joint-calling/usage-guide.md
- Network accessline 163
- [GATK joint calling tutorial](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152)
skills/bio-variant-calling-structural-variant-calling/examples/call_svs.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-calling/examples/call_variants.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-calling/usage-guide.md
skills/bio-variant-normalization/examples/normalize_vcf.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-variant-normalization/usage-guide.md
skills/bio-vcf-basics/examples/view_vcf.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-vcf-manipulation/examples/compare_vcfs.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-vcf-manipulation/usage-guide.md
- Network accessline 411
- [bcftools merge documentation](http://www.htslib.org/doc/bcftools.html#merge) - Network accessline 412
- [bcftools concat documentation](http://www.htslib.org/doc/bcftools.html#concat) - Network accessline 413
- [bcftools isec documentation](http://www.htslib.org/doc/bcftools.html#isec)
skills/bio-vcf-statistics/examples/vcf_stats.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-vcf-statistics/usage-guide.md
skills/bio-virtual-screening/examples/virtual_screen.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bio-workflow-management-cwl-workflows/examples/rnaseq.cwl
- Executable scriptline 1
#!/usr/bin/env cwl-runner
skills/bio-workflow-management-nextflow-pipelines/examples/rnaseq.nf
- Executable scriptline 1
#!/usr/bin/env nextflow
skills/bio-workflow-management-nextflow-pipelines/usage-guide.md
skills/bio-workflow-management-wdl-workflows/usage-guide.md
- Network accessline 25
# Or install Cromwell (full-featured) # Download from: https://github.com/broadinstitute/cromwell/releases - Network accessline 26
# Download from: https://github.com/broadinstitute/cromwell/releases - Network accessline 27
wget https://github.com/broadinstitute/cromwell/releases/download/91/cromwell-91.jar - Network accessline 29
# Install womtool for validation wget https://github.com/broadinstitute/cromwell/releases/download/91/womtool-91.jar - Network accessline 30
wget https://github.com/broadinstitute/cromwell/releases/download/91/womtool-91.jar
skills/bio-workflows-atacseq-pipeline/examples/atacseq_workflow.sh
skills/bio-workflows-biomarker-pipeline/examples/biomarker_pipeline.py
- Executable scriptline 1
Executable file
skills/bio-workflows-chipseq-pipeline/examples/narrow_peak_workflow.sh
skills/bio-workflows-clip-pipeline/examples/clip_full_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-cnv-pipeline/examples/cnvkit_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-crispr-editing-pipeline/examples/crispr_editing_workflow.py
- Executable scriptline 1
Executable file - Possible obfuscationline 326
target_sequence = '''ATGGATTTATCTGCTCTTCGCGTTGAAGAAGTACAAAATGTCATTAATGCTATGCAGAAAATCTTAGAGTGTCCCATCTGTCTGGAGTTGATCAAGGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAATTTTGCATGCTGAAACTTCTCAACCAGAAGAAAGGGCCTTCACAGTGTCCTTTATGTAAGAATGATATAACCAAAAGGAGCCTA
skills/bio-workflows-crispr-editing-pipeline/usage-guide.md
skills/bio-workflows-crispr-screen-pipeline/examples/crispr_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-fastq-to-variants/SKILL.md
skills/bio-workflows-fastq-to-variants/examples/bwa_bcftools_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-fastq-to-variants/examples/bwa_gatk_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-genome-assembly-pipeline/examples/bacterial_assembly.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-gwas-pipeline/examples/gwas_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-hic-pipeline/SKILL.md
- Network accessline 206
fig, ax = plt.subplots(figsize=(10, 10)) cooltools.lib.plotting.pcolormesh_45deg( ax, clr.matrix(balance=True).fetch('chr1:50000000-60000000'), - Network accessline 207
cooltools.lib.plotting.pcolormesh_45deg( ax, clr.matrix(balance=True).fetch('chr1:50000000-60000000'), start=50000000, resolution=clr.binsize - Network accessline 208
ax, clr.matrix(balance=True).fetch('chr1:50000000-60000000'),
skills/bio-workflows-hic-pipeline/examples/hic_analysis.py
- Executable scriptline 1
Executable file
skills/bio-workflows-imc-pipeline/examples/imc_analysis.py
- Executable scriptline 1
Executable file
skills/bio-workflows-longread-sv-pipeline/examples/ont_sv_calling.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-merip-pipeline/examples/merip_full_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-metabolic-modeling-pipeline/examples/metabolic_modeling_workflow.py
- Executable scriptline 1
Executable file
skills/bio-workflows-metagenomics-pipeline/examples/metagenomics_workflow.sh
skills/bio-workflows-microbiome-pipeline/usage-guide.md
skills/bio-workflows-neoantigen-pipeline/examples/neoantigen_workflow.py
- Executable scriptline 1
Executable file
skills/bio-workflows-outbreak-pipeline/examples/outbreak_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-riboseq-pipeline/examples/riboseq_full_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-rnaseq-to-de/examples/salmon_deseq2_workflow.R
- Network accessline 9
# Public RNA-seq datasets: # - Bioconductor: airway package (GSE52778, dexamethasone treatment) # - recount3: https://rna.recount.bio (precomputed counts for GEO/SRA) - Network accessline 10
# - Bioconductor: airway package (GSE52778, dexamethasone treatment) # - recount3: https://rna.recount.bio (precomputed counts for GEO/SRA) # - ENCODE: https://www.encodeproject.org (cell line RNA-seq) - Network accessline 11
# - recount3: https://rna.recount.bio (precomputed counts for GEO/SRA) - Network accessline 12
# - ENCODE: https://www.encodeproject.org (cell line RNA-seq) - Network accessline 13
# - GTEx: https://gtexportal.org (tissue expression)
skills/bio-workflows-rnaseq-to-de/examples/star_deseq2_workflow.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-scrnaseq-pipeline/examples/scanpy_workflow.py
- Executable scriptline 1
Executable file - Network accessline 22
# Public scRNA-seq datasets: # - 10x Genomics: https://www.10xgenomics.com/datasets (PBMC 3k, 10k datasets) - Network accessline 23
# - 10x Genomics: https://www.10xgenomics.com/datasets (PBMC 3k, 10k datasets) - Network accessline 24
# - CELLxGENE: https://cellxgene.cziscience.com (curated annotated datasets) - Network accessline 25
# - GEO: GSE149173 (COVID-19 PBMC), GSE136831 (human lung) # - Human Cell Atlas: https://data.humancellatlas.org # - Scanpy built-in: sc.datasets.pbmc3k_processed() - Network accessline 26
# - Human Cell Atlas: https://data.humancellatlas.org
skills/bio-workflows-scrnaseq-pipeline/examples/seurat_workflow.R
- Network accessline 8
# Public scRNA-seq datasets: # - 10x Genomics: https://www.10xgenomics.com/datasets (PBMC 3k, 10k) - Network accessline 9
# - 10x Genomics: https://www.10xgenomics.com/datasets (PBMC 3k, 10k) - Network accessline 10
# - SeuratData package: InstallData('pbmc3k') for built-in tutorial data # - CELLxGENE: https://cellxgene.cziscience.com (curated annotated datasets) # - GEO: GSE149173 (COVID-19 PBMC), GSE126030 (multi-tissue) - Network accessline 11
# - CELLxGENE: https://cellxgene.cziscience.com (curated annotated datasets) - Network accessline 13
# - Human Cell Atlas: https://data.humancellatlas.org
skills/bio-workflows-smrna-pipeline/examples/smrna_full_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-somatic-variant-pipeline/examples/run_mutect2.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-somatic-variant-pipeline/usage-guide.md
skills/bio-workflows-spatial-pipeline/examples/visium_workflow.py
- Executable scriptline 1
Executable file
skills/bio-workflows-tcr-pipeline/examples/tcr_full_pipeline.sh
- Executable scriptline 1
#!/bin/bash
skills/bio-workflows-tcr-pipeline/usage-guide.md
skills/bio-write-sequences/examples/basic_writing.py
- Executable scriptline 1
Executable file
skills/bioinformatics-singlecell/SKILL.md
- Executable scriptline 1
Executable file
skills/bioinformatics-singlecell/references/cell_markers.md
- Executable scriptline 1
Executable file
skills/biologist-analyst/QUICK_REFERENCE.md
- Network accessline 77
- **Khan Academy**: https://www.khanacademy.org/science/biology - Network accessline 78
- **Nature Scitable**: https://www.nature.com/scitable - Network accessline 79
- **Understanding Evolution**: https://evolution.berkeley.edu/ - Network accessline 80
- **NCBI**: https://www.ncbi.nlm.nih.gov/ - Network accessline 81
- **IUCN**: https://www.iucnredlist.org/
skills/biologist-analyst/README.md
- Network accessline 85
- **Khan Academy Biology**: https://www.khanacademy.org/science/biology - Network accessline 86
- **Nature Scitable**: https://www.nature.com/scitable - Network accessline 87
- **Understanding Evolution**: https://evolution.berkeley.edu/ - Network accessline 88
- **NCBI Resources**: https://www.ncbi.nlm.nih.gov/ - Network accessline 89
- **IUCN Red List**: https://www.iucnredlist.org/
skills/biologist-analyst/SKILL.md
- Network accessline 86
- [Understanding Evolution - UC Berkeley](https://evolution.berkeley.edu/) - Network accessline 87
- [Darwin Online - Complete Works](http://darwin-online.org.uk/) - Network accessline 88
- [Evolution - NCBI Bookshelf](https://www.ncbi.nlm.nih.gov/books/NBK21154/) - Network accessline 128
- [Molecular Biology of the Cell - Alberts et al.](https://www.ncbi.nlm.nih.gov/books/NBK21054/) - Network accessline 129
- [NCBI Genes and Disease](https://www.ncbi.nlm.nih.gov/books/NBK22183/) - Network accessline 130
- [Nature Scitable - Molecular Biology](https://www.nature.com/scitable/topic/genetics-5/) - Network accessline 170
- [Ecology - Khan Academy](https://www.khanacademy.org/science/biology/ecology) - Network accessline 171
- [Ecological Society of America](https://www.esa.org/) - Network accessline 172
- [Conservation Biology - Society for Conservation Biology](https://conbio.org/) - Network accessline 204
- [Cell Biology by the Numbers](http://book.bionumbers.org/) - Network accessline 205
- [The Cell - NCBI Bookshelf](https://www.ncbi.nlm.nih.gov/books/NBK9841/) - Network accessline 238
- [Genetics Home Reference - NIH](https://medlineplus.gov/genetics/) - Network accessline 239
- [Online Mendelian Inheritance in Man (OMIM)](https://www.omim.org/) - Network accessline 334
**Sources**: [The Tree of Life Web Project](http://tolweb.org/) - Network accessline 491
- [CDC Antibiotic Resistance](https://www.cdc.gov/drugresistance/) - Network accessline 492
- [Evolution of Antibiotic Resistance - Nature](https://www.nature.com/articles/s41579-018-0109-z) - Network accessline 560
- [CRISPR Sickle Cell Trials - NEJM](https://www.nejm.org/doi/full/10.1056/NEJMoa2031054) - Network accessline 561
- [Gene Editing Ethics - National Academies](https://www.nationalacademies.org/our-work/human-genome-editing) - Network accessline 631
- [Coral Reef Alliance](https://coral.org/) - Network accessline 632
- [NOAA Coral Reef Conservation Program](https://www.coralreef.noaa.gov/) - Network accessline 633
- [Reef Resilience Network](https://reefresilience.org/) - Network accessline 730
- [Khan Academy Biology](https://www.khanacademy.org/science/biology) - Network accessline 731
- [Nature Scitable](https://www.nature.com/scitable) - Network accessline 732
- [HHMI BioInteractive](https://www.biointeractive.org/) - Network accessline 736
- [Understanding Evolution - UC Berkeley](https://evolution.berkeley.edu/) - Network accessline 737
- [Darwin Online](http://darwin-online.org.uk/) - Network accessline 738
- [Tree of Life Web Project](http://tolweb.org/) - Network accessline 742
- [NCBI Resources](https://www.ncbi.nlm.nih.gov/) - Network accessline 743
- [Molecular Biology of the Cell](https://www.ncbi.nlm.nih.gov/books/NBK21054/) - Network accessline 744
- [PDB - Protein Data Bank](https://www.rcsb.org/) - Network accessline 748
- [Ecological Society of America](https://www.esa.org/) - Network accessline 749
- [Ecology.com](https://www.ecology.com/) - Network accessline 753
- [Genetics Home Reference](https://medlineplus.gov/genetics/) - Network accessline 754
- [OMIM - Genetic Disorders](https://www.omim.org/) - Network accessline 755
- [CDC](https://www.cdc.gov/) - Network accessline 759
- [IUCN Red List](https://www.iucnredlist.org/) - Network accessline 760
- [Conservation Biology - Society](https://conbio.org/) - Network accessline 761
- [WWF](https://www.worldwildlife.org/)
skills/biomaster-workflows/README.md
- Network accessline 76
- https://github.com/ai4nucleome/BioMaster
skills/biomaster-workflows/repo/README.md
- Network accessline 20
[](https://www.biorxiv.org/content/10.1101/2025.01.23.634608v1.abstract) - Network accessline 121
You can find the read the doc documentation in the [docs](https://biomaster.readthedocs.io/en/latest/) folder. - Network accessline 130
git clone https://github.com/yourusername/BioMaster.git - Network accessline 150
https://drive.google.com/drive/folders/1vA3WIAVXVo4RZSqXKsItEZHVaBgIIv_E?usp=sharing - Network accessline 173
1. **Collect the analysis workflow**, e.g.: [ChIP-seq data analysis](https://nf-co.re/chipseq/2.1.0/) - Network accessline 174
[ChIP-seq data analysis](https://nf-co.re/chipseq/2.1.0/) - Network accessline 333
# suggest base url: # https://api.bltcy.ai/v1 - Network accessline 334
# https://api.bltcy.ai/v1 - Network accessline 335
# https://gpt-api.hkust-gz.edu.cn/v1 - Network accessline 336
# https://dashscope.aliyuncs.com/compatible-mode/v1 - Network accessline 337
# https://api.openai.com/v1 - Network accessline 338
# https://api.siliconflow.cn/v1 - Network accessline 339
# https://sg.uiuiapi.com/v1 - Network accessline 341
main: key: '' base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 342
key: '' base_url: 'https://api.siliconflow.cn/v1/' embedding: - Network accessline 343
base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 344
embedding: key: '' base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 345
key: '' base_url: 'https://api.siliconflow.cn/v1/' # Ollama settings - Network accessline 346
base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 348
ollama: enabled: true base_url: 'http://localhost:11434' - Network accessline 350
base_url: 'http://localhost:11434' - Network accessline 386
ollama: enabled: true base_url: 'http://localhost:11434' - Network accessline 388
base_url: 'http://localhost:11434' - Network accessline 528
http://127.0.0.1:7860/ - Network accessline 603
[Discord](https://discord.gg/WYVyRAA6yn) - Network accessline 615
- **Code**: Licensed under the MIT License. See LICENSE for details. - **Data and Documentation**: Licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0). - Network accessline 616
- **Data and Documentation**: Licensed under the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0). - Network accessline 622
- This project uses the [langchain](https://github.com/hwchase17/langchain) library for integration with OpenAI and other tools.
skills/biomaster-workflows/repo/agents/Biomaster.py
- Executable scriptline 1
Executable file - Access to secretsline 47
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[Credential-related source omitted] - Network accessline 59
token_log_path: str = './token.txt', # Add token log path parameter use_ollama: bool = False, # Whether to use ollama ollama_base_url: str = "http://localhost:11434" # Ollama API address - Network accessline 60
use_ollama: bool = False, # Whether to use ollama ollama_base_url: str = "http://localhost:11434" # Ollama API address ): - Network accessline 61
ollama_base_url: str = "http://localhost:11434" # Ollama API address - Access to secretsline 64
[Credential-related source omitted] - Access to secretsline 66
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[Credential-related source omitted] - Network accessline 198
try: response = requests.get(f"{self.ollama_base_url}/api/tags") - Network accessline 199
response = requests.get(f"{self.ollama_base_url}/api/tags") - Access to secretsline 494
[Credential-related source omitted] - Access to secretsline 615
[Credential-related source omitted] - Access to secretsline 671
[Credential-related source omitted] - Access to secretsline 717
[Credential-related source omitted]
skills/biomaster-workflows/repo/agents/CheckAgent.py
- Executable scriptline 1
Executable file - Network accessline 28
[Credential-related source omitted] - Access to secretsline 28
[Credential-related source omitted] - Network accessline 29
use_ollama: bool = False, ollama_base_url: str = "http://localhost:11434", ollama_model: str = "qwen3:32b"): - Network accessline 30
ollama_base_url: str = "http://localhost:11434", - Access to secretsline 35
[Credential-related source omitted] - Access to secretsline 204
[Credential-related source omitted] - Network accessline 215
try: response = requests.post( - Network accessline 216
response = requests.post( - Network accessline 266
try: response = requests.post( - Network accessline 267
response = requests.post(
skills/biomaster-workflows/repo/agents/Knowledge.py
- Executable scriptline 1
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[Credential-related source omitted] - Access to secretsline 62
[Credential-related source omitted] - Network accessline 66
'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36' } response = requests.get(url, headers=headers, timeout=10) - Network accessline 67
} response = requests.get(url, headers=headers, timeout=10) response.raise_for_status() # Ensure request was successful - Network accessline 68
response = requests.get(url, headers=headers, timeout=10) - Access to secretsline 86
[Credential-related source omitted] - Access to secretsline 87
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Network accessline 115
img_response = requests.get(img_url, stream=True) - Access to secretsline 130
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skills/biomaster-workflows/repo/agents/ToolAgent.py
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try: response = requests.post( - Network accessline 97
response = requests.post(
skills/biomaster-workflows/repo/agents/__init__.py
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skills/biomaster-workflows/repo/agents/ollama.py
skills/biomaster-workflows/repo/agents/prompts.py
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skills/biomaster-workflows/repo/agents/utils.py
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skills/biomaster-workflows/repo/config.yaml
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# suggest base url: # https://api.bltcy.ai/v1 - Network accessline 21
# https://api.bltcy.ai/v1 - Network accessline 22
# https://gpt-api.hkust-gz.edu.cn/v1 - Network accessline 23
# https://dashscope.aliyuncs.com/compatible-mode/v1 - Network accessline 24
# https://api.openai.com/v1 - Network accessline 25
# https://api.siliconflow.cn/v1 - Network accessline 26
# https://sg.uiuiapi.com/v1 - Network accessline 28
main: key: '' base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 29
key: '' base_url: 'https://api.siliconflow.cn/v1/' embedding: - Network accessline 30
base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 31
embedding: key: '' base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 32
key: '' base_url: 'https://api.siliconflow.cn/v1/' # Ollama settings - Network accessline 33
base_url: 'https://api.siliconflow.cn/v1/' - Network accessline 35
ollama: enabled: true base_url: 'http://localhost:11434' - Network accessline 37
base_url: 'http://localhost:11434'
skills/biomaster-workflows/repo/data/README.md
- Network accessline 18
See the [Wiki](https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/wiki)
skills/biomaster-workflows/repo/doc/Plan_Knowledge.json
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}, { "content": "Small RNA sequencing data analysis workflow consists of several essential steps:\n\nStep 1: Quality Control and Trimming\nDescription: Perform quality control and adapter trimming on raw sequencing reads.\nInput - Network accessline 177
{ "content": "Small RNA sequencing data analysis workflow consists of several essential steps:\n\nStep 1: Quality Control and Trimming\nDescription: Perform quality control and adapter trimming on raw sequencing reads.\nInput Requir - Network accessline 178
"content": "Small RNA sequencing data analysis workflow consists of several essential steps:\n\nStep 1: Quality Control and Trimming\nDescription: Perform quality control and adapter trimming on raw sequencing reads.\nInput Required: Raw FA
skills/biomaster-workflows/repo/doc/Task_Knowledge.json
- Network accessline 92
}, { "content": "## Synopsis\nThis tutorial demonstrates how to explore, process, and manipulate SAM/BAM files using **samtools**. We will walk through installing samtools, creating a demo directory, converting between SAM and B - Network accessline 93
{ "content": "## Synopsis\nThis tutorial demonstrates how to explore, process, and manipulate SAM/BAM files using **samtools**. We will walk through installing samtools, creating a demo directory, converting between SAM and BAM form - Network accessline 94
"content": "## Synopsis\nThis tutorial demonstrates how to explore, process, and manipulate SAM/BAM files using **samtools**. We will walk through installing samtools, creating a demo directory, converting between SAM and BAM formats, sorti - Network accessline 113
}, { "content": "## Quick Guide to DiffBind\n\n**DiffBind** is an R/Bioconductor package for analyzing differential binding (peaks) in ChIP-seq or ATAC-seq data. Below is a concise workflow:\n\n---\n\n### 1. Installation & Setup - Network accessline 114
{ "content": "## Quick Guide to DiffBind\n\n**DiffBind** is an R/Bioconductor package for analyzing differential binding (peaks) in ChIP-seq or ATAC-seq data. Below is a concise workflow:\n\n---\n\n### 1. Installation & Setup\n```r\ - Network accessline 115
"content": "## Quick Guide to DiffBind\n\n**DiffBind** is an R/Bioconductor package for analyzing differential binding (peaks) in ChIP-seq or ATAC-seq data. Below is a concise workflow:\n\n---\n\n### 1. Installation & Setup\n```r\nif (!requ - Network accessline 134
}, { "content": "GO/KEGG enrichment analysis First, install the required packages.\n\n#source(\"https://bioconductor.org/biocLite.R\")\n#biocLite(\"DOSE\")\n#biocLite(\"topGO\")\n#biocLite(\"clusterProfiler\")\n#biocLite(\"pathv - Network accessline 135
{ "content": "GO/KEGG enrichment analysis First, install the required packages.\n\n#source(\"https://bioconductor.org/biocLite.R\")\n#biocLite(\"DOSE\")\n#biocLite(\"topGO\")\n#biocLite(\"clusterProfiler\")\n#biocLite(\"pathview\")\ - Network accessline 136
"content": "GO/KEGG enrichment analysis First, install the required packages.\n\n#source(\"https://bioconductor.org/biocLite.R\")\n#biocLite(\"DOSE\")\n#biocLite(\"topGO\")\n#biocLite(\"clusterProfiler\")\n#biocLite(\"pathview\")\n\nLoad th - Network accessline 179
"content": "Transcriptome Annotation Comparison (Gencode vs Chess) using rnalib must include:Step1: Set test data directory. Description: Define the global test data path for rnalib by monkey-patching `rna.__RNALIB_TESTDATA__`. Generate nec - Network accessline 187
"content": "miRNA Annotation Comparison (MirGeneDB vs FlyBase) using rnalib must include:Step1: Load transcriptome data from MirGeneDB and FlyBase. Description: Instantiate transcriptomes for MirGeneDB and FlyBase annotations. Example snipp - Network accessline 192
}, { "content": "import scanpy as sc; import nichepca as npc; # Run nichePCA on raw counts with default normalization pipeline (norm -> log1p -> agg -> pca); npc.wf.nichepca(adata, knn=25); # Use nichePCA result for neighbor gra - Network accessline 193
{ "content": "import scanpy as sc; import nichepca as npc; # Run nichePCA on raw counts with default normalization pipeline (norm -> log1p -> agg -> pca); npc.wf.nichepca(adata, knn=25); # Use nichePCA result for neighbor graph and - Network accessline 194
"content": "import scanpy as sc; import nichepca as npc; # Run nichePCA on raw counts with default normalization pipeline (norm -> log1p -> agg -> pca); npc.wf.nichepca(adata, knn=25); # Use nichePCA result for neighbor graph and Leiden clu - Network accessline 248
}, { "content": "To run PureCLIP in basic mode, it requires BAM and BAI files, the reference genome and a specified output file:\n\n```bash\npureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai -g ref.hg19.fa -iv 'ch - Network accessline 249
{ "content": "To run PureCLIP in basic mode, it requires BAM and BAI files, the reference genome and a specified output file:\n\n```bash\npureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai -g ref.hg19.fa -iv 'chr1;chr2 - Network accessline 250
"content": "To run PureCLIP in basic mode, it requires BAM and BAI files, the reference genome and a specified output file:\n\n```bash\npureclip -i aligned.prepro.R2.bam -bai aligned.prepro.R2.bam.bai -g ref.hg19.fa -iv 'chr1;chr2;chr3;' -n - Network accessline 255
}, { "content": "ribotricer: Accurate detection of short and long active ORFs using Ribo-seq data\n\nribotricer is a tool that helps in detecting actively translating open reading frames (ORFs) from Ribo-seq data. It works by as - Network accessline 256
{ "content": "ribotricer: Accurate detection of short and long active ORFs using Ribo-seq data\n\nribotricer is a tool that helps in detecting actively translating open reading frames (ORFs) from Ribo-seq data. It works by assessing - Network accessline 257
"content": "ribotricer: Accurate detection of short and long active ORFs using Ribo-seq data\n\nribotricer is a tool that helps in detecting actively translating open reading frames (ORFs) from Ribo-seq data. It works by assessing the perio
skills/biomaster-workflows/repo/docs/Makefile
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skills/biomaster-workflows/repo/docs/make.bat
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Executable file - Network accessline 20
echo. echo.If you don't have Sphinx installed, grab it from echo.https://www.sphinx-doc.org/ - Network accessline 21
echo.If you don't have Sphinx installed, grab it from echo.https://www.sphinx-doc.org/ exit /b 1 - Network accessline 22
echo.https://www.sphinx-doc.org/
skills/biomaster-workflows/repo/docs/source/conf.py
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skills/biomaster-workflows/repo/docs/source/installation.rst
skills/biomaster-workflows/repo/docs/source/introduction.rst
skills/biomaster-workflows/repo/docs/source/rag.rst
- Dangerous shell operationline 81
rm -rf ./chroma_db
skills/biomaster-workflows/repo/docs/source/usage.rst
skills/biomaster-workflows/repo/examples/WGS WES/example.py
- Executable scriptline 1
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# you can also download the data from the link below # cd data # git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git - Network accessline 25
# cd data # git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git # mv STAR-Fusion-Tutorial/* - Network accessline 26
# git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git
skills/biomaster-workflows/repo/examples/single-cell/example.py
- Executable scriptline 1
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# you can also download the data from the link below # cd data # git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git - Network accessline 25
# cd data # git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git # mv STAR-Fusion-Tutorial/* - Network accessline 26
# git clone https://github.com/STAR-Fusion/STAR-Fusion-Tutorial.git
skills/biomaster-workflows/repo/output/001_DEBUG_Input_2.json
- Network accessline 2
"input": "{\"task\": {\"step_number\": 2, \"description\": \"Convert the SAM file to a BAM file using samtools. Converting to BAM provides a compressed binary format that is more efficient for storage and faster for downstream analyses.\",
skills/biomaster-workflows/repo/output/001_Step_1.sh
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#!/bin/bash
skills/biomaster-workflows/repo/output/001_Step_2.sh
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skills/biomaster-workflows/repo/output/001_Step_3.sh
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skills/biomaster-workflows/repo/output/001_Step_4.sh
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skills/biomaster-workflows/repo/output/001_Step_5.sh
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skills/biomaster-workflows/repo/output/003_Step_1.sh
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#!/bin/bash
skills/biomaster-workflows/repo/output/003_Step_2.sh
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#!/bin/bash
skills/biomaster-workflows/repo/output/003_Step_3.sh
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#!/bin/bash
skills/biomaster-workflows/repo/output/003_Step_4.sh
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#!/bin/bash
skills/biomaster-workflows/repo/run.py
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[Credential-related source omitted] - Network accessline 48
use_ollama = use_ollama and ollama_enabled ollama_base_url = ollama_config.get('base_url', 'http://localhost:11434') - Network accessline 49
ollama_base_url = ollama_config.get('base_url', 'http://localhost:11434') - Access to secretsline 72
[Credential-related source omitted] - Access to secretsline 80
[Credential-related source omitted]
skills/biomaster-workflows/repo/run.sh
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#!/bin/bash
skills/biomaster-workflows/repo/runv.py
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skills/biomaster-workflows/repo/scripts/alignment_stats.sh
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skills/biomaster-workflows/repo/scripts/bam2fq.sh
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skills/biomaster-workflows/repo/scripts/indexbam.sh
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skills/biomaster-workflows/repo/scripts/map_fastq2_ref.sh
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skills/biomaster-workflows/repo/scripts/methy_iden.sh
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skills/biomaster-workflows/repo/scripts/quantififation.sh
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skills/biomaster-workflows/repo/scripts/raw_plot.sh
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skills/biomaster-workflows/repo/scripts/result_sum.sh
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skills/biomaster-workflows/repo/scripts/run-add-hicnormvector-to-mcool.sh
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#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-addfrag2pairs.sh
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#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-bam2pairs.sh
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#!/bin/sh
skills/biomaster-workflows/repo/scripts/run-bwa-mem.sh
skills/biomaster-workflows/repo/scripts/run-cool2multirescool.sh
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#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-cooler-balance.sh
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#!/bin/sh
skills/biomaster-workflows/repo/scripts/run-cooler.sh
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#!/bin/sh
skills/biomaster-workflows/repo/scripts/run-fastqc.sh
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#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-juicebox-pre-addnorm.sh
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#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-juicebox-pre.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-juicer.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-list.sh
- Executable scriptline 1
#!/bin/sh
skills/biomaster-workflows/repo/scripts/run-merge-pairs.sh
skills/biomaster-workflows/repo/scripts/run-pairs-patch.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-pairsam-filter.sh
- Executable scriptline 1
#!/usr/bin/env bash
skills/biomaster-workflows/repo/scripts/run-pairsam-markasdup.sh
- Executable scriptline 1
#!/usr/bin/env bash
skills/biomaster-workflows/repo/scripts/run-pairsam-merge.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-pairsam-parse-sort.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-pairsqc-merge.sh
skills/biomaster-workflows/repo/scripts/run-pairsqc-single.sh
- Executable scriptline 1
#!/bin/bash
skills/biomaster-workflows/repo/scripts/run-sort-bam.sh
- Executable scriptline 1
#!/bin/sh
skills/biomaster-workflows/repo/source/Biomaster.svg
- Network accessline 1
<svg id="图层_1" data-name="图层 1" xmlns="http://www.w3.org/2000/svg" viewBox="0 0 104.67 105.4"><defs><style>.cls-1,.cls-2{fill:#00a29a;}.cls-2{fill-rule:evenodd;}</style></defs><path class="cls-1" d="M72.19,35.49a1,1,0,0,1-.62-.64c-1.72-5.73
skills/biomcp-server/README.md
skills/biomcp-server/bio_mcp_server.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/.github/workflows/validate-codecov-config.yml
skills/biomcp-server/repo/.gitignore
skills/biomcp-server/repo/.pre-commit-config.yaml
- Network accessline 1
repos: - repo: https://github.com/pre-commit/pre-commit-hooks - Network accessline 2
- repo: https://github.com/pre-commit/pre-commit-hooks - Network accessline 12
- repo: https://github.com/astral-sh/ruff-pre-commit - Network accessline 41
- repo: https://github.com/pre-commit/mirrors-prettier
skills/biomcp-server/repo/BIOMCP_DATA_FLOW.md
- Network accessline 268
"title": "BRAF V600E mutation in melanoma", "text": "This study investigates BRAF mutations...", "url": "https://pubmed.ncbi.nlm.nih.gov/12345678" - Network accessline 269
"text": "This study investigates BRAF mutations...", "url": "https://pubmed.ncbi.nlm.nih.gov/12345678" } - Network accessline 270
"url": "https://pubmed.ncbi.nlm.nih.gov/12345678"
skills/biomcp-server/repo/CHANGELOG.md
- Network accessline 18
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Network accessline 19
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Access to secretsline 87
[Credential-related source omitted] - Network accessline 167
- Integrated into unified search syntax: `search(domain="gene", keywords=["BRAF"])` - Query language support: `gene:BRAF`, `drug:pembrolizumab`, `disease:melanoma` - Full fetch support: `fetch(domain="drug", id="DB00945")` - Network accessline 168
- Query language support: `gene:BRAF`, `drug:pembrolizumab`, `disease:melanoma` - Full fetch support: `fetch(domain="drug", id="DB00945")` - **Clinical Trial Enhancement**: - Network accessline 169
- Full fetch support: `fetch(domain="drug", id="DB00945")` - Network accessline 427
[Unreleased]: https://github.com/genomoncology/biomcp/compare/v0.6.6...HEAD - Network accessline 428
[0.6.6]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.6 - Network accessline 429
[0.6.5]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.5 - Network accessline 430
[0.6.4]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.4 - Network accessline 431
[0.6.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.3 - Network accessline 432
[0.6.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.2 - Network accessline 433
[0.6.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.1 - Network accessline 434
[0.6.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.0 - Network accessline 435
[0.5.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.5.0 - Network accessline 436
[0.4.7]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.7 - Network accessline 437
[0.4.6]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.6 - Network accessline 438
[0.4.5]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.5 - Network accessline 439
[0.4.4]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.4 - Network accessline 440
[0.4.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.3 - Network accessline 441
[0.4.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.2 - Network accessline 442
[0.4.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.1 - Network accessline 443
[0.4.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.0 - Network accessline 444
[0.3.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.3 - Network accessline 445
[0.3.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.2 - Network accessline 446
[0.3.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.1 - Network accessline 447
[0.3.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.0 - Network accessline 448
[0.2.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.2.1 - Network accessline 449
[0.2.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.2.0 - Network accessline 450
[0.1.11]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.11 - Network accessline 451
[0.1.10]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.10 - Network accessline 452
[0.1.9]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.9 - Network accessline 453
[0.1.8]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.8 - Network accessline 454
[0.1.7]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.7 - Network accessline 455
[0.1.6]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.6 - Network accessline 456
[0.1.5]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.5 - Network accessline 457
[0.1.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.3 - Network accessline 458
[0.1.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.2 - Network accessline 459
[0.1.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.1 - Network accessline 460
[0.1.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.0
skills/biomcp-server/repo/Dockerfile
- Network accessline 1
# Generated by https://smithery.ai. See: https://smithery.ai/docs/config#dockerfile - Executable scriptline 1
Executable file - Dangerous shell operationline 8
RUN apt-get update && apt-get install -y --no-install-recommends gcc build-essential git && rm -rf /var/lib/apt/lists/* - Dangerous shell operationline 25
RUN git clone https://github.com/google-deepmind/alphagenome.git /tmp/alphagenome && pip install /tmp/alphagenome && rm -rf /tmp/alphagenome - Network accessline 25
RUN git clone https://github.com/google-deepmind/alphagenome.git /tmp/alphagenome && \ - Dangerous shell operationline 27
rm -rf /tmp/alphagenome
skills/biomcp-server/repo/Makefile
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/README.md
- Network accessline 22
[](https://www.youtube.com/watch?v=bKxOWrWUUhM) - Network accessline 26
BioMCP is certified by [MCPHub](https://mcphub.com/mcp-servers/genomoncology/biomcp). This certification ensures that BioMCP follows best practices for Model Context Protocol implementation and provides reliable biomedical data access. - Network accessline 167
# Fetch article details (supports both PMID and DOI) fetch(domain="article", id="34567890") # PMID - Network accessline 168
fetch(domain="article", id="34567890") # PMID - Network accessline 169
fetch(domain="article", id="10.1101/2024.01.20.23288905") # DOI - Network accessline 171
# Fetch trial with all sections fetch(domain="trial", id="NCT04280705", detail="all") - Network accessline 172
fetch(domain="trial", id="NCT04280705", detail="all") - Network accessline 174
# Fetch variant details fetch(domain="variant", id="rs113488022") - Network accessline 175
fetch(domain="variant", id="rs113488022") - Network accessline 274
[Credential-related source omitted] - Access to secretsline 275
[Credential-related source omitted] - Network accessline 276
export CBIO_BASE_URL="https://www.cbioportal.org/api" # Custom API endpoint - Access to secretsline 281
[Credential-related source omitted] - Network accessline 313
biomcp run --mode worker # Server available at http://localhost:8000/sse - Network accessline 314
# Server available at http://localhost:8000/sse - Network accessline 417
Learn more: [GenomOncology](https://genomoncology.com/) - Network accessline 421
[](https://smithery.ai/server/@genomoncology/biomcp) - Network accessline 423
<a href="https://glama.ai/mcp/servers/@genomoncology/biomcp"> - Network accessline 424
<img width="380" height="200" src="https://glama.ai/mcp/servers/@genomoncology/biomcp/badge" /> - Network accessline 467
For comprehensive documentation, visit [https://biomcp.org](https://biomcp.org) - Network accessline 500
Check out the companion repository: 👉 **[biomcp-examples](https://github.com/genomoncology/biomcp-examples)** - Network accessline 501
👉 **[biomcp-examples](https://github.com/genomoncology/biomcp-examples)**
skills/biomcp-server/repo/THIRD_PARTY_ENDPOINTS.md
- Network accessline 28
- **URL**: `https://api.biorxiv.org/details/biorxiv` - Network accessline 36
- **URL**: `https://www.ebi.ac.uk/europepmc/webservices/rest/search` - Network accessline 44
- **URL**: `https://api.biorxiv.org/details/medrxiv` - Network accessline 52
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/` - Network accessline 60
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson` - Network accessline 68
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/` - Network accessline 78
- **URL**: `https://clinicaltrials.gov/api/v2/studies` - Network accessline 86
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers` - Access to secretsline 90
[Credential-related source omitted] - Network accessline 95
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/diseases` - Access to secretsline 99
[Credential-related source omitted] - Network accessline 104
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/interventions` - Access to secretsline 108
[Credential-related source omitted] - Network accessline 113
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/organizations` - Access to secretsline 117
[Credential-related source omitted] - Network accessline 122
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/trials` - Access to secretsline 126
[Credential-related source omitted] - Network accessline 133
- **URL**: `https://rest.ensembl.org/variation/human` - Network accessline 141
- **URL**: `https://api.gdc.cancer.gov/ssm_occurrences` - Network accessline 149
- **URL**: `https://api.gdc.cancer.gov/ssms` - Network accessline 157
- **URL**: `https://mychem.info/v1/chem` - Network accessline 165
- **URL**: `https://mychem.info/v1/query` - Network accessline 173
- **URL**: `https://mydisease.info/v1/disease` - Network accessline 181
- **URL**: `https://mydisease.info/v1/query` - Network accessline 189
- **URL**: `https://mygene.info/v3/gene` - Network accessline 197
- **URL**: `https://mygene.info/v3/query` - Network accessline 205
- **URL**: `https://myvariant.info/v1/query` - Network accessline 213
- **URL**: `https://myvariant.info/v1/variant` - Network accessline 223
- **URL**: `https://www.cbioportal.org/api` - Network accessline 232
- **URL**: `https://www.cbioportal.org/api/cancer-types` - Network accessline 240
- **URL**: `https://www.cbioportal.org/api/genes` - Network accessline 248
- **URL**: `https://www.cbioportal.org/api/molecular-profiles` - Network accessline 256
- **URL**: `https://www.cbioportal.org/api/mutations` - Network accessline 264
- **URL**: `https://www.cbioportal.org/api/studies` - Network accessline 272
- **URL**: `https://demo.oncokb.org/api/v1/utils/allCuratedGenes` - Network accessline 281
- **URL**: `https://demo.oncokb.org/api/v1/genes/{gene}` - Network accessline 290
- **URL**: `https://demo.oncokb.org/api/v1/annotate/mutations/byProteinChange` - Network accessline 301
- **URL**: `https://www.fda.gov/media/169066/download` - Network accessline 310
- **URL**: `https://api.fda.gov/device/event.json` - Access to secretsline 314
[Credential-related source omitted] - Network accessline 319
- **URL**: `https://api.fda.gov/drug/enforcement.json` - Access to secretsline 323
[Credential-related source omitted] - Network accessline 328
- **URL**: `https://api.fda.gov/drug/event.json` - Access to secretsline 332
[Credential-related source omitted] - Network accessline 337
- **URL**: `https://api.fda.gov/drug/label.json` - Access to secretsline 341
[Credential-related source omitted] - Network accessline 346
- **URL**: `https://api.fda.gov/drug/drugsfda.json` - Access to secretsline 350
[Credential-related source omitted]
skills/biomcp-server/repo/docker-compose.yml
- Access to secretsline 11
[Credential-related source omitted]
skills/biomcp-server/repo/docs/FDA_SECURITY.md
skills/biomcp-server/repo/docs/apis/error-codes.md
- Network accessline 343
"message": "NCI API key required for this operation", "details": { "get_key_url": "https://api.cancer.gov", - Network accessline 344
"details": { "get_key_url": "https://api.cancer.gov", "feature": "biomarker_search" - Network accessline 345
"get_key_url": "https://api.cancer.gov", - Access to secretsline 356
[Credential-related source omitted] - Access to secretsline 362
[Credential-related source omitted] - Network accessline 402
1. Check [FAQ](../faq-condensed.md) for common issues 2. Search [GitHub Issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 403
2. Search [GitHub Issues](https://github.com/genomoncology/biomcp/issues)
skills/biomcp-server/repo/docs/apis/overview.md
skills/biomcp-server/repo/docs/apis/python-sdk.md
skills/biomcp-server/repo/docs/backend-services-reference/01-overview.md
- Network accessline 208
- **PubTator3**: [Support Forum](https://www.ncbi.nlm.nih.gov/research/pubtator3/) - Network accessline 209
- **ClinicalTrials.gov**: [Help Desk](https://clinicaltrials.gov/help) - Network accessline 210
- **BioThings**: [Documentation](https://docs.biothings.io/) - Network accessline 211
- **cBioPortal**: [User Guide](https://docs.cbioportal.org/) - Network accessline 212
- **NCI**: [API Support](https://api.cancer.gov/support)
skills/biomcp-server/repo/docs/backend-services-reference/02-biothings-suite.md
- Network accessline 45
`https://mygene.info/v1/` - Network accessline 65
curl "https://mygene.info/v1/query?q=BRAF&fields=symbol,name,summary,type_of_gene" - Network accessline 83
curl "https://mygene.info/v1/gene/673?fields=symbol,name,summary,genomic_pos,pathway,go" - Network accessline 102
`https://myvariant.info/v1/` - Network accessline 121
curl "https://myvariant.info/v1/query?q=dbnsfp.genename:TP53&fields=_id,clinvar,gnomad_exome" - Network accessline 162
`https://mydisease.info/v1/` - Network accessline 175
curl "https://mydisease.info/v1/query?q=melanoma&fields=mondo,disease_ontology,synonyms" - Network accessline 204
`https://mychem.info/v1/` - Network accessline 217
curl "https://mychem.info/v1/query?q=imatinib&fields=drugbank,chembl,chebi" - Network accessline 247
# Step 1: Get gene info gene_response = requests.get( - Network accessline 248
gene_response = requests.get( - Network accessline 249
"https://mygene.info/v1/gene/BRAF", - Network accessline 253
# Step 2: Find variants in gene variant_response = requests.get( - Network accessline 254
variant_response = requests.get( - Network accessline 255
"https://myvariant.info/v1/query", - Network accessline 267
# Get all synonyms for a disease disease_response = requests.get( - Network accessline 268
disease_response = requests.get( - Network accessline 269
"https://mydisease.info/v1/query", - Network accessline 286
# Find drugs targeting a gene drug_response = requests.get( - Network accessline 287
drug_response = requests.get( - Network accessline 288
"https://mychem.info/v1/query", - Network accessline 320
# Good - single request for multiple genes response = requests.post( - Network accessline 321
response = requests.post( - Network accessline 322
"https://mygene.info/v1/gene", - Network accessline 326
# Bad - multiple individual requests for gene in ["BRAF", "KRAS", "EGFR"]: requests.get(f"https://mygene.info/v1/gene/{gene}") - Network accessline 328
requests.get(f"https://mygene.info/v1/gene/{gene}") - Network accessline 375
def query_biothings(api_url, query_params): try: response = requests.get(api_url, params=query_params) - Network accessline 376
try: response = requests.get(api_url, params=query_params) response.raise_for_status() - Network accessline 377
response = requests.get(api_url, params=query_params) - Network accessline 486
def normalize_gene_symbol(symbol): # Query MyGene to get official symbol response = requests.get( - Network accessline 487
# Query MyGene to get official symbol response = requests.get( f"https://mygene.info/v1/query?q={symbol}" - Network accessline 488
response = requests.get( - Network accessline 489
f"https://mygene.info/v1/query?q={symbol}"
skills/biomcp-server/repo/docs/backend-services-reference/03-cbioportal.md
skills/biomcp-server/repo/docs/backend-services-reference/04-clinicaltrials-gov.md
- Network accessline 20
The [ClinicalTrials.gov](https://clinicaltrials.gov/) API provides programmatic - Network accessline 31
**Endpoint:** `https://clinicaltrials.gov/api/v2/studies` - Network accessline 60
curl -X GET "https://clinicaltrials.gov/api/v2/studies?query.cond=Melanoma&query.intr=BRAF" - Network accessline 65
**Endpoint:** `https://clinicaltrials.gov/api/v2/studies/{NCT_ID}` - Network accessline 72
curl -X GET "https://clinicaltrials.gov/api/v2/studies/NCT04267848" - Network accessline 146
For complete API documentation, visit the [ClinicalTrials.gov API Documentation](https://clinicaltrials.gov/data-api/about-api) - Network accessline 147
the [ClinicalTrials.gov API Documentation](https://clinicaltrials.gov/data-api/about-api)
skills/biomcp-server/repo/docs/backend-services-reference/05-nci-cts-api.md
- Network accessline 28
**Base URL:** `https://clinicaltrialsapi.cancer.gov/api/v2/` - Network accessline 36
1. Visit [https://clinicaltrialsapi.cancer.gov/](https://clinicaltrialsapi.cancer.gov/) - Access to secretsline 52
[Credential-related source omitted] - Network accessline 90
curl -X GET "https://clinicaltrialsapi.cancer.gov/api/v2/trials" \ - Network accessline 133
curl -X GET "https://clinicaltrialsapi.cancer.gov/api/v2/trials/NCT04280705" \ - Network accessline 158
curl -X GET "https://clinicaltrialsapi.cancer.gov/api/v2/organizations" \ - Network accessline 189
curl -X GET "https://clinicaltrialsapi.cancer.gov/api/v2/interventions" \ - Network accessline 243
response = requests.get( - Network accessline 244
"https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Access to secretsline 245
[Credential-related source omitted] - Network accessline 273
orgs = requests.get( - Network accessline 274
"https://clinicaltrialsapi.cancer.gov/api/v2/organizations", - Access to secretsline 275
[Credential-related source omitted] - Network accessline 279
# Get trials at each center for org in orgs.json()["organizations"]: trials = requests.get( - Network accessline 280
for org in orgs.json()["organizations"]: trials = requests.get( f"https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Network accessline 281
trials = requests.get( - Network accessline 282
f"https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Access to secretsline 283
[Credential-related source omitted] - Network accessline 439
# 1. Search biomarkers biomarkers = requests.get( - Network accessline 440
biomarkers = requests.get( - Network accessline 441
"https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers", - Access to secretsline 442
[Credential-related source omitted] - Network accessline 447
all_trials = [] for biomarker in biomarkers.get("biomarkers", []): trials = requests.get( - Network accessline 448
for biomarker in biomarkers.get("biomarkers", []): trials = requests.get( "https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Network accessline 449
trials = requests.get( - Network accessline 450
"https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Access to secretsline 451
[Credential-related source omitted] - Network accessline 463
- **API Documentation**: [https://clinicaltrialsapi.cancer.gov/](https://clinicaltrialsapi.cancer.gov/) - Network accessline 464
- **Support Email**: NCICTSApiSupport@mail.nih.gov - **Status Page**: [https://status.cancer.gov/](https://status.cancer.gov/) - **Terms of Use**: [https://clinicaltrialsapi.cancer.gov/terms](https://clinicaltrialsapi.cancer.gov/terms) - Network accessline 465
- **Status Page**: [https://status.cancer.gov/](https://status.cancer.gov/) - Network accessline 466
- **Terms of Use**: [https://clinicaltrialsapi.cancer.gov/terms](https://clinicaltrialsapi.cancer.gov/terms)
skills/biomcp-server/repo/docs/backend-services-reference/06-pubtator3.md
- Network accessline 47
**Endpoint:** `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/` - Network accessline 48
`https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/` - Network accessline 64
curl "https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/?query=BRAF&concept=GENE&limit=2" - Network accessline 90
**Endpoint:** `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/` - Network accessline 104
curl "https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/?text=@CHEMICAL_remdesivir" - Network accessline 130
**Endpoint:** `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson` - Network accessline 131
`https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson` - Network accessline 146
curl "https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson?pmids=29355051&full=true" - Network accessline 222
For complete API documentation, visit the [PubTator3 API Documentation](https://www.ncbi.nlm.nih.gov/research/pubtator3/api). - Network accessline 223
the [PubTator3 API Documentation](https://www.ncbi.nlm.nih.gov/research/pubtator3/api).
skills/biomcp-server/repo/docs/backend-services-reference/07-alphagenome.md
- Network accessline 39
1. Visit [https://deepmind.google.com/science/alphagenome](https://deepmind.google.com/science/alphagenome) - Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Network accessline 69
# Clone and install git clone https://github.com/google-deepmind/alphagenome.git - Network accessline 70
git clone https://github.com/google-deepmind/alphagenome.git - Access to secretsline 95
[Credential-related source omitted] - Network accessline 476
- **Documentation**: [AlphaGenome GitHub](https://github.com/google-deepmind/alphagenome) - Network accessline 477
- **Paper**: [Nature Publication](https://www.nature.com/alphagenome)
skills/biomcp-server/repo/docs/blog/ai-assisted-clinical-trial-search-analysis.md
- Network accessline 21
Video Link: [](https://www.youtube.com/watch?v=jqGXXnVesjg&list=PLu1amIF_MEfPWhhEsXSuBi90S_xtmVJIW&index=2) - Network accessline 22
[](https://www.youtube.com/watch?v=jqGXXnVesjg&list=PLu1amIF_MEfPWhhEsXSuBi90S_xtmVJIW&index=2)
skills/biomcp-server/repo/docs/blog/researcher-persona-resource.md
- Network accessline 57
[](https://youtu.be/tBGG53O-7Hg) - Network accessline 83
[](https://github.com/genomoncology/biomcp/blob/main/src/biomcp/resources/researcher.md) - Network accessline 100
[](https://github.com/genomoncology/biomcp-examples#researcher-announcement) - Network accessline 119
We've documented this comparison in detail in the [biomcp-examples repository](https://github.com/genomoncology/biomcp-examples), - Network accessline 120
the [biomcp-examples repository](https://github.com/genomoncology/biomcp-examples), - Network accessline 154
1. Try the Researcher Persona with your own research questions 2. Contribute to the [biomcp-examples repository](https://github.com/genomoncology/biomcp-examples) - Network accessline 155
2. Contribute to the [biomcp-examples repository](https://github.com/genomoncology/biomcp-examples) with your experiments - Network accessline 156
the [biomcp-examples repository](https://github.com/genomoncology/biomcp-examples)
skills/biomcp-server/repo/docs/changelog.md
- Network accessline 18
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Network accessline 19
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). - Access to secretsline 27
[Credential-related source omitted] - Network accessline 71
- Created API parameter reference: `docs/api-changes/nci-api-parameters.md` - Updated CLAUDE.md with NCI usage instructions and parameter notes - Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Network accessline 73
- Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Network accessline 101
- **Docker deployments**: Ensure you're using `--host 0.0.0.0` for proper container networking - **Cloudflare Workers**: The worker now automatically handles both transport types on `/mcp` - See the new [Transport Protocol Guide](https://bi - Network accessline 103
- See the new [Transport Protocol Guide](https://biomcp.org/transport-protocol/) for detailed migration instructions - Network accessline 116
- Integrated into unified search syntax: `search(domain="gene", keywords=["BRAF"])` - Query language support: `gene:BRAF`, `drug:pembrolizumab`, `disease:melanoma` - Full fetch support: `fetch(domain="drug", id="DB00945")` - Network accessline 117
- Query language support: `gene:BRAF`, `drug:pembrolizumab`, `disease:melanoma` - Full fetch support: `fetch(domain="drug", id="DB00945")` - **Clinical Trial Enhancement**: - Network accessline 118
- Full fetch support: `fetch(domain="drug", id="DB00945")` - Network accessline 376
[Unreleased]: https://github.com/genomoncology/biomcp/compare/v0.6.2...HEAD - Network accessline 377
[0.6.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.2 - Network accessline 378
[0.6.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.6.0 - Network accessline 379
[0.5.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.5.0 - Network accessline 380
[0.4.6]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.6 - Network accessline 381
[0.4.5]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.5 - Network accessline 382
[0.4.4]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.4 - Network accessline 383
[0.4.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.3 - Network accessline 384
[0.4.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.2 - Network accessline 385
[0.4.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.1 - Network accessline 386
[0.4.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.4.0 - Network accessline 387
[0.3.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.3 - Network accessline 388
[0.3.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.2 - Network accessline 389
[0.3.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.1 - Network accessline 390
[0.3.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.3.0 - Network accessline 391
[0.2.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.2.1 - Network accessline 392
[0.2.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.2.0 - Network accessline 393
[0.1.11]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.11 - Network accessline 394
[0.1.10]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.10 - Network accessline 395
[0.1.9]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.9 - Network accessline 396
[0.1.8]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.8 - Network accessline 397
[0.1.7]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.7 - Network accessline 398
[0.1.6]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.6 - Network accessline 399
[0.1.5]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.5 - Network accessline 400
[0.1.3]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.3 - Network accessline 401
[0.1.2]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.2 - Network accessline 402
[0.1.1]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.1 - Network accessline 403
[0.1.0]: https://github.com/genomoncology/biomcp/releases/tag/v0.1.0
skills/biomcp-server/repo/docs/concepts/01-what-is-biomcp.md
- Network accessline 18
[](https://www.youtube.com/watch?v=bKxOWrWUUhM)
skills/biomcp-server/repo/docs/developer-guides/01-server-deployment.md
- Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 77
[Credential-related source omitted] - Access to secretsline 80
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted] - Access to secretsline 102
[Credential-related source omitted] - Dangerous shell operationline 114
sudo systemctl enable biomcp - Dangerous shell operationline 115
sudo systemctl start biomcp - Network accessline 128
location /mcp { proxy_pass http://localhost:8000; - Network accessline 129
proxy_pass http://localhost:8000; - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Network accessline 174
# Install AlphaGenome RUN git clone https://github.com/google-deepmind/alphagenome.git && \ - Network accessline 175
RUN git clone https://github.com/google-deepmind/alphagenome.git && \ - Access to secretsline 201
[Credential-related source omitted] - Access to secretsline 202
[Credential-related source omitted] - Network accessline 205
restart: unless-stopped healthcheck: test: ["CMD", "curl", "-f", "http://localhost:8000/health"] - Network accessline 206
healthcheck: test: ["CMD", "curl", "-f", "http://localhost:8000/health"] interval: 30s - Network accessline 207
test: ["CMD", "curl", "-f", "http://localhost:8000/health"] - Network accessline 257
[vars] REMOTE_MCP_SERVER_URL = "https://your-biomcp-server.com/mcp" - Network accessline 258
REMOTE_MCP_SERVER_URL = "https://your-biomcp-server.com/mcp" - Access to secretsline 259
[Credential-related source omitted] - Network accessline 298
"transport": { "type": "sse", "url": "https://your-worker.workers.dev" - Network accessline 299
"type": "sse", "url": "https://your-worker.workers.dev" }, - Network accessline 300
"url": "https://your-worker.workers.dev" - Network accessline 303
"type": "oauth", "client_id": "mcp-client", "authorization_endpoint": "https://your-worker.workers.dev/authorize", - Network accessline 304
"client_id": "mcp-client", "authorization_endpoint": "https://your-worker.workers.dev/authorize", "token_endpoint": "https://your-worker.workers.dev/token", - Network accessline 305
"authorization_endpoint": "https://your-worker.workers.dev/authorize", - Network accessline 306
"token_endpoint": "https://your-worker.workers.dev/token", - Access to secretsline 322
[Credential-related source omitted] - Network accessline 455
client = httpx.AsyncClient( - Network accessline 456
limits=httpx.Limits(max_keepalive_connections=20), - Network accessline 457
timeout=httpx.Timeout(30.0) - Network accessline 497
"mcpServers": { "biomcp": { "url": "http://localhost:8000/mcp" - Network accessline 498
"biomcp": { "url": "http://localhost:8000/mcp" } - Network accessline 499
"url": "http://localhost:8000/mcp" - Network accessline 512
"transport": { "type": "http", "url": "https://biomcp.example.com/mcp" - Network accessline 513
"type": "http", "url": "https://biomcp.example.com/mcp" } - Network accessline 514
"url": "https://biomcp.example.com/mcp" - Network accessline 539
[Credential-related source omitted] - Network accessline 540
[Credential-related source omitted] - Access to secretsline 540
[Credential-related source omitted]
skills/biomcp-server/repo/docs/developer-guides/02-contributing-and-testing.md
- Network accessline 22
- Python 3.10 or higher - [uv](https://docs.astral.sh/uv/) package manager - Network accessline 23
- [uv](https://docs.astral.sh/uv/) package manager - Network accessline 32
git clone https://github.com/YOUR_USERNAME/biomcp.git - Network accessline 550
- PubMed: https://www.ncbi.nlm.nih.gov/home/about/website-updates/ - Network accessline 551
- ClinicalTrials.gov: https://clinicaltrials.gov/about/announcements - Network accessline 552
- cBioPortal: https://www.cbioportal.org/ - Access to secretsline 568
[Credential-related source omitted] - Access to secretsline 569
[Credential-related source omitted] - Network accessline 715
- [MCP Documentation](https://modelcontextprotocol.org) - Network accessline 716
- [pytest Documentation](https://docs.pytest.org) - Network accessline 717
- [Type Hints Guide](https://mypy.readthedocs.io) - Network accessline 718
- [Ruff Documentation](https://docs.astral.sh/ruff)
skills/biomcp-server/repo/docs/developer-guides/03-third-party-endpoints.md
- Network accessline 28
- **URL**: `https://api.biorxiv.org/details/biorxiv` - Network accessline 36
- **URL**: `https://www.ebi.ac.uk/europepmc/webservices/rest/search` - Network accessline 44
- **URL**: `https://api.biorxiv.org/details/medrxiv` - Network accessline 52
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/` - Network accessline 60
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson` - Network accessline 68
- **URL**: `https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/` - Network accessline 78
- **URL**: `https://clinicaltrials.gov/api/v2/studies` - Network accessline 86
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers` - Access to secretsline 90
[Credential-related source omitted] - Network accessline 95
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/diseases` - Access to secretsline 99
[Credential-related source omitted] - Network accessline 104
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/interventions` - Access to secretsline 108
[Credential-related source omitted] - Network accessline 113
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/organizations` - Access to secretsline 117
[Credential-related source omitted] - Network accessline 122
- **URL**: `https://clinicaltrialsapi.cancer.gov/api/v2/trials` - Access to secretsline 126
[Credential-related source omitted] - Network accessline 133
- **URL**: `https://rest.ensembl.org/variation/human` - Network accessline 141
- **URL**: `https://api.gdc.cancer.gov/ssm_occurrences` - Network accessline 149
- **URL**: `https://api.gdc.cancer.gov/ssms` - Network accessline 157
- **URL**: `https://mychem.info/v1/chem` - Network accessline 165
- **URL**: `https://mychem.info/v1/query` - Network accessline 173
- **URL**: `https://mydisease.info/v1/disease` - Network accessline 181
- **URL**: `https://mydisease.info/v1/query` - Network accessline 189
- **URL**: `https://mygene.info/v3/gene` - Network accessline 197
- **URL**: `https://mygene.info/v3/query` - Network accessline 205
- **URL**: `https://myvariant.info/v1/query` - Network accessline 213
- **URL**: `https://myvariant.info/v1/variant` - Network accessline 223
- **URL**: `https://www.cbioportal.org/api` - Network accessline 232
- **URL**: `https://www.cbioportal.org/api/cancer-types` - Network accessline 240
- **URL**: `https://www.cbioportal.org/api/genes` - Network accessline 248
- **URL**: `https://www.cbioportal.org/api/molecular-profiles` - Network accessline 256
- **URL**: `https://www.cbioportal.org/api/mutations` - Network accessline 264
- **URL**: `https://www.cbioportal.org/api/studies` - Network accessline 274
- **URL**: `https://www.fda.gov/media/169066/download` - Network accessline 283
- **URL**: `https://api.fda.gov/device/event.json` - Access to secretsline 287
[Credential-related source omitted] - Network accessline 292
- **URL**: `https://api.fda.gov/drug/enforcement.json` - Access to secretsline 296
[Credential-related source omitted] - Network accessline 301
- **URL**: `https://api.fda.gov/drug/event.json` - Access to secretsline 305
[Credential-related source omitted] - Network accessline 310
- **URL**: `https://api.fda.gov/drug/label.json` - Access to secretsline 314
[Credential-related source omitted] - Network accessline 319
- **URL**: `https://api.fda.gov/drug/drugsfda.json` - Access to secretsline 323
[Credential-related source omitted]
skills/biomcp-server/repo/docs/developer-guides/04-transport-protocol.md
- Network accessline 260
location /mcp { limit_req zone=mcp burst=20; proxy_pass http://biomcp:8000; - Network accessline 261
limit_req zone=mcp burst=20; proxy_pass http://biomcp:8000; } - Network accessline 262
proxy_pass http://biomcp:8000; - Network accessline 279
# Check server health curl http://localhost:8000/health - Network accessline 280
curl http://localhost:8000/health - Network accessline 297
- Review [MCP Specification](https://spec.modelcontextprotocol.io) for protocol details - Network accessline 299
For questions or issues, please visit our [GitHub repository](https://github.com/genomoncology/biomcp).
skills/biomcp-server/repo/docs/developer-guides/05-error-handling.md
- Access to secretsline 165
[Credential-related source omitted]
skills/biomcp-server/repo/docs/developer-guides/06-http-client-and-caching.md
- Network accessline 34
async def fetch_gene(gene: str): async with httpx.AsyncClient() as client: - Network accessline 35
async with httpx.AsyncClient() as client: - Network accessline 36
response = await client.get(f"https://api.example.com/genes/{gene}") - Network accessline 46
async def fetch_gene(gene: str): data, error = await http_client.request_api( url=f"https://api.example.com/genes/{gene}", - Network accessline 47
data, error = await http_client.request_api( url=f"https://api.example.com/genes/{gene}", request={}, - Network accessline 48
url=f"https://api.example.com/genes/{gene}", - Network accessline 92
def __init__(self): self.base_url = "https://api.example.com" - Network accessline 93
self.base_url = "https://api.example.com" - Network accessline 179
# Configure in http_client_simple.py limits = httpx.Limits( - Network accessline 180
limits = httpx.Limits( - Network accessline 245
"my_api_endpoint", EndpointInfo( url="https://api.example.com/v1/data", - Network accessline 246
EndpointInfo( url="https://api.example.com/v1/data", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 247
url="https://api.example.com/v1/data",
skills/biomcp-server/repo/docs/developer-guides/generate_endpoints.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/docs/faq-condensed.md
- Network accessline 32
**Q: No results for gene search** A: Use official symbols (ERBB2 not HER2). Check at [genenames.org](https://www.genenames.org) - Network accessline 33
A: Use official symbols (ERBB2 not HER2). Check at [genenames.org](https://www.genenames.org) - Dangerous shell operationline 69
A: Clear with: `rm -rf ~/.biomcp/cache` - Network accessline 96
1. Check this FAQ 2. Read [Troubleshooting](troubleshooting.md) 3. Search [GitHub Issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 97
2. Read [Troubleshooting](troubleshooting.md) 3. Search [GitHub Issues](https://github.com/genomoncology/biomcp/issues) 4. Ask with version info: `biomcp --version` - Network accessline 98
3. Search [GitHub Issues](https://github.com/genomoncology/biomcp/issues)
skills/biomcp-server/repo/docs/getting-started/01-quickstart-cli.md
- Network accessline 20
- Python 3.10 or higher - [uv](https://docs.astral.sh/uv/) package manager (recommended) or pip - Network accessline 21
- [uv](https://docs.astral.sh/uv/) package manager (recommended) or pip - Network accessline 28
# Install uv if you haven't already curl -LsSf https://astral.sh/uv/install.sh | sh - Dangerous shell operationline 29
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 29
curl -LsSf https://astral.sh/uv/install.sh | sh - Access to secretsline 127
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted]
skills/biomcp-server/repo/docs/getting-started/02-desktop-integration.md
- Network accessline 20
- An MCP-compatible desktop application (e.g., [Claude Desktop](https://claude.ai/download)) - Network accessline 21
- One of the following: - **Option A**: Python 3.10+ and [uv](https://docs.astral.sh/uv/) (recommended) - **Option B**: [Docker](https://www.docker.com/products/docker-desktop/) - Network accessline 22
- **Option A**: Python 3.10+ and [uv](https://docs.astral.sh/uv/) (recommended) - Network accessline 23
- **Option B**: [Docker](https://www.docker.com/products/docker-desktop/) - Network accessline 34
# macOS/Linux curl -LsSf https://astral.sh/uv/install.sh | sh - Dangerous shell operationline 35
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 35
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 37
# Windows powershell -c "irm https://astral.sh/uv/install.ps1 | iex" - Network accessline 38
powershell -c "irm https://astral.sh/uv/install.ps1 | iex" - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 100
[Credential-related source omitted] - Access to secretsline 101
[Credential-related source omitted] - Network accessline 124
- Get your key from [NCI API Portal](https://api.cancer.gov) - Access to secretsline 125
[Credential-related source omitted] - Network accessline 131
- Register at [AlphaGenome Portal](https://alphagenome.google.com) - Access to secretsline 132
[Credential-related source omitted] - Network accessline 138
- Get token from [cBioPortal](https://www.cbioportal.org/webAPI) - Network accessline 250
"BIOMCP_LOG_LEVEL": "DEBUG", "BIOMCP_CACHE_DIR": "/path/to/cache", "HTTP_PROXY": "http://your-proxy:8080" - Network accessline 251
"BIOMCP_CACHE_DIR": "/path/to/cache", "HTTP_PROXY": "http://your-proxy:8080" } - Network accessline 252
"HTTP_PROXY": "http://your-proxy:8080" - Network accessline 295
- **Documentation**: [BioMCP Docs](https://github.com/genomoncology/biomcp) - Network accessline 296
- **Issues**: [GitHub Issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 297
- **Community**: [Discussions](https://github.com/genomoncology/biomcp/discussions)
skills/biomcp-server/repo/docs/getting-started/03-authentication-and-api-keys.md
- Network accessline 20
| Service | Required? | Features Enabled | Get Key | | --------------- | ---------- | ------------------------------------------------- - Network accessline 21
| --------------- | ---------- | ------------------------------------------------- | ---------------------------------------------------------------------- | | **NCI API** | Optional | Advanced clinical trial filters, biomarker search - Network accessline 22
| **NCI API** | Optional | Advanced clinical trial filters, biomarker search | [api.cancer.gov](https://api.cancer.gov) | - Network accessline 23
| **AlphaGenome** | Required\* | Variant effect predictions | [deepmind.google.com](https://deepmind.google.com/science/alphagenome) | - Network accessline 24
| **cBioPortal** | Optional | Enhanced cancer genomics queries | [cbioportal.org](https://www.cbioportal.org/webAPI) | - Network accessline 25
| **OncoKB** | Optional | Clinical actionability for all genes | [oncokb.org](https://www.oncokb.org/licensing) | - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 39
[Credential-related source omitted] - Access to secretsline 40
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 72
[Credential-related source omitted] - Network accessline 96
1. Visit [api.cancer.gov](https://api.cancer.gov) - Access to secretsline 112
[Credential-related source omitted] - Network accessline 125
1. Visit [AlphaGenome Portal](https://deepmind.google.com/science/alphagenome) - Access to secretsline 142
[Credential-related source omitted] - Network accessline 165
1. Create account at [cbioportal.org](https://www.cbioportal.org) - Access to secretsline 183
[Credential-related source omitted] - Network accessline 189
BioMCP integrates with [OncoKB](https://www.oncokb.org/), a precision oncology knowledge base, to provide clinical interpretations of cancer variants. - Network accessline 196
1. Obtain a license from [OncoKB](https://www.oncokb.org/licensing). - Network accessline 197
2. Find your token in your account settings: [www.oncokb.org/account/settings](https://www.oncokb.org/account/settings). - Access to secretsline 204
[Credential-related source omitted] - Access to secretsline 230
[Credential-related source omitted] - Access to secretsline 291
[Credential-related source omitted] - Dangerous shell operationline 316
# Add to shell: eval "$(direnv hook zsh)" - Access to secretsline 319
[Credential-related source omitted] - Access to secretsline 327
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[Credential-related source omitted]
skills/biomcp-server/repo/docs/how-to-guides/01-find-articles-and-cbioportal-data.md
- Network accessline 315
1. **Check gene symbols**: Use [genenames.org](https://www.genenames.org)
skills/biomcp-server/repo/docs/how-to-guides/02-find-trials-with-nci-and-biothings.md
- Network accessline 133
Get your key from [api.cancer.gov](https://api.cancer.gov). For detailed setup instructions, see [Authentication and API Keys](../getting-started/03-authentication-and-api-keys.md#nci-clinical-trials-api): - Access to secretsline 136
[Credential-related source omitted] - Access to secretsline 151
[Credential-related source omitted] - Access to secretsline 166
[Credential-related source omitted] - Access to secretsline 239
[Credential-related source omitted] - Access to secretsline 245
[Credential-related source omitted] - Access to secretsline 313
[Credential-related source omitted]
skills/biomcp-server/repo/docs/how-to-guides/04-predict-variant-effects-with-alphagenome.md
- Network accessline 34
1. Visit [AlphaGenome Portal](https://deepmind.google.com/science/alphagenome) - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 58
[Credential-related source omitted] - Network accessline 66
git clone https://github.com/google-deepmind/alphagenome.git
skills/biomcp-server/repo/docs/how-to-guides/05-logging-and-monitoring-with-bigquery.md
skills/biomcp-server/repo/docs/how-to-guides/06-search-nci-organizations-and-interventions.md
- Network accessline 20
All NCI tools require an API key from [api.cancer.gov](https://api.cancer.gov): - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 53
[Credential-related source omitted] - Access to secretsline 69
[Credential-related source omitted] - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 81
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[Credential-related source omitted] - Access to secretsline 126
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 179
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[Credential-related source omitted] - Access to secretsline 458
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[Credential-related source omitted] - Access to secretsline 539
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skills/biomcp-server/repo/docs/index.md
- Network accessline 16
[](https://github.com/genomoncology/biomcp/tags) - Network accessline 17
[](https://github.com/genomoncology/biomcp/actions/workflows/ci.yml?query=branch%3Amain) - Network accessline 18
[](https://img.shields.io/github/license/genomoncology/biomcp) - Network accessline 22
### Built and Maintained by <a href="https://www.genomoncology.com"><img src="./assets/logo.png" width=200 valign="middle" /></a> - Network accessline 101
1. **Install Claude Desktop** from [claude.ai/desktop](https://claude.ai/desktop) - Network accessline 257
- **GitHub**: [github.com/genomoncology/biomcp](https://github.com/genomoncology/biomcp) - Network accessline 258
- **Issues**: [Report bugs or request features](https://github.com/genomoncology/biomcp/issues) - Network accessline 259
- **Discussions**: [Ask questions and share tips](https://github.com/genomoncology/biomcp/discussions) - Network accessline 263
BioMCP is licensed under the MIT License. See [LICENSE](https://github.com/genomoncology/biomcp/blob/main/LICENSE) for details.
skills/biomcp-server/repo/docs/policies.md
- Network accessline 101
- **Breach Notification**: Users notified within 72 hours of confirmed breach - **Security Audits**: Annual third-party security assessments - **Vulnerability Reporting**: See our [SECURITY.md](https://github.com/genomoncology/biomcp/blob/m - Network accessline 103
- **Vulnerability Reporting**: See our [SECURITY.md](https://github.com/genomoncology/biomcp/blob/main/docs/biomcp-security.md) - Network accessline 143
We will update this document at `/privacy` with an updated Effective Date. Material changes will be announced by email. Version history maintained at: [github.com/genomoncology/biomcp/blob/main/docs/biomcp-privacy.md](https://github.com/gen - Network accessline 145
Version history maintained at: [github.com/genomoncology/biomcp/blob/main/docs/biomcp-privacy.md](https://github.com/genomoncology/biomcp/blob/main/docs/biomcp-privacy.md) - Network accessline 225
> This document applies to the **hosted Remote MCP service** (the "Service") provided by **GenomOncology LLC**. > > For use of the **open-source code** available at [https://github.com/genomoncology/biomcp](https://github.com/genomoncology/ - Network accessline 227
> For use of the **open-source code** available at [https://github.com/genomoncology/biomcp](https://github.com/genomoncology/biomcp), refer to the repository's LICENSE file (e.g., MIT License). - Network accessline 314
See our [Privacy Policy](https://github.com/genomoncology/biomcp/blob/main/docs/biomcp-privacy.md) for details. - Network accessline 378
We may update these Terms by posting to `/terms`. Material changes will be emailed. Continued use constitutes acceptance. Version history: [github.com/genomoncology/biomcp/blob/main/docs/biomcp-terms.md](https://github.com/genomoncology/bio - Network accessline 380
Version history: [github.com/genomoncology/biomcp/blob/main/docs/biomcp-terms.md](https://github.com/genomoncology/biomcp/blob/main/docs/biomcp-terms.md) - Network accessline 388
- Email: **security@genomoncology.com** - See: [SECURITY.md](https://github.com/genomoncology/biomcp/blob/main/SECURITY.md) - Network accessline 389
- See: [SECURITY.md](https://github.com/genomoncology/biomcp/blob/main/SECURITY.md)
skills/biomcp-server/repo/docs/reference/quick-reference.md
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# Check documentation open https://biomcp.org/ - Network accessline 425
open https://biomcp.org/ - Network accessline 427
# Report issues open https://github.com/genomoncology/biomcp/issues - Network accessline 428
open https://github.com/genomoncology/biomcp/issues
skills/biomcp-server/repo/docs/reference/visual-architecture.md
skills/biomcp-server/repo/docs/robots.txt
skills/biomcp-server/repo/docs/troubleshooting.md
- Network accessline 28
# Or using the official installer curl -LsSf https://astral.sh/uv/install.sh | sh - Dangerous shell operationline 29
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 29
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 38
# Install uv curl -LsSf https://astral.sh/uv/install.sh | sh - Dangerous shell operationline 39
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 39
curl -LsSf https://astral.sh/uv/install.sh | sh - Network accessline 41
# Install Node.js curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash - - Dangerous shell operationline 42
curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash - - Network accessline 42
curl -fsSL https://deb.nodesource.com/setup_lts.x | sudo -E bash - - Dangerous shell operationline 43
sudo apt-get install -y nodejs - Network accessline 49
# Install uv powershell -c "irm https://astral.sh/uv/install.ps1 | iex" - Network accessline 50
powershell -c "irm https://astral.sh/uv/install.ps1 | iex" - Network accessline 52
# Install Node.js from https://nodejs.org - Dangerous shell operationline 102
sudo apt update - Dangerous shell operationline 103
sudo apt install python3.11 - Access to secretsline 118
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"https://cts.nlm.nih.gov/api/v2/trials?size=1" - Dangerous shell operationline 157
sudo apt-get update - Dangerous shell operationline 158
sudo apt-get install ca-certificates - Network accessline 164
# Set proxy environment variables export HTTP_PROXY="http://proxy.company.com:8080" - Network accessline 165
export HTTP_PROXY="http://proxy.company.com:8080" - Network accessline 166
export HTTPS_PROXY="http://proxy.company.com:8080" - Network accessline 169
# Configure pip for proxy pip config set global.proxy http://proxy.company.com:8080 - Network accessline 170
pip config set global.proxy http://proxy.company.com:8080 - Network accessline 337
Open http://127.0.0.1:6274 and verify: - Network accessline 342
**2. Test with curl (HTTP mode):** - Network accessline 348
# Test health endpoint curl http://localhost:8000/health - Network accessline 349
curl http://localhost:8000/health - Network accessline 351
# Test MCP endpoint curl -X POST http://localhost:8000/mcp \ - Network accessline 352
curl -X POST http://localhost:8000/mcp \ - Dangerous shell operationline 391
- Clear cache: `rm -rf ~/.biomcp/cache` - Dangerous shell operationline 409
rm -rf ~/.biomcp/cache - Network accessline 479
Report at: https://github.com/genomoncology/biomcp/issues - Network accessline 485
1. **Check FAQ first**: [Frequently Asked Questions](faq-condensed.md) 2. **Search existing issues**: [GitHub Issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 486
2. **Search existing issues**: [GitHub Issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 500
_Still having issues? [Open a GitHub issue](https://github.com/genomoncology/biomcp/issues/new) with details._
skills/biomcp-server/repo/docs/tutorials/alphagenome-variant-analysis.md
- Network accessline 20
- **AI Assistant**: Any assistant with MCP support (e.g., Claude, Gemini, etc.) - **Python 3.11+**: Required for BioMCP and AlphaGenome - **uv**: Modern Python package manager ([installation guide](https://docs.astral.sh/uv/getting-started/ - Network accessline 21
- **Python 3.11+**: Required for BioMCP and AlphaGenome - **uv**: Modern Python package manager ([installation guide](https://docs.astral.sh/uv/getting-started/installation/)) - **AlphaGenome API Key**: Get free access at [Google DeepMind A - Network accessline 22
- **uv**: Modern Python package manager ([installation guide](https://docs.astral.sh/uv/getting-started/installation/)) - Network accessline 23
- **AlphaGenome API Key**: Get free access at [Google DeepMind AlphaGenome](https://deepmind.google.com/science/alphagenome) - Access to secretsline 51
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# Clone and install AlphaGenome git clone https://github.com/google-deepmind/alphagenome.git - Network accessline 72
git clone https://github.com/google-deepmind/alphagenome.git - Access to secretsline 124
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- [BioMCP Documentation](https://biomcp.org) - Network accessline 258
- [AlphaGenome Paper](https://deepmind.google/science/alphagenome) - Network accessline 259
- [Model Context Protocol Guide](https://modelcontextprotocol.io/) - Network accessline 260
- [uv Documentation](https://docs.astral.sh/uv/)
skills/biomcp-server/repo/docs/tutorials/biothings-prompts.md
skills/biomcp-server/repo/docs/tutorials/nci-prompts.md
- Network accessline 25
These tools require an NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 34
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skills/biomcp-server/repo/docs/tutorials/openfda-integration.md
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> **Note**: An API key is optional but recommended. Without one, you're limited to 40 requests/minute. With a key, you get 240 requests/minute. [Get a free API key here](https://open.fda.gov/apis/authentication/). - Network accessline 303
- OpenFDA documentation: https://open.fda.gov/apis/ - Network accessline 304
- OpenFDA status: https://api.fda.gov/status - Network accessline 305
- BioMCP issues: https://github.com/genomoncology/biomcp/issues - Access to secretsline 311
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skills/biomcp-server/repo/docs/tutorials/openfda-prompts.md
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The OpenFDA API has rate limits: 40 requests/minute without a key, or 240 requests/minute with a key. You can get a free API key at https://open.fda.gov/apis/authentication/ - Access to secretsline 367
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- FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/ - Network accessline 488
- ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages
skills/biomcp-server/repo/docs/tutorials/pydantic-ai-integration.md
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async def main(): # Connect to the /mcp endpoint server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 81
server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Access to secretsline 85
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async def call_biomcp_jsonrpc(method, params=None): """Direct JSON-RPC calls to BioMCP""" async with httpx.AsyncClient() as client: - Network accessline 122
"""Direct JSON-RPC calls to BioMCP""" async with httpx.AsyncClient() as client: response = await client.post( - Network accessline 123
async with httpx.AsyncClient() as client: - Network accessline 124
response = await client.post( "http://localhost:8000/", json={ - Network accessline 125
"http://localhost:8000/", - Network accessline 177
# Old (deprecated) # from pydantic_ai.mcp import MCPServerSSE # server = MCPServerSSE("http://localhost:8000/sse") - Network accessline 179
# server = MCPServerSSE("http://localhost:8000/sse") - Network accessline 181
# New (recommended) from pydantic_ai.mcp import MCPServerStreamableHTTP server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 183
server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 239
async def test_streamable_http_connection(): # Connect to the running server's /mcp endpoint server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 241
server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Access to secretsline 322
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async def main(): # Server configuration SERVER_URL = "http://localhost:8000/mcp" # Adjust port as needed - Network accessline 335
SERVER_URL = "http://localhost:8000/mcp" # Adjust port as needed - Access to secretsline 338
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[Credential-related source omitted] - Network accessline 480
# Old code (deprecated) from pydantic_ai.mcp import MCPServerSSE server = MCPServerSSE("http://localhost:8000/sse") - Network accessline 482
server = MCPServerSSE("http://localhost:8000/sse") - Network accessline 484
# New code (recommended) from pydantic_ai.mcp import MCPServerStreamableHTTP server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 486
server = MCPServerStreamableHTTP("http://localhost:8000/mcp") - Network accessline 517
1. Verify your BioMCP version: `biomcp --version` 2. Check server logs for error messages 3. Open an issue on [GitHub](https://github.com/genomoncology/biomcp/issues) with: - Network accessline 518
2. Check server logs for error messages 3. Open an issue on [GitHub](https://github.com/genomoncology/biomcp/issues) with: - Your BioMCP version - Network accessline 519
3. Open an issue on [GitHub](https://github.com/genomoncology/biomcp/issues) with:
skills/biomcp-server/repo/docs/tutorials/remote-connection.md
- Network accessline 20
The remote BioMCP server (https://remote.biomcp.org/mcp) provides cloud-hosted access to all BioMCP tools. This eliminates the need for local installation while maintaining full functionality. - Network accessline 39
- **Name**: BioMCP - **URL**: `https://remote.biomcp.org/mcp` - Network accessline 40
- **URL**: `https://remote.biomcp.org/mcp` - Network accessline 90
- Ensure you entered the URL exactly as shown: `https://remote.biomcp.org/mcp` - Network accessline 119
- GitHub Issues: [https://github.com/genomoncology/biomcp/issues](https://github.com/genomoncology/biomcp/issues) - Network accessline 120
- Documentation: [https://biomcp.org](https://biomcp.org)
skills/biomcp-server/repo/docs/user-guides/01-command-line-interface.md
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skills/biomcp-server/repo/docs/user-guides/02-mcp-tools-reference.md
- Access to secretsline 57
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fetch( - Access to secretsline 97
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# Fetch article by PMID fetch(id="38768446", domain="article") - Network accessline 115
fetch(id="38768446", domain="article") - Network accessline 117
# Fetch trial with specific details fetch(id="NCT03006926", domain="trial", detail="locations") - Network accessline 118
fetch(id="NCT03006926", domain="trial", detail="locations") - Network accessline 120
# Auto-detect domain fetch(id="rs121913529") # Variant - Network accessline 121
fetch(id="rs121913529") # Variant - Network accessline 122
fetch(id="BRAF") # Gene - Network accessline 124
# Fetch FDA records fetch(id="BLA125514", domain="fda_approval") # Drug approval - Network accessline 125
fetch(id="BLA125514", domain="fda_approval") # Drug approval - Network accessline 126
fetch(id="D-0001-2023", domain="fda_recall") # Drug recall - Access to secretsline 339
[Credential-related source omitted] - Access to secretsline 361
[Credential-related source omitted] - Network accessline 405
All NCI tools require an API key from [api.cancer.gov](https://api.cancer.gov). - Access to secretsline 416
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All OpenFDA tools support optional API keys for higher rate limits (240/min vs 40/min). Get a free key at [open.fda.gov/apis/authentication](https://open.fda.gov/apis/authentication/). - Access to secretsline 480
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# Unified fetch auto-detects domain details = fetch(id="NCT03006926") # Knows it's a trial - Network accessline 673
details = fetch(id="NCT03006926") # Knows it's a trial - Access to secretsline 698
[Credential-related source omitted] - Access to secretsline 705
[Credential-related source omitted]
skills/biomcp-server/repo/docs/user-guides/03-integrating-with-ides-and-clients.md
- Network accessline 34
- [Cursor IDE](https://cursor.sh/) installed - Network accessline 35
- [Smithery](https://smithery.ai/) account and token - Network accessline 567
4. **Invalid gene symbols** - Use official HGNC symbols - Check [genenames.org](https://www.genenames.org) - Network accessline 569
- Check [genenames.org](https://www.genenames.org)
skills/biomcp-server/repo/example_scripts/mcp_integration.py
skills/biomcp-server/repo/example_scripts/python_sdk.py
skills/biomcp-server/repo/glama.json
skills/biomcp-server/repo/mkdocs.yml
- Network accessline 1
site_name: BioMCP repo_url: https://github.com/genomoncology/biomcp - Network accessline 2
repo_url: https://github.com/genomoncology/biomcp - Network accessline 3
site_url: https://biomcp.org/ - Network accessline 6
edit_uri: edit/main/docs/ repo_name: genomoncology/biomcp copyright: Maintained by <a href="https://genomoncology.com">genomoncology</a>. - Network accessline 8
copyright: Maintained by <a href="https://genomoncology.com">genomoncology</a>. - Network accessline 132
social: - icon: fontawesome/brands/github link: https://github.com/genomoncology/biomcp - Network accessline 133
- icon: fontawesome/brands/github link: https://github.com/genomoncology/biomcp - icon: fontawesome/brands/python - Network accessline 134
link: https://github.com/genomoncology/biomcp - Network accessline 135
- icon: fontawesome/brands/python link: https://pypi.org/project/biomcp-python meta: - Network accessline 136
link: https://pypi.org/project/biomcp-python - Network accessline 143
content: AI-powered biomedical research tool integrating PubMed, ClinicalTrials.gov, and genomic databases - property: og:image content: https://biomcp.org/assets/icon.png - Network accessline 144
- property: og:image content: https://biomcp.org/assets/icon.png - property: og:url - Network accessline 145
content: https://biomcp.org/assets/icon.png - Network accessline 146
- property: og:url content: https://biomcp.org/ - name: twitter:card - Network accessline 147
content: https://biomcp.org/
skills/biomcp-server/repo/package-lock.json
- Network accessline 15
"node_modules/@cloudflare/kv-asset-handler": { "version": "0.4.0", "resolved": "https://registry.npmjs.org/@cloudflare/kv-asset-handler/-/kv-asset-handler-0.4.0.tgz", - Network accessline 16
"version": "0.4.0", "resolved": "https://registry.npmjs.org/@cloudflare/kv-asset-handler/-/kv-asset-handler-0.4.0.tgz", "integrity": "sha512-+tv3z+SPp+gqTIcImN9o0hqE9xyfQjI1XD9pL6NuKjua9B1y7mNYv0S9cP+QEbA4ppVgGZEmKOvHX5G5Ei1CVA= - Network accessline 17
"resolved": "https://registry.npmjs.org/@cloudflare/kv-asset-handler/-/kv-asset-handler-0.4.0.tgz", - Network accessline 28
"node_modules/@cloudflare/unenv-preset": { "version": "2.3.1", "resolved": "https://registry.npmjs.org/@cloudflare/unenv-preset/-/unenv-preset-2.3.1.tgz", - Network accessline 29
"version": "2.3.1", "resolved": "https://registry.npmjs.org/@cloudflare/unenv-preset/-/unenv-preset-2.3.1.tgz", "integrity": "sha512-Xq57Qd+ADpt6hibcVBO0uLG9zzRgyRhfCUgBT9s+g3+3Ivg5zDyVgLFy40ES1VdNcu8rPNSivm9A+kGP5IVaPg==", - Network accessline 30
"resolved": "https://registry.npmjs.org/@cloudflare/unenv-preset/-/unenv-preset-2.3.1.tgz", - Network accessline 44
"node_modules/@cloudflare/workerd-darwin-64": { "version": "1.20250424.0", "resolved": "https://registry.npmjs.org/@cloudflare/workerd-darwin-64/-/workerd-darwin-64-1.20250424.0.tgz", - Network accessline 45
"version": "1.20250424.0", "resolved": "https://registry.npmjs.org/@cloudflare/workerd-darwin-64/-/workerd-darwin-64-1.20250424.0.tgz", "integrity": "sha512-E+9tyQfwKwg7iz+vI50UeF9m9MhO6uCTnn6VPBTobhgi0rKcfmCteUGz6YJejG6ex9OIfFH - Network accessline 46
"resolved": "https://registry.npmjs.org/@cloudflare/workerd-darwin-64/-/workerd-darwin-64-1.20250424.0.tgz", - Network accessline 61
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skills/biomcp-server/repo/smithery.yaml
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# Smithery configuration file: https://smithery.ai/docs/config#smitheryyaml
skills/biomcp-server/repo/src/biomcp/__init__.py
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skills/biomcp-server/repo/src/biomcp/__main__.py
skills/biomcp-server/repo/src/biomcp/articles/__init__.py
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skills/biomcp-server/repo/src/biomcp/articles/autocomplete.py
skills/biomcp-server/repo/src/biomcp/articles/fetch.py
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Executable file - Network accessline 125
url = None if self.pmid: url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" - Network accessline 126
if self.pmid: url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" return url - Network accessline 127
url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" - Network accessline 133
url = None if self.pmcid: url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" - Network accessline 134
if self.pmcid: url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" return url - Network accessline 135
url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/"
skills/biomcp-server/repo/src/biomcp/articles/preprints.py
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Executable file - Network accessline 444
"full_text": "", # Europe PMC API doesn't provide full text for preprints "pubmed_url": None, "pmc_url": f"https://europepmc.org/article/PPR/{doi}" - Network accessline 445
"pubmed_url": None, "pmc_url": f"https://europepmc.org/article/PPR/{doi}" if doi - Network accessline 446
"pmc_url": f"https://europepmc.org/article/PPR/{doi}"
skills/biomcp-server/repo/src/biomcp/articles/search.py
- Executable scriptline 1
Executable file - Network accessline 79
url = None if self.pmid: url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" - Network accessline 80
if self.pmid: url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" return url - Network accessline 81
url = f"https://pubmed.ncbi.nlm.nih.gov/{self.pmid}/" - Network accessline 87
url = None if self.pmcid: url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" - Network accessline 88
if self.pmcid: url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" return url - Network accessline 89
url = f"https://www.ncbi.nlm.nih.gov/pmc/articles/{self.pmcid}/" - Network accessline 95
url = None if self.doi: url = f"https://doi.org/{self.doi}" - Network accessline 96
if self.doi: url = f"https://doi.org/{self.doi}" return url - Network accessline 97
url = f"https://doi.org/{self.doi}"
skills/biomcp-server/repo/src/biomcp/articles/search_optimized.py
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skills/biomcp-server/repo/src/biomcp/articles/unified.py
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skills/biomcp-server/repo/src/biomcp/biomarkers/__init__.py
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skills/biomcp-server/repo/src/biomcp/biomarkers/search.py
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Executable file - Access to secretsline 102
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skills/biomcp-server/repo/src/biomcp/cbioportal_helper.py
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skills/biomcp-server/repo/src/biomcp/circuit_breaker.py
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skills/biomcp-server/repo/src/biomcp/cli/__init__.py
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skills/biomcp-server/repo/src/biomcp/cli/articles.py
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skills/biomcp-server/repo/src/biomcp/cli/biomarkers.py
skills/biomcp-server/repo/src/biomcp/cli/diseases.py
skills/biomcp-server/repo/src/biomcp/cli/health.py
skills/biomcp-server/repo/src/biomcp/cli/interventions.py
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Executable file - Access to secretsline 72
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skills/biomcp-server/repo/src/biomcp/cli/main.py
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skills/biomcp-server/repo/src/biomcp/cli/openfda.py
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skills/biomcp-server/repo/src/biomcp/cli/organizations.py
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Executable file - Access to secretsline 75
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skills/biomcp-server/repo/src/biomcp/cli/server.py
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Executable file - Access to secretsline 19
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f"Starting MCP server with Streamable HTTP transport on {host}:{port}" ) logger.info(f"Endpoint: http://{host}:{port}/mcp") - Network accessline 59
) logger.info(f"Endpoint: http://{host}:{port}/mcp") logger.info("Using FastMCP's native Streamable HTTP support") - Network accessline 60
logger.info(f"Endpoint: http://{host}:{port}/mcp")
skills/biomcp-server/repo/src/biomcp/cli/trials.py
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Executable file - Access to secretsline 66
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skills/biomcp-server/repo/src/biomcp/cli/variants.py
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Executable file - Access to secretsline 276
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skills/biomcp-server/repo/src/biomcp/connection_pool.py
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Executable file - Network accessline 26
```python # Get a connection pool for the current event loop pool = await get_connection_pool(verify=True, timeout=httpx.Timeout(30)) - Network accessline 28
pool = await get_connection_pool(verify=True, timeout=httpx.Timeout(30)) - Network accessline 30
# Use the pool for multiple requests (no need to close) response = await pool.get("https://api.example.com/data") - Network accessline 31
response = await pool.get("https://api.example.com/data") - Network accessline 107
if pooled: limits = httpx.Limits( - Network accessline 108
limits = httpx.Limits( - Network accessline 115
limits = httpx.Limits(max_keepalive_connections=0) - Network accessline 117
return httpx.AsyncClient(
skills/biomcp-server/repo/src/biomcp/constants.py
- Executable scriptline 1
Executable file - Network accessline 22
# PubTator3 API # https://www.ncbi.nlm.nih.gov/research/pubtator3/api - Network accessline 23
# https://www.ncbi.nlm.nih.gov/research/pubtator3/api - Network accessline 24
PUBTATOR3_BASE_URL = "https://www.ncbi.nlm.nih.gov/research/pubtator3-api" - Network accessline 29
# ClinicalTrials.gov API # https://clinicaltrials.gov/data-api/api - Network accessline 30
# https://clinicaltrials.gov/data-api/api - Network accessline 31
CLINICAL_TRIALS_BASE_URL = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 32
CLINICAL_TRIALS_STUDY_URL = "https://clinicaltrials.gov/study/" - Network accessline 34
# NCI Clinical Trials Search API # https://clinicaltrialsapi.cancer.gov/api/v2 - Network accessline 35
# https://clinicaltrialsapi.cancer.gov/api/v2 - Network accessline 36
NCI_CTS_BASE_URL = "https://clinicaltrialsapi.cancer.gov/api/v2" - Access to secretsline 42
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# MyVariant.info API # https://docs.myvariant.info/ - Network accessline 45
# https://docs.myvariant.info/ - Network accessline 46
MYVARIANT_BASE_URL = "https://myvariant.info/v1" - Network accessline 51
BIORXIV_BASE_URL = "https://api.biorxiv.org/details/biorxiv" - Network accessline 52
MEDRXIV_BASE_URL = "https://api.biorxiv.org/details/medrxiv" - Network accessline 53
EUROPE_PMC_BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search" - Network accessline 56
GDC_BASE_URL = "https://api.gdc.cancer.gov" - Network accessline 57
GDC_SSMS_ENDPOINT_URL = f"{GDC_BASE_URL}/ssms" # Simple Somatic Mutations GDC_SSM_OCCURRENCES_URL = f"{GDC_BASE_URL}/ssm_occurrences" ENSEMBL_REST_BASE_URL = "https://rest.ensembl.org" - Network accessline 58
GDC_SSM_OCCURRENCES_URL = f"{GDC_BASE_URL}/ssm_occurrences" ENSEMBL_REST_BASE_URL = "https://rest.ensembl.org" ENSEMBL_VARIATION_URL = f"{ENSEMBL_REST_BASE_URL}/variation/human" - Network accessline 59
ENSEMBL_REST_BASE_URL = "https://rest.ensembl.org" - Network accessline 61
CBIOPORTAL_BASE_URL = "https://www.cbioportal.org/api" - Network accessline 64
PUBMED_BASE_URL = "https://pubmed.ncbi.nlm.nih.gov/" - Network accessline 65
PMC_BASE_URL = "https://www.ncbi.nlm.nih.gov/pmc/articles/" - Network accessline 66
DOI_BASE_URL = "https://doi.org/" - Network accessline 67
DBSNP_BASE_URL = "https://www.ncbi.nlm.nih.gov/snp/" - Network accessline 68
CLINVAR_BASE_URL = "https://www.ncbi.nlm.nih.gov/clinvar/variation/" - Network accessline 69
COSMIC_BASE_URL = "https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=" - Network accessline 70
CIVIC_BASE_URL = "https://civicdb.org/variants/" - Network accessline 71
ENSEMBL_VARIANT_BASE_URL = ( "https://ensembl.org/Homo_sapiens/Variation/Explore?v=" ) - Network accessline 72
"https://ensembl.org/Homo_sapiens/Variation/Explore?v=" - Network accessline 73
) GENENAMES_BASE_URL = ( "https://www.genenames.org/data/gene-symbol-report/#!/symbol/" - Network accessline 74
GENENAMES_BASE_URL = ( "https://www.genenames.org/data/gene-symbol-report/#!/symbol/" ) - Network accessline 75
"https://www.genenames.org/data/gene-symbol-report/#!/symbol/" - Network accessline 77
UCSC_GENOME_BROWSER_URL = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&"
skills/biomcp-server/repo/src/biomcp/core.py
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skills/biomcp-server/repo/src/biomcp/diseases/__init__.py
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skills/biomcp-server/repo/src/biomcp/diseases/getter.py
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Executable file - Network accessline 36
): links["MONDO Browser"] = ( f"https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/{mondo_id.replace(':', '_')}" - Network accessline 37
links["MONDO Browser"] = ( f"https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/{mondo_id.replace(':', '_')}" ) - Network accessline 38
f"https://www.ebi.ac.uk/ols/ontologies/mondo/terms?iri=http://purl.obolibrary.org/obo/{mondo_id.replace(':', '_')}" - Network accessline 48
doid_id = doid[0] if isinstance(doid[0], str) else str(doid[0]) links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid_id}" - Network accessline 49
links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid_id}" ) - Network accessline 50
f"https://www.disease-ontology.org/?id={doid_id}" - Network accessline 52
elif isinstance(doid, str): links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid}" - Network accessline 53
links["Disease Ontology"] = ( f"https://www.disease-ontology.org/?id={doid}" ) - Network accessline 54
f"https://www.disease-ontology.org/?id={doid}" - Network accessline 58
if disease_info.name: links["PubMed Search"] = ( f"https://pubmed.ncbi.nlm.nih.gov/?term={disease_info.name.replace(' ', '+')}" - Network accessline 59
links["PubMed Search"] = ( f"https://pubmed.ncbi.nlm.nih.gov/?term={disease_info.name.replace(' ', '+')}" ) - Network accessline 60
f"https://pubmed.ncbi.nlm.nih.gov/?term={disease_info.name.replace(' ', '+')}"
skills/biomcp-server/repo/src/biomcp/diseases/search.py
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skills/biomcp-server/repo/src/biomcp/domain_handlers.py
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if result.get("abstract") else "", RESULT_URL: f"https://pubmed.ncbi.nlm.nih.gov/{result['pmid']}/", - Network accessline 75
else "", RESULT_URL: f"https://pubmed.ncbi.nlm.nih.gov/{result['pmid']}/", RESULT_METADATA: { - Network accessline 76
RESULT_URL: f"https://pubmed.ncbi.nlm.nih.gov/{result['pmid']}/", - Network accessline 168
if brief_summary else "", RESULT_URL: f"https://clinicaltrials.gov/study/{nct_id}", - Network accessline 169
else "", RESULT_URL: f"https://clinicaltrials.gov/study/{nct_id}", RESULT_METADATA: { - Network accessline 170
RESULT_URL: f"https://clinicaltrials.gov/study/{nct_id}", - Network accessline 225
RESULT_TITLE: title, RESULT_SNIPPET: f"Clinical significance: {significance or DEFAULT_SIGNIFICANCE}", RESULT_URL: f"https://www.ncbi.nlm.nih.gov/snp/{rsid}" - Network accessline 226
RESULT_SNIPPET: f"Clinical significance: {significance or DEFAULT_SIGNIFICANCE}", RESULT_URL: f"https://www.ncbi.nlm.nih.gov/snp/{rsid}" if rsid - Network accessline 227
RESULT_URL: f"https://www.ncbi.nlm.nih.gov/snp/{rsid}" - Network accessline 276
RESULT_TITLE: title, RESULT_SNIPPET: snippet or "No summary available", RESULT_URL: f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{symbol}" - Network accessline 277
RESULT_SNIPPET: snippet or "No summary available", RESULT_URL: f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{symbol}" if symbol - Network accessline 278
RESULT_URL: f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{symbol}" - Network accessline 326
url = "" if drugbank_id: url = f"https://www.drugbank.ca/drugs/{drugbank_id}" - Network accessline 327
if drugbank_id: url = f"https://www.drugbank.ca/drugs/{drugbank_id}" elif result.get("pubchem_cid"): - Network accessline 328
url = f"https://www.drugbank.ca/drugs/{drugbank_id}" - Network accessline 330
url = f"https://pubchem.ncbi.nlm.nih.gov/compound/{result['pubchem_cid']}" - Network accessline 378
mondo_id = mondo_info.get("id") if isinstance(mondo_info, dict) else "" url = ( f"https://monarchinitiative.org/disease/{mondo_id}" - Network accessline 379
url = ( f"https://monarchinitiative.org/disease/{mondo_id}" if mondo_id - Network accessline 380
f"https://monarchinitiative.org/disease/{mondo_id}"
skills/biomcp-server/repo/src/biomcp/drugs/__init__.py
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Executable file
skills/biomcp-server/repo/src/biomcp/drugs/getter.py
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Executable file - Network accessline 25
if drug_info.drugbank_id: links["DrugBank"] = ( f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" - Network accessline 26
links["DrugBank"] = ( f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" ) - Network accessline 27
f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" - Network accessline 30
if drug_info.chembl_id: links["ChEMBL"] = ( f"https://www.ebi.ac.uk/chembl/compound_report_card/{drug_info.chembl_id}/" - Network accessline 31
links["ChEMBL"] = ( f"https://www.ebi.ac.uk/chembl/compound_report_card/{drug_info.chembl_id}/" ) - Network accessline 32
f"https://www.ebi.ac.uk/chembl/compound_report_card/{drug_info.chembl_id}/" - Network accessline 35
if drug_info.pubchem_cid: links["PubChem"] = ( f"https://pubchem.ncbi.nlm.nih.gov/compound/{drug_info.pubchem_cid}" - Network accessline 36
links["PubChem"] = ( f"https://pubchem.ncbi.nlm.nih.gov/compound/{drug_info.pubchem_cid}" ) - Network accessline 37
f"https://pubchem.ncbi.nlm.nih.gov/compound/{drug_info.pubchem_cid}" - Network accessline 41
chebi_id = drug_info.chebi_id.replace("CHEBI:", "") links["ChEBI"] = ( f"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{chebi_id}" - Network accessline 42
links["ChEBI"] = ( f"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{chebi_id}" ) - Network accessline 43
f"https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:{chebi_id}"
skills/biomcp-server/repo/src/biomcp/exceptions.py
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skills/biomcp-server/repo/src/biomcp/genes/__init__.py
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skills/biomcp-server/repo/src/biomcp/genes/getter.py
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if gene_info.entrezgene: result["_links"] = { "NCBI Gene": f"https://www.ncbi.nlm.nih.gov/gene/{gene_info.entrezgene}", - Network accessline 60
result["_links"] = { "NCBI Gene": f"https://www.ncbi.nlm.nih.gov/gene/{gene_info.entrezgene}", "PubMed": f"https://pubmed.ncbi.nlm.nih.gov/?term={gene_info.symbol}", - Network accessline 61
"NCBI Gene": f"https://www.ncbi.nlm.nih.gov/gene/{gene_info.entrezgene}", - Network accessline 62
"PubMed": f"https://pubmed.ncbi.nlm.nih.gov/?term={gene_info.symbol}",
skills/biomcp-server/repo/src/biomcp/http_client.py
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skills/biomcp-server/repo/src/biomcp/http_client_simple.py
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pool = httpx.AsyncClient( - Network accessline 62
http2=False, # HTTP/2 can add overhead for simple requests timeout=timeout, limits=httpx.Limits( - Network accessline 63
timeout=timeout, limits=httpx.Limits( max_keepalive_connections=20, # Reuse connections - Network accessline 64
limits=httpx.Limits( - Network accessline 70
transport=httpx.AsyncHTTPTransport( - Network accessline 111
timeout = httpx.Timeout(HTTP_TIMEOUT_SECONDS) - Network accessline 127
client = httpx.AsyncClient( - Network accessline 133
client = httpx.AsyncClient(
skills/biomcp-server/repo/src/biomcp/individual_tools.py
- Executable scriptline 1
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This tool requires: 1. AlphaGenome to be installed (see error message for instructions) 2. An API key from https://deepmind.google.com/science/alphagenome - Network accessline 695
2. An API key from https://deepmind.google.com/science/alphagenome - Access to secretsline 698
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[Credential-related source omitted] - Access to secretsline 867
[Credential-related source omitted] - Network accessline 892
Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 915
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Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 973
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Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 1047
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Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 1105
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Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 1173
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Requires NCI API key from: https://clinicaltrialsapi.cancer.gov/ - Access to secretsline 1260
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skills/biomcp-server/repo/src/biomcp/integrations/__init__.py
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skills/biomcp-server/repo/src/biomcp/integrations/biothings_client.py
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Executable file - Network accessline 13
The BioThings suite (https://biothings.io) provides high-performance biomedical - Network accessline 40
MYGENE_BASE_URL = "https://mygene.info/v3" - Network accessline 44
MYDISEASE_BASE_URL = "https://mydisease.info/v1" - Network accessline 48
MYCHEM_BASE_URL = "https://mychem.info/v1"
skills/biomcp-server/repo/src/biomcp/integrations/cts_api.py
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f"NCI API key required. Please set {NCI_API_KEY_ENV} environment " "variable or provide api_key parameter.\n" "Get a free API key at: https://www.cancer.gov/research/participate/" - Network accessline 38
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"Get a free API key at: https://www.cancer.gov/research/participate/" - Access to secretsline 43
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"```\n\n" "**Get your free API key:**\n" "Visit https://www.cancer.gov/research/participate/clinical-trials-search/developers\n\n" - Network accessline 164
"**Get your free API key:**\n" "Visit https://www.cancer.gov/research/participate/clinical-trials-search/developers\n\n" "The API key provides access to NCI's comprehensive cancer clinical trials " - Network accessline 165
"Visit https://www.cancer.gov/research/participate/clinical-trials-search/developers\n\n"
skills/biomcp-server/repo/src/biomcp/interventions/__init__.py
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skills/biomcp-server/repo/src/biomcp/interventions/getter.py
skills/biomcp-server/repo/src/biomcp/interventions/search.py
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skills/biomcp-server/repo/src/biomcp/logging_filter.py
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skills/biomcp-server/repo/src/biomcp/metrics.py
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skills/biomcp-server/repo/src/biomcp/metrics_handler.py
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skills/biomcp-server/repo/src/biomcp/oncokb_helper.py
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skills/biomcp-server/repo/src/biomcp/openfda/__init__.py
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skills/biomcp-server/repo/src/biomcp/openfda/adverse_events.py
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"• Wait a moment and try again\n" "• Provide an FDA API key for higher limits (240/min vs 40/min)\n" "• Get a free key at: https://open.fda.gov/apis/authentication/" - Network accessline 123
"• Provide an FDA API key for higher limits (240/min vs 40/min)\n" "• Get a free key at: https://open.fda.gov/apis/authentication/" ) - Network accessline 124
"• Get a free key at: https://open.fda.gov/apis/authentication/" - Access to secretsline 179
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skills/biomcp-server/repo/src/biomcp/openfda/adverse_events_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/cache.py
skills/biomcp-server/repo/src/biomcp/openfda/constants.py
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OPENFDA_BASE_URL = "https://api.fda.gov" - Network accessline 87
"🚨 **Critical Warning**: Drug shortage information is time-sensitive. " "Always verify current availability with FDA Drug Shortages Database at " "https://www.accessdata.fda.gov/scripts/drugshortages/ before making " - Network accessline 88
"Always verify current availability with FDA Drug Shortages Database at " "https://www.accessdata.fda.gov/scripts/drugshortages/ before making " "supply chain or treatment decisions." - Network accessline 89
"https://www.accessdata.fda.gov/scripts/drugshortages/ before making "
skills/biomcp-server/repo/src/biomcp/openfda/device_events.py
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skills/biomcp-server/repo/src/biomcp/openfda/device_events_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_approvals.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_labels.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_labels_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_recalls.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_recalls_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_shortages.py
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FDA_SHORTAGES_URL = ( "https://www.accessdata.fda.gov/scripts/drugshortages/default.cfm" - Network accessline 53
"https://www.accessdata.fda.gov/scripts/drugshortages/default.cfm" - Network accessline 56
FDA_SHORTAGES_JSON_URL = "https://www.fda.gov/media/169066/download" # Example URL, update as needed - Access to secretsline 61
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"This feature requires FDA to provide a machine-readable API endpoint.\n\n" "**Alternative Options:**\n" "• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" - Network accessline 214
"**Alternative Options:**\n" "• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" "• Check ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages\n\n" - Network accessline 215
"• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" - Network accessline 216
"• Check ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages\n\n" - Access to secretsline 264
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"This feature requires FDA to provide a machine-readable API endpoint.\n\n" "**Alternative Options:**\n" "• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" - Network accessline 284
"**Alternative Options:**\n" "• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" "• Check ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages\n\n" - Network accessline 285
"• Visit FDA Drug Shortages Database: https://www.accessdata.fda.gov/scripts/drugshortages/\n" - Network accessline 286
"• Check ASHP Drug Shortages: https://www.ashp.org/drug-shortages/current-shortages\n\n"
skills/biomcp-server/repo/src/biomcp/openfda/drug_shortages_detail_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/drug_shortages_helpers.py
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skills/biomcp-server/repo/src/biomcp/openfda/exceptions.py
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skills/biomcp-server/repo/src/biomcp/openfda/input_validation.py
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skills/biomcp-server/repo/src/biomcp/openfda/rate_limiter.py
skills/biomcp-server/repo/src/biomcp/openfda/utils.py
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skills/biomcp-server/repo/src/biomcp/openfda/validation.py
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skills/biomcp-server/repo/src/biomcp/organizations/__init__.py
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skills/biomcp-server/repo/src/biomcp/organizations/getter.py
skills/biomcp-server/repo/src/biomcp/organizations/search.py
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skills/biomcp-server/repo/src/biomcp/parameter_parser.py
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skills/biomcp-server/repo/src/biomcp/query_parser.py
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skills/biomcp-server/repo/src/biomcp/query_router.py
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skills/biomcp-server/repo/src/biomcp/rate_limiter.py
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skills/biomcp-server/repo/src/biomcp/render.py
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skills/biomcp-server/repo/src/biomcp/request_batcher.py
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skills/biomcp-server/repo/src/biomcp/resources/__init__.py
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skills/biomcp-server/repo/src/biomcp/resources/getter.py
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skills/biomcp-server/repo/src/biomcp/resources/instructions.md
- Network accessline 240
| **Trial** | **Combination** | **Patient Population** | **Results** | **Safety Profile** | **Reference** | | ---------------- | --------- - Network accessline 241
| ---------------- | ---------------------- | ------------------------------ | ----------- | ----------------------------------------------- | ---------------------------------------------------------------- | | CheckMate 370 | Crizotini - Network accessline 242
| CheckMate 370 | Crizotinib + Nivolumab | 13 treatment-naive ALK+ NSCLC | 38% ORR | 5/13 with grade ≥3 hepatic toxicities; 2 deaths | [Schenk et al., 2023](https://pubmed.ncbi.nlm.nih.gov/36895933/) | - Network accessline 243
| JAVELIN Lung 101 | Avelumab + Lorlatinib | 28 previously treated patients | 46.4% ORR | No DLTs; milder toxicity | [NCT02584634](https://clinicaltrials.gov/study/NCT02584634) | - Network accessline 245
- Key literature findings with proper citations: "A review by Schenk concluded that combining ALK inhibitors with checkpoint inhibitors resulted in 'significant toxicities without clear improvement in patient outcomes' [https://pubmed - Network accessline 246
"A review by Schenk concluded that combining ALK inhibitors with checkpoint inhibitors resulted in 'significant toxicities without clear improvement in patient outcomes' [https://pubmed.ncbi.nlm.nih.gov/36895933/](https://pubmed.ncbi.nlm.ni - Network accessline 250
| **Study** | **Patient Population** | **Immunotherapy Agent** | **Response Rate** | **Reference** | | --------------------- | ---------------------- | ---------------------- - Network accessline 251
| --------------------- | ---------------------- | ----------------------------- | ----------------- | ------------------------------------------------------------- | | ATLANTIC Trial | 11 ALK+ NSCLC | Durvalumab - Network accessline 252
| ATLANTIC Trial | 11 ALK+ NSCLC | Durvalumab | 0% | [Link to study](https://pubmed.ncbi.nlm.nih.gov/36895933/) | - Network accessline 253
| IMMUNOTARGET Registry | 19 ALK+ NSCLC | Various PD-1/PD-L1 inhibitors | 0% | [Link to registry](https://pubmed.ncbi.nlm.nih.gov/36895933/) | - Network accessline 295
- Specific therapeutic strategies with clickable citation links: - For Class I: BRAF inhibitors as demonstrated in [Davies et al.](https://pubmed.ncbi.nlm.nih.gov/35869122/) - Network accessline 296
- For Class I: BRAF inhibitors as demonstrated in [Davies et al.](https://pubmed.ncbi.nlm.nih.gov/35869122/) - For Class III: Alternative approaches such as MEK inhibitors shown - Network accessline 297
in [Davies et al.](https://pubmed.ncbi.nlm.nih.gov/35869122/) - Network accessline 299
in [Śmiech et al.](https://pubmed.ncbi.nlm.nih.gov/33198372/) - Network accessline 301
- Cancer-specific implications with relevant clinical evidence: - Melanoma treatment differences including clinical trial data from [NCT05767879](https://clinicaltrials.gov/study/NCT05767879) - Network accessline 302
- Melanoma treatment differences including clinical trial data from [NCT05767879](https://clinicaltrials.gov/study/NCT05767879) - Colorectal cancer approaches citing research - Network accessline 303
from [NCT05767879](https://clinicaltrials.gov/study/NCT05767879) - Network accessline 305
from [Liu et al.](https://pubmed.ncbi.nlm.nih.gov/37760573/)
skills/biomcp-server/repo/src/biomcp/retry.py
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skills/biomcp-server/repo/src/biomcp/router.py
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Executable file - Access to secretsline 207
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str | None, Field( description="NCI API key for searching NCI domains (nci_organization, nci_intervention, nci_biomarker, nci_disease). Required for NCI searches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" - Network accessline 209
Field( description="NCI API key for searching NCI domains (nci_organization, nci_intervention, nci_biomarker, nci_disease). Required for NCI searches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" ), - Network accessline 210
description="NCI API key for searching NCI domains (nci_organization, nci_intervention, nci_biomarker, nci_disease). Required for NCI searches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" - Access to secretsline 689
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@mcp_app.tool() @track_performance("biomcp.fetch") async def fetch( # noqa: C901 - Network accessline 873
@track_performance("biomcp.fetch") async def fetch( # noqa: C901 id: Annotated[ # noqa: A002 - Network accessline 874
async def fetch( # noqa: C901 - Access to secretsline 916
[Credential-related source omitted] - Network accessline 917
str | None, Field( description="NCI API key for fetching NCI records (nci_organization, nci_intervention, nci_disease). Required for NCI fetches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" - Network accessline 918
Field( description="NCI API key for fetching NCI records (nci_organization, nci_intervention, nci_disease). Required for NCI fetches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" ), - Network accessline 919
description="NCI API key for fetching NCI records (nci_organization, nci_intervention, nci_disease). Required for NCI fetches. Get a free key at: https://clinicaltrialsapi.cancer.gov/" - Network accessline 1040
Fetch article by PMID (domain auto-detected): ``` await fetch(id="35271234") - Network accessline 1041
`` await fetch(id="35271234") - Network accessline 1042
await fetch(id="35271234") - Network accessline 1045
Fetch article by DOI (domain auto-detected): ``` await fetch(id="10.1101/2024.01.20.23288905") - Network accessline 1046
`` await fetch(id="10.1101/2024.01.20.23288905") - Network accessline 1047
await fetch(id="10.1101/2024.01.20.23288905") - Network accessline 1050
Fetch complete trial information (domain auto-detected): ``` await fetch( - Network accessline 1051
`` await fetch( - Network accessline 1052
await fetch( - Network accessline 1058
Fetch variant with clinical interpretations: ``` await fetch(id="rs121913254") - Network accessline 1059
`` await fetch(id="rs121913254") - Network accessline 1060
await fetch(id="rs121913254") - Network accessline 1063
Explicitly specify domain (optional): ``` await fetch( - Network accessline 1064
`` await fetch( - Network accessline 1065
await fetch( - Network accessline 1143
"text": text_content, "url": article.get( "url", f"https://pubmed.ncbi.nlm.nih.gov/{id}/" - Network accessline 1144
"url": article.get( "url", f"https://pubmed.ncbi.nlm.nih.gov/{id}/" ), - Network accessline 1145
"url", f"https://pubmed.ncbi.nlm.nih.gov/{id}/" - Network accessline 1185
"title": f"Clinical Trial {id}", "text": f"Error parsing trial data: {e}", "url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1186
"text": f"Error parsing trial data: {e}", "url": f"https://clinicaltrials.gov/study/{id}", "metadata": { - Network accessline 1187
"url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1201
protocol_data.get("error", "Trial not found"), ), "url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1202
), "url": f"https://clinicaltrials.gov/study/{id}", "metadata": { - Network accessline 1203
"url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1350
"title": title, "text": "\n".join(text_parts), "url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1351
"text": "\n".join(text_parts), "url": f"https://clinicaltrials.gov/study/{id}", "metadata": metadata, - Network accessline 1352
"url": f"https://clinicaltrials.gov/study/{id}", - Network accessline 1449
url = variant_data.get("url", "") if not url and variant_data.get("dbsnp", {}).get("rsid"): url = f"https://www.ncbi.nlm.nih.gov/snp/{variant_data['dbsnp']['rsid']}" - Network accessline 1450
if not url and variant_data.get("dbsnp", {}).get("rsid"): url = f"https://www.ncbi.nlm.nih.gov/snp/{variant_data['dbsnp']['rsid']}" elif not url: - Network accessline 1451
url = f"https://www.ncbi.nlm.nih.gov/snp/{variant_data['dbsnp']['rsid']}" - Network accessline 1453
url = f"https://myvariant.info/v1/variant/{id}" - Network accessline 1490
url = ( f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{gene_info.symbol}" - Network accessline 1491
f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{gene_info.symbol}" - Network accessline 1547
url = "" if drug_info.drugbank_id: url = f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" - Network accessline 1548
if drug_info.drugbank_id: url = f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" elif drug_info.pubchem_cid: - Network accessline 1549
url = f"https://www.drugbank.ca/drugs/{drug_info.drugbank_id}" - Network accessline 1551
url = f"https://pubchem.ncbi.nlm.nih.gov/compound/{drug_info.pubchem_cid}" - Network accessline 1604
mondo_id = disease_info.mondo.get("id") if mondo_id: url = f"https://monarchinitiative.org/disease/{mondo_id}" - Network accessline 1606
url = f"https://monarchinitiative.org/disease/{mondo_id}" - Access to secretsline 1631
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"title": f"cBioPortal Summary for {gene_name or 'Gene'}", "text": cbioportal_summary[:5000], # Limit text length "url": f"https://www.cbioportal.org/results?gene_list={gene_name}" - Network accessline 1940
"text": cbioportal_summary[:5000], # Limit text length "url": f"https://www.cbioportal.org/results?gene_list={gene_name}" if gene_name - Network accessline 1941
"url": f"https://www.cbioportal.org/results?gene_list={gene_name}"
skills/biomcp-server/repo/src/biomcp/router_handlers.py
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skills/biomcp-server/repo/src/biomcp/shared_context.py
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skills/biomcp-server/repo/src/biomcp/thinking/__init__.py
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skills/biomcp-server/repo/src/biomcp/thinking/sequential.py
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skills/biomcp-server/repo/src/biomcp/thinking/session.py
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skills/biomcp-server/repo/src/biomcp/thinking_tool.py
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skills/biomcp-server/repo/src/biomcp/thinking_tracker.py
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skills/biomcp-server/repo/src/biomcp/trials/__init__.py
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skills/biomcp-server/repo/src/biomcp/trials/getter.py
- Executable scriptline 1
Executable file - Network accessline 103
data_to_return = studies[0] data_to_return["URL"] = ( f"https://clinicaltrials.gov/study/{nct_id}" - Network accessline 104
data_to_return["URL"] = ( f"https://clinicaltrials.gov/study/{nct_id}" ) - Network accessline 105
f"https://clinicaltrials.gov/study/{nct_id}" - Network accessline 118
data_to_return = parsed_data data_to_return["URL"] = ( f"https://clinicaltrials.gov/study/{nct_id}" - Network accessline 119
data_to_return["URL"] = ( f"https://clinicaltrials.gov/study/{nct_id}" ) - Network accessline 120
f"https://clinicaltrials.gov/study/{nct_id}" - Access to secretsline 237
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skills/biomcp-server/repo/src/biomcp/trials/nci_getter.py
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[Credential-related source omitted] - Access to secretsline 264
[Credential-related source omitted] - Access to secretsline 361
[Credential-related source omitted] - Access to secretsline 368
[Credential-related source omitted] - Access to secretsline 383
[Credential-related source omitted]
skills/biomcp-server/repo/src/biomcp/trials/nci_search.py
skills/biomcp-server/repo/src/biomcp/trials/search.py
skills/biomcp-server/repo/src/biomcp/utils/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/cancer_types_api.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/cbio_http_adapter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/endpoint_registry.py
- Executable scriptline 1
Executable file - Network accessline 75
"pubtator3_search", EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", - Network accessline 76
EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 77
url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", - Network accessline 87
"pubtator3_export", EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson", - Network accessline 88
EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 89
url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/publications/export/biocjson", - Network accessline 99
"pubtator3_autocomplete", EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/", - Network accessline 100
EndpointInfo( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 101
url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/entity/autocomplete/", - Network accessline 112
"clinicaltrials_search", EndpointInfo( url="https://clinicaltrials.gov/api/v2/studies", - Network accessline 113
EndpointInfo( url="https://clinicaltrials.gov/api/v2/studies", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 114
url="https://clinicaltrials.gov/api/v2/studies", - Network accessline 125
"myvariant_query", EndpointInfo( url="https://myvariant.info/v1/query", - Network accessline 126
EndpointInfo( url="https://myvariant.info/v1/query", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 127
url="https://myvariant.info/v1/query", - Network accessline 137
"myvariant_variant", EndpointInfo( url="https://myvariant.info/v1/variant", - Network accessline 138
EndpointInfo( url="https://myvariant.info/v1/variant", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 139
url="https://myvariant.info/v1/variant", - Network accessline 150
"biorxiv_api", EndpointInfo( url="https://api.biorxiv.org/details/biorxiv", - Network accessline 151
EndpointInfo( url="https://api.biorxiv.org/details/biorxiv", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 152
url="https://api.biorxiv.org/details/biorxiv", - Network accessline 162
"medrxiv_api", EndpointInfo( url="https://api.biorxiv.org/details/medrxiv", - Network accessline 163
EndpointInfo( url="https://api.biorxiv.org/details/medrxiv", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 164
url="https://api.biorxiv.org/details/medrxiv", - Network accessline 174
"europe_pmc", EndpointInfo( url="https://www.ebi.ac.uk/europepmc/webservices/rest/search", - Network accessline 175
EndpointInfo( url="https://www.ebi.ac.uk/europepmc/webservices/rest/search", category=EndpointCategory.BIOMEDICAL_LITERATURE, - Network accessline 176
url="https://www.ebi.ac.uk/europepmc/webservices/rest/search", - Network accessline 187
"gdc_ssms", EndpointInfo( url="https://api.gdc.cancer.gov/ssms", - Network accessline 188
EndpointInfo( url="https://api.gdc.cancer.gov/ssms", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 189
url="https://api.gdc.cancer.gov/ssms", - Network accessline 199
"gdc_ssm_occurrences", EndpointInfo( url="https://api.gdc.cancer.gov/ssm_occurrences", - Network accessline 200
EndpointInfo( url="https://api.gdc.cancer.gov/ssm_occurrences", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 201
url="https://api.gdc.cancer.gov/ssm_occurrences", - Network accessline 211
"ensembl_variation", EndpointInfo( url="https://rest.ensembl.org/variation/human", - Network accessline 212
EndpointInfo( url="https://rest.ensembl.org/variation/human", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 213
url="https://rest.ensembl.org/variation/human", - Network accessline 223
"cbioportal_api", EndpointInfo( url="https://www.cbioportal.org/api", - Network accessline 224
EndpointInfo( url="https://www.cbioportal.org/api", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 225
url="https://www.cbioportal.org/api", - Network accessline 240
"cbioportal_genes", EndpointInfo( url="https://www.cbioportal.org/api/genes", - Network accessline 241
EndpointInfo( url="https://www.cbioportal.org/api/genes", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 242
url="https://www.cbioportal.org/api/genes", - Network accessline 252
"cbioportal_cancer_types", EndpointInfo( url="https://www.cbioportal.org/api/cancer-types", - Network accessline 253
EndpointInfo( url="https://www.cbioportal.org/api/cancer-types", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 254
url="https://www.cbioportal.org/api/cancer-types", - Network accessline 264
"cbioportal_molecular_profiles", EndpointInfo( url="https://www.cbioportal.org/api/molecular-profiles", - Network accessline 265
EndpointInfo( url="https://www.cbioportal.org/api/molecular-profiles", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 266
url="https://www.cbioportal.org/api/molecular-profiles", - Network accessline 276
"cbioportal_mutations", EndpointInfo( url="https://www.cbioportal.org/api/mutations", - Network accessline 277
EndpointInfo( url="https://www.cbioportal.org/api/mutations", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 278
url="https://www.cbioportal.org/api/mutations", - Network accessline 288
"cbioportal_studies", EndpointInfo( url="https://www.cbioportal.org/api/studies", - Network accessline 289
EndpointInfo( url="https://www.cbioportal.org/api/studies", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 290
url="https://www.cbioportal.org/api/studies", - Network accessline 304
"oncokb_curated_genes", EndpointInfo( url="https://demo.oncokb.org/api/v1/utils/allCuratedGenes", - Network accessline 305
EndpointInfo( url="https://demo.oncokb.org/api/v1/utils/allCuratedGenes", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 306
url="https://demo.oncokb.org/api/v1/utils/allCuratedGenes", - Network accessline 317
"oncokb_gene_annotation", EndpointInfo( url="https://demo.oncokb.org/api/v1/genes/{gene}", - Network accessline 318
EndpointInfo( url="https://demo.oncokb.org/api/v1/genes/{gene}", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 319
url="https://demo.oncokb.org/api/v1/genes/{gene}", - Network accessline 330
"oncokb_variant_annotation", EndpointInfo( url="https://demo.oncokb.org/api/v1/annotate/mutations/byProteinChange", - Network accessline 331
EndpointInfo( url="https://demo.oncokb.org/api/v1/annotate/mutations/byProteinChange", category=EndpointCategory.CANCER_GENOMICS, - Network accessline 332
url="https://demo.oncokb.org/api/v1/annotate/mutations/byProteinChange", - Network accessline 347
"mygene_query", EndpointInfo( url="https://mygene.info/v3/query", - Network accessline 348
EndpointInfo( url="https://mygene.info/v3/query", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 349
url="https://mygene.info/v3/query", - Network accessline 359
"mygene_gene", EndpointInfo( url="https://mygene.info/v3/gene", - Network accessline 360
EndpointInfo( url="https://mygene.info/v3/gene", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 361
url="https://mygene.info/v3/gene", - Network accessline 371
"mydisease_query", EndpointInfo( url="https://mydisease.info/v1/query", - Network accessline 372
EndpointInfo( url="https://mydisease.info/v1/query", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 373
url="https://mydisease.info/v1/query", - Network accessline 383
"mydisease_disease", EndpointInfo( url="https://mydisease.info/v1/disease", - Network accessline 384
EndpointInfo( url="https://mydisease.info/v1/disease", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 385
url="https://mydisease.info/v1/disease", - Network accessline 395
"mychem_query", EndpointInfo( url="https://mychem.info/v1/query", - Network accessline 396
EndpointInfo( url="https://mychem.info/v1/query", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 397
url="https://mychem.info/v1/query", - Network accessline 407
"mychem_chem", EndpointInfo( url="https://mychem.info/v1/chem", - Network accessline 408
EndpointInfo( url="https://mychem.info/v1/chem", category=EndpointCategory.VARIANT_DATABASES, - Network accessline 409
url="https://mychem.info/v1/chem", - Network accessline 420
"nci_trials", EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Network accessline 421
EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/trials", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 422
url="https://clinicaltrialsapi.cancer.gov/api/v2/trials", - Access to secretsline 428
[Credential-related source omitted] - Network accessline 433
"nci_organizations", EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/organizations", - Network accessline 434
EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/organizations", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 435
url="https://clinicaltrialsapi.cancer.gov/api/v2/organizations", - Access to secretsline 441
[Credential-related source omitted] - Network accessline 446
"nci_diseases", EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/diseases", - Network accessline 447
EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/diseases", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 448
url="https://clinicaltrialsapi.cancer.gov/api/v2/diseases", - Access to secretsline 454
[Credential-related source omitted] - Network accessline 459
"nci_interventions", EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/interventions", - Network accessline 460
EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/interventions", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 461
url="https://clinicaltrialsapi.cancer.gov/api/v2/interventions", - Access to secretsline 467
[Credential-related source omitted] - Network accessline 472
"nci_biomarkers", EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers", - Network accessline 473
EndpointInfo( url="https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers", category=EndpointCategory.CLINICAL_TRIALS, - Network accessline 474
url="https://clinicaltrialsapi.cancer.gov/api/v2/biomarkers", - Access to secretsline 480
[Credential-related source omitted] - Network accessline 486
"openfda_drug_events", EndpointInfo( url="https://api.fda.gov/drug/event.json", - Network accessline 487
EndpointInfo( url="https://api.fda.gov/drug/event.json", category=EndpointCategory.REGULATORY_DATA, - Network accessline 488
url="https://api.fda.gov/drug/event.json", - Access to secretsline 494
[Credential-related source omitted] - Network accessline 499
"openfda_drug_labels", EndpointInfo( url="https://api.fda.gov/drug/label.json", - Network accessline 500
EndpointInfo( url="https://api.fda.gov/drug/label.json", category=EndpointCategory.REGULATORY_DATA, - Network accessline 501
url="https://api.fda.gov/drug/label.json", - Access to secretsline 507
[Credential-related source omitted] - Network accessline 512
"openfda_device_events", EndpointInfo( url="https://api.fda.gov/device/event.json", - Network accessline 513
EndpointInfo( url="https://api.fda.gov/device/event.json", category=EndpointCategory.REGULATORY_DATA, - Network accessline 514
url="https://api.fda.gov/device/event.json", - Access to secretsline 520
[Credential-related source omitted] - Network accessline 525
"openfda_drugsfda", EndpointInfo( url="https://api.fda.gov/drug/drugsfda.json", - Network accessline 526
EndpointInfo( url="https://api.fda.gov/drug/drugsfda.json", category=EndpointCategory.REGULATORY_DATA, - Network accessline 527
url="https://api.fda.gov/drug/drugsfda.json", - Access to secretsline 533
[Credential-related source omitted] - Network accessline 538
"openfda_drug_enforcement", EndpointInfo( url="https://api.fda.gov/drug/enforcement.json", - Network accessline 539
EndpointInfo( url="https://api.fda.gov/drug/enforcement.json", category=EndpointCategory.REGULATORY_DATA, - Network accessline 540
url="https://api.fda.gov/drug/enforcement.json", - Access to secretsline 546
[Credential-related source omitted] - Network accessline 553
"fda_drug_shortages", EndpointInfo( url="https://www.fda.gov/media/169066/download", - Network accessline 554
EndpointInfo( url="https://www.fda.gov/media/169066/download", category=EndpointCategory.REGULATORY_DATA, - Network accessline 555
url="https://www.fda.gov/media/169066/download",
skills/biomcp-server/repo/src/biomcp/utils/gene_validator.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/metrics.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/mutation_filter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/query_utils.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/rate_limiter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/utils/request_cache.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/alphagenome.py
- Executable scriptline 1
Executable file - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 63
[Credential-related source omitted] - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Network accessline 86
[Credential-related source omitted] - Access to secretsline 86
[Credential-related source omitted] - Network accessline 87
"```\n\n" "Get a free API key at: https://deepmind.google.com/science/alphagenome\n\n" "**ACTION REQUIRED**: Please provide your API key using Option 1 above to continue." - Network accessline 88
"Get a free API key at: https://deepmind.google.com/science/alphagenome\n\n" - Network accessline 108
"To install:\n" "```bash\n" "git clone https://github.com/google-deepmind/alphagenome.git\n" - Network accessline 109
"```bash\n" "git clone https://github.com/google-deepmind/alphagenome.git\n" "cd alphagenome && pip install .\n" - Network accessline 110
"git clone https://github.com/google-deepmind/alphagenome.git\n" - Access to secretsline 118
[Credential-related source omitted]
skills/biomcp-server/repo/src/biomcp/variants/cancer_types.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/cbio_external_client.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/cbioportal_mutations.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/cbioportal_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/cbioportal_search_helpers.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/constants.py
skills/biomcp-server/repo/src/biomcp/variants/external.py
- Executable scriptline 1
Executable file - Network accessline 31
GDC_BASE = "https://api.gdc.cancer.gov" - Network accessline 35
ENSEMBL_REST_BASE = "https://rest.ensembl.org" - Network accessline 180
occ_response, occ_error = await http_client.request_api( url="https://api.gdc.cancer.gov/ssm_occurrences", - Network accessline 181
url="https://api.gdc.cancer.gov/ssm_occurrences",
skills/biomcp-server/repo/src/biomcp/variants/filters.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/getter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/links.py
- Executable scriptline 1
Executable file - Network accessline 50
if "dbsnp" in variant and variant["dbsnp"].get("rsid"): variant["dbsnp"]["url"] = ( f"https://www.ncbi.nlm.nih.gov/snp/{variant['dbsnp']['rsid']}" - Network accessline 51
variant["dbsnp"]["url"] = ( f"https://www.ncbi.nlm.nih.gov/snp/{variant['dbsnp']['rsid']}" ) - Network accessline 52
f"https://www.ncbi.nlm.nih.gov/snp/{variant['dbsnp']['rsid']}" - Network accessline 54
_ensure_url_section(variant) variant["url"]["ensembl"] = ( f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant['dbsnp']['rsid']}" - Network accessline 55
variant["url"]["ensembl"] = ( f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant['dbsnp']['rsid']}" ) - Network accessline 56
f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant['dbsnp']['rsid']}" - Network accessline 62
if "clinvar" in variant and variant["clinvar"].get("variant_id"): variant["clinvar"]["url"] = ( f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant['clinvar']['variant_id']}/" - Network accessline 63
variant["clinvar"]["url"] = ( f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant['clinvar']['variant_id']}/" ) - Network accessline 64
f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant['clinvar']['variant_id']}/" - Network accessline 70
if "cosmic" in variant and variant["cosmic"].get("cosmic_id"): variant["cosmic"]["url"] = ( f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant['cosmic']['cosmic_id']}" - Network accessline 71
variant["cosmic"]["url"] = ( f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant['cosmic']['cosmic_id']}" ) - Network accessline 72
f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant['cosmic']['cosmic_id']}" - Network accessline 78
if "civic" in variant and variant["civic"].get("id"): variant["civic"]["url"] = ( f"https://civicdb.org/variants/{variant['civic']['id']}/summary" - Network accessline 79
variant["civic"]["url"] = ( f"https://civicdb.org/variants/{variant['civic']['id']}/summary" ) - Network accessline 80
f"https://civicdb.org/variants/{variant['civic']['id']}/summary" - Network accessline 92
_ensure_url_section(variant) variant["url"]["ucsc_genome_browser"] = ( f"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&" - Network accessline 93
variant["url"]["ucsc_genome_browser"] = ( f"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&" f"position=chr{variant['chrom']}:{variant['vcf']['position']}-{vcf_end}" - Network accessline 94
f"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&" - Network accessline 104
_ensure_url_section(variant) variant["url"]["hgnc"] = ( f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{gene}" - Network accessline 105
variant["url"]["hgnc"] = ( f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{gene}" ) - Network accessline 106
f"https://www.genenames.org/data/gene-symbol-report/#!/symbol/{gene}"
skills/biomcp-server/repo/src/biomcp/variants/oncokb_client.py
skills/biomcp-server/repo/src/biomcp/variants/oncokb_models.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/variants/search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/workers/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/workers/worker.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/src/biomcp/workers/worker_entry.js
- Executable scriptline 1
Executable file - Network accessline 8
let REMOTE_MCP_SERVER_URL = "http://localhost:8000"; // Default fallback - Network accessline 30
export default { async fetch(req, env, ctx) { - Network accessline 31
async fetch(req, env, ctx) { - Network accessline 89
const resp = await fetch(target, { - Network accessline 171
try { const u = await fetch(`${REMOTE_MCP_SERVER_URL}/sse`, { - Network accessline 172
const u = await fetch(`${REMOTE_MCP_SERVER_URL}/sse`, {
skills/biomcp-server/repo/src/biomcp/workers/worker_entry_stytch.js
- Executable scriptline 1
Executable file - Access to secretsline 22
[Credential-related source omitted] - Network accessline 167
const getStytchUrl = (env, path, isPublic = false) => { const base = env.STYTCH_API_URL || "https://test.stytch.com/v1"; - Network accessline 168
const base = env.STYTCH_API_URL || "https://test.stytch.com/v1"; - Possible obfuscationline 183
const json = atob(base64); - Network accessline 192
/** * Fetch (and cache) a BigQuery OAuth token. - Network accessline 193
* Fetch (and cache) a BigQuery OAuth token. - Network accessline 205
const assertion = await new SignJWT({ iss: key.client_email, scope: "https://www.googleapis.com/auth/bigquery.insertdata", - Network accessline 206
iss: key.client_email, scope: "https://www.googleapis.com/auth/bigquery.insertdata", aud: "https://oauth2.googleapis.com/token", - Network accessline 207
scope: "https://www.googleapis.com/auth/bigquery.insertdata", - Network accessline 208
aud: "https://oauth2.googleapis.com/token", - Network accessline 216
const resp = await fetch("https://oauth2.googleapis.com/token", { - Access to secretsline 224
[Credential-related source omitted] - Access to secretsline 225
[Credential-related source omitted] - Network accessline 237
const url = `https://bigquery.googleapis.com/bigquery/v2/projects/` + - Network accessline 238
`https://bigquery.googleapis.com/bigquery/v2/projects/` + - Network accessline 242
const response = await fetch(url, { - Access to secretsline 282
[Credential-related source omitted] - Network accessline 360
const authenticateResp = await fetch(getStytchUrl(c.env, endpoint), { - Access to secretsline 365
[Credential-related source omitted] - Network accessline 455
try { const response = await fetch(targetUrl, { - Network accessline 456
const response = await fetch(targetUrl, { - Network accessline 584
.get("/status", (c) => { const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 585
const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; return new Response( - Network accessline 586
c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 602
.get("/debug", (c) => { const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 603
const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; return new Response( - Network accessline 604
c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 836
const stytchLoginUrl = `${ c.env.STYTCH_OAUTH_URL || "https://test.stytch.com/v1/public/oauth/google/start" - Network accessline 837
[Credential-related source omitted] - Network accessline 838
"https://test.stytch.com/v1/public/oauth/google/start" - Access to secretsline 840
[Credential-related source omitted] - Network accessline 960
oauthRequest = { client_id: "biomcp-client", redirect_uri: "https://claude.ai/api/mcp/auth_callback", - Network accessline 961
client_id: "biomcp-client", redirect_uri: "https://claude.ai/api/mcp/auth_callback", code_challenge: null, - Network accessline 962
redirect_uri: "https://claude.ai/api/mcp/auth_callback", - Access to secretsline 1096
[Credential-related source omitted] - Access to secretsline 1136
[Credential-related source omitted] - Access to secretsline 1138
[Credential-related source omitted] - Access to secretsline 1173
[Credential-related source omitted] - Network accessline 1196
log("All messages endpoints hit"); const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1197
const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; const sid = new URL(c.req.url).searchParams.get("session_id"); - Network accessline 1198
c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1319
log("MCP GET endpoint hit - Streamable HTTP transport"); const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1321
c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1340
try { const response = await fetch(targetUrl, { - Network accessline 1341
const response = await fetch(targetUrl, { - Network accessline 1383
log("MCP POST endpoint hit - Streamable HTTP transport"); const REMOTE_MCP_SERVER_URL = c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1385
c.env.REMOTE_MCP_SERVER_URL || "http://localhost:8000"; - Network accessline 1422
return app.fetch(request, env, ctx);
skills/biomcp-server/repo/tests/bdd/cli_help/test_help.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/conftest.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/features/alphagenome_integration.feature
- Access to secretsline 16
[Credential-related source omitted]
skills/biomcp-server/repo/tests/bdd/fetch_articles/test_fetch.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/get_trials/test_get.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/get_variants/test_get.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/search_articles/test_autocomplete.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/search_articles/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/search_trials/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/search_variants/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/bdd/steps/test_alphagenome_steps.py
- Executable scriptline 1
Executable file - Access to secretsline 35
[Credential-related source omitted] - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 47
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Access to secretsline 52
[Credential-related source omitted] - Access to secretsline 74
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Network accessline 258
result = alphagenome_context["result"] assert "AlphaGenome API key required" in result assert "https://deepmind.google.com/science/alphagenome" in result - Network accessline 259
assert "AlphaGenome API key required" in result assert "https://deepmind.google.com/science/alphagenome" in result assert "ACTION REQUIRED" in result - Network accessline 260
assert "https://deepmind.google.com/science/alphagenome" in result
skills/biomcp-server/repo/tests/config/test_smithery_config.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/conftest.py
skills/biomcp-server/repo/tests/data/ct_gov/clinical_trials_api_v2.yaml
- Network accessline 14
description: "Version info" servers: - url: "https://clinicaltrials.gov/api/v2" - Network accessline 15
servers: - url: "https://clinicaltrials.gov/api/v2" description: "This server" - Network accessline 16
- url: "https://clinicaltrials.gov/api/v2" - Network accessline 60
in: "query" description: "Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\ - Network accessline 61
description: "Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\ \ format\n* `legacy`- compatible with classic PRS\n\nApplicable only to\ - Network accessline 62
"Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\ - Network accessline 541
* `json`- return JSON object; format of `markup` fields depends on `markupFormat`\ \ parameter\n* `json.zip`- put JSON object into a .json file and download\ \ it as zip archive; field values of type `markup` are in - Network accessline 542
\ parameter\n* `json.zip`- put JSON object into a .json file and download\ \ it as zip archive; field values of type `markup` are in [markdown](https://spec.commonmark.org/0.28/)\ \ format\n* `fhir.json` - return FHI - Network accessline 543
\ it as zip archive; field values of type `markup` are in [markdown](https://spec.commonmark.org/0.28/)\ - Network accessline 558
in: "query" description: "Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\ - Network accessline 559
description: "Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\ \ format\n* `legacy`- compatible with classic PRS\n\nApplicable only to\ - Network accessline 560
"Format of `markup` type fields:\n* `markdown`- [markdown](https://spec.commonmark.org/0.28/)\
skills/biomcp-server/repo/tests/data/myvariant/myvariant_api.yaml
- Network accessline 4
email: help@myvariant.info name: Chunlei Wu x-id: https://github.com/newgene - Network accessline 5
name: Chunlei Wu x-id: https://github.com/newgene x-role: responsible developer - Network accessline 6
x-id: https://github.com/newgene - Network accessline 8
description: Documentation of the MyVariant.info genetic variant query web services. Learn more about [MyVariant.info](https://docs.myvariant.info/en/latest/index.html) - Network accessline 9
Documentation of the MyVariant.info genetic variant query web services. Learn more about [MyVariant.info](https://docs.myvariant.info/en/latest/index.html) termsOfService: https://myvariant.info/terms/ - Network accessline 10
Learn more about [MyVariant.info](https://docs.myvariant.info/en/latest/index.html) - Network accessline 11
termsOfService: https://myvariant.info/terms/ - Network accessline 20
servers: - description: Encrypted Production server url: https://myvariant.info/v1 - Network accessline 21
- description: Encrypted Production server url: https://myvariant.info/v1 x-maturity: production - Network accessline 22
url: https://myvariant.info/v1 - Network accessline 58
- description: Required, passing user query. The detailed query syntax for parameter is explained [here](https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax). - Network accessline 59
Required, passing user query. The detailed query syntax for parameter is explained [here](https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax). example: rs58991260 - Network accessline 60
is explained [here](https://docs.myvariant.info/en/latest/doc/variant_query_service.html#query-syntax). - Network accessline 112
'Optional, specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/d - Network accessline 113
search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id - Network accessline 114
to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). - Network accessline 151
'Specify one or more fields (separated by commas) to search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/la - Network accessline 152
search, e.g., "scopes=dbsnp.rsid". The available "fields" can be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). Default: _id' - Network accessline 153
be passed to "scopes" parameter are listed [here](https://docs.myvariant.info/en/latest/doc/data.html#available-fields). - Network accessline 218
description: 'By default, this will return the complete variant annotation object in JSON format. See [here](https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#returned-object) for - Network accessline 219
'By default, this will return the complete variant annotation object in JSON format. See [here](https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#returned-object) for an example and [here](https://d - Network accessline 220
in JSON format. See [here](https://docs.myvariant.info/en/latest/doc/variant_annotation_service.html#returned-object) for - Network accessline 221
an example and [here](https://docs.myvariant.info/en/latest/doc/data.html#variant-object) - Network accessline 294
description: Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). - Network accessline 295
Optional, an integer (1 <= facet_size <= 1000) that specifies how many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). in: query - Network accessline 296
many buckets to return in a [faceted query](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). - Network accessline 305
Optional, a single field or comma-separated fields to return facets, can only be used on non-free text fields. E.g. "facets=chembl.molecule_properties.full_mwt". See [examples of faceted queries here](https://docs.mychem.i - Network accessline 306
can only be used on non-free text fields. E.g. "facets=chembl.molecule_properties.full_mwt". See [examples of faceted queries here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). - Network accessline 307
See [examples of faceted queries here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#faceted-queries). - Network accessline 320
returns the next 1000 query results. Setting fetch_all = TRUE causes the results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all here](https://docs.m - Network accessline 321
results to be inherently unsorted, therefore the sort parameter is ignored. For more information, see [examples using fetch_all here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries) - Network accessline 322
For more information, see [examples using fetch_all here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). Default: - Network accessline 332
"Optional, can be a comma-separated list to limit the fields returned\ \ from the object. If \"fields=all\", all available fields will be returned.\ \ Look [here](https://docs.mychem.info/en/latest/doc/data.html#available- - Network accessline 333
\ from the object. If \"fields=all\", all available fields will be returned.\ \ Look [here](https://docs.mychem.info/en/latest/doc/data.html#available-fields)\ \ for a list of available fields. \n\nNote that it supports do - Network accessline 334
\ Look [here](https://docs.mychem.info/en/latest/doc/data.html#available-fields)\ - Network accessline 360
a new one must be obtained with another query request with fetch_all = TRUE. All other parameters are ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id here](https://docs - Network accessline 361
All other parameters are ignored when the scroll_id parameter is supplied. For more information see [examples using scroll_id here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries). - Network accessline 362
For more information see [examples using scroll_id here](https://docs.mychem.info/en/latest/doc/chem_query_service.html?highlight=from#scrolling-queries).
skills/biomcp-server/repo/tests/data/myvariant/variants_full_braf_v600e.json
- Network accessline 8
"_score": 26.326775, "cadd": { "_license": "http://bit.ly/2TIuab9", - Network accessline 9
"cadd": { "_license": "http://bit.ly/2TIuab9", "alt": "T", - Network accessline 10
"_license": "http://bit.ly/2TIuab9", - Network accessline 114
"cgi": [ { "_license": "http://bit.ly/2FqS871", - Network accessline 115
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 116
"_license": "http://bit.ly/2FqS871", - Network accessline 127
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 128
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 129
"_license": "http://bit.ly/2FqS871", - Network accessline 140
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 141
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 142
"_license": "http://bit.ly/2FqS871", - Network accessline 153
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 154
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 155
"_license": "http://bit.ly/2FqS871", - Network accessline 166
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 167
{ "_license": "http://bit.ly/2FqS871", "association": "Resistant", - Network accessline 168
"_license": "http://bit.ly/2FqS871", - Network accessline 179
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 180
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 181
"_license": "http://bit.ly/2FqS871", - Network accessline 192
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 193
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 194
"_license": "http://bit.ly/2FqS871", - Network accessline 205
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 206
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 207
"_license": "http://bit.ly/2FqS871", - Network accessline 218
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 219
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 220
"_license": "http://bit.ly/2FqS871", - Network accessline 231
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 232
{ "_license": "http://bit.ly/2FqS871", "association": "Resistant", - Network accessline 233
"_license": "http://bit.ly/2FqS871", - Network accessline 244
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 245
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 246
"_license": "http://bit.ly/2FqS871", - Network accessline 257
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 258
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 259
"_license": "http://bit.ly/2FqS871", - Network accessline 270
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 271
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 272
"_license": "http://bit.ly/2FqS871", - Network accessline 283
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 284
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 285
"_license": "http://bit.ly/2FqS871", - Network accessline 296
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 297
{ "_license": "http://bit.ly/2FqS871", "association": "Resistant", - Network accessline 298
"_license": "http://bit.ly/2FqS871", - Network accessline 309
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 310
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 311
"_license": "http://bit.ly/2FqS871", - Network accessline 322
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 323
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 324
"_license": "http://bit.ly/2FqS871", - Network accessline 335
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 336
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 337
"_license": "http://bit.ly/2FqS871", - Network accessline 348
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 349
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 350
"_license": "http://bit.ly/2FqS871", - Network accessline 361
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 362
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 363
"_license": "http://bit.ly/2FqS871", - Network accessline 374
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 375
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 376
"_license": "http://bit.ly/2FqS871", - Network accessline 387
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 388
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 389
"_license": "http://bit.ly/2FqS871", - Network accessline 400
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 401
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 402
"_license": "http://bit.ly/2FqS871", - Network accessline 413
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 414
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 415
"_license": "http://bit.ly/2FqS871", - Network accessline 426
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 427
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 428
"_license": "http://bit.ly/2FqS871", - Network accessline 439
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 440
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 441
"_license": "http://bit.ly/2FqS871", - Network accessline 452
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 453
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 454
"_license": "http://bit.ly/2FqS871", - Network accessline 465
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 466
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 467
"_license": "http://bit.ly/2FqS871", - Network accessline 478
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 479
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 480
"_license": "http://bit.ly/2FqS871", - Network accessline 491
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 492
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 493
"_license": "http://bit.ly/2FqS871", - Network accessline 504
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 505
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 506
"_license": "http://bit.ly/2FqS871", - Network accessline 517
}, { "_license": "http://bit.ly/2FqS871", - Network accessline 518
{ "_license": "http://bit.ly/2FqS871", "association": "Responsive", - Network accessline 519
"_license": "http://bit.ly/2FqS871", - Network accessline 532
"chrom": "7", "civic": { "_license": "http://bit.ly/2FqS871", - Network accessline 533
"civic": { "_license": "http://bit.ly/2FqS871", "alleleRegistryId": "CA123643", - Network accessline 534
"_license": "http://bit.ly/2FqS871", - Network accessline 787
"Thyroid Neoplasm" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1781", - Network accessline 788
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1781", "displayName": "Thyroid Cancer", - Network accessline 789
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1781", - Network accessline 825
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21594703", - Network accessline 826
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21594703", "title": "Both BRAF V600E mutation and older age (≥ 65 years) are associated with recurrent papillary thyroid cancer." - Network accessline 827
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21594703", - Network accessline 834
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 835
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 836
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 872
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24583796", - Network accessline 873
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24583796", "title": "Dabrafenib and trametinib, alone and in combination for BRAF-mutant metastatic melanoma." - Network accessline 874
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24583796", - Network accessline 895
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 896
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 897
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 933
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24388723", - Network accessline 934
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24388723", "title": "Prognostic value of BRAF mutations in localized cutaneous melanoma." - Network accessline 935
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24388723", - Network accessline 942
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 943
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 944
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 981
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24576830", - Network accessline 982
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24576830", "title": "Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence." - Network accessline 983
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24576830", - Network accessline 1002
"Thyroid Gland Papillary Carcinoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 1003
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", "displayName": "Papillary Thyroid Carcinoma", - Network accessline 1004
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 1041
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24396464", - Network accessline 1042
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24396464", "title": "Prognostic value of the BRAF V600E mutation in papillary thyroid carcinoma." - Network accessline 1043
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24396464", - Network accessline 1054
"Thyroid Gland Papillary Carcinoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 1055
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", "displayName": "Papillary Thyroid Carcinoma", - Network accessline 1056
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 1092
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/21594703", - Network accessline 1093
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"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4197
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4232
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19603024", - Network accessline 4233
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19603024", "title": "Prognostic and predictive value of common mutations for treatment response and survival in patients with metas - Network accessline 4234
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19603024", - Network accessline 4253
"Thyroid Gland Papillary Carcinoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4254
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", "displayName": "Papillary Thyroid Carcinoma", - Network accessline 4255
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4292
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25024077", - Network accessline 4293
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25024077", "title": "BRAF V600E and TERT promoter mutations cooperatively identify the most aggressive papillary thyroid cancer wit - Network accessline 4294
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25024077", - Network accessline 4305
"Thyroid Gland Papillary Carcinoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4306
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", "displayName": "Papillary Thyroid Carcinoma", - Network accessline 4307
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4343
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24570209", - Network accessline 4344
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24570209", "title": "Immunohistochemistry for BRAF(V600E) antibody VE1 performed in core needle biopsy samples identifies mutated p - Network accessline 4345
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24570209", - Network accessline 4352
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4353
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 4354
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4390
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25265492", - Network accessline 4391
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25265492", "title": "Combined BRAF and MEK inhibition versus BRAF inhibition alone in melanoma." - Network accessline 4392
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25265492", - Network accessline 4413
"disease": { "diseaseAliases": ["Benign Glioma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080829", - Network accessline 4414
"diseaseAliases": ["Benign Glioma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080829", "displayName": "Low Grade Glioma", - Network accessline 4415
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080829", - Network accessline 4450
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32523649", - Network accessline 4451
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32523649", "title": "Phase I study of vemurafenib in children with recurrent or progressive BRAFV600E mutant brain tumors: Pacific - Network accessline 4452
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32523649", - Network accessline 4466
"description": "Patients with completely resected colorectal adenocarcinoma (Stage II-III) were treated with fluorouracil and leucovorin +/- ironotecan. Of the 1,307 FFPE samples tested, V600E was observed in 31 Stage II samples (7.6%) and - Network accessline 4467
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4468
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4503
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20008640", - Network accessline 4504
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20008640", "title": "Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study - Network accessline 4505
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20008640", - Network accessline 4516
"Thyroid Gland Papillary Carcinoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4517
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", "displayName": "Papillary Thyroid Carcinoma", - Network accessline 4518
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:3969", - Network accessline 4554
"retracted": false, "sourceType": "ASCO", "sourceUrl": "https://meetinglibrary.asco.org/record/145877/abstract", - Network accessline 4555
"sourceType": "ASCO", "sourceUrl": "https://meetinglibrary.asco.org/record/145877/abstract", "title": "Results of randomized phase II trial of dabrafenib versus dabrafenib plus trametinib in BRAF-mutated - Network accessline 4556
"sourceUrl": "https://meetinglibrary.asco.org/record/145877/abstract", - Network accessline 4581
"Primary Cancer" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:162", - Network accessline 4582
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:162", "displayName": "Cancer", - Network accessline 4583
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:162", - Network accessline 4618
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32758030", - Network accessline 4619
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32758030", "title": "Dabrafenib and Trametinib in Patients With Tumors With BRAFV600E Mutations: Results of the NCI-MATCH Trial Sub - Network accessline 4620
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/32758030", - Network accessline 4640
"description": "This preclinical study examined vemurafenib efficacy on various colorectal cancer cell lines and in mouse xenograft experiments. Of the cell lines tested, six harbored BRAF V600E (and WT KRAS) and three harbored BRAF WT (but - Network accessline 4641
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4642
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4677
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", - Network accessline 4678
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", "title": "Antitumor activity of BRAF inhibitor vemurafenib in preclinical models of BRAF-mutant colorectal cancer." - Network accessline 4679
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", - Network accessline 4693
"description": "This in vivo study examined the efficacy of various treatments on athymic nude mice xenografted with colorectal cancer HT29 cells, which harbor BRAF V600E. The authors sought to understand whether the addition of vemurafenib - Network accessline 4694
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4695
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4730
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", - Network accessline 4731
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", "title": "Antitumor activity of BRAF inhibitor vemurafenib in preclinical models of BRAF-mutant colorectal cancer." - Network accessline 4732
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22180495", - Network accessline 4752
"description": "This study examined outcomes of 240 rectum cancer patients treated with total mesorectal excision therapy. Tumor samples were obtained at the time of surgery and genotyped for BRAF exon 15 mutations. BRAF V600E was identifie - Network accessline 4753
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4754
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4789
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19903786", - Network accessline 4790
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19903786", "title": "PIK3CA mutations predict local recurrences in rectal cancer patients." - Network accessline 4791
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19903786", - Network accessline 4797
"description": "In a study of metastatic colorectal cancer patients treated with capecitabine, oxaliplatin, bevacizumab, and cetuximab those with BRAF V600E mutations had reduced progression-free survival (6.6mo vs. 10.4mo, P=0.01) and redu - Network accessline 4798
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 4799
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 4833
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19571295", - Network accessline 4834
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19571295", "title": "BRAF mutation in metastatic colorectal cancer." - Network accessline 4835
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/19571295", - Network accessline 4868
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4869
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 4870
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4907
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20818844", - Network accessline 4908
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20818844", "title": "Inhibition of mutated, activated BRAF in metastatic melanoma." - Network accessline 4909
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/20818844", - Network accessline 4924
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4925
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 4926
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 4962
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25524477", - Network accessline 4963
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25524477", "title": "A multicenter DeCOG study on predictors of vemurafenib therapy outcome in melanoma: pretreatment impacts survi - Network accessline 4964
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/25524477", - Network accessline 4978
"description": "A stage 4B, low-grade papillary serous ovarian adenocarcinoma patient, harboring a BRAF V600E mutation was associated with response to vemurafenib monotherapy. The patient was treated with standard chemotherapy, hormone ther - Network accessline 4979
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0050933", "displayName": "Ovarian Serous Carcinoma", - Network accessline 4980
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0050933", - Network accessline 5013
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26490654", - Network accessline 5014
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26490654", "title": "Sustained response to vemurafenib in a low grade serous ovarian cancer with a BRAF V600E mutation." - Network accessline 5015
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/26490654", - Network accessline 5030
"disease": { "diseaseAliases": ["Thyroid Gland Anaplastic Carcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", - Network accessline 5031
"diseaseAliases": ["Thyroid Gland Anaplastic Carcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", "displayName": "Anaplastic Thyroid Carcinoma", - Network accessline 5032
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", - Network accessline 5065
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/23406047", - Network accessline 5066
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/23406047", "title": "BRAF V600E inhibition in anaplastic thyroid cancer." - Network accessline 5067
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/23406047", - Network accessline 5088
"disease": { "diseaseAliases": ["Pediatric Low-grade Glioma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080830", - Network accessline 5089
"diseaseAliases": ["Pediatric Low-grade Glioma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080830", "displayName": "Childhood Low-grade Glioma", - Network accessline 5090
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080830", - Network accessline 5116
"link": "/phenotypes/15320", "name": "Pediatric onset", "url": "https://hpo.jax.org/app/browse/term/HP:0410280" - Network accessline 5117
"name": "Pediatric onset", "url": "https://hpo.jax.org/app/browse/term/HP:0410280" }, - Network accessline 5118
"url": "https://hpo.jax.org/app/browse/term/HP:0410280" - Network accessline 5124
"link": "/phenotypes/16642", "name": "Early young adult onset", "url": "https://hpo.jax.org/app/browse/term/HP:0025708" - Network accessline 5125
"name": "Early young adult onset", "url": "https://hpo.jax.org/app/browse/term/HP:0025708" } - Network accessline 5126
"url": "https://hpo.jax.org/app/browse/term/HP:0025708" - Network accessline 5141
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29948154", - Network accessline 5142
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29948154", "title": "Pediatric low-grade gliomas can be molecularly stratified for risk." - Network accessline 5143
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29948154", - Network accessline 5150
"disease": { "diseaseAliases": ["Thyroid Gland Anaplastic Carcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", - Network accessline 5151
"diseaseAliases": ["Thyroid Gland Anaplastic Carcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", "displayName": "Anaplastic Thyroid Carcinoma", - Network accessline 5152
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:0080522", - Network accessline 5187
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29072975", - Network accessline 5188
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29072975", "title": "Dabrafenib and Trametinib Treatment in Patients With Locally Advanced or Metastatic BRAF V600-Mutant Anaplasti - Network accessline 5189
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29072975", - Network accessline 5209
"description": "Thirty-two patients with BRAF V600E positive metastatic colorectal cancer (mCRC) and 7 patients with other cancers were treated with a combination of BRAF-inhibitor vemurafenib (960 mg twice daily) and EGFR-inhibitor erlotin - Network accessline 5210
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 5211
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 5247
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/36638198", - Network accessline 5248
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/36638198", "title": "A Phase Ib/II Trial of Combined BRAF and EGFR Inhibition in BRAF V600E Positive Metastatic Colorectal Cancer a - Network accessline 5249
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/36638198", - Network accessline 5269
"description": "In this trial, 665 patients having metastatic colorectal cancer were randomly assigned in 1:1:1 ratio to receive encorafenib plus cetuximab plus binimetinib, encorafenib plus cetuximab, investigators' choice of irinotecan pl - Network accessline 5270
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 5271
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 5307
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/33503393", - Network accessline 5308
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/33503393", "title": "Encorafenib Plus Cetuximab as a New Standard of Care for Previously Treated BRAF V600E-Mutant Metastatic Color - Network accessline 5309
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/33503393", - Network accessline 5324
"disease": { "diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 5325
"diseaseAliases": ["Malignant Melanoma", "Naevocarcinoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", "displayName": "Melanoma", - Network accessline 5326
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1909", - Network accessline 5362
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22735384", - Network accessline 5363
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22735384", "title": "Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial - Network accessline 5364
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22735384", - Network accessline 5378
"description": "Five colorectal cancer (CRC) cell lines with BRAF V600E mutation were resistant to treatment with the BRAF inhibitor vemurafenib. An RNAi screen in the WiDr cell line (a V600E CRC line) identified EGFR as an enhancer for sur - Network accessline 5379
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 5380
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 5415
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", - Network accessline 5416
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", "title": "Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR." - Network accessline 5417
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", - Network accessline 5437
"description": "Five colorectal cancer (CRC) cell lines (VACO432, HT29, SNU-C5, KM20, WiDr) with BRAF V600E mutation were resistant to treatment with the BRAF inhibitor vemurafenib. An RNAi screen in the WiDr cell line (a V600E CRC line) id - Network accessline 5438
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 5439
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 5474
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", - Network accessline 5475
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", "title": "Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR." - Network accessline 5476
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/22281684", - Network accessline 5517
"Letterer-Siwe Disease Of Spleen" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:2571", - Network accessline 5518
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:2571", "displayName": "Langerhans-cell Histiocytosis", - Network accessline 5519
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:2571", - Network accessline 5556
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29472347", - Network accessline 5557
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29472347", "title": "Single-agent dabrafenib for BRAFV600E-mutated histiocytosis." - Network accessline 5558
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/29472347", - Network accessline 5572
"description": "In this case series, the authors assessed the efficacy and safety of swapping cetuximab for panitumumab as some patients are unable to tolerate treatment with the mouse/human chimeric monoclonal IgG1 antibody cetuximab. Pani - Network accessline 5573
"disease": { "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", "displayName": "Colorectal Cancer", - Network accessline 5574
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 5608
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/35970034", - Network accessline 5609
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/35970034", "title": "Panitumumab can safely and effectively be substituted for cetuximab in the treatment of BRAF V600Emut metastat - Network accessline 5610
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/35970034", - Network accessline 5635
"Childhood Ganglioglioma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:5078", - Network accessline 5636
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:5078", "displayName": "Ganglioglioma", - Network accessline 5637
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:5078", - Network accessline 5673
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31985841", - Network accessline 5674
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31985841", "title": "Combination of BRAF and MEK inhibition in BRAF V600E mutant low-grade ganglioglioma." - Network accessline 5675
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/31985841", - Network accessline 5696
"disease": { "diseaseAliases": ["Pleomorphic Xantho-astrocytoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:4852", - Network accessline 5697
"diseaseAliases": ["Pleomorphic Xantho-astrocytoma"], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:4852", "displayName": "Pleomorphic Xanthoastrocytoma", - Network accessline 5698
"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:4852", - Network accessline 5734
"retracted": false, "sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28984141", - Network accessline 5735
"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28984141", "title": "Dabrafenib and trametinib in BRAFV600E mutated glioma." - Network accessline 5736
"sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/28984141", - Network accessline 5757
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"Thyroid Neoplasm" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1781", - Network accessline 6063
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1781", "displayName": "Thyroid Cancer", - Network accessline 6064
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"Malignant Upper Limb Melanoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:8923", - Network accessline 6130
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:8923", "displayName": "Skin Melanoma", - Network accessline 6131
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"Piloid Astrocytoma" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:4851", - Network accessline 6187
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"sourceType": "PUBMED", "sourceUrl": "http://www.ncbi.nlm.nih.gov/pubmed/24821190", "title": "Pilomyxoid astrocytoma treated successfully with vemurafenib." - Network accessline 6225
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"diseaseUrl": "https://www.disease-ontology.org/?id=DOID:9256", - Network accessline 6277
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"Primary Cancer" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:162", - Network accessline 6305
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"description": "AURELIA trial indicated substantial improvement in progression-free survival and overall survival in ovarian cancer patients with PD-L1 positive expression in response to bevacizumab plus single regime chemotherapy (BC) trea - Network accessline 6560
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"description": "The Medical Research Council (MRC) COIN trial consisted of patients with histologically confirmed adenocarcinoma of the colon or rectum, inoperable metastatic or locoregional measurable disease, and who had not received chem - Network accessline 6778
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"description": "This clinical study was conducted with 30 patients with colorectal cancer harboring BRAF V600E (n = 29) or BRAF K601E (n=1) mutations, treated with a combination of cobimetinib and vemurafenib. Of the 30 patients, only 27 we - Network accessline 7264
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"Pancreatic Tumor" ], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1793", - Network accessline 7537
], "diseaseUrl": "https://www.disease-ontology.org/?id=DOID:1793", "displayName": "Pancreatic Cancer", - Network accessline 7538
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"_license": "http://bit.ly/2VMkY7R", - Network accessline 8359
}, "dbnsfp": { "_license": "http://bit.ly/2VLnQBz", - Network accessline 8360
"dbnsfp": { "_license": "http://bit.ly/2VLnQBz", "aa": { - Network accessline 8361
"_license": "http://bit.ly/2VLnQBz", - Network accessline 8898
}, "dbsnp": { "_license": "http://bit.ly/2AqoLOc", - Network accessline 8899
"dbsnp": { "_license": "http://bit.ly/2AqoLOc", "alleles": [ - Network accessline 8900
"_license": "http://bit.ly/2AqoLOc", - Network accessline 9499
"type": "SNP", "ucsc_cons": 1, "url": "http://www.mycancergenome.org/content/disease/thyroid-cancer/braf/54" - Network accessline 9500
"ucsc_cons": 1, "url": "http://www.mycancergenome.org/content/disease/thyroid-cancer/braf/54" }, - Network accessline 9501
"url": "http://www.mycancergenome.org/content/disease/thyroid-cancer/braf/54" - Network accessline 9502
}, "emv": { "_license": "http://bit.ly/2RieoY1", - Network accessline 9503
"emv": { "_license": "http://bit.ly/2RieoY1", "egl_classification": "Pathogenic", - Network accessline 9504
"_license": "http://bit.ly/2RieoY1", - Network accessline 9519
}, "exac": { "_license": "http://bit.ly/2H9c4hg", - Network accessline 9520
"exac": { "_license": "http://bit.ly/2H9c4hg", "ac": { - Network accessline 9521
"_license": "http://bit.ly/2H9c4hg", - Network accessline 9589
}, "exac_nontcga": { "_license": "http://bit.ly/2H9c4hg", - Network accessline 9590
"exac_nontcga": { "_license": "http://bit.ly/2H9c4hg", "ac": { - Network accessline 9591
"_license": "http://bit.ly/2H9c4hg", - Network accessline 9659
}, "gnomad_exome": { "_license": "http://bit.ly/2I1cl1I", - Network accessline 9660
"gnomad_exome": { "_license": "http://bit.ly/2I1cl1I", "ac": { - Network accessline 9661
"_license": "http://bit.ly/2I1cl1I", - Network accessline 9841
}, "mutdb": { "_license": "http://bit.ly/2SQ6fXA", - Network accessline 9842
"mutdb": { "_license": "http://bit.ly/2SQ6fXA", "alt": "A", - Network accessline 9843
"_license": "http://bit.ly/2SQ6fXA", - Network accessline 9857
"observed": true, "snpeff": { "_license": "http://bit.ly/2suyRKt", - Network accessline 9858
"snpeff": { "_license": "http://bit.ly/2suyRKt", "ann": { - Network accessline 9859
"_license": "http://bit.ly/2suyRKt",
skills/biomcp-server/repo/tests/data/myvariant/variants_full_braf_v600e.txt
- Network accessline 11
## Cadd License: http://bit.ly/2TIuab9 - Network accessline 12
License: http://bit.ly/2TIuab9 - Network accessline 116
## Civic License: http://bit.ly/2FqS871 - Network accessline 117
License: http://bit.ly/2FqS871 - Network accessline 122
Name: V600E Open Cravat Url: https://run.opencravat.org/webapps/variantreport/index.html?alt_base=T&c - Network accessline 123
Open Cravat Url: https://run.opencravat.org/webapps/variantreport/index.html?alt_base=T&c hrom=chr7&pos=140753336&ref_base=A - Network accessline 124
https://run.opencravat.org/webapps/variantreport/index.html?alt_base=T&c - Network accessline 361
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 362
Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 425
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 426
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 Title: - Network accessline 427
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 446
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 447
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 502
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24583796 - Network accessline 503
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24583796 Title: - Network accessline 504
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24583796 - Network accessline 535
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 536
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 584
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24388723 - Network accessline 585
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24388723 Title: Prognostic value of BRAF mutations in localized cutaneous melanoma. - Network accessline 586
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24388723 - Network accessline 603
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 604
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 667
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 - Network accessline 668
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 Title: - Network accessline 669
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 - Network accessline 694
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 695
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 754
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24396464 - Network accessline 755
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24396464 Title: - Network accessline 756
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24396464 - Network accessline 775
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 776
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 838
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 839
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 Title: - Network accessline 840
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 859
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 860
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 922
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 923
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 Title: - Network accessline 924
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21594703 - Network accessline 943
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9538 - Network accessline 944
Disease Url: https://www.disease-ontology.org/?id=DOID:9538 - Network accessline 993
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23612012 - Network accessline 994
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23612012 Title: Targeting the BRAF V600E mutation in multiple myeloma. - Network accessline 995
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23612012 - Network accessline 1011
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1012
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1063
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1064
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 Title: - Network accessline 1065
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1089
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1090
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1141
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1142
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 Title: - Network accessline 1143
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1168
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1169
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1232
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 - Network accessline 1233
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 Title: - Network accessline 1234
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24576830 - Network accessline 1266
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1267
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1318
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16273091 - Network accessline 1319
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16273091 Title: BRAF mutation predicts sensitivity to MEK inhibition. - Network accessline 1320
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16273091 - Network accessline 1342
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1343
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1394
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1395
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 Title: - Network accessline 1396
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1420
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1421
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1483
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 - Network accessline 1484
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 Title: Inhibition of mutated, activated BRAF in metastatic melanoma. - Network accessline 1485
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 - Network accessline 1507
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1508
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1575
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 - Network accessline 1576
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 Title: - Network accessline 1577
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 - Network accessline 1606
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1607
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1668
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18172275 - Network accessline 1669
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18172275 Title: - Network accessline 1670
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18172275 - Network accessline 1702
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 1703
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 1763
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26460303 - Network accessline 1764
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26460303 Title: - Network accessline 1765
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26460303 - Network accessline 1789
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1790
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1841
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1842
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 Title: - Network accessline 1843
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 1869
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1870
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 1937
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107323 - Network accessline 1938
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107323 Title: - Network accessline 1939
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107323 - Network accessline 1964
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 1965
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2023
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24594804 - Network accessline 2024
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24594804 Title: - Network accessline 2025
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24594804 - Network accessline 2049
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0050626 - Network accessline 2050
Disease Url: https://www.disease-ontology.org/?id=DOID:0050626 - Network accessline 2109
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27048246 - Network accessline 2110
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27048246 Title: - Network accessline 2111
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27048246 - Network accessline 2152
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 2153
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 2240
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24508103 - Network accessline 2241
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24508103 Title: - Network accessline 2242
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24508103 - Network accessline 2273
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 2274
Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 2349
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22356324 - Network accessline 2350
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22356324 Title: Survival in BRAF V600-mutant advanced melanoma treated with vemurafenib. - Network accessline 2351
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22356324 - Network accessline 2374
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 2375
Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 2436
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21351275 - Network accessline 2437
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21351275 Title: - Network accessline 2438
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21351275 - Network accessline 2468
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 2469
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 2544
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 - Network accessline 2545
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 Title: Targeting Mutant BRAF in Relapsed or Refractory Hairy-Cell Leukemia. - Network accessline 2546
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 - Network accessline 2572
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9538 - Network accessline 2573
Disease Url: https://www.disease-ontology.org/?id=DOID:9538 - Network accessline 2603
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24997557 - Network accessline 2604
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24997557 Title: - Network accessline 2605
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24997557 - Network accessline 2635
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2636
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2696
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27729313 - Network accessline 2697
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27729313 Title: - Network accessline 2698
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27729313 - Network accessline 2736
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2737
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2795
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19001320 - Network accessline 2796
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19001320 Title: - Network accessline 2797
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19001320 - Network accessline 2830
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2831
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2896
Retraction Reasons: +Conflict of Interest; Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26287849 - Network accessline 2897
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26287849 Title: Vemurafenib in Multiple Nonmelanoma Cancers with BRAF V600 Mutations. - Network accessline 2898
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26287849 - Network accessline 2925
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2926
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 2977
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26989027 - Network accessline 2978
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26989027 Title: - Network accessline 2979
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26989027 - Network accessline 3006
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3007
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3074
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 - Network accessline 3075
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 Title: - Network accessline 3076
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21107320 - Network accessline 3103
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3104
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3155
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20149136 - Network accessline 3156
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20149136 Title: - Network accessline 3157
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20149136 - Network accessline 3189
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:2394 - Network accessline 3190
Disease Url: https://www.disease-ontology.org/?id=DOID:2394 - Network accessline 3258
Retracted: False Source Type: ASCO Source Url: https://meetinglibrary.asco.org/record/172039/abstract - Network accessline 3259
Source Type: ASCO Source Url: https://meetinglibrary.asco.org/record/172039/abstract Title: - Network accessline 3260
Source Url: https://meetinglibrary.asco.org/record/172039/abstract - Network accessline 3291
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3292
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3343
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 3344
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 Title: - Network accessline 3345
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16424035 - Network accessline 3371
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3372
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3427
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24463458 - Network accessline 3428
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24463458 Title: - Network accessline 3429
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24463458 - Network accessline 3457
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3458
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3522
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18287029 - Network accessline 3523
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18287029 Title: - Network accessline 3524
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/18287029 - Network accessline 3551
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3552
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3607
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26070258 - Network accessline 3608
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26070258 Title: - Network accessline 3609
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26070258 - Network accessline 3636
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 3637
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 3701
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21882184 - Network accessline 3702
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21882184 Title: - Network accessline 3703
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21882184 - Network accessline 3726
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3727
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3780
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20551065 - Network accessline 3781
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20551065 Title: - Network accessline 3782
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20551065 - Network accessline 3808
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3809
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3871
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22241959 - Network accessline 3872
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22241959 Title: - Network accessline 3873
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22241959 - Network accessline 3899
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3900
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 3958
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19671763 - Network accessline 3959
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19671763 Title: - Network accessline 3960
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19671763 - Network accessline 3989
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 3990
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 4024
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23278307 - Network accessline 4025
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23278307 Title: - Network accessline 4026
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23278307 - Network accessline 4054
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 4055
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 4104
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25815361 - Network accessline 4105
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25815361 Title: - Network accessline 4106
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25815361 - Network accessline 4134
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 4135
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 4168
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27116997 - Network accessline 4169
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27116997 Title: - Network accessline 4170
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27116997 - Network accessline 4195
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4196
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4264
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25353071 - Network accessline 4265
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25353071 Title: - Network accessline 4266
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25353071 - Network accessline 4300
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4301
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4363
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23489023 - Network accessline 4364
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23489023 Title: - Network accessline 4365
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23489023 - Network accessline 4392
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4393
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 4460
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23729178 - Network accessline 4461
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23729178 Title: Src inhibitors in suppression of papillary thyroid carcinoma growth. - Network accessline 4462
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23729178 - Network accessline 4486
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:219 - Network accessline 4487
Disease Url: https://www.disease-ontology.org/?id=DOID:219 - Network accessline 4541
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26865419 - Network accessline 4542
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26865419 Title: - Network accessline 4543
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26865419 - Network accessline 4571
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 4572
Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 4635
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26200454 - Network accessline 4636
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26200454 Title: - Network accessline 4637
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26200454 - Network accessline 4668
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 4669
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 4722
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 - Network accessline 4723
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 Title: - Network accessline 4724
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 - Network accessline 4746
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 4747
Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 4792
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24888229 - Network accessline 4793
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24888229 Title: - Network accessline 4794
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24888229 - Network accessline 4822
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3963 - Network accessline 4823
Disease Url: https://www.disease-ontology.org/?id=DOID:3963 - Network accessline 4880
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26456083 - Network accessline 4881
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26456083 Title: - Network accessline 4882
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26456083 - Network accessline 4909
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 4910
Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 4942
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25092772 - Network accessline 4943
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25092772 Title: - Network accessline 4944
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25092772 - Network accessline 4973
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:5940 - Network accessline 4974
Disease Url: https://www.disease-ontology.org/?id=DOID:5940 - Network accessline 5014
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24335681 - Network accessline 5015
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24335681 Title: - Network accessline 5016
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24335681 - Network accessline 5044
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4231 - Network accessline 5045
Disease Url: https://www.disease-ontology.org/?id=DOID:4231 - Network accessline 5076
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25209580 - Network accessline 5077
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25209580 Title: - Network accessline 5078
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25209580 - Network accessline 5106
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1751 - Network accessline 5107
Disease Url: https://www.disease-ontology.org/?id=DOID:1751 - Network accessline 5148
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27520988 - Network accessline 5149
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27520988 Title: - Network accessline 5150
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27520988 - Network accessline 5177
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4947 - Network accessline 5178
Disease Url: https://www.disease-ontology.org/?id=DOID:4947 - Network accessline 5246
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28480077 - Network accessline 5247
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28480077 Title: - Network accessline 5248
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28480077 - Network accessline 5284
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4928 - Network accessline 5285
Disease Url: https://www.disease-ontology.org/?id=DOID:4928 - Network accessline 5339
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28078132 - Network accessline 5340
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28078132 Title: - Network accessline 5341
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28078132 - Network accessline 5375
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4928 - Network accessline 5376
Disease Url: https://www.disease-ontology.org/?id=DOID:4928 - Network accessline 5431
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25435907 - Network accessline 5432
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25435907 Title: - Network accessline 5433
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25435907 - Network accessline 5467
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5468
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5529
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29320312 - Network accessline 5530
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29320312 Title: - Network accessline 5531
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29320312 - Network accessline 5561
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5562
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5623
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29431699 - Network accessline 5624
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29431699 Title: - Network accessline 5625
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29431699 - Network accessline 5663
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5664
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 5717
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 - Network accessline 5718
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 Title: - Network accessline 5719
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19603024 - Network accessline 5747
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 5748
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 5816
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25024077 - Network accessline 5817
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25024077 Title: - Network accessline 5818
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25024077 - Network accessline 5837
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 5838
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 5901
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24570209 - Network accessline 5902
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24570209 Title: - Network accessline 5903
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24570209 - Network accessline 5930
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 5931
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 6002
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25265492 - Network accessline 6003
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25265492 Title: - Network accessline 6004
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25265492 - Network accessline 6039
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0080829 - Network accessline 6040
Disease Url: https://www.disease-ontology.org/?id=DOID:0080829 - Network accessline 6098
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32523649 - Network accessline 6099
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32523649 Title: - Network accessline 6100
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32523649 - Network accessline 6135
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6136
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6194
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20008640 - Network accessline 6195
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20008640 Title: - Network accessline 6196
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20008640 - Network accessline 6219
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 6220
Disease Url: https://www.disease-ontology.org/?id=DOID:3969 - Network accessline 6289
Retracted: False Source Type: ASCO Source Url: https://meetinglibrary.asco.org/record/145877/abstract - Network accessline 6290
Source Type: ASCO Source Url: https://meetinglibrary.asco.org/record/145877/abstract Title: - Network accessline 6291
Source Url: https://meetinglibrary.asco.org/record/145877/abstract - Network accessline 6326
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:162 - Network accessline 6327
Disease Url: https://www.disease-ontology.org/?id=DOID:162 - Network accessline 6388
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32758030 - Network accessline 6389
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32758030 Title: - Network accessline 6390
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/32758030 - Network accessline 6436
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6437
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6493
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 - Network accessline 6494
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 Title: - Network accessline 6495
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 - Network accessline 6529
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6530
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6586
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 - Network accessline 6587
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 Title: - Network accessline 6588
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22180495 - Network accessline 6623
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6624
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6680
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19903786 - Network accessline 6681
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19903786 Title: PIK3CA mutations predict local recurrences in rectal cancer patients. - Network accessline 6682
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19903786 - Network accessline 6702
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6703
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 6731
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19571295 - Network accessline 6732
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19571295 Title: BRAF mutation in metastatic colorectal cancer. - Network accessline 6733
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19571295 - Network accessline 6777
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 6778
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 6840
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 - Network accessline 6841
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 Title: Inhibition of mutated, activated BRAF in metastatic melanoma. - Network accessline 6842
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20818844 - Network accessline 6868
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 6869
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 6939
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25524477 - Network accessline 6940
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25524477 Title: - Network accessline 6941
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25524477 - Network accessline 6971
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0050933 - Network accessline 6972
Disease Url: https://www.disease-ontology.org/?id=DOID:0050933 - Network accessline 7017
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26490654 - Network accessline 7018
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26490654 Title: - Network accessline 7019
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26490654 - Network accessline 7048
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0080522 - Network accessline 7049
Disease Url: https://www.disease-ontology.org/?id=DOID:0080522 - Network accessline 7075
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23406047 - Network accessline 7076
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23406047 Title: BRAF V600E inhibition in anaplastic thyroid cancer. - Network accessline 7077
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23406047 - Network accessline 7109
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0080830 - Network accessline 7110
Disease Url: https://www.disease-ontology.org/?id=DOID:0080830 - Network accessline 7171
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29948154 - Network accessline 7172
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29948154 Title: Pediatric low-grade gliomas can be molecularly stratified for risk. - Network accessline 7173
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29948154 - Network accessline 7182
Link: /phenotypes/15320 Name: Pediatric onset Url: https://hpo.jax.org/app/browse/term/HP:0410280 - Network accessline 7184
Url: https://hpo.jax.org/app/browse/term/HP:0410280 - Network accessline 7192
Link: /phenotypes/16642 Name: Early young adult onset Url: https://hpo.jax.org/app/browse/term/HP:0025708 - Network accessline 7194
Url: https://hpo.jax.org/app/browse/term/HP:0025708 - Network accessline 7215
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0080522 - Network accessline 7216
Disease Url: https://www.disease-ontology.org/?id=DOID:0080522 - Network accessline 7274
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29072975 - Network accessline 7275
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29072975 Title: - Network accessline 7276
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29072975 - Network accessline 7317
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7318
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7379
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/36638198 - Network accessline 7380
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/36638198 Title: - Network accessline 7381
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/36638198 - Network accessline 7421
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7422
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7487
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/33503393 - Network accessline 7488
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/33503393 Title: - Network accessline 7489
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/33503393 - Network accessline 7522
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 7523
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 7591
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 - Network accessline 7592
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 Title: - Network accessline 7593
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 - Network accessline 7623
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7624
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7679
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 - Network accessline 7680
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 Title: - Network accessline 7681
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 - Network accessline 7720
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7721
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7776
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 - Network accessline 7777
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 Title: - Network accessline 7778
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22281684 - Network accessline 7818
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:2571 - Network accessline 7819
Disease Url: https://www.disease-ontology.org/?id=DOID:2571 - Network accessline 7879
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29472347 - Network accessline 7880
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29472347 Title: Single-agent dabrafenib for BRAFV600E-mutated histiocytosis. - Network accessline 7881
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29472347 - Network accessline 7935
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7936
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 7966
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/35970034 - Network accessline 7967
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/35970034 Title: - Network accessline 7968
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/35970034 - Network accessline 8021
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:5078 - Network accessline 8022
Disease Url: https://www.disease-ontology.org/?id=DOID:5078 - Network accessline 8065
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31985841 - Network accessline 8066
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31985841 Title: - Network accessline 8067
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31985841 - Network accessline 8137
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 8138
Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 8180
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28984141 - Network accessline 8181
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28984141 Title: Dabrafenib and trametinib in BRAFV600E mutated glioma. - Network accessline 8182
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/28984141 - Network accessline 8227
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 8228
Disease Url: https://www.disease-ontology.org/?id=DOID:4852 - Network accessline 8311
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 - Network accessline 8312
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 Title: - Network accessline 8313
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 - Network accessline 8362
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 8363
Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 8446
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 - Network accessline 8447
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 Title: - Network accessline 8448
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/34838156 - Network accessline 8483
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3908 - Network accessline 8484
Disease Url: https://www.disease-ontology.org/?id=DOID:3908 - Network accessline 8548
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19010912 - Network accessline 8549
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19010912 Title: Genetic predictors of MEK dependence in non-small cell lung cancer. - Network accessline 8550
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/19010912 - Network accessline 8594
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 8595
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 8670
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 - Network accessline 8671
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 Title: Targeting Mutant BRAF in Relapsed or Refractory Hairy-Cell Leukemia. - Network accessline 8672
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/26352686 - Network accessline 8696
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3070 - Network accessline 8697
Disease Url: https://www.disease-ontology.org/?id=DOID:3070 - Network accessline 8761
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20806365 - Network accessline 8762
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20806365 Title: - Network accessline 8763
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/20806365 - Network accessline 8788
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 8789
Disease Url: https://www.disease-ontology.org/?id=DOID:1781 - Network accessline 8854
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16533790 - Network accessline 8855
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16533790 Title: BRAF is a therapeutic target in aggressive thyroid carcinoma. - Network accessline 8856
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/16533790 - Network accessline 8883
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 8884
Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 8961
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 - Network accessline 8962
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 Title: - Network accessline 8963
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/22735384 - Network accessline 8992
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 8993
Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 9035
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24821190 - Network accessline 9036
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24821190 Title: Pilomyxoid astrocytoma treated successfully with vemurafenib. - Network accessline 9037
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24821190 - Network accessline 9062
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9063
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9116
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23845441 - Network accessline 9117
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23845441 Title: - Network accessline 9118
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23845441 - Network accessline 9154
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:162 - Network accessline 9155
Disease Url: https://www.disease-ontology.org/?id=DOID:162 - Network accessline 9212
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23934108 - Network accessline 9213
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23934108 Title: - Network accessline 9214
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23934108 - Network accessline 9244
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9245
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9301
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25989278 - Network accessline 9302
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25989278 Title: - Network accessline 9303
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/25989278 - Network accessline 9335
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 9336
Disease Url: https://www.disease-ontology.org/?id=DOID:285 - Network accessline 9405
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21663470 - Network accessline 9406
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21663470 Title: BRAF mutations in hairy-cell leukemia. - Network accessline 9407
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21663470 - Network accessline 9437
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 9438
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 9494
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23031422 - Network accessline 9495
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23031422 Title: - Network accessline 9496
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/23031422 - Network accessline 9547
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:2152 - Network accessline 9548
Disease Url: https://www.disease-ontology.org/?id=DOID:2152 - Network accessline 9609
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31105696 - Network accessline 9610
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31105696 Title: - Network accessline 9611
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31105696 - Network accessline 9647
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9648
Disease Url: https://www.disease-ontology.org/?id=DOID:9256 - Network accessline 9706
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21098728 - Network accessline 9707
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21098728 Title: - Network accessline 9708
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21098728 - Network accessline 9759
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 9760
Disease Url: https://www.disease-ontology.org/?id=DOID:1909 - Network accessline 9815
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24265155 - Network accessline 9816
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24265155 Title: - Network accessline 9817
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/24265155 - Network accessline 9883
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0050861 - Network accessline 9884
Disease Url: https://www.disease-ontology.org/?id=DOID:0050861 - Network accessline 9962
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21641636 - Network accessline 9963
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21641636 Title: - Network accessline 9964
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/21641636 - Network accessline 10017
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 10018
Disease Url: https://www.disease-ontology.org/?id=DOID:8923 - Network accessline 10081
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27135738 - Network accessline 10082
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27135738 Title: - Network accessline 10083
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/27135738 - Network accessline 10128
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 10129
Disease Url: https://www.disease-ontology.org/?id=DOID:3910 - Network accessline 10160
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29074209 - Network accessline 10161
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29074209 Title: - Network accessline 10162
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/29074209 - Network accessline 10229
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:5078 - Network accessline 10230
Disease Url: https://www.disease-ontology.org/?id=DOID:5078 - Network accessline 10266
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/30120137 - Network accessline 10267
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/30120137 Title: - Network accessline 10268
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/30120137 - Network accessline 10349
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 10350
Disease Url: https://www.disease-ontology.org/?id=DOID:4851 - Network accessline 10439
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31151904 - Network accessline 10440
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31151904 Title: - Network accessline 10441
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/31151904 - Network accessline 10473
##### Disease Disease Url: https://www.disease-ontology.org/?id=DOID:0080830 - Network accessline 10474
Disease Url: https://www.disease-ontology.org/?id=DOID:0080830 - Network accessline 10537
Retracted: False Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/37978284 - Network accessline 10538
Source Type: PUBMED Source Url: http://www.ncbi.nlm.nih.gov/pubmed/37978284 Title: - Network accessline 10539
Source Url: http://www.ncbi.nlm.nih.gov/pubmed/37978284
skills/biomcp-server/repo/tests/data/myvariant/variants_part_braf_v600_multiple.json
- Network accessline 4
"_score": 19.419012, "cadd": { "_license": "http://bit.ly/2TIuab9", - Network accessline 5
"cadd": { "_license": "http://bit.ly/2TIuab9", "phred": 21.2 - Network accessline 6
"_license": "http://bit.ly/2TIuab9", - Network accessline 9
"chrom": "7", "clinvar": { "_license": "http://bit.ly/2SQdcI0", - Network accessline 10
"clinvar": { "_license": "http://bit.ly/2SQdcI0", "rcv": { - Network accessline 11
"_license": "http://bit.ly/2SQdcI0", - Network accessline 16
}, "cosmic": { "_license": "http://bit.ly/2VMkY7R", - Network accessline 17
"cosmic": { "_license": "http://bit.ly/2VMkY7R", "cosmic_id": "COSM18443" - Network accessline 18
"_license": "http://bit.ly/2VMkY7R", - Network accessline 20
}, "dbnsfp": { "_license": "http://bit.ly/2VLnQBz", - Network accessline 21
"dbnsfp": { "_license": "http://bit.ly/2VLnQBz", "genename": ["BRAF", "BRAF", "BRAF", "BRAF"], - Network accessline 22
"_license": "http://bit.ly/2VLnQBz", - Network accessline 32
}, "dbsnp": { "_license": "http://bit.ly/2AqoLOc", - Network accessline 33
"dbsnp": { "_license": "http://bit.ly/2AqoLOc", "rsid": "rs113488022" - Network accessline 34
"_license": "http://bit.ly/2AqoLOc", - Network accessline 45
"_score": 18.693962, "cadd": { "_license": "http://bit.ly/2TIuab9", - Network accessline 46
"cadd": { "_license": "http://bit.ly/2TIuab9", "phred": 32 - Network accessline 47
"_license": "http://bit.ly/2TIuab9", - Network accessline 50
"chrom": "7", "civic": { "_license": "http://bit.ly/2FqS871", - Network accessline 51
"civic": { "_license": "http://bit.ly/2FqS871", "id": 12, - Network accessline 52
"_license": "http://bit.ly/2FqS871", - Network accessline 53
"id": 12, "openCravatUrl": "https://run.opencravat.org/webapps/variantreport/index.html?alt_base=T&chrom=chr7&pos=140753336&ref_base=A" }, - Network accessline 54
"openCravatUrl": "https://run.opencravat.org/webapps/variantreport/index.html?alt_base=T&chrom=chr7&pos=140753336&ref_base=A" - Network accessline 55
}, "clinvar": { "_license": "http://bit.ly/2SQdcI0", - Network accessline 56
"clinvar": { "_license": "http://bit.ly/2SQdcI0", "rcv": [ - Network accessline 57
"_license": "http://bit.ly/2SQdcI0", - Network accessline 148
}, "cosmic": { "_license": "http://bit.ly/2VMkY7R", - Network accessline 149
"cosmic": { "_license": "http://bit.ly/2VMkY7R", "cosmic_id": "COSM476" - Network accessline 150
"_license": "http://bit.ly/2VMkY7R", - Network accessline 152
}, "dbnsfp": { "_license": "http://bit.ly/2VLnQBz", - Network accessline 153
"dbnsfp": { "_license": "http://bit.ly/2VLnQBz", "genename": ["BRAF", "BRAF", "BRAF", "BRAF"], - Network accessline 154
"_license": "http://bit.ly/2VLnQBz", - Network accessline 164
}, "dbsnp": { "_license": "http://bit.ly/2AqoLOc", - Network accessline 165
"dbsnp": { "_license": "http://bit.ly/2AqoLOc", "rsid": "rs113488022" - Network accessline 166
"_license": "http://bit.ly/2AqoLOc", - Network accessline 168
}, "exac": { "_license": "http://bit.ly/2H9c4hg", - Network accessline 169
"exac": { "_license": "http://bit.ly/2H9c4hg", "af": 1.647e-5 - Network accessline 170
"_license": "http://bit.ly/2H9c4hg", - Network accessline 172
}, "gnomad_exome": { "_license": "http://bit.ly/2I1cl1I", - Network accessline 173
"gnomad_exome": { "_license": "http://bit.ly/2I1cl1I", "af": { - Network accessline 174
"_license": "http://bit.ly/2I1cl1I", - Network accessline 187
"_score": 18.476965, "cadd": { "_license": "http://bit.ly/2TIuab9", - Network accessline 188
"cadd": { "_license": "http://bit.ly/2TIuab9", "phred": 26.0 - Network accessline 189
"_license": "http://bit.ly/2TIuab9", - Network accessline 192
"chrom": "7", "clinvar": { "_license": "http://bit.ly/2SQdcI0", - Network accessline 193
"clinvar": { "_license": "http://bit.ly/2SQdcI0", "rcv": [ - Network accessline 194
"_license": "http://bit.ly/2SQdcI0", - Network accessline 210
}, "cosmic": { "_license": "http://bit.ly/2VMkY7R", - Network accessline 211
"cosmic": { "_license": "http://bit.ly/2VMkY7R", "cosmic_id": "COSM6137" - Network accessline 212
"_license": "http://bit.ly/2VMkY7R", - Network accessline 214
}, "dbnsfp": { "_license": "http://bit.ly/2VLnQBz", - Network accessline 215
"dbnsfp": { "_license": "http://bit.ly/2VLnQBz", "genename": ["BRAF", "BRAF", "BRAF", "BRAF"], - Network accessline 216
"_license": "http://bit.ly/2VLnQBz", - Network accessline 226
}, "dbsnp": { "_license": "http://bit.ly/2AqoLOc", - Network accessline 227
"dbsnp": { "_license": "http://bit.ly/2AqoLOc", "rsid": "rs113488022" - Network accessline 228
"_license": "http://bit.ly/2AqoLOc",
skills/biomcp-server/repo/tests/data/openfda/drugsfda_detail.json
- Network accessline 65
{ "id": "52674", "url": "https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/125514lbl.pdf", - Network accessline 66
"id": "52674", "url": "https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/125514lbl.pdf", "date": "20140905", - Network accessline 67
"url": "https://www.accessdata.fda.gov/drugsatfda_docs/label/2014/125514lbl.pdf",
skills/biomcp-server/repo/tests/data/pubtator/pubtator3_paper.txt
- Network accessline 1
Nucleic Acids Research, 2024, 52, W540–W546 https://doi.org/10.1093/nar/gkae235 - Network accessline 2
https://doi.org/10.1093/nar/gkae235 - Network accessline 20
Abstract PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer - Network accessline 21
PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer - Network accessline 54
Downloaded from https://academic.oup.com/nar/article/52/W1/W540/7640526 by guest on 10 March 2025 - Network accessline 102
Data sources and article processing PubTator 3.0 downloads new articles weekly from the BioC PubMed API (https://www.ncbi.nlm.nih.gov/research/bionlp/ - Network accessline 103
PubTator 3.0 downloads new articles weekly from the BioC PubMed API (https://www.ncbi.nlm.nih.gov/research/bionlp/ APIs/BioC-PubMed/) and the BioC PMC API (https://www. - Network accessline 104
PubMed API (https://www.ncbi.nlm.nih.gov/research/bionlp/ - Network accessline 105
APIs/BioC-PubMed/) and the BioC PMC API (https://www. - Network accessline 142
Downloaded from https://academic.oup.com/nar/article/52/W1/W540/7640526 by guest on 10 March 2025 - Network accessline 176
Programmatic access and data formats PubTator 3.0 offers programmatic access through its API and bulk download. The API (https://www.ncbi. - Network accessline 177
PubTator 3.0 offers programmatic access through its API and bulk download. The API (https://www.ncbi. nlm.nih.gov/research/pubtator3/) supports keyword, entity and relation search, and also supports exporting - Network accessline 178
API and bulk download. The API (https://www.ncbi. - Network accessline 179
nlm.nih.gov/research/pubtator3/) supports keyword, entity and relation search, and also supports exporting annotations in XML and JSON-based BioC (16) formats and tab-delimited free text. The PubTator 3.0 FTP site (https://ftp.ncbi.nlm.nih. - Network accessline 180
annotations in XML and JSON-based BioC (16) formats and tab-delimited free text. The PubTator 3.0 FTP site (https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator3) provides bulk downloads of annotated articles and extraction summaries for entities a - Network accessline 181
site (https://ftp.ncbi.nlm.nih.gov/pub/lu/PubTator3) provides bulk downloads of annotated articles and extraction - Network accessline 190
Downloaded from https://academic.oup.com/nar/article/52/W1/W540/7640526 by guest on 10 March 2025 - Network accessline 224
Downloaded from https://academic.oup.com/nar/article/52/W1/W540/7640526 by guest on 10 March 2025 - Network accessline 303
Downloaded from https://academic.oup.com/nar/article/52/W1/W540/7640526 by guest on 10 March 2025 - Network accessline 348
Data is available through the online interface at https:// www.ncbi.nlm.nih.gov/research/pubtator3/, through the API at https://www.ncbi.nlm.nih.gov/research/pubtator3/api or - Network accessline 349
www.ncbi.nlm.nih.gov/research/pubtator3/, through the API at https://www.ncbi.nlm.nih.gov/research/pubtator3/api or bulk FTP download at https://ftp.ncbi.nlm.nih.gov/pub/lu/ - Network accessline 350
at https://www.ncbi.nlm.nih.gov/research/pubtator3/api or bulk FTP download at https://ftp.ncbi.nlm.nih.gov/pub/lu/ PubTator3/. - Network accessline 351
bulk FTP download at https://ftp.ncbi.nlm.nih.gov/pub/lu/ - Network accessline 353
The source code for each component of PubTator 3.0 is openly accessible. The AIONER named entity recognizer is available at https://github.com/ncbi/AIONER. GNorm2, - Network accessline 354
is openly accessible. The AIONER named entity recognizer is available at https://github.com/ncbi/AIONER. GNorm2, for gene name normalization, is available at https://github. - Network accessline 355
is available at https://github.com/ncbi/AIONER. GNorm2, - Network accessline 356
for gene name normalization, is available at https://github. - Network accessline 357
com/ncbi/GNorm2. The tmVar3 variant name normalizer is available at https://github.com/ncbi/tmVar3. The NLMChem Tagger, for chemical name normalization, is available at https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem. The TaggerOne system, for - Network accessline 358
is available at https://github.com/ncbi/tmVar3. The NLMChem Tagger, for chemical name normalization, is available - Network accessline 359
at https://ftp.ncbi.nlm.nih.gov/pub/lu/NLMChem. The TaggerOne system, for disease and cell line normalization, is available at https://www.ncbi.nlm.nih.gov/research/bionlp/Tools/ - Network accessline 360
taggerone. The BioREx relation extraction system is available at https://github.com/ncbi/BioREx. The code for customizing ChatGPT with the PubTator 3.0 API is available at https: - Network accessline 361
at https://github.com/ncbi/BioREx. The code for customizing - Network accessline 363
//github.com/ncbi-nlp/pubtator-gpt. The details of the applications, performance, evaluation data, and citations for each tool are shown in Supplementary Table S7. All source code is also available at https://doi.org/10.5281/zenodo.10839630 - Network accessline 365
also available at https://doi.org/10.5281/zenodo.10839630.
skills/biomcp-server/repo/tests/integration/test_oncokb_integration.py
- Executable scriptline 1
Executable file - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 83
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 135
[Credential-related source omitted] - Access to secretsline 137
[Credential-related source omitted] - Access to secretsline 193
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Access to secretsline 201
[Credential-related source omitted] - Access to secretsline 249
[Credential-related source omitted] - Access to secretsline 260
[Credential-related source omitted] - Access to secretsline 265
[Credential-related source omitted] - Access to secretsline 280
[Credential-related source omitted] - Access to secretsline 310
[Credential-related source omitted] - Access to secretsline 311
[Credential-related source omitted] - Access to secretsline 312
[Credential-related source omitted] - Access to secretsline 325
[Credential-related source omitted] - Access to secretsline 368
[Credential-related source omitted] - Access to secretsline 416
[Credential-related source omitted] - Access to secretsline 418
[Credential-related source omitted] - Access to secretsline 440
[Credential-related source omitted] - Access to secretsline 445
[Credential-related source omitted] - Access to secretsline 447
[Credential-related source omitted] - Access to secretsline 470
[Credential-related source omitted] - Access to secretsline 475
[Credential-related source omitted] - Access to secretsline 477
[Credential-related source omitted] - Access to secretsline 503
[Credential-related source omitted] - Access to secretsline 510
[Credential-related source omitted] - Access to secretsline 512
[Credential-related source omitted] - Access to secretsline 543
[Credential-related source omitted]
skills/biomcp-server/repo/tests/integration/test_openfda_integration.py
- Executable scriptline 1
Executable file - Access to secretsline 121
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 145
[Credential-related source omitted]
skills/biomcp-server/repo/tests/integration/test_preprints_integration.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/integration/test_simple.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/integration/test_variants_integration.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_autocomplete.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_cbioportal_integration.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_fetch.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_preprints.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/articles/test_unified.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/conftest.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/drugs/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/drugs/test_drug_getter.py
- Executable scriptline 1
Executable file - Network accessline 73
assert "Trade Names**: Gleevec, Glivec" in result assert "External Links" in result assert "DrugBank](https://www.drugbank.ca/drugs/DB00619)" in result - Network accessline 75
assert "DrugBank](https://www.drugbank.ca/drugs/DB00619)" in result - Network accessline 108
assert ( data["_links"]["DrugBank"] == "https://www.drugbank.ca/drugs/DB00619" - Network accessline 109
data["_links"]["DrugBank"] == "https://www.drugbank.ca/drugs/DB00619" ) - Network accessline 110
== "https://www.drugbank.ca/drugs/DB00619"
skills/biomcp-server/repo/tests/tdd/openfda/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_adverse_events.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_device_events.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_drug_approvals.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_drug_labels.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_drug_recalls.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/openfda/test_drug_shortages.py
- Executable scriptline 1
Executable file - Network accessline 100
assert "Drug shortage information is time-sensitive" in result assert ( "https://www.accessdata.fda.gov/scripts/drugshortages/" - Network accessline 101
assert ( "https://www.accessdata.fda.gov/scripts/drugshortages/" in result - Network accessline 102
"https://www.accessdata.fda.gov/scripts/drugshortages/"
skills/biomcp-server/repo/tests/tdd/openfda/test_security.py
- Executable scriptline 1
Executable file - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 73
[Credential-related source omitted] - Access to secretsline 74
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Access to secretsline 79
[Credential-related source omitted] - Access to secretsline 80
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted] - Access to secretsline 88
[Credential-related source omitted] - Access to secretsline 98
[Credential-related source omitted] - Access to secretsline 111
[Credential-related source omitted] - Network accessline 116
cache_key = _generate_cache_key( "https://api.fda.gov/drug/event.json", params - Network accessline 117
"https://api.fda.gov/drug/event.json", params - Network accessline 125
safe_params = {"drug": "aspirin", "limit": 10} expected_input = f"https://api.fda.gov/drug/event.json:{json.dumps(safe_params, sort_keys=True)}" - Network accessline 126
expected_input = f"https://api.fda.gov/drug/event.json:{json.dumps(safe_params, sort_keys=True)}" - Network accessline 148
set_cached_response( "https://api.fda.gov/test", {"drug": "test"}, large_response - Network accessline 149
"https://api.fda.gov/test", {"drug": "test"}, large_response - Network accessline 153
cached = get_cached_response( "https://api.fda.gov/test", {"drug": "test"} - Network accessline 154
"https://api.fda.gov/test", {"drug": "test"} - Network accessline 248
_, error = await make_openfda_request( "https://api.fda.gov/drug/event.json", - Network accessline 249
"https://api.fda.gov/drug/event.json", - Dangerous shell operationline 297
await search_device_events(device="pump; rm -rf /", limit=10) - Access to secretsline 314
[Credential-related source omitted] - Access to secretsline 321
[Credential-related source omitted] - Network accessline 343
for i in range(3): task = make_openfda_request( "https://api.fda.gov/test", {"drug": f"test{i}"} - Network accessline 344
task = make_openfda_request( "https://api.fda.gov/test", {"drug": f"test{i}"} ) - Network accessline 345
"https://api.fda.gov/test", {"drug": f"test{i}"}
skills/biomcp-server/repo/tests/tdd/test_biothings_integration.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_biothings_integration_real.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_circuit_breaker.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_concurrent_requests.py
- Executable scriptline 1
Executable file - Network accessline 36
tasks = [ http_client.request_api( url=f"https://api.example.com/resource/{i}", - Network accessline 37
http_client.request_api( url=f"https://api.example.com/resource/{i}", request={}, - Network accessline 38
url=f"https://api.example.com/resource/{i}", - Network accessline 75
tasks = [ http_client.request_api( "https://domain1.com/api", {}, domain="domain1" - Network accessline 76
http_client.request_api( "https://domain1.com/api", {}, domain="domain1" ), - Network accessline 77
"https://domain1.com/api", {}, domain="domain1" - Network accessline 78
), http_client.request_api( "https://domain2.com/api", {}, domain="domain2" - Network accessline 79
http_client.request_api( "https://domain2.com/api", {}, domain="domain2" ), - Network accessline 80
"https://domain2.com/api", {}, domain="domain2" - Network accessline 81
), http_client.request_api( "https://domain3.com/api", {}, domain="domain3" - Network accessline 82
http_client.request_api( "https://domain3.com/api", {}, domain="domain3" ), - Network accessline 83
"https://domain3.com/api", {}, domain="domain3" - Network accessline 103
await http_client.request_api( url="https://api.example.com/data", - Network accessline 104
url="https://api.example.com/data", - Network accessline 114
tasks = [ http_client.request_api( url="https://api.example.com/data", - Network accessline 115
http_client.request_api( url="https://api.example.com/data", request={}, - Network accessline 116
url="https://api.example.com/data", - Network accessline 144
tasks = [ http_client.request_api( url=f"https://failing.com/api/{i}", - Network accessline 145
http_client.request_api( url=f"https://failing.com/api/{i}", request={}, - Network accessline 146
url=f"https://failing.com/api/{i}", - Network accessline 161
_, error = await http_client.request_api( url="https://failing.com/api/test", - Network accessline 162
url="https://failing.com/api/test",
skills/biomcp-server/repo/tests/tdd/test_connection_pool.py
- Executable scriptline 1
Executable file - Network accessline 37
timeout = httpx.Timeout(30) - Network accessline 49
timeout = httpx.Timeout(30) - Network accessline 60
timeout = httpx.Timeout(30) - Network accessline 71
ssl_context = ssl.create_default_context() timeout = httpx.Timeout(30) - Network accessline 72
timeout = httpx.Timeout(30) - Network accessline 83
timeout = httpx.Timeout(30) - Network accessline 97
with patch("asyncio.get_running_loop", side_effect=RuntimeError): timeout = httpx.Timeout(30) - Network accessline 98
timeout = httpx.Timeout(30) - Network accessline 110
timeout = httpx.Timeout(30) - Network accessline 131
timeout = httpx.Timeout(30) - Network accessline 145
[Credential-related source omitted] - Access to secretsline 145
[Credential-related source omitted] - Network accessline 146
timeout = httpx.Timeout(30) - Network accessline 158
timeout = httpx.Timeout(30) - Network accessline 174
timeout = httpx.Timeout(30) - Network accessline 189
pool_manager = EventLoopConnectionPools() timeout = httpx.Timeout(30) - Network accessline 190
timeout = httpx.Timeout(30)
skills/biomcp-server/repo/tests/tdd/test_domain_handlers.py
- Executable scriptline 1
Executable file - Network accessline 43
assert len(result["snippet"]) == 203 # 200 + "..." assert result["snippet"].endswith("...") assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" - Network accessline 44
assert result["snippet"].endswith("...") assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" assert result["metadata"]["year"] == "2023" - Network accessline 45
assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" - Network accessline 55
"title": "Preprint Title", "abstract": "Short abstract", "url": "https://www.biorxiv.org/content/10.1101/2023.01.01.12345", - Network accessline 56
"abstract": "Short abstract", "url": "https://www.biorxiv.org/content/10.1101/2023.01.01.12345", "pub_year": "2023", - Network accessline 57
"url": "https://www.biorxiv.org/content/10.1101/2023.01.01.12345", - Network accessline 68
assert ( result["url"] == "https://www.biorxiv.org/content/10.1101/2023.01.01.12345" - Network accessline 69
result["url"] == "https://www.biorxiv.org/content/10.1101/2023.01.01.12345" ) - Network accessline 70
== "https://www.biorxiv.org/content/10.1101/2023.01.01.12345" - Network accessline 86
) # Should use default for missing title assert result["snippet"] == "" # Empty when no abstract assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/67890/" - Network accessline 88
assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/67890/" - Network accessline 143
assert result["title"] == "Brief Title" assert "brief summary" in result["snippet"] assert result["url"] == "https://clinicaltrials.gov/study/NCT12345" - Network accessline 144
assert "brief summary" in result["snippet"] assert result["url"] == "https://clinicaltrials.gov/study/NCT12345" assert result["metadata"]["status"] == "RECRUITING" - Network accessline 145
assert result["url"] == "https://clinicaltrials.gov/study/NCT12345" - Network accessline 166
assert result["title"] == "Legacy Trial Title" assert result["snippet"].startswith("Legacy summary") assert result["url"] == "https://clinicaltrials.gov/study/NCT67890" - Network accessline 167
assert result["snippet"].startswith("Legacy summary") assert result["url"] == "https://clinicaltrials.gov/study/NCT67890" assert result["metadata"]["status"] == "COMPLETED" - Network accessline 168
assert result["url"] == "https://clinicaltrials.gov/study/NCT67890"
skills/biomcp-server/repo/tests/tdd/test_drug_approvals.py
- Executable scriptline 1
Executable file - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 79
[Credential-related source omitted] - Access to secretsline 140
[Credential-related source omitted] - Access to secretsline 150
[Credential-related source omitted] - Access to secretsline 159
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/test_drug_recalls.py
- Executable scriptline 1
Executable file - Access to secretsline 73
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted] - Access to secretsline 141
[Credential-related source omitted] - Access to secretsline 151
[Credential-related source omitted] - Access to secretsline 159
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/test_drug_shortages.py
- Executable scriptline 1
Executable file - Network accessline 39
assert "FDA drug shortage database cannot be accessed" in result assert ( "https://www.accessdata.fda.gov/scripts/drugshortages/" - Network accessline 40
assert ( "https://www.accessdata.fda.gov/scripts/drugshortages/" in result - Network accessline 41
"https://www.accessdata.fda.gov/scripts/drugshortages/" - Network accessline 43
) assert ( "https://www.ashp.org/drug-shortages/current-shortages" - Network accessline 44
assert ( "https://www.ashp.org/drug-shortages/current-shortages" in result - Network accessline 45
"https://www.ashp.org/drug-shortages/current-shortages" - Access to secretsline 219
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/test_endpoint_documentation.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_error_scenarios.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_europe_pmc_fetch.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_mcp_integration.py
skills/biomcp-server/repo/tests/tdd/test_mcp_tools.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_metrics.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_nci_integration.py
- Executable scriptline 1
Executable file - Access to secretsline 31
[Credential-related source omitted] - Access to secretsline 34
[Credential-related source omitted] - Network accessline 35
pytest.raises(CTSAPIError, match="NCI API key required"), ): await make_cts_request("https://example.com/api") - Network accessline 37
await make_cts_request("https://example.com/api") - Access to secretsline 40
[Credential-related source omitted] - Network accessline 45
[Credential-related source omitted] - Network accessline 46
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 73
[Credential-related source omitted] - Access to secretsline 94
[Credential-related source omitted] - Access to secretsline 118
[Credential-related source omitted] - Access to secretsline 140
[Credential-related source omitted] - Access to secretsline 165
[Credential-related source omitted] - Access to secretsline 228
[Credential-related source omitted] - Access to secretsline 250
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/test_nci_mcp_tools.py
- Executable scriptline 1
Executable file - Access to secretsline 68
[Credential-related source omitted] - Access to secretsline 79
[Credential-related source omitted] - Access to secretsline 111
[Credential-related source omitted] - Access to secretsline 118
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 164
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Access to secretsline 207
[Credential-related source omitted] - Access to secretsline 218
[Credential-related source omitted] - Access to secretsline 257
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted] - Access to secretsline 326
[Credential-related source omitted] - Access to secretsline 335
[Credential-related source omitted] - Access to secretsline 377
[Credential-related source omitted] - Access to secretsline 387
[Credential-related source omitted] - Access to secretsline 408
[Credential-related source omitted] - Access to secretsline 427
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/test_network_policies.py
- Executable scriptline 1
Executable file - Network accessline 82
endpoint = EndpointInfo( url="https://api.example.com/test", - Network accessline 83
url="https://api.example.com/test", - Network accessline 142
result, error = await request_api( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", - Network accessline 143
url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", - Network accessline 155
with pytest.raises(ValueError, match="Unknown endpoint key"): await request_api( url="https://api.example.com/test", - Network accessline 156
await request_api( url="https://api.example.com/test", request={"test": "data"}, - Network accessline 157
url="https://api.example.com/test", - Network accessline 170
result, error = await request_api( url="https://api.example.com/test", - Network accessline 171
url="https://api.example.com/test",
skills/biomcp-server/repo/tests/tdd/test_offline_mode.py
- Executable scriptline 1
Executable file - Access to secretsline 25
[Credential-related source omitted] - Network accessline 27
result, error = await request_api( url="https://api.example.com/test", - Network accessline 28
url="https://api.example.com/test", - Access to secretsline 46
[Credential-related source omitted] - Network accessline 52
result, error = await request_api( url="https://api.example.com/cached", - Network accessline 53
url="https://api.example.com/cached", - Access to secretsline 62
[Credential-related source omitted] - Network accessline 64
result, error = await request_api( url="https://api.example.com/cached", - Network accessline 65
url="https://api.example.com/cached", - Network accessline 81
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted] - Network accessline 82
result, error = await request_api( url="https://api.example.com/test", request={"test": "data"}, - Network accessline 83
url="https://api.example.com/test", - Access to secretsline 99
[Credential-related source omitted] - Network accessline 104
result, error = await request_api( url="https://api.example.com/test", - Network accessline 105
url="https://api.example.com/test", - Network accessline 119
[Credential-related source omitted] - Access to secretsline 119
[Credential-related source omitted] - Network accessline 120
result, error = await request_api( url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/", request={"text": "BRAF"}, - Network accessline 121
url="https://www.ncbi.nlm.nih.gov/research/pubtator3-api/search/",
skills/biomcp-server/repo/tests/tdd/test_openfda_unified.py
skills/biomcp-server/repo/tests/tdd/test_pten_r173_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_render.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/test_retry.py
- Executable scriptline 1
Executable file - Network accessline 267
call_count += 1 if call_count < 3: raise httpx.ConnectError("Connection failed") - Network accessline 269
raise httpx.ConnectError("Connection failed") - Network accessline 283
status, content = await call_http( "GET", "https://api.example.com/test", {}, retry_config=config - Network accessline 284
"GET", "https://api.example.com/test", {}, retry_config=config - Network accessline 300
mock_client.get.side_effect = httpx.TimeoutException( - Network accessline 310
with pytest.raises(TimeoutError): await call_http( "GET", "https://api.example.com/test", {}, retry_config=config - Network accessline 311
await call_http( "GET", "https://api.example.com/test", {}, retry_config=config ) - Network accessline 312
"GET", "https://api.example.com/test", {}, retry_config=config
skills/biomcp-server/repo/tests/tdd/test_router.py
- Executable scriptline 1
Executable file - Network accessline 49
assert result["title"] == "Test Article" assert "test abstract" in result["text"] assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" - Network accessline 51
assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/12345/" - Network accessline 329
result = await fetch( - Network accessline 341
result = await fetch(domain="article", id="not_a_number") - Network accessline 372
result = await fetch(domain="trial", id="NCT123", detail="all") - Network accessline 382
with pytest.raises(InvalidParameterError) as exc_info: await fetch( - Network accessline 383
await fetch( - Network accessline 397
"clinvar": {"clinical_significance": "Pathogenic"}, "tcga": {"cancer_types": {}}, "external_links": {"dbSNP": "https://example.com"}, - Network accessline 398
"tcga": {"cancer_types": {}}, "external_links": {"dbSNP": "https://example.com"}, } - Network accessline 399
"external_links": {"dbSNP": "https://example.com"}, - Network accessline 406
result = await fetch(domain="variant", id="rs123") - Network accessline 421
result = await fetch(domain="variant", id="rs123") - Network accessline 427
with pytest.raises(InvalidDomainError): await fetch(domain="invalid", id="123") - Network accessline 428
await fetch(domain="invalid", id="123") - Network accessline 435
with pytest.raises(SearchExecutionError) as exc_info: await fetch(domain="article", id="123") - Network accessline 436
await fetch(domain="article", id="123") - Network accessline 448
result = await fetch(id="12345") - Network accessline 462
result = await fetch(id="NCT12345") - Network accessline 474
await fetch(id="10.1038/nature12345") - Network accessline 483
await fetch(id="rs12345") - Network accessline 492
await fetch(id="chr7:g.140453136A>T")
skills/biomcp-server/repo/tests/tdd/test_unified_biothings.py
- Executable scriptline 1
Executable file - Network accessline 167
result = await fetch(id="BRAF", domain="gene") - Network accessline 200
result = await fetch(id="imatinib", domain="drug") - Network accessline 235
result = await fetch(id="melanoma", domain="disease") - Network accessline 374
result = await fetch(id="INVALID:12345", domain="disease")
skills/biomcp-server/repo/tests/tdd/thinking/__init__.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/thinking/test_sequential.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/trials/test_backward_compatibility.py
skills/biomcp-server/repo/tests/tdd/trials/test_getter.py
- Executable scriptline 1
Executable file - Network accessline 14
async def test_get_protocol(anyio_backend): markdown = await get_trial("NCT04280705", Module.PROTOCOL) assert markdown.startswith("Url: https://clinicaltrials.gov/study/") - Network accessline 15
markdown = await get_trial("NCT04280705", Module.PROTOCOL) assert markdown.startswith("Url: https://clinicaltrials.gov/study/") assert len(markdown) > 10000 # 10370 on 2025-03-23 - Network accessline 16
assert markdown.startswith("Url: https://clinicaltrials.gov/study/") - Network accessline 20
async def test_get_locations(anyio_backend): markdown = await get_trial("NCT04280705", Module.LOCATIONS) starts_with = """Url: https://clinicaltrials.gov/study/NCT04280705 - Network accessline 22
starts_with = """Url: https://clinicaltrials.gov/study/NCT04280705
skills/biomcp-server/repo/tests/tdd/trials/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/utils/test_gene_validator.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/utils/test_mutation_filter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/utils/test_rate_limiter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/utils/test_request_cache.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/constants.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_alphagenome.py
- Executable scriptline 1
Executable file - Access to secretsline 21
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 31
assert "AlphaGenome API key required" in result assert "https://deepmind.google.com/science/alphagenome" in result - Network accessline 32
assert "https://deepmind.google.com/science/alphagenome" in result - Access to secretsline 33
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 72
[Credential-related source omitted] - Access to secretsline 74
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/variants/test_alphagenome_api_key.py
- Executable scriptline 1
Executable file - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 26
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 85
[Credential-related source omitted] - Access to secretsline 86
[Credential-related source omitted] - Network accessline 94
assert "My AlphaGenome API key is" in result assert "ACTION REQUIRED" in result assert "https://deepmind.google.com/science/alphagenome" in result - Network accessline 96
assert "https://deepmind.google.com/science/alphagenome" in result - Access to secretsline 103
[Credential-related source omitted] - Access to secretsline 120
[Credential-related source omitted] - Access to secretsline 121
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/variants/test_alphagenome_comprehensive.py
- Executable scriptline 1
Executable file - Access to secretsline 86
[Credential-related source omitted] - Access to secretsline 104
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 179
[Credential-related source omitted] - Access to secretsline 195
[Credential-related source omitted] - Access to secretsline 214
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/variants/test_cbioportal_mutations.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_cbioportal_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_external.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_external_integration.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_extract_gene_aa_change.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_filters.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_getter.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_links.py
- Executable scriptline 1
Executable file - Network accessline 39
assert ( variant0["dbsnp"]["url"] == f"https://www.ncbi.nlm.nih.gov/snp/{variant0['dbsnp']['rsid']}" - Network accessline 40
variant0["dbsnp"]["url"] == f"https://www.ncbi.nlm.nih.gov/snp/{variant0['dbsnp']['rsid']}" ) - Network accessline 41
== f"https://www.ncbi.nlm.nih.gov/snp/{variant0['dbsnp']['rsid']}" - Network accessline 43
assert ( variant0["clinvar"]["url"] == f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant0['clinvar']['variant_id']}/" - Network accessline 44
variant0["clinvar"]["url"] == f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant0['clinvar']['variant_id']}/" ) - Network accessline 45
== f"https://www.ncbi.nlm.nih.gov/clinvar/variation/{variant0['clinvar']['variant_id']}/" - Network accessline 47
assert ( variant0["cosmic"]["url"] == f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant0['cosmic']['cosmic_id']}" - Network accessline 48
variant0["cosmic"]["url"] == f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant0['cosmic']['cosmic_id']}" ) - Network accessline 49
== f"https://cancer.sanger.ac.uk/cosmic/mutation/overview?id={variant0['cosmic']['cosmic_id']}" - Network accessline 52
assert ( variant0["url"]["ensembl"] == f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant0['dbsnp']['rsid']}" - Network accessline 53
variant0["url"]["ensembl"] == f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant0['dbsnp']['rsid']}" ) - Network accessline 54
== f"https://ensembl.org/Homo_sapiens/Variation/Explore?v={variant0['dbsnp']['rsid']}" - Network accessline 55
) assert variant0["url"]["ucsc_genome_browser"].startswith( "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:" - Network accessline 56
assert variant0["url"]["ucsc_genome_browser"].startswith( "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:" ) - Network accessline 57
"https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:" - Network accessline 59
assert ( variant0["url"]["hgnc"] == "https://www.genenames.org/data/gene-symbol-report/#!/symbol/BRAF" - Network accessline 60
variant0["url"]["hgnc"] == "https://www.genenames.org/data/gene-symbol-report/#!/symbol/BRAF" ) - Network accessline 61
== "https://www.genenames.org/data/gene-symbol-report/#!/symbol/BRAF" - Network accessline 66
assert ( variant1["civic"]["url"] == f"https://civicdb.org/variants/{variant1['civic']['id']}/summary" - Network accessline 67
variant1["civic"]["url"] == f"https://civicdb.org/variants/{variant1['civic']['id']}/summary" ) - Network accessline 68
== f"https://civicdb.org/variants/{variant1['civic']['id']}/summary" - Network accessline 81
assert ( result["url"]["ucsc_genome_browser"] == "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-124" - Network accessline 82
result["url"]["ucsc_genome_browser"] == "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-124" ) - Network accessline 83
== "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-124" - Network accessline 93
assert ( result["url"]["ucsc_genome_browser"] == "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-126" - Network accessline 94
result["url"]["ucsc_genome_browser"] == "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-126" ) - Network accessline 95
== "https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr7:123-126"
skills/biomcp-server/repo/tests/tdd/variants/test_oncokb_client.py
- Executable scriptline 1
Executable file - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 58
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 88
[Credential-related source omitted] - Access to secretsline 97
[Credential-related source omitted] - Access to secretsline 107
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 174
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 209
[Credential-related source omitted] - Access to secretsline 240
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted] - Access to secretsline 297
[Credential-related source omitted] - Access to secretsline 315
[Credential-related source omitted] - Access to secretsline 374
[Credential-related source omitted] - Access to secretsline 397
[Credential-related source omitted] - Access to secretsline 420
[Credential-related source omitted] - Access to secretsline 439
[Credential-related source omitted] - Access to secretsline 454
[Credential-related source omitted] - Access to secretsline 487
[Credential-related source omitted] - Access to secretsline 511
[Credential-related source omitted]
skills/biomcp-server/repo/tests/tdd/variants/test_oncokb_helper.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/variants/test_search.py
- Executable scriptline 1
Executable file
skills/biomcp-server/repo/tests/tdd/workers/test_worker_sanitization.js
- Executable scriptline 1
Executable file - Access to secretsline 10
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 58
[Credential-related source omitted] - Access to secretsline 85
[Credential-related source omitted] - Access to secretsline 86
[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 99
[Credential-related source omitted] - Access to secretsline 100
[Credential-related source omitted] - Access to secretsline 105
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted]
skills/biomcp-server/repo/tests/test_pydantic_ai_integration.py
- Executable scriptline 1
Executable file - Network accessline 63
with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s: - Network accessline 84
try: async with httpx.AsyncClient() as client: - Network accessline 85
async with httpx.AsyncClient() as client: - Access to secretsline 145
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 148
[Credential-related source omitted] - Network accessline 195
await wait_for_server( f"http://localhost:{port}/health", process=server_process - Network accessline 196
f"http://localhost:{port}/health", process=server_process - Network accessline 200
server = MCPServerStreamableHTTP(f"http://localhost:{port}/mcp") - Network accessline 246
await wait_for_server( f"http://localhost:{port}/health", process=server_process - Network accessline 247
f"http://localhost:{port}/health", process=server_process - Network accessline 251
server = MCPServerStreamableHTTP(f"http://localhost:{port}/mcp") - Network accessline 297
await wait_for_server( f"http://localhost:{port}/health", process=server_process - Network accessline 298
f"http://localhost:{port}/health", process=server_process - Network accessline 302
async with httpx.AsyncClient() as client: - Network accessline 304
response = await client.post( f"http://localhost:{port}/mcp", - Network accessline 305
f"http://localhost:{port}/mcp", - Network accessline 327
health_response = await client.get( f"http://localhost:{port}/health" - Network accessline 328
f"http://localhost:{port}/health" - Network accessline 409
await wait_for_server( f"http://localhost:{port}/health", process=server_process - Network accessline 410
f"http://localhost:{port}/health", process=server_process - Network accessline 413
async with httpx.AsyncClient() as client: - Network accessline 414
response = await client.get(f"http://localhost:{port}/health")
skills/biomcp-server/repo/uv.lock
- Network accessline 12
name = "absl-py" version = "2.3.1" source = { registry = "https://pypi.org/simple" } - Network accessline 13
version = "2.3.1" source = { registry = "https://pypi.org/simple" } sdist = { url = "https://files.pythonhosted.org/packages/10/2a/c93173ffa1b39c1d0395b7e842bbdc62e556ca9d8d3b5572926f3e4ca752/absl_py-2.3.1.tar.gz", hash = "sha256:a97820526f - Network accessline 14
source = { registry = "https://pypi.org/simple" } - Network accessline 15
sdist = { url = "https://files.pythonhosted.org/packages/10/2a/c93173ffa1b39c1d0395b7e842bbdc62e556ca9d8d3b5572926f3e4ca752/absl_py-2.3.1.tar.gz", hash = "sha256:a97820526f7fbfd2ec1bce83f3f25e3a14840dac0d8e02a0b71cd75db3f77fc9", size = 1165 - Network accessline 16
wheels = [ { url = "https://files.pythonhosted.org/packages/8f/aa/ba0014cc4659328dc818a28827be78e6d97312ab0cb98105a770924dc11e/absl_py-2.3.1-py3-none-any.whl", hash = "sha256:eeecf07f0c2a93ace0772c92e596ace6d3d3996c042b2128459aaae2a76de - Network accessline 17
{ url = "https://files.pythonhosted.org/packages/8f/aa/ba0014cc4659328dc818a28827be78e6d97312ab0cb98105a770924dc11e/absl_py-2.3.1-py3-none-any.whl", hash = "sha256:eeecf07f0c2a93ace0772c92e596ace6d3d3996c042b2128459aaae2a76de11d", size = 13 - Network accessline 21
name = "ag-ui-protocol" version = "0.1.8" source = { registry = "https://pypi.org/simple" } - Network accessline 22
version = "0.1.8" source = { registry = "https://pypi.org/simple" } dependencies = [ - Network accessline 23
source = { registry = "https://pypi.org/simple" } - Network accessline 25
{ name = "pydantic" }, ] sdist = { url = "https://files.pythonhosted.org/packages/27/de/0bddf7f26d5f38274c99401735c82ad59df9cead6de42f4bb2ad837286fe/ag_ui_protocol-0.1.8.tar.gz", hash = "sha256:eb745855e9fc30964c77e953890092f8bd7d4bbe6550d6 - Network accessline 26
] sdist = { url = "https://files.pythonhosted.org/packages/27/de/0bddf7f26d5f38274c99401735c82ad59df9cead6de42f4bb2ad837286fe/ag_ui_protocol-0.1.8.tar.gz", hash = "sha256:eb745855e9fc30964c77e953890092f8bd7d4bbe6550d6413845428dd0faac0b", si - Network accessline 27
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{ url = "https://files.pythonhosted.org/packages/c4/00/40c6b0313c25d1ab6fac2ecba1cd5b15b1cd3c3a71b3d267ad890e405889/ag_ui_protocol-0.1.8-py3-none-any.whl", hash = "sha256:1567ccb067b7b8158035b941a985e7bb185172d660d4542f3f9c6fff77b55c6e", si - Network accessline 33
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version = "2.6.1" source = { registry = "https://pypi.org/simple" } sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c - Network accessline 35
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sdist = { url = "https://files.pythonhosted.org/packages/26/30/f84a107a9c4331c14b2b586036f40965c128aa4fee4dda5d3d51cb14ad54/aiohappyeyeballs-2.6.1.tar.gz", hash = "sha256:c3f9d0113123803ccadfdf3f0faa505bc78e6a72d1cc4806cbd719826e943558", si - Network accessline 37
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{ url = "https://files.pythonhosted.org/packages/0f/15/5bf3b99495fb160b63f95972b81750f18f7f4e02ad051373b669d17d44f2/aiohappyeyeballs-2.6.1-py3-none-any.whl", hash = "sha256:f349ba8f4b75cb25c99c5c2d84e997e485204d2902a9597802b0371f09331fb8", - Network accessline 42
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version = "3.12.15" source = { registry = "https://pypi.org/simple" } dependencies = [ - Network accessline 44
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{ name = "yarl" }, ] sdist = { url = "https://files.pythonhosted.org/packages/9b/e7/d92a237d8802ca88483906c388f7c201bbe96cd80a165ffd0ac2f6a8d59f/aiohttp-3.12.15.tar.gz", hash = "sha256:4fc61385e9c98d72fcdf47e6dd81833f47b2f77c114c29cd64a361b - Network accessline 54
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{ url = "https://files.pythonhosted.org/packages/47/dc/ef9394bde9080128ad401ac7ede185267ed637df03b51f05d14d1c99ad67/aiohttp-3.12.15-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:b6fc902bff74d9b1879ad55f5404153e2b33a82e72a95c89cec5 - Network accessline 58
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# 1. In the Cloudflare dashboard under Workers & Pages > your-worker > Settings > Variables # 2. Using wrangler CLI: wrangler secret put REMOTE_MCP_SERVER_URL # 3. During local development: wrangler dev --var REMOTE_MCP_SERVER_URL="http://l - Network accessline 9
# 2. Using wrangler CLI: wrangler secret put REMOTE_MCP_SERVER_URL # 3. During local development: wrangler dev --var REMOTE_MCP_SERVER_URL="http://localhost:8000" # 4. In your CI/CD pipeline using environment variables with the format CF_RE - Network accessline 10
# 3. During local development: wrangler dev --var REMOTE_MCP_SERVER_URL="http://localhost:8000" - Network accessline 12
REMOTE_MCP_SERVER_URL = "http://localhost:8000" # Replace with your MCP server URL in production - Network accessline 14
# Stytch OAuth Configuration # Replace these placeholder values with your actual Stytch credentials # For development, use test credentials from https://stytch.com/dashboard - Network accessline 15
# Replace these placeholder values with your actual Stytch credentials # For development, use test credentials from https://stytch.com/dashboard # For production, use production credentials and api.stytch.com instead of test.stytch.com - Network accessline 16
# For development, use test credentials from https://stytch.com/dashboard - Network accessline 19
[Credential-related source omitted] - Network accessline 20
[Credential-related source omitted] - Network accessline 21
STYTCH_API_URL = "https://test.stytch.com/v1" # Use https://api.stytch.com/v1 for production - Network accessline 22
STYTCH_OAUTH_URL = "https://test.stytch.com/v1/public/oauth/google/start" # Update for production
skills/biomedical-data-analysis/README.md
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| Repository | Description | Source | |------------|-------------|--------| | **numpy-tutorials** | Official NumPy educational content | [numpy/numpy-tutorials](https://github.com/numpy/numpy-tutorials) | - Network accessline 455
|------------|-------------|--------| | **numpy-tutorials** | Official NumPy educational content | [numpy/numpy-tutorials](https://github.com/numpy/numpy-tutorials) | | **pandas-workshop** | Conference workshop (ODSC, PyCon, SciPy 2025) | [ - Network accessline 456
| **numpy-tutorials** | Official NumPy educational content | [numpy/numpy-tutorials](https://github.com/numpy/numpy-tutorials) | - Network accessline 457
| **pandas-workshop** | Conference workshop (ODSC, PyCon, SciPy 2025) | [stefmolin/pandas-workshop](https://github.com/stefmolin/pandas-workshop) | - Network accessline 458
| **pandas-cookbook** | Real-world examples with practical data | [jvns/pandas-cookbook](https://github.com/jvns/pandas-cookbook) | - Network accessline 470
| Repository | Description | Source | |------------|-------------|--------| | **tidyverse-workshop** | RStudio Education official workshop | [rstudio-education/welcome-to-the-tidyverse](https://github.com/rstudio-education/welcome-to-the-ti - Network accessline 471
|------------|-------------|--------| | **tidyverse-workshop** | RStudio Education official workshop | [rstudio-education/welcome-to-the-tidyverse](https://github.com/rstudio-education/welcome-to-the-tidyverse) | | **r-tidyverse-series** | - Network accessline 472
| **tidyverse-workshop** | RStudio Education official workshop | [rstudio-education/welcome-to-the-tidyverse](https://github.com/rstudio-education/welcome-to-the-tidyverse) | - Network accessline 473
| **r-tidyverse-series** | Northwestern IT workshop series | [nuitrcs/r-tidyverse](https://github.com/nuitrcs/r-tidyverse) | - Network accessline 483
| Repository | Description | Source | |------------|-------------|--------| | **biomedsql** | NIH biomedical text-to-SQL benchmark | [NIH-CARD/biomedsql](https://github.com/NIH-CARD/biomedsql) | - Network accessline 484
|------------|-------------|--------| | **biomedsql** | NIH biomedical text-to-SQL benchmark | [NIH-CARD/biomedsql](https://github.com/NIH-CARD/biomedsql) | | **sql-for-analytics** | SQL for data analytics (Packt) | [TrainingByPackt/SQL-for - Network accessline 485
| **biomedsql** | NIH biomedical text-to-SQL benchmark | [NIH-CARD/biomedsql](https://github.com/NIH-CARD/biomedsql) | - Network accessline 486
| **sql-for-analytics** | SQL for data analytics (Packt) | [TrainingByPackt/SQL-for-Data-Analytics](https://github.com/TrainingByPackt/SQL-for-Data-Analytics) | - Network accessline 487
| **healthcare-sql** | Healthcare dataset analysis | [SPARTANX21/SQL-Data-Analysis-Healthcare-Project](https://github.com/SPARTANX21/SQL-Data-Analysis-Healthcare-Project) | - Network accessline 496
| Repository | Description | Source | |------------|-------------|--------| | **tableau-powerbi-learning** | Hands-on learning path | [Ashleshk/TableaU-PowerBI-Visualisation-Learning-path](https://github.com/Ashleshk/TableaU-PowerBI-Visuali - Network accessline 497
|------------|-------------|--------| | **tableau-powerbi-learning** | Hands-on learning path | [Ashleshk/TableaU-PowerBI-Visualisation-Learning-path](https://github.com/Ashleshk/TableaU-PowerBI-Visualisation-Learning-path) | | **data-viz-p - Network accessline 498
| **tableau-powerbi-learning** | Hands-on learning path | [Ashleshk/TableaU-PowerBI-Visualisation-Learning-path](https://github.com/Ashleshk/TableaU-PowerBI-Visualisation-Learning-path) | - Network accessline 499
| **data-viz-projects** | MySQL, PostgreSQL, Tableau, Spark projects | [ptyadana/SQL-Data-Analysis-and-Visualization-Projects](https://github.com/ptyadana/SQL-Data-Analysis-and-Visualization-Projects) |
skills/biomedical-data-analysis/tutorials/README.md
- Network accessline 31
### numpy-tutorials (Official) **Source:** [numpy/numpy-tutorials](https://github.com/numpy/numpy-tutorials) - Network accessline 32
**Source:** [numpy/numpy-tutorials](https://github.com/numpy/numpy-tutorials) - Network accessline 43
### pandas-workshop **Source:** [stefmolin/pandas-workshop](https://github.com/stefmolin/pandas-workshop) - Network accessline 44
**Source:** [stefmolin/pandas-workshop](https://github.com/stefmolin/pandas-workshop) - Network accessline 54
### pandas-cookbook **Source:** [jvns/pandas-cookbook](https://github.com/jvns/pandas-cookbook) - Network accessline 55
**Source:** [jvns/pandas-cookbook](https://github.com/jvns/pandas-cookbook) - Network accessline 70
### tidyverse-workshop (RStudio Education) **Source:** [rstudio-education/welcome-to-the-tidyverse](https://github.com/rstudio-education/welcome-to-the-tidyverse) - Network accessline 71
**Source:** [rstudio-education/welcome-to-the-tidyverse](https://github.com/rstudio-education/welcome-to-the-tidyverse) - Network accessline 81
### r-tidyverse-series (Northwestern IT) **Source:** [nuitrcs/r-tidyverse](https://github.com/nuitrcs/r-tidyverse) - Network accessline 82
**Source:** [nuitrcs/r-tidyverse](https://github.com/nuitrcs/r-tidyverse) - Network accessline 97
### biomedsql (NIH) **Source:** [NIH-CARD/biomedsql](https://github.com/NIH-CARD/biomedsql) - Network accessline 98
**Source:** [NIH-CARD/biomedsql](https://github.com/NIH-CARD/biomedsql) - Network accessline 108
### sql-for-analytics (Packt) **Source:** [TrainingByPackt/SQL-for-Data-Analytics](https://github.com/TrainingByPackt/SQL-for-Data-Analytics) - Network accessline 109
**Source:** [TrainingByPackt/SQL-for-Data-Analytics](https://github.com/TrainingByPackt/SQL-for-Data-Analytics) - Network accessline 120
### healthcare-sql **Source:** [SPARTANX21/SQL-Data-Analysis-Healthcare-Project](https://github.com/SPARTANX21/SQL-Data-Analysis-Healthcare-Project) - Network accessline 121
**Source:** [SPARTANX21/SQL-Data-Analysis-Healthcare-Project](https://github.com/SPARTANX21/SQL-Data-Analysis-Healthcare-Project) - Network accessline 136
### tableau-powerbi-learning **Source:** [Ashleshk/TableaU-PowerBI-Visualisation-Learning-path](https://github.com/Ashleshk/TableaU-PowerBI-Visualisation-Learning-path) - Network accessline 137
**Source:** [Ashleshk/TableaU-PowerBI-Visualisation-Learning-path](https://github.com/Ashleshk/TableaU-PowerBI-Visualisation-Learning-path) - Network accessline 148
### data-viz-projects **Source:** [ptyadana/SQL-Data-Analysis-and-Visualization-Projects](https://github.com/ptyadana/SQL-Data-Analysis-and-Visualization-Projects) - Network accessline 149
**Source:** [ptyadana/SQL-Data-Analysis-and-Visualization-Projects](https://github.com/ptyadana/SQL-Data-Analysis-and-Visualization-Projects)
skills/biomedical-search/SKILL.md
- Network accessline 30
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 31
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 52
1. **Ask the user for their API key:** "To search biomedical databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 53
"To search biomedical databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Title", "url": "https://...", - Network accessline 79
"title": "Title", "url": "https://...", "content": "Full content...", - Network accessline 80
"url": "https://...", - Network accessline 82
"source": "pubmed|biorxiv|medrxiv|clinical-trials|drug-labels", "relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] } - Network accessline 84
"images": ["https://example.com/figure1.jpg"] - Network accessline 157
- Base URL: `https://api.valyu.ai/v1` - Network accessline 169
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 180
[Credential-related source omitted] - Network accessline 214
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/biomedical-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/biomedical-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/biomni-general-agent/README.md
- Network accessline 16
**Source:** [snap-stanford/Biomni](https://github.com/snap-stanford/Biomni)
skills/biomni-general-agent/repo/DETAILS.md
skills/biomni-general-agent/repo/LICENSE
skills/biomni-general-agent/repo/README.md
- Network accessline 18
<p align="center"> <a href="https://join.slack.com/t/biomnigroup/shared_invite/zt-3avks4913-dotMBt8D_apQnJ3mG~ak6Q"> - Network accessline 19
<a href="https://join.slack.com/t/biomnigroup/shared_invite/zt-3avks4913-dotMBt8D_apQnJ3mG~ak6Q"> - Network accessline 20
<img src="https://img.shields.io/badge/Join-Slack-4A154B?style=for-the-badge&logo=slack" alt="Join Slack" /> - Network accessline 21
</a> <a href="https://biomni.stanford.edu"> <img src="https://img.shields.io/badge/Try-Web%20UI-blue?style=for-the-badge" alt="Web UI" /> - Network accessline 22
<a href="https://biomni.stanford.edu"> - Network accessline 23
<img src="https://img.shields.io/badge/Try-Web%20UI-blue?style=for-the-badge" alt="Web UI" /> - Network accessline 24
</a> <a href="https://x.com/ProjectBiomni"> <img src="https://img.shields.io/badge/Follow-on%20X-black?style=for-the-badge&logo=x" alt="Follow on X" /> - Network accessline 25
<a href="https://x.com/ProjectBiomni"> - Network accessline 26
<img src="https://img.shields.io/badge/Follow-on%20X-black?style=for-the-badge&logo=x" alt="Follow on X" /> - Network accessline 27
</a> <a href="https://www.linkedin.com/company/project-biomni"> <img src="https://img.shields.io/badge/Follow-LinkedIn-0077B5?style=for-the-badge&logo=linkedin" alt="Follow on LinkedIn" /> - Network accessline 28
<a href="https://www.linkedin.com/company/project-biomni"> - Network accessline 29
<img src="https://img.shields.io/badge/Follow-LinkedIn-0077B5?style=for-the-badge&logo=linkedin" alt="Follow on LinkedIn" /> - Network accessline 30
</a> <a href="https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1"> <img src="https://img.shields.io/badge/Read-Paper-green?style=for-the-badge" alt="Paper" /> - Network accessline 31
<a href="https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1"> - Network accessline 32
<img src="https://img.shields.io/badge/Read-Paper-green?style=for-the-badge" alt="Paper" /> - Network accessline 68
pip install git+https://github.com/snap-stanford/Biomni.git@main - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 82
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Access to secretsline 94
[Credential-related source omitted] - Network accessline 96
[Credential-related source omitted] - Access to secretsline 97
[Credential-related source omitted] - Network accessline 98
OPENAI_ENDPOINT=https://your-resource-name.openai.azure.com/ - Access to secretsline 101
[Credential-related source omitted] - Access to secretsline 104
[Credential-related source omitted] - Network accessline 114
# Optional: Custom model serving configuration # CUSTOM_MODEL_BASE_URL=http://localhost:8000/v1 - Network accessline 115
# CUSTOM_MODEL_BASE_URL=http://localhost:8000/v1 - Access to secretsline 116
[Credential-related source omitted] - Network accessline 130
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Network accessline 131
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Network accessline 132
export OPENAI_ENDPOINT="https://your-resource-name.openai.azure.com/" # optional unless you are using Azure - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 135
[Credential-related source omitted] - Access to secretsline 136
[Credential-related source omitted] - Network accessline 200
The interface will be available at `http://localhost:7860` - Network accessline 253
# See [WeasyPrint Installation Guide](https://doc.courtbouillon.org/weasyprint/stable/first_steps.html) for detailed instructions. - Network accessline 262
# Or download prebuilt binaries from: # https://github.com/theiskaa/markdown2pdf/releases/latest - Network accessline 263
# https://github.com/theiskaa/markdown2pdf/releases/latest - Network accessline 290
- 🤗 Model: [biomni/Biomni-R0-32B-Preview](https://huggingface.co/biomni/Biomni-R0-32B-Preview) - Network accessline 291
- 📝 Technical Report: [biomni.stanford.edu/blog/biomni-r0-technical-report](https://biomni.stanford.edu/blog/biomni-r0-technical-report) - Network accessline 313
llm="biomni/Biomni-R0-32B-Preview", source="Custom", base_url="http://localhost:30000/v1", - Network accessline 314
[Credential-related source omitted] - Network accessline 315
base_url="http://localhost:30000/v1", - Access to secretsline 316
[Credential-related source omitted] - Network accessline 335
**Resources:** - 🤗 Dataset: [biomni/Eval1](https://huggingface.co/datasets/biomni/Eval1) - Network accessline 336
- 🤗 Dataset: [biomni/Eval1](https://huggingface.co/datasets/biomni/Eval1) - Network accessline 383
If you have particular tool/database/software in mind that you want to add, you can also submit to [this form](https://forms.gle/nu2n1unzAYodTLVj6) and the biomni team will implement them. - Network accessline 410
Experience Biomni through our no-code web interface at **[biomni.stanford.edu](https://biomni.stanford.edu)**. - Network accessline 412
[](https://youtu.be/E0BRvl23hLs)
skills/biomni-general-agent/repo/biomni/__init__.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/agent/__init__.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/agent/a1.py
- Executable scriptline 1
Executable file - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 58
[Credential-related source omitted] - Access to secretsline 75
[Credential-related source omitted] - Network accessline 85
use_tool_retriever: If True, use a tool retriever timeout_seconds: Timeout for code execution in seconds base_url: Base URL for custom model serving (e.g., "http://localhost:8000/v1") - Network accessline 86
[Credential-related source omitted] - Network accessline 87
base_url: Base URL for custom model serving (e.g., "http://localhost:8000/v1") - Access to secretsline 88
[Credential-related source omitted] - Access to secretsline 105
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 155
[Credential-related source omitted] - Network accessline 177
print("Checking and downloading missing data lake files...") check_and_download_s3_files( s3_bucket_url="https://biomni-release.s3.amazonaws.com", - Network accessline 178
check_and_download_s3_files( s3_bucket_url="https://biomni-release.s3.amazonaws.com", local_data_lake_path=data_lake_dir, - Network accessline 179
s3_bucket_url="https://biomni-release.s3.amazonaws.com", - Network accessline 193
print("Checking and downloading benchmark files...") check_and_download_s3_files( s3_bucket_url="https://biomni-release.s3.amazonaws.com", - Network accessline 194
check_and_download_s3_files( s3_bucket_url="https://biomni-release.s3.amazonaws.com", local_data_lake_path=benchmark_dir, - Network accessline 195
s3_bucket_url="https://biomni-release.s3.amazonaws.com", local_data_lake_path=benchmark_dir, expected_files=[], # Empty list - will download entire folder - Access to secretsline 212
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/agent/env_collection.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/agent/function_generator.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/agent/qa_llm.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/agent/react.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/biorxiv_scripts/extract_biorxiv_tasks.py
skills/biomni-general-agent/repo/biomni/biorxiv_scripts/generate_function.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/biorxiv_scripts/process_all_subjects.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/config.py
- Executable scriptline 1
Executable file - Access to secretsline 28
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 63
[Credential-related source omitted] - Access to secretsline 83
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Access to secretsline 103
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/env_desc.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/env_desc_cm.py
- Executable scriptline 1
Executable file - Network accessline 54
# "McPAS-TCR.parquet": "T-cell receptor sequences and specificity data from McPAS database.", # CC BY-NC-SA 4.0 - Non-commercial only # "miRDB_v6.0_results.parquet": "Predicted microRNA targets from miRDB.", # Non-commercial use only - Network accessline 55
# "miRDB_v6.0_results.parquet": "Predicted microRNA targets from miRDB.", # Non-commercial use only # "miRTarBase_microRNA_target_interaction.parquet": "Experimentally validated microRNA-target interactions from miRTarBase.", # CC BY- - Network accessline 56
# "miRTarBase_microRNA_target_interaction.parquet": "Experimentally validated microRNA-target interactions from miRTarBase.", # CC BY-NC 4.0 - Non-commercial only - Network accessline 57
# "miRTarBase_microRNA_target_interaction_pubmed_abtract.txt": "PubMed abstracts for microRNA-target interactions in miRTarBase.", # CC BY-NC 4.0 - Non-commercial only - Network accessline 58
# "miRTarBase_MicroRNA_Target_Sites.parquet": "Binding sites of microRNAs on target genes from miRTarBase.", # CC BY-NC 4.0 - Non-commercial only
skills/biomni-general-agent/repo/biomni/eval/__init__.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/eval/biomni_eval1.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/know_how/__init__.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/know_how/loader.py
- Executable scriptline 1
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skills/biomni-general-agent/repo/biomni/know_how/resource/CRISPick_download_links.txt
- Network accessline 1
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_8030_ICSASG_v2_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230421.txt.gz - Network accessline 2
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_8030_ICSASG_v2_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230421.summary.txt - Network accessline 3
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_8030_ICSASG_v2_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230421.txt.gz - Network accessline 4
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_8030_ICSASG_v2_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230421.summary.txt - Network accessline 5
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRa_Azimuth_2.0_Ensembl_20241114.txt.gz - Network accessline 6
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRa_Azimuth_2.0_Ensembl_20241114.summary.txt - Network accessline 7
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRi_Azimuth_2.0_Ensembl_20241114.txt.gz - Network accessline 8
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRi_Azimuth_2.0_Ensembl_20241114.summary.txt - Network accessline 9
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRko_Azimuth_2.0_Ensembl_20241114.txt.gz - Network accessline 10
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SaurCas9_CRISPRko_Azimuth_2.0_Ensembl_20241114.summary.txt - Network accessline 11
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SpyoCas9_CRISPRa_RS3seq-Chen2013_Ensembl_20241114.txt.gz - Network accessline 12
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SpyoCas9_CRISPRa_RS3seq-Chen2013_Ensembl_20241114.summary.txt - Network accessline 13
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_Ensembl_20241114.txt.gz - Network accessline 14
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10029_CHOK1GS_HDv1_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_Ensembl_20241114.summary.txt - Network accessline 15
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_74940_Otsh_v1.0_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230424.txt.gz - Network accessline 16
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_74940_Otsh_v1.0_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230424.summary.txt - Network accessline 17
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_74940_Otsh_v1.0_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230424.txt.gz - Network accessline 18
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_74940_Otsh_v1.0_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230424.summary.txt - Network accessline 19
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9913_ARS-UCD1.2_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230418.txt.gz - Network accessline 20
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9913_ARS-UCD1.2_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20230418.summary.txt - Network accessline 21
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9913_ARS-UCD1.2_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230418.txt.gz - Network accessline 22
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9913_ARS-UCD1.2_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20230418.summary.txt - Network accessline 23
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https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10116_Rnor_6.0_SaurCas9_CRISPRko_Azimuth_2.0_NCBI_20220907.txt.gz - Network accessline 230
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https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10116_Rnor_6.0_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20220907.txt.gz - Network accessline 232
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10116_Rnor_6.0_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20220907.summary.txt - Network accessline 233
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10116_Rnor_6.0_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20220907.txt.gz - Network accessline 234
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_10116_Rnor_6.0_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20220907.summary.txt - Network accessline 235
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9544_Mmul_10_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20241025.txt.gz - Network accessline 236
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9544_Mmul_10_SpyoCas9_CRISPRa_RS3seq-Chen2013_NCBI_20241025.summary.txt - Network accessline 237
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9544_Mmul_10_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20241025.txt.gz - Network accessline 238
https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/sgRNA_design_9544_Mmul_10_SpyoCas9_CRISPRko_RS3seq-Chen2013+RS3target_NCBI_20241025.summary.txt
skills/biomni-general-agent/repo/biomni/know_how/resource/addgene_grna_sequences.csv
- Network accessline 1
Application,Cas9 Species,Depositor,Plasmid ID,PubMed ID,Target Gene,Target Sequence,Target Species cut,S. pyogenes,Goncalves,"<a href=""/58252/"">58252</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24870050/"">24870050</a>",AAVS1,GGGG - Network accessline 2
cut,S. pyogenes,Goncalves,"<a href=""/58252/"">58252</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24870050/"">24870050</a>",AAVS1,GGGGCCACTAGGGACAGGAT,H. sapiens - Network accessline 3
cut,S. pyogenes,Church,"<a href=""/41818/"">41818</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",AAVS1,GGGGCCACTAGGGACAGGAT,H. sapiens - Network accessline 4
cut,S. pyogenes,Sabatini,"<a href=""/50662/"">50662</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336569/"">24336569</a>",AAVS1,GGGGCCACTAGGGACAGGAT,H. sapiens - Network accessline 5
cut,S. pyogenes,Sabatini,"<a href=""/70661/"">70661</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",AAVS1,GGGGCCACTAGGGACAGGAT,H. sapiens - Network accessline 6
cut,S. pyogenes,Church,"<a href=""/41817/"">41817</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",AAVS1,GTCCCCTCCACCCCACAGTG,H. sapiens - Network accessline 7
cut,S. pyogenes,Kanemaki,"<a href=""/72833/"">72833</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27052166/"">27052166</a>",AAVS1,GGGGCCACTAGGGACAGGAT,H. sapiens - Network accessline 8
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",AAVS1,TGTCCCTAGTGGCCCCACTG,H. sapiens - Network accessline 9
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",AAVS1,ACAGTGGGGCCACTAGGGAC,H. sapiens - Network accessline 10
RNA targeting,S. pyogenes,Yeo,"<a href=""/74705/"">74705</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26997482/"">26997482</a>",ACTB,UGGAGCGAGCAUCCCCCAAA,H. sapiens - Network accessline 11
cut,S. pyogenes,Jiang,"<a href=""/62552/"">62552</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25739462/"">25739462</a>",actII-orf4,ATTACCAGGGACCGGAGTTC,S. coelicolor - Network accessline 12
cut,S. pyogenes,Zaratiegui,"<a href=""/52225/"">52225</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25352017/"">25352017</a>",ade6+,TCTATTGTTCAGATGCCTCG,S. pombe - Network accessline 13
cut,S. pyogenes,Zaratiegui,"<a href=""/52227/"">52227</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25352017/"">25352017</a>",ade6-L469,TCTATTGTTCAGATGCCTTG,S. pombe - Network accessline 14
cut,S. pyogenes,Zaratiegui,"<a href=""/52226/"">52226</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25352017/"">25352017</a>",ade6-M210,TCTATTGTTCAGATGCTTCG,S. pombe - Network accessline 15
cut,S. pyogenes,Ventura,"<a href=""/64071/"">64071</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25337876/"">25337876</a>",Alk and Eml,,M. musculus - Network accessline 16
nick,S. pyogenes,Shaw,"<a href=""/74374/"">74374</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26816379/"">26816379</a>",AMPK alpha 1,GGCTGTCGCCATCTTTCTCC,H. sapiens - Network accessline 17
nick,S. pyogenes,Shaw,"<a href=""/74375/"">74375</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26816379/"">26816379</a>",AMPK alpha 1,GAAGATCGGCCACTACATTC,H. sapiens - Network accessline 18
nick,S. pyogenes,Shaw,"<a href=""/74376/"">74376</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26816379/"">26816379</a>",AMPK alpha 2,GTCAGCCATCTTCGGCGCGCG,H. sapiens - Network accessline 19
nick,S. pyogenes,Shaw,"<a href=""/74377/"">74377</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26816379/"">26816379</a>",AMPK alpha 2,GAAGATCGGACACTACGTGC,H. sapiens - Network accessline 20
cut,S. pyogenes,Sabatini,"<a href=""/70660/"">70660</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>","Amplicon, JAK2",GAGGCATATTCTTCTCCTGG,H. sapiens - Network accessline 21
cut,S. pyogenes,Voytas,"<a href=""/70019/"">70019</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26541286/"">26541286</a>",ANT1,TGTCGTTTATAATTTGTAGA,S. lycopersicum - Network accessline 22
cut,S. pyogenes,Voytas,"<a href=""/70018/"">70018</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26541286/"">26541286</a>",ANT1,ACAATTTAATACACCTTTT,S. lycopersicum - Network accessline 23
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",AOC,CAAAAGACTGTCAATTCCCT,N. attenuata - Network accessline 24
cut/nick,S. pyogenes,Yamamoto,"<a href=""/58780/"">58780</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",APC,GAAGCGGGCAAAGGGGCGAC,H. sapiens - Network accessline 25
cut,S. pyogenes,Joung,"<a href=""/42241/"">42241</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",apoea,GGATGAGCCAAGAAGCCGCT,D. rerio - Network accessline 26
activate,S. pyogenes,Sato,"<a href=""/64131/"">64131</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",ASCL1,TGGATGGAGAGTTTGCAAGGAGC,H. sapiens - Network accessline 27
activate,S. pyogenes,Sato,"<a href=""/64130/"">64130</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",ASCL1,TGGGCAGCCGCTCGCTGCAGCAG,H. sapiens - Network accessline 28
activate,S. pyogenes,Sato,"<a href=""/64129/"">64129</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",ASCL1,TGGGGCTGGGTGTCCCATTGAAA,H. sapiens - Network accessline 29
activate,S. pyogenes,Sato,"<a href=""/64132/"">64132</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",ASCL1,TGGTGTTTATTCAGCCGGGAGTC,H. sapiens - Network accessline 30
cut,S. pyogenes,Mashimo,"<a href=""/60968/"">60968</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Asip,ATGACAGGAGTCTAACTCAC,R. norvegicus - Network accessline 31
tag,S. pyogenes,Mendenhall,"<a href=""/64690/"">64690</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",ATF1,TAGGAATCAAACACTTTTATTGG,H. sapiens - Network accessline 32
cut,S. pyogenes,Yamamoto,"<a href=""/58779/"">58779</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",ATM,TGAATTGGGATGCTGTTTTT,H. sapiens - Network accessline 33
cut,S. pyogenes,Mello,"<a href=""/58981/"">58981</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24879462/"">24879462</a>",avr-14,GATTGGAGAGTTAGACCACG,C. elegans - Network accessline 34
cut,S. pyogenes,Mello,"<a href=""/58982/"">58982</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24879462/"">24879462</a>",avr-15,GTTTGCAATATAAGTCACCC,C. elegans - Network accessline 35
cut,S. pyogenes,Yamamoto,"<a href=""/58782/"">58782</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",AXIN2,TATGTTGGTGACTTGCCTCC,H. sapiens - Network accessline 36
methylation,S. pyogenes,Zoldoš,"<a href=""/71828/"">71828</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26969735/"">26969735</a>",BACH2,AATGTAGCGATTGAGAGTGTGGG,H. sapiens - Network accessline 37
cut,S. pyogenes,Sabatini,"<a href=""/70658/"">70658</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",BCR/ABL amplicon,GGCTCCCTTCAAGTGGGATG,H. sapiens - Network accessline 38
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",BFP,ATGGCGTGCAGTGCTTCAGC, - Network accessline 39
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",BIN2,ATCACAGTGATGCTCGTCAA,L. sativa - Network accessline 40
cut,S. pyogenes,Hanna,"<a href=""/59724/"">59724</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25543152/"">25543152</a>",BLIMP1,CGGATGGGGTAAACGACCCG,H. sapiens - Network accessline 41
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",BRI1,TTTGAAAGATGGAAGCGCGG,A. thaliana - Network accessline 42
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",BRI1,TGAAACTAAACTGGTCCACA,A. thaliana - Network accessline 43
interfere,S. pyogenes,Lu,"<a href=""/68892/"">68892</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",BT1754,GAAAATGGGGTGTATCCTGC,B. thetaiotaomicron - Network accessline 44
interfere,S. pyogenes,Lu,"<a href=""/68891/"">68891</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",BT1854,ATTGAAGAACAAAAGCAGTT,B. thetaiotaomicron - Network accessline 45
cut,S. pyogenes,Sabatini,"<a href=""/70650/"">70650</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C16orf80,CGATGCTGTAGAGGATGGAG,H. sapiens - Network accessline 46
cut,S. pyogenes,Sabatini,"<a href=""/70651/"">70651</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C16orf80,TGTCTGAGAAGTAAACCCGT,H. sapiens - Network accessline 47
cut,S. pyogenes,Sabatini,"<a href=""/70653/"">70653</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C3orf17,GGGCCAAATGGGGTTTGTGG,H. sapiens - Network accessline 48
cut,S. pyogenes,Sabatini,"<a href=""/70652/"">70652</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C3orf17,GTGTGAGAATCCCTAAGGCG,H. sapiens - Network accessline 49
cut,S. pyogenes,Sabatini,"<a href=""/70654/"">70654</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C9orf114,CAGGCGGGCTCACCTCCGTG,H. sapiens - Network accessline 50
cut,S. pyogenes,Sabatini,"<a href=""/70655/"">70655</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",C9orf114,GCGGCAGAGAAGGAGGACCG,H. sapiens - Network accessline 51
cut,S. pyogenes,Church,"<a href=""/43803/"">43803</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23460208/"">23460208</a>",CAN1,GATACGTTCTCTATGGAGGA,S. cerevisiae - Network accessline 52
cut,S. pyogenes,Bornhauser,"<a href=""/75164/"">75164</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27194728/"">27194728</a>",Caspase-8,GCCTGGACTACATTCCGCAA,H. sapiens - Network accessline 53
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",CCR5,TGACATCAATTATTATACAT,H. sapiens - Network accessline 54
interfere,S. pyogenes,Qi,"<a href=""/46918/"">46918</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",CD71,GGACGCGCTAGTGTGAGTGC,H. sapiens - Network accessline 55
cut,S. pyogenes,Yamamoto,"<a href=""/58781/"">58781</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",CDH1,TGACTTGCGAGGGACGCATT,H. sapiens - Network accessline 56
activate,S. pyogenes,Vale,"<a href=""/60905/"">60905</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25307933/"">25307933</a>",CDKN1B,GAAGCCGGGACCTGGACCAG,H. sapiens - Network accessline 57
tag,S. pyogenes,Mendenhall,"<a href=""/64036/"">64036</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",CEBPB,CTCCGGCCACTGCTAGCGCGG,H. sapiens - Network accessline 58
tag,S. pyogenes,Mendenhall,"<a href=""/64047/"">64047</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",CEBPB,GCCGGCAGGGGGACGCGCGCGG,H. sapiens - Network accessline 59
cut,S. pyogenes,Ikawa,"<a href=""/50718/"">50718</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24284873/"">24284873</a>",Cent1,GGCAACGTTTGACTTCCTGA,M. musculus - Network accessline 60
cut,S. pyogenes,Yamamoto,"<a href=""/58783/"">58783</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",CFTR,TCTGTATCTATATTCATCAT,H. sapiens - Network accessline 61
tag,S. pyogenes,Mendenhall,"<a href=""/64940/"">64940</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",CREB1,GCCACAAATCAGATTAATTTGG,H. sapiens - Network accessline 62
tag,S. pyogenes,Mendenhall,"<a href=""/64939/"">64939</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",CREB1,GCCACAAATCAGATTAATTTGGG,H. sapiens - Network accessline 63
cut,S. pyogenes,Hong,"<a href=""/68060/"">68060</a>","<a href=""http://fungalbiolbiotech.biomedcentral.com/articles/10.1186/s40694-015-0015-1"">Fungal Biology and Biotechnology 2015, 2:4</a>",csr-1,GAGTGGGAGGGTCCCGTCCT,N. crassa - Network accessline 64
cut,S. pyogenes,Jacks,"<a href=""/59912/"">59912</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25119044/"">25119044</a>",Ctnnb1,AGCTCCTTCCCTGAGTGGCA,M. musculus - Network accessline 65
cut,S. pyogenes,Jacks,"<a href=""/59911/"">59911</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25119044/"">25119044</a>",Ctnnb1,CTGTGGTGGTGGCACCAGAA,M. musculus - Network accessline 66
interfere,S. pyogenes,Qi,"<a href=""/46917/"">46917</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",CXCR4,GCAGGTAGCAAAGTGACGCCGA,H. sapiens - Network accessline 67
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",CXCR4,CCTCTTTGTCATCACGCTTC,H. sapiens - Network accessline 68
activate,S. pyogenes,Lu,"<a href=""/64385/"">64385</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,ACAGAGCACATGCATGCCAT,S. cerevisiae - Network accessline 69
activate,S. pyogenes,Lu,"<a href=""/64387/"">64387</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,ACTAATACTTTCAACATTTT,S. cerevisiae - Network accessline 70
activate,S. pyogenes,Lu,"<a href=""/64382/"">64382</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,ATATCGAATTCCTGCAGCCC,S. cerevisiae - Network accessline 71
activate,S. pyogenes,Lu,"<a href=""/64380/"">64380</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,ATATTCTTTCCTTATACATT,S. cerevisiae - Network accessline 72
activate,S. pyogenes,Lu,"<a href=""/64379/"">64379</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,CTAGATATTAAAATGTCTAA,S. cerevisiae - Network accessline 73
activate,S. pyogenes,Lu,"<a href=""/64388/"">64388</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,GTTGAAAGTATTAGTTAAAG,S. cerevisiae - Network accessline 74
activate,S. pyogenes,Lu,"<a href=""/64381/"">64381</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,TACATACAGTAGGATCCTA,S. cerevisiae - Network accessline 75
activate,S. pyogenes,Lu,"<a href=""/64383/"">64383</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,TATAGTAATTTATGCTGCAA,S. cerevisiae - Network accessline 76
activate,S. pyogenes,Lu,"<a href=""/64384/"">64384</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,TGCAAAGGTCCTAATGTATA,S. cerevisiae - Network accessline 77
activate,S. pyogenes,Lu,"<a href=""/64386/"">64386</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,TGTATGTACATACAGTACCC,S. cerevisiae - Network accessline 78
activate,S. pyogenes,Lu,"<a href=""/64378/"">64378</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23977949/"">23977949</a>",CYC1m promoter,TTACTGTATGTACATACAGT,S. cerevisiae - Network accessline 79
cut,S. pyogenes,Wente,"<a href=""/47932/"">47932</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23918387/"">23918387</a>",ddx19,GGCAACAGATTCGTGGGCCC,D. rerio - Network accessline 80
cut,S. pyogenes,Sabatini,"<a href=""/70656/"">70656</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",DDX3Y,GCAGTTTAGCGATATTGACA,H. sapiens - Network accessline 81
cut,S. pyogenes,Sabatini,"<a href=""/70657/"">70657</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",DDX3Y,TCTTGTTGGGGCTAAAACCA,H. sapiens - Network accessline 82
cut,S. pyogenes,Church,"<a href=""/41822/"">41822</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",DNMT3A,GAGATGATCGCCCCTTCTTC,H. sapiens - Network accessline 83
cut,S. pyogenes,Church,"<a href=""/41821/"">41821</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",DNMT3A,GCATGATGCGCGGCCCAAGG,H. sapiens - Network accessline 84
cut,S. pyogenes,Church,"<a href=""/41823/"">41823</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",DNMT3B,GAATTACTCACGCCCCAAGG,H. sapiens - Network accessline 85
cut,VRER Cas9 mutant,Fire,"<a href=""/71516/"">71516</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26680661/"">26680661</a>",dpy-10,CGCTACCATAGGCACCACG,C. elegans - Network accessline 86
cut,S. pyogenes,Katic,"<a href=""/65630/"">65630</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26044730/"">26044730</a>",dpy-10,GCTACCATAGGCACCACGAG,C.elegans - Network accessline 87
cut,S. pyogenes,Fire,"<a href=""/59933/"">59933</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",dpy-10,GCTACCATAGGCACCACGAG,C. elegans - Network accessline 88
cut,VQR Cas9 variant,Fire,"<a href=""/71479/"">71479</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26680661/"">26680661</a>",dpy-10,TCCGCTACCATAGGCACCA,C. elegans - Network accessline 89
cut,S. pyogenes,Seydoux,"<a href=""/70047/"">70047</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26187122/"">26187122</a>",dpy‐10,GCTACCATAGGCACCACGAG,C. elegans - Network accessline 90
cut,S. pyogenes,Joung,"<a href=""/42242/"">42242</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",drd3,GGAAACTACAGCCCAGCGTC,D. rerio - Network accessline 91
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",DWD1,TGCATCGTCCAAGCGCACAG,O. sativa - Network accessline 92
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",DWD1,CTACGACGTCAGGTTCTACC,O. sativa - Network accessline 93
cut,S. pyogenes,Christiaen,"<a href=""/59990/"">59990</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25336740/"">25336740</a>",Ebf,GCTGAGGGTTGGACAACAGG,C. intestinalis - Network accessline 94
dCas9-FokI,S. pyogenes,Joung,"<a href=""/60071/"">60071</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24770325/"">24770325</a>",EGFP,"multiple, see article",A. victoria - Network accessline 95
cut,S. pyogenes,Zhang,"<a href=""/51764/"">51764</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GAAGTTCGAGGGCGACACCC,A. victoria - Network accessline 96
cut,S. pyogenes,Zhang,"<a href=""/51761/"">51761</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GAGCTGGACGGCGACGTAAA,A. victoria - Network accessline 97
cut,S. pyogenes,Joung,"<a href=""/47512/"">47512</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",EGFP,GATGCCGTTCTTCTGCTTGT,A. victoria - Network accessline 98
cut,S. pyogenes,Zhang,"<a href=""/51763/"">51763</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GGAGCGCACCATCTTCTTCA,A. victoria - Network accessline 99
cut,S. pyogenes,Zhang,"<a href=""/51762/"">51762</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GGCCACAAGTTCAGCGTGTC,A. victoria - Network accessline 100
cut,S. pyogenes,Del Bene,"<a href=""/61051/"">61051</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24179142/"">24179142</a>",EGFP,GGCGAGGGCGATGCCACCTA,A. victoria - Network accessline 101
cut,S. pyogenes,Chen,"<a href=""/46760/"">46760</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23918387/"">23918387</a>",EGFP,GGGCACGGGCAGCTTGCCGG,A. victoria - Network accessline 102
cut,S. pyogenes,Joung,"<a href=""/47511/"">47511</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",EGFP,GGGCACGGGCAGCTTGCCGG,A. victoria - Network accessline 103
cut,S. pyogenes,Zhang,"<a href=""/51760/"">51760</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GGGCGAGGAGCTGTTCACCG,A. victoria - Network accessline 104
cut,S. pyogenes,Zhang,"<a href=""/51765/"">51765</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24336571/"">24336571</a>",EGFP,GGTGAACCGCATCGAGCTGA,A. victoria - Network accessline 105
cut,S. pyogenes,Joung,"<a href=""/47513/"">47513</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",EGFP,GGTGGTGCAGATGAACTTCA,A. victoria - Network accessline 106
cut,S. pyogenes,Goncalves,"<a href=""/58255/"">58255</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24870050/"">24870050</a>",EGFP,TGAAGAAGATGGTGCGCTC,A. victoria - Network accessline 107
cut,S. pyogenes,Moffat,"<a href=""/74187/"">74187</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",EIF3D,TGTAGGTTGCCTCCATGGCC,H. sapiens - Network accessline 108
cut,S. pyogenes,Moffat,"<a href=""/74188/"">74188</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",EIF3D,AGACGACCCTGTCATCCGCA,H. sapiens - Network accessline 109
cut,S. pyogenes,Zhang,"<a href=""/42337/"">42337</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287718/"">23287718</a>",Emx1,,H. sapiens - Network accessline 110
cut,S. pyogenes,Joung,"<a href=""/47508/"">47508</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",EMX1,GAGTCCGAGCAGAAGAAGAA,H. sapiens - Network accessline 111
cut,S. pyogenes,Corn,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26789497/"">26789497</a>",EMX1,CGATGTCACCTCCAATGACT,H. sapiens - Network accessline 112
cut,S. pyogenes,Chen,"<a href=""/71288/"">71288</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26193878/"">26193878</a>","ETC2, TRY, and CPC",,A. thaliana - Network accessline 113
cut,S. pyogenes,Bornhauser,"<a href=""/75166/"">75166</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27194728/"">27194728</a>",FADD,ACTCCCGCACACGCTCTGTC,H. sapiens - Network accessline 114
cut,S. pyogenes,Joung,"<a href=""/47510/"">47510</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",FANCF,GGAATCCCTTCTGCAGCACC,H. sapiens - Network accessline 115
cut,S. pyogenes,Seydoux,"<a href=""/65597/"">65597</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",fbf-2,GTAGTCACGGCGATGATTA,C. elegans - Network accessline 116
cut,S. pyogenes,Seydoux,"<a href=""/65591/"">65591</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",fbf-2,TAATCATCGCCGTGACTAC,C. elegans - Network accessline 117
cut,S. pyogenes,Joung,"<a href=""/42244/"">42244</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",fh,GGAGCGAGCGGAGCGGTACA,D. rerio - Network accessline 118
cut,S. pyogenes,Joung,"<a href=""/42243/"">42243</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",fh,GGAGCGGTACATGGCGACCG,D. rerio - Network accessline 119
tag,S. pyogenes,Mendenhall,"<a href=""/64254/"">64254</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",GABPA,GAAAAGGATAATTGAGCCCCAGG,H. sapiens - Network accessline 120
tag,S. pyogenes,Mendenhall,"<a href=""/64255/"">64255</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",GABPA,TTTGGAGTCTCAGAATGTCCTGG,H. sapiens - Network accessline 121
activate,S. pyogenes,Qi,"<a href=""/46916/"">46916</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",GAL4 UAS,GAACGACTAGTTAGGCGTGTA, - Network accessline 122
activate,S. pyogenes,Qi,"<a href=""/46915/"">46915</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",GAL4 UAS,GTTGGAGCACTGTCCTCCGAACGT, - Network accessline 123
activate,S. pyogenes,Sato,"<a href=""/64158/"">64158</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",GAL4UAS,TGGGGACAGTACTCCGCTCGAGT, - Network accessline 124
activate,S. pyogenes,Sato,"<a href=""/64157/"">64157</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",GAL4UAS,TGGGTCTTCGGAGGACAGTACTC, - Network accessline 125
activate,S. pyogenes,Sato,"<a href=""/64159/"">64159</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",GAL4UAS,TGGTCCGTCTAGAAACTCGGTAC, - Network accessline 126
cut,S. pyogenes,Du,"<a href=""/65566/"">65566</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25849248/"">25849248</a>",gfap,GTGCGCAACACATAGCACCA,D. rerio - Network accessline 127
interfere,S. pyogenes,Qi,"<a href=""/46914/"">46914</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",GFP,GAATAGCTCAGAGGCCGAGG,A. victoria - Network accessline 128
cut,S. pyogenes,Church,"<a href=""/41820/"">41820</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",GFP,GGAGCGCACCATCTTCTTCA,A. victoria - Network accessline 129
cut,S. pyogenes,Church,"<a href=""/41819/"">41819</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23287722/"">23287722</a>",GFP,GTGAACCGCATCGAGCTGAA,A. victoria - Network accessline 130
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72619/"">72619</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",GFP,gRNA1: GAGCTGGACGGCGACGTAAA; gRNA2: CAGAACACCCCCATCGGCGA,Synthetic - Network accessline 131
interfere,S. pyogenes,Hudson,"<a href=""/73221/"">73221</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26689101/"">26689101</a>",GFPmut3b,ACCATCTAATTCAACAAGAATT,A. victoria - Network accessline 132
interfere,S. pyogenes,Hudson,"<a href=""/73224/"">73224</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26689101/"">26689101</a>",GFPmut3b,ACCATCTAATTCAACAAGAATT,synthetic - Network accessline 133
CRISPR-display,S. pyogenes,Rinn,"<a href=""/68422/"">68422</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26030444/"">26030444</a>",GLuc,GATCTAGATACGACTCACTAT,synthetic - Network accessline 134
cut,S. pyogenes,Ye,"<a href=""/61833/"">61833</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24424410/"">24424410</a>",gp78,GCCCAGCCTCCGCACCTACA,H. sapiens - Network accessline 135
cut,S. pyogenes,Joung,"<a href=""/42245/"">42245</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",gsk3b,GGGACCTGACCGGCCGCAGG,D. rerio - Network accessline 136
cut,S. pyogenes,Jin,"<a href=""/64333/"">64333</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25281382/"">25281382</a>",his3,ATTGCGATCTCTTTAAAGGG,S. cerevisiae - Network accessline 137
cut,S. pyogenes,Yan,"<a href=""/69539/"">69539</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26130722/"">26130722</a>",HPRT,GACTGTAAGTGAATTACTT,H. sapiens - Network accessline 138
cut,S. pyogenes,Yamamoto,"<a href=""/58778/"">58778</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",HPRT1,CTGATAAAATCTACAGTCAT,H. sapiens - Network accessline 139
cut,S. pyogenes,Yamamoto,"<a href=""/58771/"">58771</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24954249/"">24954249</a>",HPRT1,TTATGCTGAGGATTTGGAAA,H. sapiens - Network accessline 140
activate,S. pyogenes,Sato,"<a href=""/64142/"">64142</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",IL1RN,TGGACGCAGATAAGAACCAGTT,H. sapiens - Network accessline 141
activate,S. pyogenes,Sato,"<a href=""/64151/"">64151</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",IL1RN,TGGCATCAAGTCAGCCATCAGC,H. sapiens - Network accessline 142
activate,S. pyogenes,Sato,"<a href=""/64152/"">64152</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",IL1RN,TGGGAGTCACCCTCCTGGAAAC,H. sapiens - Network accessline 143
activate,S. pyogenes,Sato,"<a href=""/64140/"">64140</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",IL1RN,TGGTGTACTCTCTGAGGTGCTC,H. sapiens - Network accessline 144
cut,S. pyogenes,Xue,"<a href=""/66582/"">66582</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",inverted GFP,GAGCGGCCGCTCGAGTCTAG,A. victoria - Network accessline 145
cut,S. pyogenes,Xue,"<a href=""/66583/"">66583</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",inverted GFP,GATATCGAATTCCTGCAGCC,A. victoria - Network accessline 146
cut,S. pyogenes,Xue,"<a href=""/66581/"">66581</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",inverted GFP,GTATCGATACCGTCGACCTCG,A. victoria - Network accessline 147
cut,S. pyogenes,Xue,"<a href=""/66584/"">66584</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",inverted GFP,GTTGATCCATAACTTCGTAT,A. victoria - Network accessline 148
purify,S. pyogenes,Fujii,"<a href=""/61079/"">61079</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23942116/"">23942116</a>",IRF1,CCGGGGGCGCTGGGCTGTCCCGG,H. sapiens - Network accessline 149
purify,S. pyogenes,Fujii,"<a href=""/61080/"">61080</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25051498/"">25051498</a>",IRF1,GCGCTTACACTTTAGGAGACACTC,H. sapiens - Network accessline 150
cut,S. pyogenes,Sabatini,"<a href=""/70679/"">70679</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26472758/"">26472758</a>",JAK2 amplicon ,GGTTTAATGGAAGAGAAGGG,H. sapiens - Network accessline 151
cut,S. pyogenes,Seydoux,"<a href=""/66085/"">66085</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",K08F4.2,AATCACTCCCTGTTTGTGT,C. elegans - Network accessline 152
cut,S. pyogenes,Seydoux,"<a href=""/66095/"">66095</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",K08F4.2,CACGAGGTGGTATGCGCAG,C. elegans - Network accessline 153
cut,S. pyogenes,Seydoux,"<a href=""/66092/"">66092</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",K08F4.2,CGCAGCGGTTTCCAAAATG,C. elegans - Network accessline 154
cut,S. pyogenes,Seydoux,"<a href=""/66087/"">66087</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",K08F4.2,GCCTTAACCCAGAATAAGA,C. elegans - Network accessline 155
cut,S. pyogenes,Seydoux,"<a href=""/66089/"">66089</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",K08F4.2,TATTAAATGCAGATAACCT,C. elegans - Network accessline 156
cut,S. pyogenes,Wolfe,"<a href=""/69238/"">69238</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",KANK3,GCATGGGTGATGTCAATGCC,H. sapiens - Network accessline 157
cut,S. pyogenes,Mashimo,"<a href=""/60969/"">60969</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Kit-1,CATCTGTGCGGCCGTTGGCT,R. norvegicus - Network accessline 158
cut,S. pyogenes,Mashimo,"<a href=""/60970/"">60970</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Kit-2,CTAACGTTCCAGCGCTCGTT,R. norvegicus - Network accessline 159
cut,S. pyogenes,Mashimo,"<a href=""/60971/"">60971</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Kit-2,GTCAAGATGTCATCTTACGG,R. norvegicus - Network accessline 160
cut,S. pyogenes,Calarco,"<a href=""/46170/"">46170</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23817069/"">23817069</a>",klp-12,GATCCACAAGTTACAATTGG,C. elegans - Network accessline 161
cut,S. pyogenes,Zhang,"<a href=""/60224/"">60224</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25263330/"">25263330</a>","Kras, p53, and Lkb1","multiple, see article",M. musculus - Network accessline 162
cut,S. pyogenes,Zhang,"<a href=""/60225/"">60225</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25263330/"">25263330</a>",LacZ,TGCGAATACGCCCACGCGAT,E. coli - Network accessline 163
cut,S. pyogenes,Moffat,"<a href=""/74179/"">74179</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",LacZ,CCCGAATCTCTATCGTGCGG,E.coli - Network accessline 164
cut,S. pyogenes,Patron,"<a href=""/68256/"">68256</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26616834/"">26616834</a>",lC.GA4a,GTTGAGAGGGGAGCCGGTGA,B. oleracea - Network accessline 165
cut,S. pyogenes,Patron,"<a href=""/68255/"">68255</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26616834/"">26616834</a>",lC.GA4a,GTTTTCACTTGCGGCCGGAG,B. oleracea - Network accessline 166
cut,S. pyogenes,Jin,"<a href=""/64332/"">64332</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25281382/"">25281382</a>",leu2,AATCACAGCCGAAGCCATTA,S. cerevisiae - Network accessline 167
cut,S. pyogenes,Winslow,"<a href=""/66894/"">66894</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26178787/"">26178787</a>",Lkb1,GTGGTGGGCCGCAGTCACAA,M. musculus - Network accessline 168
cut,S. pyogenes,Xue,"<a href=""/66586/"">66586</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",Lox-STOP-Lox,GCGTATAGCATACATTATACG,synthetic - Network accessline 169
cut,S. pyogenes,Xue,"<a href=""/66585/"">66585</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",Lox-STOP-Lox,GCGTATAGTACACATTATACG,synthetic - Network accessline 170
cut,S. pyogenes,Wolfe,"<a href=""/69237/"">69237</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",LRTM2,GCTGGCGGAAGACAGAGTGC,H. sapiens - Network accessline 171
cut,S. pyogenes,Moffat,"<a href=""/74190/"">74190</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",Luciferase,ACAACTTTACCGACCGCGCC, - Network accessline 172
cut,S. pyogenes,Cate,"<a href=""/60847/"">60847</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25139909/"">25139909</a>",LYP1,CATAATAACGTCCAATAAAT,S. cerevisiae - Network accessline 173
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72620/"">72620</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",Malat1,gRNA1: GAACCGGTGGGGCTGCGTCA; gRNA2: GGCAGGAGAGGCCAGTTGCG,H. sapiens - Network accessline 174
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72621/"">72621</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",Malat1,gRNA1: GCAACTTCCATTTTCAGTCT; gRNA2: GGAAGCCTCAGCTCGCCTGA,H. sapiens - Network accessline 175
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72622/"">72622</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",Malat1,gRNA1:GCTGGGGCTCAGTTGCGTAA; gRNA2:AGGTTTCTAAAACATGACGG,H. sapiens - Network accessline 176
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72623/"">72623</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",Malat1,gRNA1:GTTGAGATGAAGCTTCTTCA; gRNA2:TCAACCGTCCCTGCAAGGCT,H. sapiens - Network accessline 177
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72624/"">72624</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",Malat1,gRNA1: GAAACCTCGTGTAGCTATCA; gRNA2: AATGTGAAGGACTTTCGTAA,H. sapiens - Network accessline 178
nick,S. pyogenes,Hanna,"<a href=""/61514/"">61514</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25569111/"">25569111</a>",Mettl14,GCCGCTCCCGGATCTCCTGC,M. musculus - Network accessline 179
nick,S. pyogenes,Hanna,"<a href=""/61515/"">61515</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25569111/"">25569111</a>",Mettl14,GCGGCAGCTCCTAGCTCAGC,M. musculus - Network accessline 180
cut,S. pyogenes,Zhao,"<a href=""/69801/"">69801</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26293209/"">26293209</a>",mitf,CTTTCGGATATAATCCACGG,S. scrofa - Network accessline 181
cut,S. pyogenes,Chen,"<a href=""/47931/"">47931</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23918387/"">23918387</a>",mitfa,GGTCTCTCGCAGGATGTTGC,D. rerio - Network accessline 182
cut,S. pyogenes,Bleris,"<a href=""/62715/"">62715</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25527740/"">25527740</a>",mKate,ATGAGAATCAAGGCGGTCGA,synthetic - Network accessline 183
cut,S. pyogenes,Bornhauser,"<a href=""/75167/"">75167</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27194728/"">27194728</a>",MLKL,ATCCCCGTGGATTCTGCTAA,H. sapiens - Network accessline 184
cut,S. pyogenes,Katsanis,"<a href=""/72890/"">72890</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26429889/"">26429889</a>",mmp21,CGGAGCTGATCACTGACA,D. rerio - Network accessline 185
visualize,S. pyogenes,Qi,"<a href=""/51025/"">51025</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24360272/"">24360272</a>",MUC4,GTGGCGTGACCTGTGGATGCTG,H. sapiens - Network accessline 186
activate,S. pyogenes,Sato,"<a href=""/64138/"">64138</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",MYOD1,TGGCCTCCCTCCCTGCCCGGTAG,H. sapiens - Network accessline 187
activate,S. pyogenes,Sato,"<a href=""/64139/"">64139</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",MYOD1,TGGGAGGTTTGGAAAGGGCGTGC,H. sapiens - Network accessline 188
activate,S. pyogenes,Sato,"<a href=""/64136/"">64136</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",MYOD1,TGGGCCTGGGCTCCGGGGCGTTT,H. sapiens - Network accessline 189
activate,S. pyogenes,Sato,"<a href=""/64137/"">64137</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",MYOD1,TGGGGGCCCCTGCGGCCACCCCG,H. sapiens - Network accessline 190
activate,S. pyogenes,Sato,"<a href=""/64156/"">64156</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",NANOG,TGGCATATTCCTGATTTAAAAGT,H. sapiens - Network accessline 191
activate,S. pyogenes,Sato,"<a href=""/64153/"">64153</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",NANOG,TGGCGCCAGGAGGGGTGGGTCTA,H. sapiens - Network accessline 192
activate,S. pyogenes,Sato,"<a href=""/64154/"">64154</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",NANOG,TGGGCCTTGGTGAGACTGGTAGA,H. sapiens - Network accessline 193
activate,S. pyogenes,Sato,"<a href=""/64155/"">64155</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",NANOG,TGGTGTCTTCAGGTTCTGTTGCT,H. sapiens - Network accessline 194
interfere,S. pyogenes,Lu,"<a href=""/68897/"">68897</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",NanoLuc,AGCTTACGCCACCCTGTTCC,synthetic - Network accessline 195
interfere,S. pyogenes,Lu,"<a href=""/68898/"">68898</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",NanoLuc,GACAGAACGATGCGCTGAAT,synthetic - Network accessline 196
interfere,S. pyogenes,Lu,"<a href=""/68895/"">68895</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",NanoLuc,TCACGCTCACACCCAGGTTC,synthetic - Network accessline 197
interfere,S. pyogenes,Lu,"<a href=""/68896/"">68896</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",NanoLuc,TTGATCCAAATTATAACCCG,synthetic - Network accessline 198
cut,S. pyogenes,Lu,"<a href=""/61270/"">61270</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25240928/"">25240928</a>",NDM-1,GGGCAGTCGCTTCCAACGGTTTGATCGTCA, - Network accessline 199
cut,S. pyogenes,Cepko,"<a href=""/69992/"">69992</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25155555/"">25155555</a>",near LoxP sites,CGAAGTTATATTAAGGGTTC,synthetic - Network accessline 200
interfere,S. pyogenes,Lu,"<a href=""/68893/"">68893</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",negative control,CTGGAATGAATTGGCCTATG, - Network accessline 201
cut,S. pyogenes,Winslow,"<a href=""/66895/"">66895</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26178787/"">26178787</a>",negative control,GCGAGGTATTCGGCTCCGCG,M. musculus - Network accessline 202
cut,S. pyogenes,Christiaen,"<a href=""/60006/"">60006</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25336740/"">25336740</a>",negative control,GCTTTGCTACGATCTACATT,C. intestinalis - Network accessline 203
cut,S. pyogenes,Bleris,"<a href=""/64955/"">64955</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25527740/"">25527740</a>",negative control,GTCAAGGCACTCTTGCCTA,synthetic - Network accessline 204
,S. pyogenes,Wolfe,"<a href=""/50927/"">50927</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",negative control,GTTCCGCGTTACATAACTTA,H. sapiens - Network accessline 205
cut,S. pyogenes,Winslow,"<a href=""/67594/"">67594</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26178787/"">26178787</a>",Neomycin,TCATGGCTGATGCAATGCGG, - Network accessline 206
cut,S. pyogenes,Zhang,"<a href=""/60227/"">60227</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25263330/"">25263330</a>",NeuN,TCCGGTTCAGGGACCCCGAC,M. musculus - Network accessline 207
activate,S. pyogenes,Sato,"<a href=""/64161/"">64161</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",Neurog2,GTCTCTATCACTGATAGGGA,H. sapiens - Network accessline 208
activate,S. pyogenes,Sato,"<a href=""/64160/"">64160</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25619936/"">25619936</a>",Neurog2,GTGAATGATGATAATACGAT,H. sapiens - Network accessline 209
methylation,S. pyogenes,Zoldoš,"<a href=""/71830/"">71830</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26969735/"">26969735</a>",Non-targeting,GTAGGCGCGCCGCTCTCTAC,H. sapiens - Network accessline 210
cut,S. pyogenes,Huangfu,"<a href=""/66989/"">66989</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26028531/"">26028531</a>",OCT4,CTCCCATGCATTCAAACTG,H. sapiens - Network accessline 211
activate,S. pyogenes,Otonkoski,"<a href=""/69537/"">69537</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26352799/"">26352799</a>",OCT4,"multiple, see article",H. sapiens - Network accessline 212
cut,N. meningitidis,Thomson,"<a href=""/47870/"">47870</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23940360/"">23940360</a>",OCT4,GTTGTAGCTCCCTTTCTCATTTCG,H. sapiens - Network accessline 213
interfere,S. pyogenes,Wolfe,"<a href=""/50922/"">50922</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Oct4A (POU5F1),GGGGCGCCAGTTGTGTCTCC,H. sapiens - Network accessline 214
interfere,S. pyogenes,Wolfe,"<a href=""/50921/"">50921</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Oct4A (POU5F1),GTGGGACTGGGGAGGGAGAG,H. sapiens - Network accessline 215
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",P450,CATATAGTTGGGTCATGGCA,O. sativa - Network accessline 216
cut,S. pyogenes,Sherwood,"<a href=""/71483/"">71483</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26527385/"">26527385</a>",Pal1,GCTCTGTGACTAGTCACAGAG,synthetic - Network accessline 217
cut,S. pyogenes,Sherwood,"<a href=""/71484/"">71484</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26527385/"">26527385</a>",Pal7,GGCTTAGTACTAGTACTAAGC,synthetic - Network accessline 218
cut,S. pyogenes,Zhang,"<a href=""/68466/"">68466</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26145478/"">26145478</a>",PAX6,GATACTGGAGAAGCAGGGGC,H. sapiens - Network accessline 219
cut,S. pyogenes,Zhang,"<a href=""/68465/"">68465</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26145478/"">26145478</a>",PAX6,GTAGATTTTGTATGCACTGC,H. sapiens - Network accessline 220
interfere,S. pyogenes,Lu,"<a href=""/68900/"">68900</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",PcfiA,AAACAAAACCTCATCAGGCA, - Network accessline 221
interfere,S. pyogenes,Lu,"<a href=""/68899/"">68899</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26918244/"">26918244</a>",PcfiA,GAAGCTCACTCCTTAGCACG, - Network accessline 222
interfere,S. pyogenes,Lu,"<a href=""/74068/"">74068</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pck,AGGGCGAGGCGCCGACCAAGAATA,C. glutamicum - Network accessline 223
interfere,S. pyogenes,Lu,"<a href=""/74069/"">74069</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pck,TCCAGTTCAGCAGTTCCTTATTCT,C. glutamicum - Network accessline 224
cut,S. pyogenes,Kamoun,"<a href=""/46966/"">46966</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23929340/"">23929340</a>",PDS,GCCGTTAATTTGAGAGTCCA,N. benthamiana - Network accessline 225
cut,S. pyogenes,Kamoun,"<a href=""/49772/"">49772</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24112467/"">24112467</a>",PDS1,"multiple, see article",N. benthamiana - Network accessline 226
cut,S. pyogenes,Sheen,"<a href=""/52255/"">52255</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23929339/"">23929339</a>",PDS3,GGACTTTTGCCAGCCATGGT,A. thaliana - Network accessline 227
interfere,S. pyogenes,Lu,"<a href=""/74066/"">74066</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pgi,TGACCGATCATTACTCAAACTTCC,C. glutamicum - Network accessline 228
interfere,S. pyogenes,Lu,"<a href=""/74067/"">74067</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pgi,TTGCCTGGAAGTTTGAGTAATGAT,C. glutamicum - Network accessline 229
activate,S. pyogenes,Gersbach,"<a href=""/60719/"">60719</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25664691/"">25664691</a>",pGL3-Basic-8x-gRNA-eGFP reporter,AAAGGTCGAGAAACTGCAAA,synthetic - Network accessline 230
cut,S. pyogenes,Ward,"<a href=""/61252/"">61252</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25491644/"">25491644</a>",pha-1,ATGAATAACTTGATGAACAT,C. elegans - Network accessline 231
cut,S. pyogenes,Kim,"<a href=""//""></a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26479191/"">26479191</a>",PHYB,CACTAGGAGCAACACCCAA,A. thaliana - Network accessline 232
cut,S. pyogenes,Wolfe,"<a href=""/69240/"">69240</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",PLXNB2,GGGCCCAACCTAGGGCATGG,H. sapiens - Network accessline 233
cut,S. pyogenes,Patron,"<a href=""/68253/"">68253</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26616834/"">26616834</a>",PM19,GCTCTCCACTCTGGGCTCTT,H. vulgare - Network accessline 234
cut,S. pyogenes,Patron,"<a href=""/68254/"">68254</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26616834/"">26616834</a>",PM19,GGCTGGCGTTGGTCGTAACA,H. vulgare - Network accessline 235
cut,S. pyogenes,Shaw,"<a href=""/79004/"">79004</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26944679/"">26944679</a>",Prkaa1,TTATTGTCACAGGCATATGG,M. musculus - Network accessline 236
cut,S. pyogenes,Shaw,"<a href=""/79005/"">79005</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26944679/"">26944679</a>",Prkaa2,ACAGGCATATGGTTGTCCAT,M. musculus - Network accessline 237
cut,S. pyogenes,Schmitt-Ulms,"<a href=""/61857/"">61857</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25490046/"">25490046</a>",Prnp,GGTGGAACACCGGTGGAAGC,M. musculus - Network accessline 238
cut,S. pyogenes,Schmitt-Ulms,"<a href=""/61856/"">61856</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25490046/"">25490046</a>",Prnp,TTGGCCCCATCCACCGCCAT,M. musculus - Network accessline 239
cut,N. meningitidis,Church,"<a href=""/48651/"">48651</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer A,TACCATCTCAAGCTTGTTGA,Synthetic - Network accessline 240
cut,S. thermophilus,Church,"<a href=""/48653/"">48653</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer A,TACCATCTCAAGCTTGTTGA,Synthetic - Network accessline 241
cut,T. denticola,Church,"<a href=""/48655/"">48655</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer A,TACCATCTCAAGCTTGTTGA,Synthetic - Network accessline 242
cut,N. meningitidis,Church,"<a href=""/48652/"">48652</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer B,ACTTTAAAAGTATTCGCCAT,Synthetic - Network accessline 243
cut,S. thermophilus,Church,"<a href=""/48654/"">48654</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer B,ACTTTAAAAGTATTCGCCAT,Synthetic - Network accessline 244
cut,T. denticola,Church,"<a href=""/48656/"">48656</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24076762/"">24076762</a>",Protospacer B,ACTTTAAAAGTATTCGCCAT,Synthetic - Network accessline 245
cut,S. pyogenes,Moffat,"<a href=""/74184/"">74184</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",PSMB2,ATGTTCTTGTCGCCTCCGAC,H. sapiens - Network accessline 246
cut,S. pyogenes,Moffat,"<a href=""/74185/"">74185</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",PSMB2,AATATTGTCCAGATGAAGGA,H. sapiens - Network accessline 247
cut,S. pyogenes,Moffat,"<a href=""/74180/"">74180</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",PSMD1,TGTGCGCTACGGAGCTGCAA,H. sapiens - Network accessline 248
cut,S. pyogenes,Moffat,"<a href=""/74181/"">74181</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26627737/"">26627737</a>",PSMD1,ACCAGAGCCACAATAAGCCA,H. sapiens - Network accessline 249
cut,S. pyogenes,Jacks,"<a href=""/59909/"">59909</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25119044/"">25119044</a>",Pten,AGATCGTTAGCAGAAACAAA,M. musculus - Network accessline 250
cut,S. pyogenes,Xue,"<a href=""/66588/"">66588</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",Pten,GCTGTAGTAATATCTGCTAT,M. musculus - Network accessline 251
cut,S. pyogenes,Xue,"<a href=""/66587/"">66587</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26018130/"">26018130</a>",Pten,GTTTCATAGCGGCCACGAAGT,M. musculus - Network accessline 252
interfere,S. pyogenes,Lu,"<a href=""/74070/"">74070</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pyk,AGATTGTATGTACCCTAGGCCCAG,C. glutamicum - Network accessline 253
interfere,S. pyogenes,Lu,"<a href=""/74072/"">74072</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",pyk,ATTCCATCTGCACTAGCCACCGCT,C. glutamicum - Network accessline 254
tag,S. pyogenes,Mendenhall,"<a href=""/64057/"">64057</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26355004/"">26355004</a>",RAD21,CCAAGGTTCCATATTATATAAGG,H. sapiens - Network accessline 255
cut,S. pyogenes,Fire,"<a href=""/59927/"">59927</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",rde-1(D718),TGCCATTAACTATGTATGT,C. elegans - Network accessline 256
cut,S. pyogenes,Fire,"<a href=""/59928/"">59928</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",rde-1(D801),GATATTGTAGTCTATCGAGA,C. elegans - Network accessline 257
cut,S. pyogenes,Fire,"<a href=""/59929/"">59929</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",rde-1(H974),GATAAATGAGCATAATGAAC,C. elegans - Network accessline 258
interfere,S. pyogenes,Lu,"<a href=""/74075/"">74075</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26829286/"">26829286</a>",rfp,AAGTTCGTATGGAAGGTTCCGTTAA, - Network accessline 259
cut,S. pyogenes,Joung,"<a href=""/42246/"">42246</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",rgs4,GGAGAAGGTGAAGGACACTG,D. rerio - Network accessline 260
cut,S. pyogenes,Bornhauser,"<a href=""/75165/"">75165</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27194728/"">27194728</a>",RIP3,TACACGAGTGATGGTTCGGT,H. sapiens - Network accessline 261
cut,S. pyogenes,Bornhauser,"<a href=""/75163/"">75163</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27194728/"">27194728</a>",RIPK1,GCTCTGCTGGGAAGCGAATC,H. sapiens - Network accessline 262
cut,S. pyogenes,Joung,"<a href=""/47509/"">47509</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",RNF2,GTCATCTTAGTCATTACCTG,H. sapiens - Network accessline 263
cut,S. pyogenes,Fire,"<a href=""/59930/"">59930</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",rol-6(su1006),GTGAGACGTCAACAATATGG,C. elegans - Network accessline 264
cut,S. pyogenes,Kuhn,"<a href=""/64216/"">64216</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25803306/"">25803306</a>",Rosa26,ACTCCAGTCTTTCTAGAAGA,M.musculus - Network accessline 265
cut,S. pyogenes,Marraffini,"<a href=""/44505/"">44505</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360965/"">23360965</a>",rpsL,AAAAAACCGAACTCCGCGCTGCGTAAAGTA,E. coli - Network accessline 266
interfere,S. pyogenes,Voigt,"<a href=""/62285/"">62285</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25422271/"">25422271</a>",scramble,AACCCCTGATTGTATCCGCA,synthetic - Network accessline 267
cut,S. pyogenes,Chen,"<a href=""/47930/"">47930</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23918387/"">23918387</a>",slc24a5 (golden),GGTCTCTCGCAGGATGTTGC,D. rerio - Network accessline 268
cut,S. pyogenes,Hanna,"<a href=""/59725/"">59725</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25543152/"">25543152</a>",SOX17,GCCCAGCCCGGCCATCACCG,H. sapiens - Network accessline 269
activate,S. pyogenes,Wolfe,"<a href=""/50925/"">50925</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Sox17,GCTCCGGCTAGTTTTCCCGG,H. sapiens - Network accessline 270
activate,S. pyogenes,Wolfe,"<a href=""/50924/"">50924</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Sox17,GGAGGGGCAAGGGGCGGGCG,H. sapiens - Network accessline 271
activate,S. pyogenes,Wolfe,"<a href=""/50926/"">50926</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Sox17,GGGCAAGTACGTCGATTCCA,H. sapiens - Network accessline 272
activate,S. pyogenes,Wolfe,"<a href=""/50923/"">50923</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24346702/"">24346702</a>",Sox17,GGGCGTGGGCCTAACGACGC,H. sapiens - Network accessline 273
cut,S. pyogenes,Fire,"<a href=""/59935/"">59935</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",sqt-1,GGAAGGACATAGTTGTCAT,C. elegans - Network accessline 274
cut,S. pyogenes,Fire,"<a href=""/60212/"">60212</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",sqt-1,TGTGGAGTTGGGGTAGCGT,C. elegans - Network accessline 275
activate/interfere,S. pyogenes,Qi,"<a href=""/62338/"">62338</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",sv40 promoter,CATACTTCTGCCTGCTGGGGAGCCTG,synthetic - Network accessline 276
scaffold,S. pyogenes,Qi & Lim,"<a href=""/62340/"">62340</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",SV40.NT1,GAATAGCTCAGAGGCCGAGG,H. sapiens - Network accessline 277
cut,S. pyogenes,Seydoux,"<a href=""/66100/"">66100</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",swan-2,ACAAATTGATATCCAATCA,C. elegans - Network accessline 278
cut,S. pyogenes,Seydoux,"<a href=""/66099/"">66099</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25249454/"">25249454</a>",swan-2,TGAAGAAAGTTATACTCGA,C. elegans - Network accessline 279
cut,S. pyogenes,Hanna,"<a href=""/59726/"">59726</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25543152/"">25543152</a>",T (BRACHYURY),CACGCGCAGTTCGCGCTCTG,H. sapiens - Network accessline 280
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72627/"">72627</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",TCRC,gRNA1:GGGGAGCGGGAAAGCGGTCG; gRNA2:AACTGACCTTCAGGCCCGTA,H. sapiens - Network accessline 281
cut,N. meningitidis,Thomson,"<a href=""/47869/"">47869</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23940360/"">23940360</a>",tdtomato,CGAAATGAGAAAGGGAGCTACAAC,Synthetic - Network accessline 282
scaffold,S. pyogenes,Qi & Lim,"<a href=""/62320/"">62320</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",TEF,TTGATATTTAAGTTAATAAA,S. cerevisiae - Network accessline 283
interfere,S. pyogenes,Weissman,"<a href=""/46922/"">46922</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",TEF1,TTGATATTTAAGTTAATAAA,S. cerevisiae - Network accessline 284
visualize,S. pyogenes,Qi,"<a href=""/51024/"">51024</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24360272/"">24360272</a>",telomeres,GTTAGGGTTAGGGTTAGGGTTA,H. sapiens - Network accessline 285
scaffold,S. pyogenes,Qi & Lim,"<a href=""/62313/"">62313</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",TET,ACTTTTCTCTATCACTGATA,S. cerevisiae - Network accessline 286
interfere,S. pyogenes,Weissman,"<a href=""/46923/"">46923</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23849981/"">23849981</a>",TET promoter,TATCAGTGATAGAGAAAAGT, - Network accessline 287
activate/interfere,S. pyogenes,Qi,"<a href=""/62327/"">62327</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",Tet3G,GTACGTTCTCTATCACTGATA,synthetic - Network accessline 288
cut,S. pyogenes,Shaw,"<a href=""/79006/"">79006</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26944679/"">26944679</a>",Tfeb,AGCACTGTTGCCGGCCGAGG,M. musculus - Network accessline 289
RNA targeting,S. pyogenes,Yeo,"<a href=""/74709/"">74709</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26997482/"">26997482</a>",TFRC,GCACUGACCAGAUAAGAAUG,H. sapiens - Network accessline 290
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72626/"">72626</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",TFRC,"gRNA1:GCAGCCTCAGAAATACAAAA, gRNA2CGGGATATCGGGTGGCGGCT",H. sapiens - Network accessline 291
cut,S. pyogenes,Wolfe,"<a href=""/69239/"">69239</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",TGM2,CCTGGACCCAACGCCCCAGG,H. sapiens - Network accessline 292
cut,S. pyogenes,Sibley,"<a href=""/59855/"">59855</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25480939/"">25480939</a>",TGME49_290860,ATTGGTCTGACAGCGATGTG,T. gondii - Network accessline 293
cut,S. pyogenes,Joung,"<a href=""/42247/"">42247</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",th,GGATGCGCGTAAGGAGCGCG,D. rerio - Network accessline 294
cut,S. pyogenes,Du,"<a href=""/65565/"">65565</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25849248/"">25849248</a>",th,GGGTTGTTACACTCATAAAG,D. rerio - Network accessline 295
cut,S. pyogenes,Joung,"<a href=""/42248/"">42248</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",tia1l,GGTATGTCGGGAACCTCTCC,D. rerio - Network accessline 296
cut,S. pyogenes,Joung,"<a href=""/42249/"">42249</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23360964/"">23360964</a>",tph1a,GGGAAAACACAACCGCAGCC,D. rerio - Network accessline 297
scaffold,S. pyogenes,Qi & Lim,"<a href=""/62325/"">62325</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25533786/"">25533786</a>",TRE3G,GTACGTTCTCTATCACTGATA,H. sapiens - Network accessline 298
cut,S. pyogenes,Jin,"<a href=""/64331/"">64331</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25281382/"">25281382</a>",trp1,GTCAATTGTTCTCTTTCTAT,S. cerevisiae - Network accessline 299
cut,S. pyogenes,Jacks,"<a href=""/59910/"">59910</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25119044/"">25119044</a>",Trp53,CCTCGAGCTCCCTCTGAGCC,M. musculus - Network accessline 300
cut,S. pyogenes,Wolfe,"<a href=""/69234/"">69234</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",TS2,GACCCCCTCCACCCCGCCTC,H. sapiens - Network accessline 301
cut,S. pyogenes,Wolfe,"<a href=""/69235/"">69235</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",TS3,GGTGAGTGAGTGTGTGCGTG,H. sapiens - Network accessline 302
cut,S. pyogenes,Wolfe,"<a href=""/69236/"">69236</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26480473/"">26480473</a>",TS4,GAGTCCGAGCAGAAGAAGAA,H. sapiens - Network accessline 303
cut,S. pyogenes,Goldstein,"<a href=""/47550/"">47550</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23995389/"">23995389</a>",ttTi5605 Mos1 insertion site,ATATCAGTCTGTTTCGTAA,C. elegans - Network accessline 304
cut,S. pyogenes,Chen,"<a href=""/46761/"">46761</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23918387/"">23918387</a>",tyr,CCCCAGAAGTCCTCCAGTCC,D. rerio - Network accessline 305
cut,S. pyogenes,Chen,"<a href=""/64250/"">64250</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25855067/"">25855067</a>",tyr,GGACTGGAGGACTTCTGGGG,D. rerio - Network accessline 306
cut,S. pyogenes,Mashimo,"<a href=""/60966/"">60966</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Tyr (albino),TTTCCAGGATTATGTAATAG,R. norvegicus - Network accessline 307
cut,S. pyogenes,Mashimo,"<a href=""/60967/"">60967</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24967838/"">24967838</a>",Tyr (wild type),TTTCCAGGATTACGTAATAG,R. norvegicus - Network accessline 308
cut,S. pyogenes,"Guigo, Johnson","<a href=""/72628/"">72628</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/26493208/"">26493208</a>",UCA1,gRNA1:GGTTTCCTTTTAGATGACGG; gRNA2:TCTGAAAAGAGAGTCAGCGA,H. sapiens - Network accessline 309
cut,S. pyogenes,Fire,"<a href=""/59932/"">59932</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",unc-109(n499),GGAACTCGTGTCAAAACAAC,C. elegans - Network accessline 310
cut,S. pyogenes,Calarco,"<a href=""/46169/"">46169</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23817069/"">23817069</a>",unc-119,GAATTTTCTGAAATTAAAGA,C. elegans - Network accessline 311
cut,S. pyogenes,Mello,"<a href=""/58202/"">58202</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24879462/"">24879462</a>",unc-22,GAACCCGTTGCCGAATACAC,C. elegans - Network accessline 312
cut,S. pyogenes,Fire,"<a href=""/59931/"">59931</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25161212/"">25161212</a>",unc-58(e665),TCCACGCACATGGTCACTA,C. elegans - Network accessline 313
cut,S. pyogenes,Sibley,"<a href=""/54467/"">54467</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24825012/"">24825012</a>",UPRT,GGCGTCTCGATTGTGAGAGC,Toxoplasma gondii - Network accessline 314
cut,S. pyogenes,Jin,"<a href=""/64330/"">64330</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25281382/"">25281382</a>",ura3,GAGTAAAAAATTGTACTTGG,S. cerevisiae - Network accessline 315
cut,S. pyogenes,Ye,"<a href=""/61812/"">61812</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24424410/"">24424410</a>",USP13,GCCGCCCGGCATGCCGAACA,H. sapiens - Network accessline 316
cut,S. pyogenes,Joung,"<a href=""/47506/"">47506</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",VEGF,GACCCCCTCCACCCCGCCTC,H. sapiens - Network accessline 317
cut,S. pyogenes,Joung,"<a href=""/47505/"">47505</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",VEGF,GGGTGGGGGGAGTTTGCTCC,H. sapiens - Network accessline 318
cut,S. pyogenes,Joung,"<a href=""/47507/"">47507</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/23792628/"">23792628</a>",VEGF,GGTGAGTGAGTGTGTGCGTG,H. sapiens - Network accessline 319
interfere,S. pyogenes,Voigt,"<a href=""/62286/"">62286</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25422271/"">25422271</a>",VR,TGCGCTCGGTCGTTCGGCTG,synthetic - Network accessline 320
nick,S. pyogenes,Yang,"<a href=""/73228/"">73228</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/27213844/"">27213844</a>",xylR,CGAGTTAGACATAATAGTGA,C. beijerinckii - Network accessline 321
cut,S. pyogenes,Ward,"<a href=""/61250/"">61250</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/25491644/"">25491644</a>",Y61A9LA.1,GGATGGATGTGTAGTCAATT,C. elegans - Network accessline 322
cut,S. pyogenes,Liu,"<a href=""/49331/"">49331</a>","<a href=""https://www.ncbi.nlm.nih.gov/pubmed/24326186/"">24326186</a>",yellow,GGTTTTGGACACTGGAACCG,D. melanogaster
skills/biomni-general-agent/repo/biomni/know_how/sgRNA_design_guide.md
- Network accessline 34
### If you use validated sgRNAs from our database (Option 1): - **Database Source**: Addgene (https://www.addgene.org) - Network accessline 35
- **Database Source**: Addgene (https://www.addgene.org) - Network accessline 37
- **Acknowledgment**: "Validated sgRNA sequences obtained from Addgene (https://www.addgene.org/crispr/reference/grna-sequence/)" - Network accessline 222
# Copy the URL from download_links.txt, then: wget [PASTE_URL_HERE] - Network accessline 223
wget [PASTE_URL_HERE] - Network accessline 400
# Download human GRCh38 SpCas9 knockout dataset wget https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/\ - Network accessline 401
wget https://portals.broadinstitute.org/gppx/public/sgrna_design/api/downloads/\
skills/biomni-general-agent/repo/biomni/know_how/single_cell_annotation.md
- Network accessline 34
**Source**: https://www.sc-best-practices.org/cellular_structure/annotation.html - Network accessline 205
### Tools: - **Scanpy**: https://scanpy.readthedocs.io/ - Network accessline 206
- **Scanpy**: https://scanpy.readthedocs.io/ - Network accessline 207
- **CellTypist**: https://www.celltypist.org/ - Network accessline 208
- **scArches**: https://scarches.readthedocs.io/ - Network accessline 209
- **Seurat**: https://satijalab.org/seurat/
skills/biomni-general-agent/repo/biomni/llm.py
- Executable scriptline 1
Executable file - Access to secretsline 29
[Credential-related source omitted] - Network accessline 39
source (str): Source provider: "OpenAI", "AzureOpenAI", "Anthropic", "Ollama", "Gemini", "Bedrock", or "Custom" If None, will attempt to auto-detect from model name base_url (str): The base URL for custom model - Network accessline 40
If None, will attempt to auto-detect from model name base_url (str): The base URL for custom model serving (e.g., "http://localhost:8000/v1"), default is None api_key (str): The API key for the custom llm - Network accessline 41
base_url (str): The base URL for custom model serving (e.g., "http://localhost:8000/v1"), default is None - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 63
[Credential-related source omitted] - Access to secretsline 64
[Credential-related source omitted] - Access to secretsline 162
[Credential-related source omitted] - Access to secretsline 177
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[Credential-related source omitted] - Access to secretsline 183
[Credential-related source omitted] - Access to secretsline 189
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[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 206
[Credential-related source omitted] - Network accessline 216
[Credential-related source omitted] - Network accessline 217
[Credential-related source omitted] - Access to secretsline 217
[Credential-related source omitted] - Network accessline 218
base_url="https://generativelanguage.googleapis.com/v1beta/openai/", - Network accessline 231
[Credential-related source omitted] - Network accessline 232
[Credential-related source omitted] - Access to secretsline 232
[Credential-related source omitted] - Network accessline 233
base_url="https://api.groq.com/openai/v1", - Access to secretsline 278
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/model/__init__.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/model/retriever.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/task/__init__.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/task/base_task.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/task/hle.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/task/lab_bench.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/__init__.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/biochemistry.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/bioengineering.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/bioimaging.py
- Executable scriptline 1
Executable file - Access to secretsline 175
[Credential-related source omitted] - Access to secretsline 176
[Credential-related source omitted] - Access to secretsline 177
[Credential-related source omitted] - Access to secretsline 180
[Credential-related source omitted] - Access to secretsline 181
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted] - Access to secretsline 185
[Credential-related source omitted] - Access to secretsline 186
[Credential-related source omitted] - Access to secretsline 187
[Credential-related source omitted] - Access to secretsline 191
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 193
[Credential-related source omitted] - Access to secretsline 198
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Access to secretsline 200
[Credential-related source omitted] - Network accessline 217
try: response = requests.get(url, headers=headers, stream=True, timeout=300) - Network accessline 218
response = requests.get(url, headers=headers, stream=True, timeout=300) - Access to secretsline 239
[Credential-related source omitted] - Network accessline 256
download_url = f"https://zenodo.org/record/4003545/files/{task_id}.zip?download=1" - Access to secretsline 347
[Credential-related source omitted] - Access to secretsline 368
[Credential-related source omitted] - Access to secretsline 369
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/tool/biophysics.py
- Executable scriptline 1
Executable file - Network accessline 38
url = "https://iupred2a.elte.hu/iupred2a" - Network accessline 45
try: response = requests.post(url, data=payload) - Network accessline 46
response = requests.post(url, data=payload) - Network accessline 442
# Calculate curl (rotation) - Network accessline 443
u_y = cv2.Sobel(u, cv2.CV_64F, 0, 1, ksize=3) / (8.0 * pixel_scale) v_x = cv2.Sobel(v, cv2.CV_64F, 1, 0, ksize=3) / (8.0 * pixel_scale) curl = v_x - u_y - Network accessline 445
curl = v_x - u_y - Network accessline 517
log += f"- Flow visualization images: {output_dir}/flow_viz_*.png\n" log += f"- Divergence maps: {output_dir}/divergence_*.npy\n" log += f"- Curl maps: {output_dir}/curl_*.npy\n" - Network accessline 518
log += f"- Divergence maps: {output_dir}/divergence_*.npy\n" log += f"- Curl maps: {output_dir}/curl_*.npy\n" log += f"- Strain maps: {output_dir}/strain_*.npy\n" - Network accessline 519
log += f"- Curl maps: {output_dir}/curl_*.npy\n"
skills/biomni-general-agent/repo/biomni/tool/cancer_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/cell_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/database.py
- Executable scriptline 1
Executable file - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 67
[Credential-related source omitted] - Access to secretsline 70
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 86
[Credential-related source omitted] - Network accessline 150
if method.upper() == "GET": response = requests.get(endpoint, params=params, headers=headers) - Network accessline 151
response = requests.get(endpoint, params=params, headers=headers) - Network accessline 152
elif method.upper() == "POST": response = requests.post(endpoint, params=params, headers=headers, json=json_data) else: - Network accessline 153
response = requests.post(endpoint, params=params, headers=headers, json=json_data) - Access to secretsline 221
[Credential-related source omitted] - Network accessline 232
esearch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 263
esummary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 289
esummary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 467
prompt (str, required): Natural language query about proteins (e.g., "Find information about human insulin") endpoint (str, optional): Full or partial UniProt API endpoint URL to query directly (e.g., "https: - Network accessline 468
endpoint (str, optional): Full or partial UniProt API endpoint URL to query directly (e.g., "https://rest.uniprot.org/uniprotkb/P01308") max_results (int): Maximum number of results to return - Network accessline 469
(e.g., "https://rest.uniprot.org/uniprotkb/P01308") - Network accessline 477
-------- - Natural language: query_uniprot(prompt="Find information about human insulin protein") - Direct endpoint: query_uniprot(endpoint="https://rest.uniprot.org/uniprotkb/P01308") - Network accessline 479
- Direct endpoint: query_uniprot(endpoint="https://rest.uniprot.org/uniprotkb/P01308") - Network accessline 483
base_url = "https://rest.uniprot.org" - Network accessline 509
SPECIAL NOTES: - Base URL is "https://rest.uniprot.org" - Network accessline 510
- Base URL is "https://rest.uniprot.org" - Network accessline 590
base_url = "https://alphafold.ebi.ac.uk/api" - Network accessline 614
response = requests.get(url) - Network accessline 634
download_url = f"https://alphafold.ebi.ac.uk/files/{filename}" - Network accessline 637
download_response = requests.get(download_url) - Network accessline 712
prompt (str, required): Natural language query about protein domains or families endpoint (str, optional): Direct endpoint path or full URL (e.g., "/entry/interpro/IPR023411" or "https://www.ebi.ac.uk/interp - Network accessline 713
endpoint (str, optional): Direct endpoint path or full URL (e.g., "/entry/interpro/IPR023411" or "https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR023411") max_results (int): Maximum number of results to - Network accessline 714
or "https://www.ebi.ac.uk/interpro/api/entry/interpro/IPR023411") - Network accessline 728
base_url = "https://www.ebi.ac.uk/interpro/api" - Network accessline 753
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://www.ebi.ac.uk/interpro/api") - Network accessline 754
1. "full_url": The complete URL to query (including the base URL "https://www.ebi.ac.uk/interpro/api") - Network accessline 916
search_url = "https://search.rcsb.org/rcsbsearch/v2/query" - Network accessline 956
if return_type == "entry": data_url = f"https://data.rcsb.org/rest/v1/core/entry/{identifier}" - Network accessline 957
data_url = f"https://data.rcsb.org/rest/v1/core/entry/{identifier}" - Network accessline 958
elif return_type == "polymer_entity": entry_id, entity_id = identifier.split("_") data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity/{entry_id}/{entity_id}" - Network accessline 959
entry_id, entity_id = identifier.split("_") data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity/{entry_id}/{entity_id}" elif return_type == "nonpolymer_entity": - Network accessline 960
data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity/{entry_id}/{entity_id}" - Network accessline 961
elif return_type == "nonpolymer_entity": entry_id, entity_id = identifier.split("_") data_url = f"https://data.rcsb.org/rest/v1/core/nonpolymer_entity/{entry_id}/{entity_id}" - Network accessline 962
entry_id, entity_id = identifier.split("_") data_url = f"https://data.rcsb.org/rest/v1/core/nonpolymer_entity/{entry_id}/{entity_id}" elif return_type == "polymer_instance": - Network accessline 963
data_url = f"https://data.rcsb.org/rest/v1/core/nonpolymer_entity/{entry_id}/{entity_id}" - Network accessline 964
elif return_type == "polymer_instance": entry_id, asym_id = identifier.split(".") data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity_instance/{entry_id}/{asym_id}" - Network accessline 965
entry_id, asym_id = identifier.split(".") data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity_instance/{entry_id}/{asym_id}" elif return_type == "assembly": - Network accessline 966
data_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity_instance/{entry_id}/{asym_id}" - Network accessline 967
elif return_type == "assembly": entry_id, assembly_id = identifier.split("-") data_url = f"https://data.rcsb.org/rest/v1/core/assembly/{entry_id}/{assembly_id}" - Network accessline 968
entry_id, assembly_id = identifier.split("-") data_url = f"https://data.rcsb.org/rest/v1/core/assembly/{entry_id}/{assembly_id}" elif return_type == "mol_definition": - Network accessline 969
data_url = f"https://data.rcsb.org/rest/v1/core/assembly/{entry_id}/{assembly_id}" - Network accessline 971
data_url = f"https://data.rcsb.org/rest/v1/core/chem_comp/{identifier}" - Network accessline 974
data_response = requests.get(data_url) - Network accessline 1012
pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" - Network accessline 1013
pdb_response = requests.get(pdb_url) - Network accessline 1054
base_url = "https://rest.kegg.jp" - Network accessline 1071
The KEGG API has the following general form: https://rest.kegg.jp/<operation>/<argument>[/<argument2>[/<argument3> ...]] - Network accessline 1072
https://rest.kegg.jp/<operation>/<argument>[/<argument2>[/<argument3> ...]] - Network accessline 1079
Output only a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://rest.kegg.jp") - Network accessline 1080
1. "full_url": The complete URL to query (including the base URL "https://rest.kegg.jp") - Network accessline 1085
EXAMPLES OF CORRECT OUTPUTS: - For "Find information about glycolysis pathway": {{"full_url": "https://rest.kegg.jp/info/pathway/hsa00010", "description": "Finding information about the glycolysis pathway"}} - Network accessline 1086
- For "Find information about glycolysis pathway": {{"full_url": "https://rest.kegg.jp/info/pathway/hsa00010", "description": "Finding information about the glycolysis pathway"}} - Network accessline 1087
- For "Get information about the human BRCA1 gene": {{"full_url": "https://rest.kegg.jp/get/hsa:672", "description": "Retrieving information about BRCA1 gene in human"}} - Network accessline 1088
- For "List all human pathways": {{"full_url": "https://rest.kegg.jp/list/pathway/hsa", "description": "Listing all human-specific pathways"}} - Network accessline 1089
- For "Convert NCBI gene ID 672 to KEGG ID": {{"full_url": "https://rest.kegg.jp/conv/genes/ncbi-geneid:672", "description": "Converting NCBI Gene ID 672 to KEGG gene identifier"}} - Network accessline 1150
-------- - Natural language: query_stringdb("Show protein interactions for BRCA1 and BRCA2 in humans") - Direct endpoint: query_stringdb(endpoint="https://string-db.org/api/json/network?identifiers=BRCA1,BRCA2&species=9606") - Network accessline 1152
- Direct endpoint: query_stringdb(endpoint="https://string-db.org/api/json/network?identifiers=BRCA1,BRCA2&species=9606") - Network accessline 1156
base_url = "https://version-12-0.string-db.org/api" - Network accessline 1232
try: response = requests.get(endpoint, stream=True) - Network accessline 1233
response = requests.get(endpoint, stream=True) - Network accessline 1322
base_url = "https://apiv3.iucnredlist.org/api/v3" - Network accessline 1329
[Credential-related source omitted] - Network accessline 1330
return {"error": "IUCN API token is required. Get one at https://apiv3.iucnredlist.org/api/v3/token"} - Network accessline 1348
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://apiv3.iucnredlist.org/api/v3" and any path parameters) - Network accessline 1349
1. "full_url": The complete URL to query (including the base URL "https://apiv3.iucnredlist.org/api/v3" and any path parameters) - Network accessline 1427
base_url = "https://paleobiodb.org/data1.2" - Network accessline 1449
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://paleobiodb.org/data1.2" and format extension) - Network accessline 1450
1. "full_url": The complete URL to query (including the base URL "https://paleobiodb.org/data1.2" and format extension) - Network accessline 1497
try: response = requests.get(endpoint) - Network accessline 1498
response = requests.get(endpoint) - Network accessline 1555
base_url = "https://jaspar.elixir.no/api/v1" - Network accessline 1577
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://jaspar.elixir.no/api/v1" and any parameters) - Network accessline 1578
1. "full_url": The complete URL to query (including the base URL "https://jaspar.elixir.no/api/v1" and any parameters) - Network accessline 1653
-------- - Natural language: query_worms("Find information about the blue whale") - Direct endpoint: query_worms(endpoint="https://www.marinespecies.org/rest/AphiaRecordByName/Balaenoptera%20musculus") - Network accessline 1655
- Direct endpoint: query_worms(endpoint="https://www.marinespecies.org/rest/AphiaRecordByName/Balaenoptera%20musculus") - Network accessline 1659
base_url = "https://www.marinespecies.org/rest" - Network accessline 1681
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://www.marinespecies.org/rest" and any path/query parameters) - Network accessline 1682
1. "full_url": The complete URL to query (including the base URL "https://www.marinespecies.org/rest" and any path/query parameters) - Network accessline 1756
base_url = "https://www.cbioportal.org/api" - Network accessline 1778
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://www.cbioportal.org/api" and any parameters) - Network accessline 1779
1. "full_url": The complete URL to query (including the base URL "https://www.cbioportal.org/api" and any parameters) - Network accessline 2121
-------- - Natural language: query_ucsc("Get DNA sequence of chromosome M positions 1-100 in human genome") - Direct endpoint: query_ucsc(endpoint="https://api.genome.ucsc.edu/getData/sequence?genome=hg38&chrom=chrM&start=1&end=100" - Network accessline 2123
- Direct endpoint: query_ucsc(endpoint="https://api.genome.ucsc.edu/getData/sequence?genome=hg38&chrom=chrM&start=1&end=100") - Network accessline 2127
base_url = "https://api.genome.ucsc.edu" - Network accessline 2149
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://api.genome.ucsc.edu" and all parameters) - Network accessline 2150
1. "full_url": The complete URL to query (including the base URL "https://api.genome.ucsc.edu" and all parameters) - Network accessline 2229
base_url = "https://rest.ensembl.org" - Network accessline 2352
OPENTARGETS_URL = "https://api.platform.opentargets.org/api/v4/graphql" - Network accessline 2446
-------- - Natural language: query_monarch("Find phenotypes associated with BRCA1") - Direct endpoint: query_monarch(endpoint="https://api.monarchinitiative.org/v3/api/search?q=marfan&category=biolink:Disease&limit=10") - Network accessline 2447
- Natural language: query_monarch("Find phenotypes associated with BRCA1") - Direct endpoint: query_monarch(endpoint="https://api.monarchinitiative.org/v3/api/search?q=marfan&category=biolink:Disease&limit=10") - Direct endpoint: qu - Network accessline 2448
- Direct endpoint: query_monarch(endpoint="https://api.monarchinitiative.org/v3/api/search?q=marfan&category=biolink:Disease&limit=10") - Network accessline 2449
- Direct endpoint: query_monarch(endpoint="https://api.monarchinitiative.org/v3/api/entity/MONDO:0007947") - Network accessline 2451
base_url = "https://api.monarchinitiative.org/v3/api" - Network accessline 2568
-------- - Natural language: query_openfda("Find adverse events for Lipitor") - Direct endpoint: query_openfda(endpoint="https://api.fda.gov/drug/event.json?search=patient.drug.medicinalproduct:lipitor") - Network accessline 2569
- Natural language: query_openfda("Find adverse events for Lipitor") - Direct endpoint: query_openfda(endpoint="https://api.fda.gov/drug/event.json?search=patient.drug.medicinalproduct:lipitor") - Search params: query_openfda(search - Network accessline 2570
- Direct endpoint: query_openfda(endpoint="https://api.fda.gov/drug/event.json?search=patient.drug.medicinalproduct:lipitor") - Network accessline 2574
base_url = "https://api.fda.gov" - Network accessline 2596
Your response should be a JSON object with the following fields: 1. "full_url": The complete URL to query (including the base URL "https://api.fda.gov" and any parameters) - Network accessline 2597
1. "full_url": The complete URL to query (including the base URL "https://api.fda.gov" and any parameters) - Network accessline 2670
---------- prompt (str, required): Natural language query about GWAS data endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/gwas/rest/api/studies?diseaseTraitId=EFO_0001360") - Network accessline 2671
prompt (str, required): Natural language query about GWAS data endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/gwas/rest/api/studies?diseaseTraitId=EFO_0001360") max_results (int): Maximum number o - Network accessline 2672
endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/gwas/rest/api/studies?diseaseTraitId=EFO_0001360") - Network accessline 2686
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 2787
base_url = "https://gnomad.broadinstitute.org/api" - Network accessline 2992
content_base_url = "https://reactome.org/ContentService" - Network accessline 2993
analysis_base_url = "https://reactome.org/AnalysisService" - Network accessline 3110
diagram_url = f"{content_base_url}/data/pathway/{pathway_id}/diagram" try: diagram_response = requests.get(diagram_url) - Network accessline 3111
try: diagram_response = requests.get(diagram_url) diagram_response.raise_for_status() - Network accessline 3112
diagram_response = requests.get(diagram_url) - Network accessline 3138
---------- prompt (str, required): Natural language query about regulatory elements endpoint (str, optional): The full endpoint to query (e.g., "https://regulomedb.org/regulome-search/?regions=chr11:5246919-5246919&genome=GRCh38") - Network accessline 3139
prompt (str, required): Natural language query about regulatory elements endpoint (str, optional): The full endpoint to query (e.g., "https://regulomedb.org/regulome-search/?regions=chr11:5246919-5246919&genome=GRCh38") verbose (boo - Network accessline 3140
endpoint (str, optional): The full endpoint to query (e.g., "https://regulomedb.org/regulome-search/?regions=chr11:5246919-5246919&genome=GRCh38") - Network accessline 3168
Your response should be a JSON object with ONLY ONE of the following fields: 1. "endpoint": The API endpoint to query (e.g., "https://regulomedb.org/regulome-search/?regions=chr11:5246919-5246919&genome=GRCh38") - Network accessline 3169
1. "endpoint": The API endpoint to query (e.g., "https://regulomedb.org/regulome-search/?regions=chr11:5246919-5246919&genome=GRCh38") - Network accessline 3172
SPECIAL NOTES: - RegulomeDB only works with human genome data - Variant IDs should be rsIDs from dbSNP when possible. The endpoint should be in the format https://regulomedb.org/regulome-search/?regions=rsID&genome=GRCh38 - Network accessline 3173
- RegulomeDB only works with human genome data - Variant IDs should be rsIDs from dbSNP when possible. The endpoint should be in the format https://regulomedb.org/regulome-search/?regions=rsID&genome=GRCh38 - Thumbnails for - Network accessline 3174
- Variant IDs should be rsIDs from dbSNP when possible. The endpoint should be in the format https://regulomedb.org/regulome-search/?regions=rsID&genome=GRCh38 - Network accessline 3175
- Thumbnails for chip and chromatin should be in the format https://regulomedb.org/regulome-search?regions=chr11:5246919-5246919&genome=GRCh38/thumbnail=chip - Network accessline 3226
---------- prompt (str, required): Natural language query about proteomics data endpoint (str, optional): The full endpoint to query (e.g., "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=breast%20cancer") - Network accessline 3227
prompt (str, required): Natural language query about proteomics data endpoint (str, optional): The full endpoint to query (e.g., "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=breast%20cancer") max_results (int): Maximu - Network accessline 3228
endpoint (str, optional): The full endpoint to query (e.g., "https://www.ebi.ac.uk/pride/ws/archive/v2/projects?keyword=breast%20cancer") - Network accessline 3242
base_url = "https://www.ebi.ac.uk/pride/ws/archive/v2" - Network accessline 3325
---------- prompt (str, required): Natural language query about drug targets, ligands, and interactions endpoint (str, optional): Full API endpoint to query (e.g., "https://www.guidetopharmacology.org/services/targets?type=GPCR&name - Network accessline 3326
prompt (str, required): Natural language query about drug targets, ligands, and interactions endpoint (str, optional): Full API endpoint to query (e.g., "https://www.guidetopharmacology.org/services/targets?type=GPCR&name=beta-2") v - Network accessline 3327
endpoint (str, optional): Full API endpoint to query (e.g., "https://www.guidetopharmacology.org/services/targets?type=GPCR&name=beta-2") - Network accessline 3341
base_url = "https://www.guidetopharmacology.org/services" - Network accessline 3439
url = "https://screen-beta-api.wenglab.org/dataws/cre_table" - Network accessline 3451
response = requests.post(url, json=data) - Network accessline 3546
url = "https://screen-beta-api.wenglab.org/dataws/re_detail/nearbyGenomic" - Network accessline 3549
steps_log += "Sending POST request to API with given data.\n" response = requests.post(url, json=data) - Network accessline 3550
response = requests.post(url, json=data) - Network accessline 3593
---------- prompt (str, required): Natural language query about transcription factors and binding sites endpoint (str, optional): Full API endpoint to query (e.g., "https://remap.univ-amu.fr/api/v1/catalogue/tf?tf=CTCF") - Network accessline 3594
prompt (str, required): Natural language query about transcription factors and binding sites endpoint (str, optional): Full API endpoint to query (e.g., "https://remap.univ-amu.fr/api/v1/catalogue/tf?tf=CTCF") verbose (bool): Whethe - Network accessline 3595
endpoint (str, optional): Full API endpoint to query (e.g., "https://remap.univ-amu.fr/api/v1/catalogue/tf?tf=CTCF") - Network accessline 3609
base_url = "https://remap.univ-amu.fr/api/v1" - Network accessline 3694
---------- prompt (str, required): Natural language query about mouse phenotypes, strains, or measurements endpoint (str, optional): Full API endpoint to query (e.g., "https://phenomedoc.jax.org/MPD_API/strains") - Network accessline 3695
prompt (str, required): Natural language query about mouse phenotypes, strains, or measurements endpoint (str, optional): Full API endpoint to query (e.g., "https://phenomedoc.jax.org/MPD_API/strains") verbose (bool): Whether to ret - Network accessline 3696
endpoint (str, optional): Full API endpoint to query (e.g., "https://phenomedoc.jax.org/MPD_API/strains") - Network accessline 3710
base_url = "https://phenome.jax.org" - Network accessline 3732
Your response should be a JSON object with the following fields: 1. "endpoint": The full url endpoint to query (e.g. https://phenome.jax.org/api/strains) - Network accessline 3733
1. "endpoint": The full url endpoint to query (e.g. https://phenome.jax.org/api/strains) - Network accessline 3795
---------- prompt (str, required): Natural language query about EM structures and associated data endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/emdb/api/search") - Network accessline 3796
prompt (str, required): Natural language query about EM structures and associated data endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/emdb/api/search") verbose (bool): Whether to return detailed r - Network accessline 3797
endpoint (str, optional): Full API endpoint to query (e.g., "https://www.ebi.ac.uk/emdb/api/search") - Network accessline 3811
base_url = "https://www.ebi.ac.uk/emdb/api" - Access to secretsline 3904
[Credential-related source omitted] - Access to secretsline 3931
[Credential-related source omitted] - Network accessline 3946
base_url = "https://repo-prod.prod.sagebase.org" - Access to secretsline 3954
[Credential-related source omitted] - Network accessline 4064
base_url = "https://pubchem.ncbi.nlm.nih.gov/rest/pug" - Network accessline 4085
2. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://pubchem.ncbi.nlm.nih.gov/rest/pug" - Network accessline 4086
SPECIAL NOTES: - Base URL is "https://pubchem.ncbi.nlm.nih.gov/rest/pug" - Common operations: property, synonyms, record, xrefs - Network accessline 4087
- Base URL is "https://pubchem.ncbi.nlm.nih.gov/rest/pug" - Network accessline 4175
base_url = "https://www.ebi.ac.uk/chembl/api/data" - Network accessline 4203
2. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://www.ebi.ac.uk/chembl/api/data" - Network accessline 4205
- Base URL is "https://www.ebi.ac.uk/chembl/api/data" - Network accessline 4407
base_url = "https://www.ebi.ac.uk/unichem/api/v1" - Network accessline 4430
4. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://www.ebi.ac.uk/unichem/api/v1" - Network accessline 4431
SPECIAL NOTES: - Base URL is "https://www.ebi.ac.uk/unichem/api/v1" - Compound searches use POST method to /compounds endpoint - Network accessline 4432
- Base URL is "https://www.ebi.ac.uk/unichem/api/v1" - Network accessline 4518
base_url = "https://clinicaltrials.gov/api/v2" - Network accessline 4539
2. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://clinicaltrials.gov/api/v2" - Network accessline 4540
SPECIAL NOTES: - Base URL is "https://clinicaltrials.gov/api/v2" - Main endpoint is /studies for searching clinical trials - Network accessline 4541
- Base URL is "https://clinicaltrials.gov/api/v2" - Network accessline 4636
base_url = "https://dailymed.nlm.nih.gov/dailymed/services/v2" - Network accessline 4661
2. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://dailymed.nlm.nih.gov/dailymed/services/v2" - Network accessline 4662
SPECIAL NOTES: - Base URL is "https://dailymed.nlm.nih.gov/dailymed/services/v2" - Available resources: applicationnumbers, drugclasses, drugnames, ndcs, rxcuis, spls, uniis - Network accessline 4663
- Base URL is "https://dailymed.nlm.nih.gov/dailymed/services/v2" - Network accessline 4739
base_url = "https://www.ebi.ac.uk/QuickGO/services" - Network accessline 4769
2. "description": A brief description of what the query is doing SPECIAL NOTES: - Base URL is "https://www.ebi.ac.uk/QuickGO/services" - Network accessline 4770
SPECIAL NOTES: - Base URL is "https://www.ebi.ac.uk/QuickGO/services" - Main services: /ontology (GO/ECO terms), /annotation (GO annotations), /geneproduct (gene products) - Network accessline 4771
- Base URL is "https://www.ebi.ac.uk/QuickGO/services" - Network accessline 4859
base_url = "https://www.encodeproject.org"
skills/biomni-general-agent/repo/biomni/tool/example_mcp_tools/pubmed_mcp.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/genetics.py
- Executable scriptline 1
Executable file - Network accessline 896
jaspar_url = f"https://jaspar.genereg.net/api/v1/matrix/?name={tf_name}" response = requests.get(jaspar_url) - Network accessline 897
response = requests.get(jaspar_url) - Network accessline 909
pwm_url = f"https://jaspar.genereg.net/api/v1/matrix/{matrix_id}.pfm" pwm_response = requests.get(pwm_url) - Network accessline 910
pwm_response = requests.get(pwm_url)
skills/biomni-general-agent/repo/biomni/tool/genomics.py
- Executable scriptline 1
Executable file - Access to secretsline 52
[Credential-related source omitted] - Network accessline 218
try: source_dataset = Dataset(name=source_dataset_name, host="http://www.ensembl.org") - Network accessline 219
source_dataset = Dataset(name=source_dataset_name, host="http://www.ensembl.org") - Network accessline 249
steps.append(f"Error during gene conversion from {source_species} to {target_species}: {e}") try: source_dataset = Dataset(name=source_dataset_name, host="http://www.ensembl.org") - Network accessline 251
source_dataset = Dataset(name=source_dataset_name, host="http://www.ensembl.org") - Network accessline 307
url = f"https://rest.ensembl.org/sequence/id/{ensembl_gene_id}?type=protein;multiple_sequences=1" headers = {"Content-Type": "text/x-fasta"} response = requests.get(url, headers=headers) - Network accessline 308
headers = {"Content-Type": "text/x-fasta"} response = requests.get(url, headers=headers) if not response.ok or not response.text.startswith(">"): - Network accessline 309
response = requests.get(url, headers=headers) - Network accessline 660
subprocess.run( ["conda", "run", "-n", env_name, "pip", "install", "git+https://github.com/satijalab/panhumanpy.git"], - Network accessline 661
["conda", "run", "-n", env_name, "pip", "install", "git+https://github.com/satijalab/panhumanpy.git"], - Network accessline 853
# https://pypi.org/project/harmony-pytorch/ - Network accessline 888
steps.append("Successfully imported UCE main function") except Exception: steps.append("Please install the UCE package first. Follow https://github.com/snap-stanford/UCE.git.") - Network accessline 889
except Exception: steps.append("Please install the UCE package first. Follow https://github.com/snap-stanford/UCE.git.") return "\n".join(steps) - Network accessline 890
steps.append("Please install the UCE package first. Follow https://github.com/snap-stanford/UCE.git.") - Network accessline 1164
if balance_if_possible and has_weights: return c.matrix(balance=True).fetch(chrom) - Network accessline 1165
return c.matrix(balance=True).fetch(chrom) - Network accessline 1166
else: return c.matrix(balance=False).fetch(chrom) except Exception as e: - Network accessline 1167
return c.matrix(balance=False).fetch(chrom) - Network accessline 1171
if balance_if_possible: log.append("Falling back to unbalanced matrix") return c.matrix(balance=False).fetch(chrom) - Network accessline 1172
log.append("Falling back to unbalanced matrix") return c.matrix(balance=False).fetch(chrom) else: - Network accessline 1173
return c.matrix(balance=False).fetch(chrom) - Dangerous shell operationline 2286
"sudo apt-get install git-lfs\n" - Network accessline 2306
steps.append("This may take a while and final model weights are approx 25GB!...") process = subprocess.Popen( ["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder], - Network accessline 2307
process = subprocess.Popen( ["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder], stdout=subprocess.PIPE, - Network accessline 2308
["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder], - Network accessline 2323
if process.returncode != 0: raise subprocess.CalledProcessError( process.returncode, ["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder] - Network accessline 2324
raise subprocess.CalledProcessError( process.returncode, ["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder] ) - Network accessline 2325
process.returncode, ["git", "clone", "https://huggingface.co/arcinstitute/SE-600M", model_folder] - Access to secretsline 2351
[Credential-related source omitted] - Access to secretsline 2531
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/tool/glycoengineering.py
- Executable scriptline 1
Executable file - Network accessline 133
lines.append("1) Glycoshield-md") lines.append(" - MD workflows for glycan shielding analysis around proteins.") lines.append(" - URL: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/") - Network accessline 134
lines.append(" - MD workflows for glycan shielding analysis around proteins.") lines.append(" - URL: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/") lines.append("") - Network accessline 135
lines.append(" - URL: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/") - Network accessline 145
lines.append("4) Copenhagen Center for Glycomics (CCG)") lines.append(" - Consortium hosting many glyco-related datasets, tools, and protocols.") lines.append(" - URL: https://github.com/CopenhagenCenterForGlycomics") - Network accessline 146
lines.append(" - Consortium hosting many glyco-related datasets, tools, and protocols.") lines.append(" - URL: https://github.com/CopenhagenCenterForGlycomics") lines.append("") - Network accessline 147
lines.append(" - URL: https://github.com/CopenhagenCenterForGlycomics") - Network accessline 149
lines.append("5) NetOGlyc 4.0 (O-glycosite predictor)") lines.append(" - Web service for O-GalNAc site prediction; check license/usage terms.") lines.append(" - URL: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/") - Network accessline 150
lines.append(" - Web service for O-GalNAc site prediction; check license/usage terms.") lines.append(" - URL: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/") lines.append("") - Network accessline 151
lines.append(" - URL: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/")
skills/biomni-general-agent/repo/biomni/tool/immunology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/lab_automation.py
- Executable scriptline 1
Executable file - Network accessline 76
url = f"https://github.com/{repo}/archive/{ref}.zip" - Network accessline 78
data = None try: with urllib.request.urlopen(url, timeout=20) as resp: - Network accessline 79
try: with urllib.request.urlopen(url, timeout=20) as resp: data = resp.read() - Network accessline 80
with urllib.request.urlopen(url, timeout=20) as resp: - Dangerous shell operationline 580
exec(script_content, namespace)
skills/biomni-general-agent/repo/biomni/tool/literature.py
- Executable scriptline 1
Executable file - Network accessline 38
crossref_url = f"https://doi.org/{doi}" headers = {"User-Agent": "Mozilla/5.0"} response = requests.get(crossref_url, headers=headers) - Network accessline 40
response = requests.get(crossref_url, headers=headers) - Network accessline 51
response = requests.get(publisher_url, headers=headers) - Network accessline 81
for link in supplementary_links: file_name = os.path.join(output_dir, link.split("/")[-1]) file_response = requests.get(link, headers=headers) - Network accessline 82
file_name = os.path.join(output_dir, link.split("/")[-1]) file_response = requests.get(link, headers=headers) if file_response.status_code == 200: - Network accessline 83
file_response = requests.get(link, headers=headers) - Access to secretsline 259
[Credential-related source omitted] - Access to secretsline 260
[Credential-related source omitted] - Access to secretsline 261
[Credential-related source omitted] - Access to secretsline 264
[Credential-related source omitted] - Access to secretsline 269
[Credential-related source omitted] - Access to secretsline 270
[Credential-related source omitted] - Access to secretsline 272
[Credential-related source omitted] - Network accessline 323
response = requests.get(url, headers={"User-Agent": "Mozilla/5.0"}) - Network accessline 367
response = requests.get(url, timeout=30) - Network accessline 383
response = requests.get(url, timeout=30)
skills/biomni-general-agent/repo/biomni/tool/microbiology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/molecular_biology.py
skills/biomni-general-agent/repo/biomni/tool/pathology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/pharmacology.py
- Executable scriptline 1
Executable file - Network accessline 2985
BASE_URL = "https://api.fda.gov" - Network accessline 2992
self.requests = requests self.time = time self.session = requests.Session() - Network accessline 2993
self.time = time self.session = requests.Session() self.session.headers.update({"User-Agent": "Biomni-Agent/1.0 (https://biomni.stanford.edu)"}) - Network accessline 2994
self.session = requests.Session() - Network accessline 2995
self.session.headers.update({"User-Agent": "Biomni-Agent/1.0 (https://biomni.stanford.edu)"})
skills/biomni-general-agent/repo/biomni/tool/physiology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/protocols.py
- Executable scriptline 1
Executable file - Network accessline 31
PROTOCOLS_IO_API_BASE = "https://www.protocols.io/api/v3" - Access to secretsline 34
[Credential-related source omitted] - Access to secretsline 35
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 68
[Credential-related source omitted] - Access to secretsline 70
[Credential-related source omitted] - Network accessline 74
url = "https://www.protocols.io/api/v3/protocols" - Access to secretsline 76
[Credential-related source omitted] - Network accessline 88
response = requests.get(url, headers=headers, params=params) - Network accessline 140
except requests.exceptions.RequestException as e: raise requests.RequestException(f"Failed to search protocols.io: {str(e)}") from e - Network accessline 141
raise requests.RequestException(f"Failed to search protocols.io: {str(e)}") from e - Access to secretsline 159
[Credential-related source omitted] - Access to secretsline 161
[Credential-related source omitted] - Network accessline 164
url = f"https://www.protocols.io/api/v3/protocols/{protocol_id}" - Access to secretsline 166
[Credential-related source omitted] - Network accessline 168
try: response = requests.get(url, headers=headers, timeout=timeout) - Network accessline 169
response = requests.get(url, headers=headers, timeout=timeout) - Network accessline 179
except requests.exceptions.RequestException as e: raise requests.RequestException(f"Failed to get protocol details: {str(e)}") from e - Network accessline 180
raise requests.RequestException(f"Failed to get protocol details: {str(e)}") from e
skills/biomni-general-agent/repo/biomni/tool/support_tools.py
- Executable scriptline 1
Executable file - Dangerous shell operationline 41
exec(command, _persistent_namespace) - Access to secretsline 220
[Credential-related source omitted] - Access to secretsline 257
[Credential-related source omitted] - Access to secretsline 287
[Credential-related source omitted] - Access to secretsline 291
[Credential-related source omitted] - Access to secretsline 292
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/tool/synthetic_biology.py
- Executable scriptline 1
Executable file - Network accessline 1250
url = "https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan" - Network accessline 1254
try: response = requests.post(url, data=json.dumps(data), headers=headers) - Network accessline 1255
response = requests.post(url, data=json.dumps(data), headers=headers) - Network accessline 1269
result_response = requests.get(f"{result_url}.json")
skills/biomni-general-agent/repo/biomni/tool/systems_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/biochemistry.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/bioengineering.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/bioimaging.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/biophysics.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/cancer_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/cell_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/database.py
- Executable scriptline 1
Executable file - Network accessline 16
{ "default": None, "description": "Full or partial UniProt API endpoint URL to query directly (e.g., 'https://rest.uniprot.org/uniprotkb/P01308')", - Network accessline 17
"default": None, "description": "Full or partial UniProt API endpoint URL to query directly (e.g., 'https://rest.uniprot.org/uniprotkb/P01308')", "name": "endpoint", - Network accessline 18
"description": "Full or partial UniProt API endpoint URL to query directly (e.g., 'https://rest.uniprot.org/uniprotkb/P01308')", - Access to secretsline 523
[Credential-related source omitted]
skills/biomni-general-agent/repo/biomni/tool/tool_description/genetics.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/genomics.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/glycoengineering.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/immunology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/lab_automation.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/literature.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/microbiology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/molecular_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/pathology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/pharmacology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/physiology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/protocols.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/support_tools.py
skills/biomni-general-agent/repo/biomni/tool/tool_description/synthetic_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_description/systems_biology.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/tool/tool_registry.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni/utils.py
- Executable scriptline 1
Executable file - Access to secretsline 128
[Credential-related source omitted] - Network accessline 352
query: str, variables: dict, api_address: str = "https://api.genetics.opentargets.org/graphql", - Network accessline 353
variables: dict, api_address: str = "https://api.genetics.opentargets.org/graphql", ) -> dict: - Network accessline 354
api_address: str = "https://api.genetics.opentargets.org/graphql", - Network accessline 357
headers = {"Content-Type": "application/json"} response = requests.post(api_address, json={"query": query, "variables": variables}, headers=headers) - Network accessline 358
response = requests.post(api_address, json={"query": query, "variables": variables}, headers=headers) - Dangerous shell operationline 575
annotations[param["name"]] = eval(param_type) - Network accessline 621
api_call = f"https://mygene.info/v3/query?species=human&q=symbol:{gene_symbol}" response = requests.get(api_call) - Network accessline 622
response = requests.get(api_call) - Network accessline 635
api_call = f"https://mygene.info/v3/query?species=human&fields=ensembl&q=symbol:{gene_symbol}" response = requests.get(api_call) - Network accessline 636
response = requests.get(api_call) - Network accessline 655
api_base = "https://gtexportal.org/api/v2/reference/gene" params = {"geneId": gene_symbol} response_json = requests.get(api_base, params=params).json() - Network accessline 657
response_json = requests.get(api_base, params=params).json() - Network accessline 901
os.makedirs(dest_dir, exist_ok=True) print(f"Downloading from {url} ...") with requests.get(url, stream=True) as r: - Network accessline 902
print(f"Downloading from {url} ...") with requests.get(url, stream=True) as r: r.raise_for_status() - Network accessline 903
with requests.get(url, stream=True) as r: - Network accessline 936
Args: s3_bucket_url: Base URL of the S3 bucket (e.g., "https://biomni-release.s3.amazonaws.com") - Network accessline 937
s3_bucket_url: Base URL of the S3 bucket (e.g., "https://biomni-release.s3.amazonaws.com") - Network accessline 951
try: response = requests.get(url, stream=True) - Network accessline 952
response = requests.get(url, stream=True)
skills/biomni-general-agent/repo/biomni/version.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/biomni_env/README.md
- Network accessline 20
git clone https://github.com/snap-stanford/Biomni.git
skills/biomni-general-agent/repo/biomni_env/cli_tools_config.json
- Network accessline 5
"function_name": "install_plink2", "description": "Whole genome association analysis toolset", "website": "https://www.cog-genomics.org/plink/2.0/", - Network accessline 6
"description": "Whole genome association analysis toolset", "website": "https://www.cog-genomics.org/plink/2.0/", "downloads": { - Network accessline 7
"website": "https://www.cog-genomics.org/plink/2.0/", - Network accessline 8
"downloads": { "linux": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_linux_avx2_20250129.zip", "macos_intel": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_mac_avx2_20250129.zip", - Network accessline 9
"linux": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_linux_avx2_20250129.zip", - Network accessline 10
"macos_intel": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_mac_avx2_20250129.zip", - Network accessline 11
"macos_arm64": "https://s3.amazonaws.com/plink2-assets/alpha6/plink2_mac_arm64_20250129.zip" - Network accessline 18
"function_name": "install_iqtree", "description": "Efficient phylogenetic software by maximum likelihood", "website": "http://www.iqtree.org/", - Network accessline 19
"description": "Efficient phylogenetic software by maximum likelihood", "website": "http://www.iqtree.org/", "downloads": { - Network accessline 20
"website": "http://www.iqtree.org/", "downloads": { "linux": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz", - Network accessline 21
"downloads": { "linux": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz", "macos_intel": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-MacOSX.zip", - Network accessline 22
"linux": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-Linux.tar.gz", - Network accessline 23
"macos_intel": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-MacOSX.zip", - Network accessline 24
"macos_arm64": "https://github.com/iqtree/iqtree2/releases/download/v2.2.2.7/iqtree-2.2.2.7-MacOSX.zip" - Network accessline 31
"function_name": "install_gcta", "description": "Genome-wide Complex Trait Analysis", "website": "https://yanglab.westlake.edu.cn/software/gcta/", - Network accessline 32
"description": "Genome-wide Complex Trait Analysis", "website": "https://yanglab.westlake.edu.cn/software/gcta/", "downloads": { - Network accessline 33
"website": "https://yanglab.westlake.edu.cn/software/gcta/", - Network accessline 34
"downloads": { "linux": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.4-linux-kernel-3-x86_64.zip", "macos_intel": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.1-macOS-x86_64.zip", - Network accessline 35
"linux": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.4-linux-kernel-3-x86_64.zip", - Network accessline 36
"macos_intel": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.1-macOS-x86_64.zip", - Network accessline 37
"macos_arm64": "https://yanglab.westlake.edu.cn/software/gcta/bin/gcta-1.94.3-macOS-arm64.zip" - Network accessline 44
"function_name": "install_bwa", "description": "Burrow-Wheeler Aligner for short-read alignment", "website": "https://github.com/lh3/bwa", - Network accessline 45
"description": "Burrow-Wheeler Aligner for short-read alignment", "website": "https://github.com/lh3/bwa", "downloads": { - Network accessline 46
"website": "https://github.com/lh3/bwa", - Network accessline 47
"downloads": { "linux": "https://github.com/lh3/bwa.git", "macos_intel": "https://github.com/lh3/bwa.git", - Network accessline 48
"linux": "https://github.com/lh3/bwa.git", - Network accessline 49
"macos_intel": "https://github.com/lh3/bwa.git", - Network accessline 50
"macos_arm64": "https://github.com/lh3/bwa.git" - Network accessline 57
"function_name": "install_fasttree", "description": "Approximately-Maximum-Likelihood phylogenetic trees from alignments", "website": "https://morgannprice.github.io/fasttree/", - Network accessline 58
"description": "Approximately-Maximum-Likelihood phylogenetic trees from alignments", "website": "https://morgannprice.github.io/fasttree/", "downloads": { - Network accessline 59
"website": "https://morgannprice.github.io/fasttree/", - Network accessline 60
"downloads": { "linux": "https://morgannprice.github.io/fasttree/FastTree.c", "macos_intel": "https://morgannprice.github.io/fasttree/FastTree.c", - Network accessline 61
"linux": "https://morgannprice.github.io/fasttree/FastTree.c", - Network accessline 62
"macos_intel": "https://morgannprice.github.io/fasttree/FastTree.c", - Network accessline 63
"macos_arm64": "https://morgannprice.github.io/fasttree/FastTree.c" - Network accessline 70
"function_name": "install_muscle", "description": "Multiple sequence alignment with high accuracy and performance", "website": "https://github.com/rcedgar/muscle", - Network accessline 71
"description": "Multiple sequence alignment with high accuracy and performance", "website": "https://github.com/rcedgar/muscle", "downloads": { - Network accessline 72
"website": "https://github.com/rcedgar/muscle", "downloads": { "linux": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-linux-x86.v5.3", - Network accessline 73
"downloads": { "linux": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-linux-x86.v5.3", "macos_arm64": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-osx-arm64.v5.3" - Network accessline 74
"linux": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-linux-x86.v5.3", - Network accessline 75
"macos_arm64": "https://github.com/rcedgar/muscle/releases/download/v5.3/muscle-osx-arm64.v5.3" - Network accessline 82
"function_name": "install_homer", "description": "Software for motif discovery and next-gen sequencing analysis", "website": "http://homer.ucsd.edu/homer/", - Network accessline 83
"description": "Software for motif discovery and next-gen sequencing analysis", "website": "http://homer.ucsd.edu/homer/", "downloads": { - Network accessline 84
"website": "http://homer.ucsd.edu/homer/", - Network accessline 85
"downloads": { "linux": "http://homer.ucsd.edu/homer/configureHomer.pl", "macos_intel": "http://homer.ucsd.edu/homer/configureHomer.pl", - Network accessline 86
"linux": "http://homer.ucsd.edu/homer/configureHomer.pl", - Network accessline 87
"macos_intel": "http://homer.ucsd.edu/homer/configureHomer.pl", - Network accessline 88
"macos_arm64": "http://homer.ucsd.edu/homer/configureHomer.pl"
skills/biomni-general-agent/repo/biomni_env/install_cli_tools.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 12
# Check for wget or fallback to curl - Network accessline 13
if command -v wget &> /dev/null; then - Network accessline 14
DOWNLOADER="wget -v -O" - Network accessline 15
elif command -v curl &> /dev/null; then - Network accessline 16
DOWNLOADER="curl -L -o" - Network accessline 17
echo -e "${YELLOW}Warning: wget not found, using curl instead.${NC}" - Network accessline 18
else echo -e "${RED}Error: Neither wget nor curl is installed.${NC}" echo -e "${YELLOW}Please install one of them (e.g., brew install wget on macOS).${NC}" - Network accessline 19
echo -e "${RED}Error: Neither wget nor curl is installed.${NC}" - Network accessline 20
echo -e "${YELLOW}Please install one of them (e.g., brew install wget on macOS).${NC}" - Dangerous shell operationline 27
# Use conda to install jq (no sudo required) - Network accessline 30
if [ $? -ne 0 ]; then echo -e "${RED}Failed to install jq with conda. Please install it manually.${NC}" echo "Visit: https://stedolan.github.io/jq/download/" - Network accessline 31
echo -e "${RED}Failed to install jq with conda. Please install it manually.${NC}" echo "Visit: https://stedolan.github.io/jq/download/" exit 1 - Network accessline 32
echo "Visit: https://stedolan.github.io/jq/download/" - Dangerous shell operationline 46
rm -rf "$old_afs_dir/bin" - Dangerous shell operationline 55
rm -rf "$old_home_dir/bin" - Dangerous shell operationline 77
rm -rf "$TOOLS_DIR/bin" - Network accessline 147
$DOWNLOADER "$TOOLS_DIR/bin/configureHomer.pl" "$download_url" - Network accessline 204
$DOWNLOADER "$TOOLS_DIR/$tool_dir_name/FastTree.c" "$download_url" - Network accessline 301
$DOWNLOADER "$TOOLS_DIR/$tool_dir_name.zip" "$download_url" - Dangerous shell operationline 319
rm "$TOOLS_DIR/$tool_dir_name.zip" - Network accessline 322
$DOWNLOADER "$TOOLS_DIR/$tool_dir_name.tar.gz" "$download_url" - Dangerous shell operationline 341
rm "$TOOLS_DIR/$tool_dir_name.tar.gz" - Network accessline 343
elif [[ "$tool_name" = "MUSCLE" ]]; then echo -e "${YELLOW}Downloading $tool_name binary...${NC}" $DOWNLOADER "$TOOLS_DIR/$tool_dir_name/$binary_name" "$download_url" - Network accessline 345
$DOWNLOADER "$TOOLS_DIR/$tool_dir_name/$binary_name" "$download_url"
skills/biomni-general-agent/repo/biomni_env/install_r_packages.R
- Executable scriptline 1
#!/usr/bin/env Rscript - Network accessline 7
options(repos = c(CRAN = "https://cran.rstudio.com/")) - Network accessline 86
# Install WGCNA (from CRAN, not Bioconductor) # Following official instructions from https://cran.r-project.org/web/packages/WGCNA/index.html - Network accessline 87
# Following official instructions from https://cran.r-project.org/web/packages/WGCNA/index.html
skills/biomni-general-agent/repo/biomni_env/new_software_v008.sh
- Executable scriptline 1
Executable file - Network accessline 3
pip install transformers sentencepiece langchain-google-genai langchain_ollama mcp pip install lazyslide pip install "git+https://github.com/YosefLab/popV.git@refs/pull/100/head" - Network accessline 4
pip install lazyslide pip install "git+https://github.com/YosefLab/popV.git@refs/pull/100/head" pip install uv - Network accessline 5
pip install "git+https://github.com/YosefLab/popV.git@refs/pull/100/head" - Dangerous shell operationline 7
sudo apt-get install git-lfs # or brew install git-lfs if you are on macOS - Network accessline 15
pip install nnunet nibabel nilearn pip install mi-googlesearch-python pip install git+https://github.com/pylabrobot/pylabrobot.git - Network accessline 16
pip install mi-googlesearch-python pip install git+https://github.com/pylabrobot/pylabrobot.git conda install weasyprint - Network accessline 17
pip install git+https://github.com/pylabrobot/pylabrobot.git
skills/biomni-general-agent/repo/biomni_env/setup.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 22
echo -e "${RED}Error: Conda is not installed or not in PATH.${NC}" echo "Please install Miniconda or Anaconda first." echo "Visit: https://docs.conda.io/en/latest/miniconda.html" - Network accessline 23
echo "Please install Miniconda or Anaconda first." echo "Visit: https://docs.conda.io/en/latest/miniconda.html" exit 1 - Network accessline 24
echo "Visit: https://docs.conda.io/en/latest/miniconda.html" - Dangerous shell operationline 161
eval "$("$MAMBA_EXE" shell hook --shell bash)" - Dangerous shell operationline 164
eval "$(conda shell.bash hook)"
skills/biomni-general-agent/repo/docs/Makefile
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/docs/configuration.md
- Access to secretsline 28
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 44
[Credential-related source omitted] - Network accessline 92
default_config.source = "Custom" default_config.base_url = "http://localhost:8000/v1" - Network accessline 93
default_config.base_url = "http://localhost:8000/v1" - Access to secretsline 94
[Credential-related source omitted] - Access to secretsline 104
[Credential-related source omitted] - Access to secretsline 105
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Access to secretsline 107
[Credential-related source omitted] - Network accessline 111
# Azure OpenAI OPENAI_ENDPOINT=https://your-resource.openai.azure.com/ - Network accessline 112
OPENAI_ENDPOINT=https://your-resource.openai.azure.com/ - Network accessline 119
BIOMNI_USE_TOOL_RETRIEVER=true # Default: true BIOMNI_SOURCE=Anthropic # Auto-detected if not set BIOMNI_CUSTOM_BASE_URL=http://localhost:8000/v1 - Network accessline 120
[Credential-related source omitted] - Network accessline 121
BIOMNI_CUSTOM_BASE_URL=http://localhost:8000/v1 - Access to secretsline 122
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 151
[Credential-related source omitted]
skills/biomni-general-agent/repo/docs/generate_api_docs.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/docs/make.bat
- Executable scriptline 1
Executable file - Network accessline 20
echo. echo.If you don't have Sphinx installed, grab it from echo.https://www.sphinx-doc.org/ - Network accessline 21
echo.If you don't have Sphinx installed, grab it from echo.https://www.sphinx-doc.org/ exit /b 1 - Network accessline 22
echo.https://www.sphinx-doc.org/
skills/biomni-general-agent/repo/docs/mcp_integration.md
- Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 59
[Credential-related source omitted] - Access to secretsline 90
[Credential-related source omitted] - Access to secretsline 128
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted]
skills/biomni-general-agent/repo/docs/source/conf.py
- Executable scriptline 1
Executable file - Network accessline 12
# # For the full list of built-in configuration values, see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html - Network accessline 14
# https://www.sphinx-doc.org/en/master/usage/configuration.html - Network accessline 16
# -- Project information ----------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information - Network accessline 17
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information - Network accessline 28
# -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - Network accessline 29
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration - Network accessline 55
# -- Options for HTML output ------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output - Network accessline 56
# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
skills/biomni-general-agent/repo/license_info.md
- Network accessline 22
| Data Source Category | Example Files | License | Internal Hosting | Source | | :--- | :--- | :--- | :--- | :--- | | **COSMIC** | `Cosmic_*.csv`, `Cosmic_*.parquet` | Requires commercial license for commercial use. | Yes, with a valid comm - Network accessline 23
| :--- | :--- | :--- | :--- | :--- | | **COSMIC** | `Cosmic_*.csv`, `Cosmic_*.parquet` | Requires commercial license for commercial use. | Yes, with a valid commercial license. | [Sanger Institute](https://cancer.sanger.ac.uk/cosmic) | | ** - Network accessline 24
| **COSMIC** | `Cosmic_*.csv`, `Cosmic_*.parquet` | Requires commercial license for commercial use. | Yes, with a valid commercial license. | [Sanger Institute](https://cancer.sanger.ac.uk/cosmic) | - Network accessline 25
| **BindingDB** | `BindingDB_All_202409.tsv` | Custom, non-commercial use granted. Commercial use requires a license. | Yes, with a commercial license. | [BindingDB](https://www.bindingdb.org) | | **Broad Repurposing Hub** | `broad_repurpos - Network accessline 26
| **Broad Repurposing Hub** | `broad_repurposing_hub_*.parquet` | CC BY 4.0 | Yes | [Broad Institute](https://www.broadinstitute.org/drug-repurposing-hub) | | **DDInter** | `ddinter_*.csv` | CC BY-NC-SA 4.0 | No, non-commercial use only. | - Network accessline 27
| **DDInter** | `ddinter_*.csv` | CC BY-NC-SA 4.0 | No, non-commercial use only. | [DDInter](http://ddinter.scbdd.com/) | - Network accessline 28
| **DisGeNET** | `DisGeNET.parquet` | CC BY-NC-SA 4.0 | No, non-commercial use only. | [DisGeNET](https://www.disgenet.org/) | - Network accessline 29
| **Enamine** | `enamine_cloud_library_smiles.pkl` | Proprietary. Requires license for screening. | Yes, with a valid license. | [Enamine](https://enamine.net/) | - Network accessline 30
| **EveBio** | `evebio_*.csv` | Appears to be proprietary data from EveBio. | Requires permission from EveBio. | EveBio | | **Gene Ontology (GO)** | `go-plus.json` | CC BY 4.0 | Yes | [Gene Ontology Consortium](http://geneontology.org/) | | - Network accessline 31
| **Gene Ontology (GO)** | `go-plus.json` | CC BY 4.0 | Yes | [Gene Ontology Consortium](http://geneontology.org/) | - Network accessline 32
| **GTEx** | `gtex_tissue_gene_tpm.parquet` | dbGaP controlled access. | Yes, with authorization. | [GTEx Portal](https://gtexportal.org/) | - Network accessline 33
| **Human Protein Atlas** | `proteinatlas.tsv` | CC BY-SA 3.0 | Yes | [Human Protein Atlas](https://www.proteinatlas.org/) | - Network accessline 34
| **MSigDB** | `msigdb_human_*.parquet` | Custom, requires license for commercial use. | Yes, with a license. | [Broad Institute](https://www.gsea-msigdb.org/gsea/msigdb) | - Network accessline 35
| **OMIM** | `omim.parquet` | Custom, requires license for commercial use. | Yes, with a license. | [OMIM](https://omim.org/) | - Network accessline 36
| **BioGRID** | `affinity_capture-ms.parquet`, etc. | OSL 3.0 | Yes | [BioGRID](https://thebiogrid.org/) | - Network accessline 37
| **CZI Cell Census** | `czi_census_datasets_v4.parquet` | CC BY 4.0 | Yes | [Chan Zuckerberg Initiative](https://cellxgene.cziscience.com/census) | - Network accessline 38
| **DepMap** | `DepMap_*.csv` | CC BY 4.0 | Yes | [Broad Institute DepMap](https://depmap.org/) | - Network accessline 39
| **Genebass** | `genebass_*.pkl` | ODC-By v1.0 | Yes | [Genebass](https://genebass.org/) | - Network accessline 40
| **GWAS Catalog** | `gwas_catalog.pkl` | Apache 2.0 | Yes | [EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/) | | **HPO** | `hp.obo` | Custom, free for all uses. | Yes | [Human Phenotype Ontology](https://hpo.jax.org/) | | **McPAS-TCR** | `M - Network accessline 41
| **HPO** | `hp.obo` | Custom, free for all uses. | Yes | [Human Phenotype Ontology](https://hpo.jax.org/) | | **McPAS-TCR** | `McPAS-TCR.parquet` | CC BY-NC-SA 4.0 | No, non-commercial use only. | [McPAS-TCR](http://friedmanlab.weizmann.ac - Network accessline 42
| **McPAS-TCR** | `McPAS-TCR.parquet` | CC BY-NC-SA 4.0 | No, non-commercial use only. | [McPAS-TCR](http://friedmanlab.weizmann.ac.il/McPAS-TCR/) | - Network accessline 43
| **miRDB** | `miRDB_v6.0_results.parquet` | Custom, free for non-commercial use. | No, non-commercial use only. | [miRDB](http://mirdb.org/) | | **miRTarBase** | `miRTarBase_*.parquet` | CC BY-NC 4.0 | No, non-commercial use only. | [miRTa - Network accessline 44
| **miRTarBase** | `miRTarBase_*.parquet` | CC BY-NC 4.0 | No, non-commercial use only. | [miRTarBase](https://mirtarbase.cuhk.edu.cn/) | - Network accessline 45
| **MouseMine** | `mousemine_*.parquet` | CC BY 4.0 | Yes | [MouseMine](http://www.mousemine.org/) | - Network accessline 46
| **P-HIPSTER** | `Virus-Host_PPI_P-HIPSTER_2020.parquet` | CC BY 4.0 | Yes | [P-HIPSTER](http://phipster.org) |
skills/biomni-general-agent/repo/pyproject.toml
skills/biomni-general-agent/repo/tutorials/biomni_101.ipynb
- Executable scriptline 1
Executable file - Network accessline 91
"\u001b[31mKeyboardInterrupt\u001b[39m Traceback (most recent call last)", "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 7\u001b[39m\n\u001b[32m 3\u001b[39m sys.pa - Network accessline 92
"\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[1]\u001b[39m\u001b[32m, line 7\u001b[39m\n\u001b[32m 3\u001b[39m sys.path.append(\u001b[33m\"\u001b[39m\u001b[33m../\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 5\u001b[3 - Network accessline 93
[Credential-related source omitted] - Possible obfuscationline 93
[Credential-related source omitted] - Access to secretsline 93
[Credential-related source omitted] - Possible obfuscationline 94
"\u001b[36mFile \u001b[39m\u001b[32m~/Desktop/Biomni/tutorials/../biomni/utils.py:1011\u001b[39m, in \u001b[36mcheck_and_download_s3_files\u001b[39m\u001b[34m(s3_bucket_url, local_data_lake_path, expected_files, folder)\u001b[39m\n\u001b[32 - Possible obfuscationline 95
"\u001b[36mFile \u001b[39m\u001b[32m~/Desktop/Biomni/tutorials/../biomni/utils.py:949\u001b[39m, in \u001b[36mcheck_and_download_s3_files.<locals>.download_with_progress\u001b[39m\u001b[34m(url, file_path, desc)\u001b[39m\n\u001b[32m 947 - Possible obfuscationline 98
"\u001b[36mFile \u001b[39m\u001b[32m~/miniconda3/envs/biomni_fixed/lib/python3.11/site-packages/urllib3/response.py:980\u001b[39m, in \u001b[36mHTTPResponse.read\u001b[39m\u001b[34m(self, amt, decode_content, cache_content)\u001b[39m\n\u001 - Possible obfuscationline 99
"\u001b[36mFile \u001b[39m\u001b[32m~/miniconda3/envs/biomni_fixed/lib/python3.11/site-packages/urllib3/response.py:904\u001b[39m, in \u001b[36mHTTPResponse._raw_read\u001b[39m\u001b[34m(self, amt, read1)\u001b[39m\n\u001b[32m 901\u001b[ - Possible obfuscationline 100
"\u001b[36mFile \u001b[39m\u001b[32m~/miniconda3/envs/biomni_fixed/lib/python3.11/site-packages/urllib3/response.py:887\u001b[39m, in \u001b[36mHTTPResponse._fp_read\u001b[39m\u001b[34m(self, amt, read1)\u001b[39m\n\u001b[32m 884\u001b[3 - Possible obfuscationline 101
"\u001b[36mFile \u001b[39m\u001b[32m~/miniconda3/envs/biomni_fixed/lib/python3.11/http/client.py:473\u001b[39m, in \u001b[36mHTTPResponse.read\u001b[39m\u001b[34m(self, amt)\u001b[39m\n\u001b[32m 470\u001b[39m \u001b[38;5;28;01mif\u001b[ - Possible obfuscationline 103
"\u001b[36mFile \u001b[39m\u001b[32m~/miniconda3/envs/biomni_fixed/lib/python3.11/ssl.py:1314\u001b[39m, in \u001b[36mSSLSocket.recv_into\u001b[39m\u001b[34m(self, buffer, nbytes, flags)\u001b[39m\n\u001b[32m 1310\u001b[39m \u001b[38; - Network accessline 177
"=== Step 1: Researching T cell exhaustion biology ===\n", "Reactome pathways for T cell exhaustion:\n", "{'success': True, 'query_info': {'endpoint': 'https://reactome.org/ContentService/search/query', 'method': 'GET', 'descrip - Network accessline 178
"Reactome pathways for T cell exhaustion:\n", "{'success': True, 'query_info': {'endpoint': 'https://reactome.org/ContentService/search/query', 'method': 'GET', 'description': 'Search Reactome for pathways related to T cell exhaustion - Network accessline 179
"{'success': True, 'query_info': {'endpoint': 'https://reactome.org/ContentService/search/query', 'method': 'GET', 'description': 'Search Reactome for pathways related to T cell exhaustion, T cell receptor signaling, and chronic T cell stim - Possible obfuscationline 179
"{'success': True, 'query_info': {'endpoint': 'https://reactome.org/ContentService/search/query', 'method': 'GET', 'description': 'Search Reactome for pathways related to T cell exhaustion, T cell receptor signaling, and chronic T cell stim
skills/biomni-general-agent/repo/tutorials/examples/add_mcp_server/mcp_config.yaml
skills/biomni-general-agent/repo/tutorials/examples/add_mcp_server/mcp_example.ipynb
- Executable scriptline 1
Executable file - Network accessline 29
"from biomni.agent import A1\n", "\n", "# configure here: https://github.com/settings/personal-access-tokens\n", - Network accessline 30
"\n", "# configure here: https://github.com/settings/personal-access-tokens\n", "os.environ.setdefault(\"GITHUB_TOKEN\", \"XXX\")\n", - Network accessline 31
"# configure here: https://github.com/settings/personal-access-tokens\n", - Access to secretsline 32
[Credential-related source omitted] - Network accessline 626
"21:45:50 - INFO - Performing Enrichr analysis using database GO_Biological_Process_2021. \n", " Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.clou - Network accessline 627
" Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", " \n" - Network accessline 628
" Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", - Network accessline 679
"21:45:51 - INFO - Performing Enrichr analysis using database GO_Biological_Process_2021. \n", " Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.clou - Network accessline 680
" Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", " \n", - Network accessline 681
" Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", - Network accessline 683
"21:45:51 - INFO - Performing Enrichr analysis using database GO_Biological_Process_2021. \n", " Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.clou - Network accessline 684
" Please note that there might be a more appropriate database for your application. \n", " Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", " \n" - Network accessline 685
" Go to https://maayanlab.cloud/Enrichr/#libraries for a full list of supported databases.\n", - Network accessline 1178
"<observation>Uploading files to mcp_gene repository...\n", "Upload successful!\n", "Result: {\"type\":\"text\",\"text\":\"failed to get branch reference: GET https://api.github.com/repos/mcp_gene/mcp_gene/git/ref/heads/main: 40 - Network accessline 1179
"Upload successful!\n", "Result: {\"type\":\"text\",\"text\":\"failed to get branch reference: GET https://api.github.com/repos/mcp_gene/mcp_gene/git/ref/heads/main: 404 Not Found []\",\"annotations\":null,\"meta\":null}\n", "</ - Network accessline 1180
"Result: {\"type\":\"text\",\"text\":\"failed to get branch reference: GET https://api.github.com/repos/mcp_gene/mcp_gene/git/ref/heads/main: 404 Not Found []\",\"annotations\":null,\"meta\":null}\n", - Network accessline 1209
"\n", "<observation>Checking user information and creating repository...\n", "User info: {\"type\":\"text\",\"text\":\"{\\\"login\\\":\\\"kexinhuang12345\\\",\\\"id\\\":27795075,\\\"profile_url\\\":\\\"https://github.com/kexinhu - Network accessline 1210
"<observation>Checking user information and creating repository...\n", "User info: {\"type\":\"text\",\"text\":\"{\\\"login\\\":\\\"kexinhuang12345\\\",\\\"id\\\":27795075,\\\"profile_url\\\":\\\"https://github.com/kexinhuang12345\\\" - Network accessline 1211
"User info: {\"type\":\"text\",\"text\":\"{\\\"login\\\":\\\"kexinhuang12345\\\",\\\"id\\\":27795075,\\\"profile_url\\\":\\\"https://github.com/kexinhuang12345\\\",\\\"avatar_url\\\":\\\"https://avatars.githubusercontent.com/u/27795075?v=4\ - Network accessline 1212
"Repository creation result: {\"type\":\"text\",\"text\":\"failed to create repository: POST https://api.github.com/user/repos: 422 Repository creation failed. [{Resource:Repository Field:name Code:custom Message:name already exists on this - Network accessline 1415
"print(\"ANALYSIS COMPLETE!\")\n", "print(\"=\"*60)\n", "print(f\"Repository: https://github.com/kexinhuang12345/mcp_gene\")\n", - Network accessline 1416
"print(\"=\"*60)\n", "print(f\"Repository: https://github.com/kexinhuang12345/mcp_gene\")\n", "print(f\"Files uploaded: 6 (including README.md)\")\n", - Network accessline 1417
"print(f\"Repository: https://github.com/kexinhuang12345/mcp_gene\")\n", - Network accessline 1429
"ANALYSIS COMPLETE!\n", "============================================================\n", "Repository: https://github.com/kexinhuang12345/mcp_gene\n", - Network accessline 1430
"============================================================\n", "Repository: https://github.com/kexinhuang12345/mcp_gene\n", "Files uploaded: 6 (including README.md)\n", - Network accessline 1431
"Repository: https://github.com/kexinhuang12345/mcp_gene\n", - Network accessline 1476
"- 13 additional cell types\n", "\n", "**Repository Contents (https://github.com/kexinhuang12345/mcp_gene):**\n", - Network accessline 1477
"\n", "**Repository Contents (https://github.com/kexinhuang12345/mcp_gene):**\n", "- `README.md` - Comprehensive documentation\n", - Network accessline 1478
"**Repository Contents (https://github.com/kexinhuang12345/mcp_gene):**\n",
skills/biomni-general-agent/repo/tutorials/examples/cloning.ipynb
- Executable scriptline 1
Executable file - Network accessline 126
"`st.cache_data` or `st.cache_resource`.\n", "\n", "More information [in our docs](https://docs.streamlit.io/library/advanced-features/caching).\n", - Network accessline 127
"\n", "More information [in our docs](https://docs.streamlit.io/library/advanced-features/caching).\n", "/dfs/user/kexinh/miniconda3/envs/biomni_env/lib/python3.11/site-packages/plannotate/annotate.py:138: FutureWarning: errors= - Network accessline 128
"More information [in our docs](https://docs.streamlit.io/library/advanced-features/caching).\n", - Possible obfuscationline 141
"{'explanation': 'Output fields for each annotation:\\n- sseqid: Subject sequence identifier (name of the feature)\\n- qstart/qend: Start and end positions in query sequence\\n- sstart/send: Start and end positions in subject sequence\\n- s - Possible obfuscationline 642
" \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>The output is too long to be added to context. Here are the first 10K characters...\\nAnalyzing plentiCRISPR v2 plasmid - Possible obfuscationline 644
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>Looking for BsmBI restriction sites in plentiCRISPR v2...\\n{\\'explanation\\': \"Output fields:\\\\n- sequence_info: Inf - Possible obfuscationline 647
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<execute>\\n# Now let\\'s simulate the Golden Gate assembly to create the final plasmid\\nfrom biomni.tool.molecular_biology import go - Possible obfuscationline 650
" \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>The output is too long to be added to context. Here are the first 10K characters...\\nChecking digestion result structur - Possible obfuscationline 651
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<execute>\\n# Let me work with the actual fragment sequences from the digestion\\nprint(\"Working with digestion fragments...\")\\n\\n - Possible obfuscationline 655
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<execute>\\n# Now I understand the correct format. Let me create the final assembled plasmid manually\\nprint(\"Creating the final ass - Possible obfuscationline 657
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nNow let me provide the step-by-step experimental protocols:\\n\\n<execute>\\n# Get the experimental protocols\\nfrom biomni.tool.molec - Possible obfuscationline 658
" \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>=== STEP-BY-STEP EXPERIMENTAL PROTOCOLS ===\\n\\n1. OLIGONUCLEOTIDE ANNEALING PROTOCOL\\n=============================== - Possible obfuscationline 659
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nLet me update the plan with completed steps:\\n\\n## Updated Plan:\\n1. [✓] Load and examine the plentiCRISPR v2 plasmid sequence\\n2. - Possible obfuscationline 661
" \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<solution>\\nI have successfully designed a complete cloning strategy to insert a CRISPR sgRNA targeting human B2M into the plentiCRI - Possible obfuscationline 662
" \"==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<solution>\\nI have successfully designed a complete cloning strategy to insert a CRISPR sgRNA targeting human B2M into the plentiCRI
skills/biomni-general-agent/repo/tutorials/examples/expose_biomni_server/run_mcp_server.py
- Executable scriptline 1
Executable file
skills/biomni-general-agent/repo/tutorials/examples/expose_biomni_server/test_mcp_server.py
skills/biomni-general-agent/repo/tutorials/examples/pylabrobot.ipynb
- Executable scriptline 1
Executable file - Network accessline 77
"Video of what this code does:\n", "\n", "<iframe width=\"640\" height=\"360\" src=\"https://www.youtube.com/embed/NN6ltrRj3bU\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; - Network accessline 78
"\n", "<iframe width=\"640\" height=\"360\" src=\"https://www.youtube.com/embed/NN6ltrRj3bU\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-pi - Network accessline 79
"<iframe width=\"640\" height=\"360\" src=\"https://www.youtube.com/embed/NN6ltrRj3bU\" title=\"YouTube video player\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allo - Network accessline 230
"# Z-probing\n", "\n", "With PyLabRobot, one can probe the surface of any object on a STAR(let) deck. This effectively makes the STAR act as a [Coordinate-Measurement Machine (CMM)](https://en.wikipedia.org/wiki/Coordinate-measu - Network accessline 231
"\n", "With PyLabRobot, one can probe the surface of any object on a STAR(let) deck. This effectively makes the STAR act as a [Coordinate-Measurement Machine (CMM)](https://en.wikipedia.org/wiki/Coordinate-measuring_machine).\n", - Network accessline 232
"With PyLabRobot, one can probe the surface of any object on a STAR(let) deck. This effectively makes the STAR act as a [Coordinate-Measurement Machine (CMM)](https://en.wikipedia.org/wiki/Coordinate-measuring_machine).\n", - Network accessline 971
"(['================================\\x1b[1m Human Message \\x1b[0m=================================\\n\\nCan you generate a script to use PyLabRobot to move water from one range of wells to another using the Hamilton STAR backend?',\n", - Network accessline 972
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\nI\\'ll help you generate a PyLabRobot script to move water from one range of wells to another using the Hamilton STAR backend. Let me - Network accessline 973
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>The output is too long to be added to context. Here are the first 10K characters...\\nPyLabRobot Liquid Handling Document - Possible obfuscationline 973
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>The output is too long to be added to context. Here are the first 10K characters...\\nPyLabRobot Liquid Handling Document - Possible obfuscationline 975
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>Generated PyLabRobot Script:\\n================================================================================\\n\\n\"\" - Possible obfuscationline 979
" '==================================\\x1b[1m Ai Message \\x1b[0m==================================\\n\\n<observation>Fixed PyLabRobot Script:\\n================================================================================\\n\\n\"\"\"\\
skills/biomni-research-agent/SKILL.md
skills/biomni/SKILL.md
- Access to secretsline 43
[Credential-related source omitted] - Network accessline 268
### External Resources - **GitHub**: https://github.com/snap-stanford/biomni - Network accessline 269
- **GitHub**: https://github.com/snap-stanford/biomni - Network accessline 270
- **Web Platform**: https://biomni.stanford.edu - Network accessline 271
- **Paper**: https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1 - Network accessline 272
- **Model**: https://huggingface.co/biomni/Biomni-R0-32B-Preview - Network accessline 273
- **Evaluation Dataset**: https://huggingface.co/datasets/biomni/Eval1 - Access to secretsline 289
[Credential-related source omitted] - Access to secretsline 290
[Credential-related source omitted] - Network accessline 306
For issues or questions: - GitHub Issues: https://github.com/snap-stanford/biomni/issues - Network accessline 307
- GitHub Issues: https://github.com/snap-stanford/biomni/issues
skills/biomni/references/api_reference.md
skills/biomni/references/llm_providers.md
- Access to secretsline 27
[Credential-related source omitted] - Access to secretsline 29
[Credential-related source omitted] - Access to secretsline 30
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 74
[Credential-related source omitted] - Access to secretsline 96
[Credential-related source omitted] - Network accessline 113
[Credential-related source omitted] - Access to secretsline 113
[Credential-related source omitted] - Network accessline 114
export AZURE_OPENAI_ENDPOINT="https://your-resource.openai.azure.com/" - Network accessline 124
[Credential-related source omitted] - Network accessline 125
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Network accessline 126
default_config.azure_openai_endpoint = "https://your-resource.openai.azure.com/" - Access to secretsline 149
[Credential-related source omitted] - Access to secretsline 168
[Credential-related source omitted] - Access to secretsline 184
[Credential-related source omitted] - Access to secretsline 203
[Credential-related source omitted] - Access to secretsline 219
[Credential-related source omitted] - Network accessline 258
default_config.llm = "custom" default_config.custom_llm_endpoint = "http://localhost:8000/v1/chat/completions" - Network accessline 259
default_config.custom_llm_endpoint = "http://localhost:8000/v1/chat/completions" - Access to secretsline 260
[Credential-related source omitted] - Network accessline 283
# Configure biomni export CUSTOM_LLM_ENDPOINT="http://localhost:8000/v1/chat/completions" - Network accessline 284
export CUSTOM_LLM_ENDPOINT="http://localhost:8000/v1/chat/completions" - Access to secretsline 363
[Credential-related source omitted] - Access to secretsline 367
[Credential-related source omitted]
skills/biomni/scripts/generate_report.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 187
<div class="footer"> <p>Generated with Biomni | Stanford SNAP Lab</p> <p><a href="https://github.com/snap-stanford/biomni">github.com/snap-stanford/biomni</a></p> - Network accessline 188
<p>Generated with Biomni | Stanford SNAP Lab</p> <p><a href="https://github.com/snap-stanford/biomni">github.com/snap-stanford/biomni</a></p> </div> - Network accessline 189
<p><a href="https://github.com/snap-stanford/biomni">github.com/snap-stanford/biomni</a></p>
skills/biomni/scripts/setup_environment.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 39
if not check_conda_installed(): print("❌ Conda not found. Please install Miniconda or Anaconda:") print(" https://docs.conda.io/en/latest/miniconda.html") - Network accessline 40
print("❌ Conda not found. Please install Miniconda or Anaconda:") print(" https://docs.conda.io/en/latest/miniconda.html") return False - Network accessline 41
print(" https://docs.conda.io/en/latest/miniconda.html") - Network accessline 91
print("\n1. Anthropic Claude (Recommended)") print(" Get your API key from: https://console.anthropic.com/") - Network accessline 92
print(" Get your API key from: https://console.anthropic.com/") - Access to secretsline 93
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Network accessline 98
print("\n2. OpenAI") print(" Get your API key from: https://platform.openai.com/api-keys") - Network accessline 99
print(" Get your API key from: https://platform.openai.com/api-keys") - Access to secretsline 100
[Credential-related source omitted] - Access to secretsline 102
[Credential-related source omitted] - Network accessline 105
print("\n3. Google Gemini") print(" Get your API key from: https://makersuite.google.com/app/apikey") - Network accessline 106
print(" Get your API key from: https://makersuite.google.com/app/apikey") - Access to secretsline 107
[Credential-related source omitted] - Access to secretsline 109
[Credential-related source omitted] - Network accessline 112
print("\n4. Groq") print(" Get your API key from: https://console.groq.com/keys") - Network accessline 113
print(" Get your API key from: https://console.groq.com/keys") - Access to secretsline 114
[Credential-related source omitted] - Access to secretsline 116
[Credential-related source omitted] - Access to secretsline 128
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 298
[Credential-related source omitted] - Network accessline 342
print("\nFor documentation, see:") print(" - GitHub: https://github.com/snap-stanford/biomni") - Network accessline 343
print(" - GitHub: https://github.com/snap-stanford/biomni") - Network accessline 344
print(" - Paper: https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1")
skills/biopython/SKILL.md
- Access to secretsline 56
[Credential-related source omitted] - Network accessline 406
- **Official Documentation**: https://biopython.org/docs/latest/ - Network accessline 407
- **Tutorial**: https://biopython.org/docs/latest/Tutorial/ - Network accessline 408
- **Cookbook**: https://biopython.org/docs/latest/Tutorial/ (advanced examples) - Network accessline 409
- **GitHub**: https://github.com/biopython/biopython
skills/biopython/references/databases.md
skills/biorxiv-database/SKILL.md
- Network accessline 119
python scripts/biorxiv_search.py \ --doi "https://doi.org/10.1101/2024.01.15.123456" - Network accessline 120
--doi "https://doi.org/10.1101/2024.01.15.123456" - Network accessline 208
"category": "genomics", "abstract": "Full abstract text...", "pdf_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf", - Network accessline 209
"abstract": "Full abstract text...", "pdf_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf", "html_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1", - Network accessline 210
"pdf_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf", - Network accessline 211
"html_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1", - Network accessline 212
"jatsxml": "https://www.biorxiv.org/content/...",
skills/biorxiv-database/references/api_reference.md
- Network accessline 10
https://api.biorxiv.org - Network accessline 39
GET https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31 - Network accessline 40
GET https://api.biorxiv.org/details/biorxiv/2024-01-01/2024-01-31/neuroscience - Network accessline 63
"license": "cc_by", "category": "neuroscience", "jatsxml": "https://www.biorxiv.org/content/...", - Network accessline 64
"category": "neuroscience", "jatsxml": "https://www.biorxiv.org/content/...", "abstract": "This is the abstract...", - Network accessline 65
"jatsxml": "https://www.biorxiv.org/content/...", - Network accessline 87
GET https://api.biorxiv.org/details/biorxiv/10.1101/2024.01.15.123456 - Network accessline 106
GET https://api.biorxiv.org/pubs/biorxiv/1/0/json - Network accessline 183
https://www.biorxiv.org/content/{doi}v{version}.full.pdf - Network accessline 188
https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf - Network accessline 194
https://www.biorxiv.org/content/{doi}v{version} - Network accessline 278
- bioRxiv homepage: https://www.biorxiv.org/ - Network accessline 279
- API documentation: https://api.biorxiv.org/ - Network accessline 280
- JATS XML specification: https://jats.nlm.nih.gov/
skills/biorxiv-database/scripts/biorxiv_search.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 23
BASE_URL = "https://api.biorxiv.org" - Network accessline 39
self.verbose = verbose self.session = requests.Session() - Network accessline 40
self.session = requests.Session() - Network accessline 247
pdf_url = f"https://www.biorxiv.org/content/{doi}v1.full.pdf" - Network accessline 294
if result["doi"]: result["pdf_url"] = f"https://www.biorxiv.org/content/{result['doi']}v{result['version']}.full.pdf" - Network accessline 295
result["pdf_url"] = f"https://www.biorxiv.org/content/{result['doi']}v{result['version']}.full.pdf" - Network accessline 296
result["html_url"] = f"https://www.biorxiv.org/content/{result['doi']}v{result['version']}"
skills/bioservices/SKILL.md
- Network accessline 352
For detailed API documentation and advanced features, refer to: - Official documentation: https://bioservices.readthedocs.io/ - Network accessline 353
- Official documentation: https://bioservices.readthedocs.io/ - Network accessline 354
- Source code: https://github.com/cokelaer/bioservices
skills/bioservices/references/services_reference.md
- Network accessline 127
**Key Methods:** - `search(query)`: Search gene symbols/names - `fetch(format, query)`: Retrieve gene information - Network accessline 129
- `fetch(format, query)`: Retrieve gene information - Network accessline 633
For detailed API documentation: - Official docs: https://bioservices.readthedocs.io/ - Network accessline 634
- Official docs: https://bioservices.readthedocs.io/ - Network accessline 636
- Source code: https://github.com/cokelaer/bioservices
skills/bioservices/scripts/batch_id_converter.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bioservices/scripts/compound_cross_reference.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bioservices/scripts/pathway_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/bioservices/scripts/protein_analysis_workflow.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/boltzgen/SKILL.md
- Network accessline 16
tags: [structure-design, sequence-design, diffusion, all-atom, binder] proteinbase_slug: boltzgen proteinbase_url: https://proteinbase.com/design-methods/boltzgen - Network accessline 17
proteinbase_slug: boltzgen proteinbase_url: https://proteinbase.com/design-methods/boltzgen biomodals_script: modal_boltzgen.py - Network accessline 18
proteinbase_url: https://proteinbase.com/design-methods/boltzgen - Network accessline 39
# Clone biomodals git clone https://github.com/hgbrian/biomodals && cd biomodals - Network accessline 40
git clone https://github.com/hgbrian/biomodals && cd biomodals - Network accessline 61
git clone https://github.com/HannesStark/boltzgen.git
skills/boltzgen/references/yaml-spec.md
- Network accessline 286
Then visualize the output CIF in Molstar (https://molstar.org/viewer/) to confirm:
skills/brenda-database/SKILL.md
- Access to secretsline 302
[Credential-related source omitted] - Network accessline 314
3. **Register for BRENDA access**: - Visit https://www.brenda-enzymes.org/ - Network accessline 315
- Visit https://www.brenda-enzymes.org/ - Access to secretsline 674
[Credential-related source omitted] - Network accessline 710
- BRENDA Home: https://www.brenda-enzymes.org/ - Network accessline 711
- BRENDA SOAP API Documentation: https://www.brenda-enzymes.org/soap.php - Network accessline 712
- Enzyme Commission (EC) Numbers: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/ - Network accessline 713
- Zeep SOAP Client: https://python-zeep.readthedocs.io/ - Network accessline 714
- Enzyme Nomenclature: https://www.iubmb.org/enzyme/
skills/brenda-database/references/api_reference.md
- Network accessline 11
https://www.brenda-enzymes.org/soap/brenda_zeep.wsdl - Access to secretsline 214
[Credential-related source omitted] - Access to secretsline 215
[Credential-related source omitted] - Access to secretsline 216
[Credential-related source omitted] - Access to secretsline 217
[Credential-related source omitted] - Network accessline 509
- **BRENDA Website**: https://www.brenda-enzymes.org/ - Network accessline 510
- **SOAP API Documentation**: https://www.brenda-enzymes.org/soap.php - Network accessline 511
- **Enzyme Nomenclature**: https://www.iubmb.org/enzyme/ - Network accessline 512
- **EC Number Database**: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/ - Network accessline 516
- **Zeep (SOAP Client)**: https://python-zeep.readthedocs.io/ - Network accessline 517
- **PubChemPy**: https://pubchempy.readthedocs.io/ - Network accessline 518
- **BioPython**: https://biopython.org/ - Network accessline 519
- **RDKit**: https://www.rdkit.org/
skills/brenda-database/scripts/brenda_queries.py
- Executable scriptline 1
Executable file
skills/brenda-database/scripts/brenda_visualization.py
- Executable scriptline 1
Executable file
skills/brenda-database/scripts/enzyme_pathway_builder.py
- Executable scriptline 1
Executable file
skills/bulk-stringdb-ppi/SKILL.md
- Network accessline 46
## References - Tutorial notebook: [`t_network.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_network.ipynb) - STRING background: [string-db.org](https://string-db.org/) - Network accessline 47
- Tutorial notebook: [`t_network.ipynb`](../../omicverse_guide/docs/Tutorials-bulk/t_network.ipynb) - STRING background: [string-db.org](https://string-db.org/) - Quick copy/paste commands: [`reference.md`](reference.md) - Network accessline 48
- STRING background: [string-db.org](https://string-db.org/)
skills/care-coordination/coworker.py
skills/cbioportal-database/SKILL.md
- Network accessline 13
cBioPortal for Cancer Genomics (https://www.cbioportal.org/) is an open-access resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. It hosts data from The Cancer Genome Atlas (TCGA), AACR Project GENIE, - Network accessline 15
**Key resources:** - cBioPortal website: https://www.cbioportal.org/ - Network accessline 16
- cBioPortal website: https://www.cbioportal.org/ - Network accessline 17
- REST API: https://www.cbioportal.org/api/ - API docs (Swagger): https://www.cbioportal.org/api/swagger-ui/index.html - Python client: `bravado` or `requests` - Network accessline 18
- API docs (Swagger): https://www.cbioportal.org/api/swagger-ui/index.html - Python client: `bravado` or `requests` - GitHub: https://github.com/cBioPortal/cbioportal - Network accessline 20
- GitHub: https://github.com/cBioPortal/cbioportal - Network accessline 39
Base URL: `https://www.cbioportal.org/api` - Network accessline 46
BASE_URL = "https://www.cbioportal.org/api" - Network accessline 49
def cbioportal_get(endpoint, params=None): url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers=HEADERS) - Network accessline 50
url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers=HEADERS) response.raise_for_status() - Network accessline 51
response = requests.get(url, params=params, headers=HEADERS) - Network accessline 55
def cbioportal_post(endpoint, body): url = f"{BASE_URL}/{endpoint}" response = requests.post(url, json=body, headers=HEADERS) - Network accessline 56
url = f"{BASE_URL}/{endpoint}" response = requests.post(url, json=body, headers=HEADERS) response.raise_for_status() - Network accessline 57
response = requests.post(url, json=body, headers=HEADERS) - Network accessline 175
# Get sample list samples = requests.get( - Network accessline 176
samples = requests.get( - Network accessline 181
(s["sampleListId"] for s in samples if s["category"] == "all_cases_in_study"), None ) total_samples = len(requests.get( - Network accessline 182
) total_samples = len(requests.get( f"{BASE_URL}/sample-lists/{all_samples_id}/sample-ids", - Network accessline 183
total_samples = len(requests.get( - Network accessline 188
# Get gene Entrez IDs gene_data = requests.post( - Network accessline 189
gene_data = requests.post( - Network accessline 245
# 1. Get gene Entrez ID gene_info = requests.post( - Network accessline 246
gene_info = requests.post( - Network accessline 308
gene_info = requests.post( - Network accessline 355
# Download TCGA BRCA data wget https://cbioportal-datahub.s3.amazonaws.com/brca_tcga.tar.gz - Network accessline 356
wget https://cbioportal-datahub.s3.amazonaws.com/brca_tcga.tar.gz - Network accessline 361
- **cBioPortal website**: https://www.cbioportal.org/ - Network accessline 362
- **API Swagger UI**: https://www.cbioportal.org/api/swagger-ui/index.html - Network accessline 363
- **Documentation**: https://docs.cbioportal.org/ - Network accessline 364
- **GitHub**: https://github.com/cBioPortal/cbioportal - Network accessline 365
- **Data hub**: https://datahub.cbioportal.org/ - Network accessline 367
- **API clients**: https://docs.cbioportal.org/web-api-and-clients/
skills/cell-free-expression/SKILL.md
- Network accessline 258
### CFPS Overview - [User's Guide to CFPS - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6481089/) - Network accessline 259
- [User's Guide to CFPS - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6481089/) - Network accessline 260
- [Optimising Protein Synthesis in Cell-Free Systems - PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996726/) - Network accessline 261
- [CFPS Systems Comparison - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC8258279/) - Network accessline 263
### Extract Preparation - [Crude Extract Preparation - MDPI Methods](https://www.mdpi.com/2409-9279/2/3/68) - Network accessline 264
- [Crude Extract Preparation - MDPI Methods](https://www.mdpi.com/2409-9279/2/3/68) - Network accessline 265
- [Simple Rapid Cell-Free Lysate - PLOS One](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0165137) - Network accessline 266
- [High-Throughput Extract Preparation - Nature Scientific Reports](https://www.nature.com/articles/srep08663) - Network accessline 268
### PURE System - [PURE System Evolution - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10521753/) - Network accessline 269
- [PURE System Evolution - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10521753/) - Network accessline 270
- [PURE System for Membrane Proteins - Nature Protocols](https://www.nature.com/articles/nprot.2015.082) - Network accessline 272
### Wheat Germ - [Wheat Germ Systems Review - FEBS Letters](https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2014.05.061) - Network accessline 273
- [Wheat Germ Systems Review - FEBS Letters](https://febs.onlinelibrary.wiley.com/doi/10.1016/j.febslet.2014.05.061) - Network accessline 274
- [Wheat Germ for Structural Biology - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC8027086/) - Network accessline 276
### Codon Optimization - [Rare Codons and Solubility - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2723077/) - Network accessline 277
- [Rare Codons and Solubility - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC2723077/) - Network accessline 278
- [Codon Influence on Expression - Nature](https://www.nature.com/articles/nature16509) - Network accessline 279
- [Synonymous Codon Substitutions Perturb Folding - PNAS](https://www.pnas.org/doi/10.1073/pnas.1907126117) - Network accessline 281
### Disulfide Formation - [Oxidative Protein Folding in ER - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4312752/) - Network accessline 282
- [Oxidative Protein Folding in ER - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4312752/) - Network accessline 283
- [PDI-Regulated Disulfide Formation - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC7794689/) - Network accessline 285
### Solubility Tags - [SUMO Fusion for Difficult Proteins - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC7129290/) - Network accessline 286
- [SUMO Fusion for Difficult Proteins - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC7129290/) - Network accessline 287
- [Fusion Tags Review - Frontiers Microbiol](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2014.00063/full) - Network accessline 289
### Temperature Effects - [Cold Shock Promoters - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC9800685/) - Network accessline 290
- [Cold Shock Promoters - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC9800685/) - Network accessline 291
- [Strategies to Optimize E. coli Expression - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC7162232/)
skills/cellagent-annotation/README.md
- Network accessline 68
- https://github.com/jianghao-zhang/CellTypeAgent
skills/cellagent-annotation/repo/.gitignore
- Access to secretsline 6
[Credential-related source omitted]
skills/cellagent-annotation/repo/CellTypeAgent/LLM.py
- Executable scriptline 1
Executable file - Network accessline 11
""" This file contains the code for calling all LLM APIs. Ref: https://github.com/snap-stanford/BioDiscoveryAgent/blob/master/LLM.py""" - Access to secretsline 20
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Access to secretsline 32
[Credential-related source omitted] - Access to secretsline 47
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted]
skills/cellagent-annotation/repo/CellTypeAgent/__init__.py
- Executable scriptline 1
Executable file
skills/cellagent-annotation/repo/CellTypeAgent/config.py
- Executable scriptline 1
Executable file
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/Azimuth.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/BCL.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/HCA.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/HCL.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/MCA.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/all.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/all_human.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/all_human_mixed.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/all_mouse.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/coloncancer.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/literature.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/datasets/lungcancer.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/src/all.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/src/compiled.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/GPTCellType/src/relation.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/Gene-Expression-Atlas.png
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/CellTypeAgent/data/README.md
- Network accessline 16
## GPTCellType - [all.csv](https://github.com/Winnie09/GPTCelltype_Paper/blob/master/anno/compiled/all.csv) - Network accessline 17
- [all.csv](https://github.com/Winnie09/GPTCelltype_Paper/blob/master/anno/compiled/all.csv) - Network accessline 18
- [compiled.csv](https://github.com/Winnie09/GPTCelltype_Paper/blob/master/anno/cl/compiled.csv) - Network accessline 19
- [relation.csv](https://github.com/Winnie09/GPTCelltype_Paper/blob/master/anno/cl/relation.csv) - Network accessline 21
## CellxGene gene expression data - [TS part 1](https://cellxgene.cziscience.com/gene-expression?tissues=UBERON%3A0001013%2CUBERON%3A0018707%2CUBERON%3A0000178%2CUBERON%3A0002371%2CUBERON%3A0000310%2CUBERON%3A0000970%2CUBERON%3A0000033%2CUB - Network accessline 22
- [TS part 1](https://cellxgene.cziscience.com/gene-expression?tissues=UBERON%3A0001013%2CUBERON%3A0018707%2CUBERON%3A0000178%2CUBERON%3A0002371%2CUBERON%3A0000310%2CUBERON%3A0000970%2CUBERON%3A0000033%2CUBERON%3A0000948%2CUBERON%3A0002113% - Network accessline 23
- [Azimuth part 1](https://cellxgene.cziscience.com/gene-expression?tissues=UBERON%3A0001013%2CUBERON%3A0000178%2CUBERON%3A0002371%2CUBERON%3A0001851%2CUBERON%3A0000922%2CUBERON%3A0000948%2CUBERON%3A0002113%2CUBERON%3A0002107%2CUBERON%3A000 - Network accessline 24
- [HCA](https://cellxgene.cziscience.com/gene-expression?tissues=UBERON%3A0000310%2CUBERON%3A0001043%2CUBERON%3A0000948%2CUBERON%3A0002048%2CUBERON%3A0001015%2CUBERON%3A0002367%2CUBERON%3A0002097&genes=ACACB%2CFASN%2CLPIN1%2CMLXIPL%2CEBF1%2 - Network accessline 25
- [MCA](https://cellxgene.cziscience.com/gene-expression?organism=NCBITaxon%3A10090&genes=F13a1%2CStar%2CLpl%2CPtn%2CTff1%2CSmc1b%2CScg2%2CCsf1r%2CSparc%2CAgr2%2CCd3g%2CKlk1%2CLgals4%2CNap1l5%2CGzmb%2CTtr%2CSerpinh1%2CCol11a1%2CCtla2a%2CCsn - Network accessline 26
- [HCL](https://cellxgene.cziscience.com/gene-expression?genes=PGC%2CKRT6A%2CUROD%2CLYZ%2CEPYC%2CRPS17%2CPOSTN%2CIYD%2CALDOC%2CTSPAN8%2CPRCP%2CFGFBP1%2CKRT14%2CCLU%2CADIRF%2CHLA-B%2CACP5%2CCST7%2CSPARCL1%2CSTMN1%2CAQP3%2CHNRNPA1%2CCD52%2CRP - Network accessline 27
- [literature](https://cellxgene.cziscience.com/gene-expression?genes=EBF1%2CG0S2%2CPLIN1%2CPLIN2%2CLPIN1%2CFOXO1%2CPPARG%2CACSL1%2CADIPOQ%2CGHR%2CLDB2%2CEGFL7%2CPECAM1%2CCDH5%2CVWF%2CRAMP3%2CCD300LG%2CBACE2%2CEPHB4%2CNOSTRIN%2CPTPRB%2CCLDN - Network accessline 28
- [lungcancer](https://cellxgene.cziscience.com/gene-expression?diseases=MONDO%3A0005061%2CMONDO%3A0003050%2CMONDO%3A0005233%2CMONDO%3A0008433%2CMONDO%3A0005097&genes=LYZ%2CC1QA%2CC1QB%2CAIF1%2CTYROBP%2CFCER1G%2CCD68%2CC1QC%2CAPOC1%2CLST1%2 - Network accessline 29
- [coloncancer](https://cellxgene.cziscience.com/gene-expression?diseases=MONDO%3A0005575&genes=KRT18%2CKRT8%2CEPCAM%2CCLDN3%2CKRT19%2CTFF3%2CCLDN4%2CTSPAN8%2CCD24%2CCEACAM5%2CPHGR1%2CGUCA2A%2CMT1G%2CPIGR%2CMT1E%2CGUCA2B%2CFABP1%2CLGALS4%2C - Network accessline 30
- [BCL](https://cellxgene.cziscience.com/gene-expression?diseases=MONDO%3A0004947%2CMONDO%3A0015759%2CMONDO%3A0018906&genes=IL32%2CZBTB16%2CANXA1%2CTXNIP%2CPTGDS%2CNKG7%2CCD8A%2CTRDV2%2CCTLA4%2CCD3E%2CIFI30%2CFGFBP2%2CCST7%2CTF%2CIFITM3%2CF - Network accessline 33
### How can you obtain your own gene expression data from the CZ CellxGene gene expression atlas? 1. Go to the [atlas page](https://cellxgene.cziscience.com/gene-expression). - Network accessline 34
1. Go to the [atlas page](https://cellxgene.cziscience.com/gene-expression). 2. Fill in the corresponding options according to your own dataset, and then paste all the marker genes of your dataset. (It may take some time to load all the dat
skills/cellagent-annotation/repo/CellTypeAgent/eval.py
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Executable file
skills/cellagent-annotation/repo/CellTypeAgent/get_expression_score.py
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Executable file
skills/cellagent-annotation/repo/CellTypeAgent/get_gene_summary.py
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Executable file - Network accessline 15
def get_gene_id(gene_name, species="human"): base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 16
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 19
response = requests.get(esearch_url) - Network accessline 33
def get_gene_summary(gene_id): base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 34
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 37
response = requests.get(efetch_url)
skills/cellagent-annotation/repo/CellTypeAgent/get_lit_review.py
- Executable scriptline 1
Executable file - Network accessline 214
def query_LitSense(query, max_results, rerank=True): base_url = "https://www.ncbi.nlm.nih.gov/research/litsense-api/api/" - Network accessline 215
base_url = "https://www.ncbi.nlm.nih.gov/research/litsense-api/api/" - Network accessline 222
} full_url = f"{base_url}?{urllib.parse.urlencode(params)}" response = requests.get(full_url) - Network accessline 223
full_url = f"{base_url}?{urllib.parse.urlencode(params)}" response = requests.get(full_url) reviews = [] - Network accessline 224
response = requests.get(full_url)
skills/cellagent-annotation/repo/CellTypeAgent/get_prediction.py
skills/cellagent-annotation/repo/CellTypeAgent/get_selection.py
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cell_type_pred_CLname = eval(sample['cell_type_pred_CLname']) if isinstance(sample['cell_type_pred_CLname'], str) else sample['cell_type_pred_CLname'] - Dangerous shell operationline 475
pred_ls = pred[pred_name].apply(lambda x: eval(x) if isinstance(x, str) else x).tolist() - Dangerous shell operationline 525
lambda x: eval(x) if isinstance(x, str) and '[[' in x else ([ [x] ] if isinstance(x, str) else x) - Dangerous shell operationline 551
lambda x: eval(x) if isinstance(x, str) and '[[' in x else ([ [x] ] if isinstance(x, str) else x) - Dangerous shell operationline 554
lambda x: eval(x) if isinstance(x, str) and '[[' in x else ([ [x] ] if isinstance(x, str) else x) - Dangerous shell operationline 572
sep_avg_score += eval(data[f'final_score_{j}'][i]) if isinstance(data[f'final_score_{j}'][i], str) else data[f'final_score_{j}'][i] - Dangerous shell operationline 581
data['best_candidate_index'] = data['agreement_score'].apply(lambda x: np.argmax(eval(x)))
skills/cellagent-annotation/repo/CellTypeAgent/utils.py
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skills/cellagent-annotation/repo/Figs/Fig_a - Results table like f2d in GPTCellType.ipynb
skills/cellagent-annotation/repo/Figs/Fig_b - Average agreement score on all datasets accross different base models.ipynb
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/comparison.ipynb
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/gene_summary_augmented/test_gene_summary_augmented.ipynb
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/lit_review_augmented/lit_dict_MCA (claude-3.5-sonnet).json
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"Tagln" ], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated - Network accessline 700
], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHe - Network accessline 701
"prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHere are the
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/lit_review_augmented/lit_dict_MCA (deepseek-r1).json
- Network accessline 699
"Tagln" ], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated - Network accessline 700
], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHe - Network accessline 701
"prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHere are the
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/lit_review_augmented/lit_dict_MCA (o1-mini).json
- Network accessline 15
"H2afz" ], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated - Network accessline 16
], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHe - Network accessline 17
"prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHere are the - Network accessline 699
"Tagln" ], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated - Network accessline 700
], "prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHe - Network accessline 701
"prompt": "\nIdentify most likely top 3 cell types of mouse cells using the following markers. Only provide the lists of top 3 cell type names. The higher the probability, the further left it is ranked, separated by commas.\n\nHere are the
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/lit_review_augmented/logs/deepseek-r1/MCA/38.log
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pmcid: PMC11236323 section: RESULTS content: So, we redid the analysis manually to analyze the top 10 expressed genes in the cluster 14, including TAGLN, RGS5, IGFBP5, ACTA2, IGFBP7, CALD1, MYL9, TPM2, TIMP3, NR2F2 through the online websit - Network accessline 16
section: RESULTS content: So, we redid the analysis manually to analyze the top 10 expressed genes in the cluster 14, including TAGLN, RGS5, IGFBP5, ACTA2, IGFBP7, CALD1, MYL9, TPM2, TIMP3, NR2F2 through the online website Cell Taxonomy (ht - Network accessline 17
content: So, we redid the analysis manually to analyze the top 10 expressed genes in the cluster 14, including TAGLN, RGS5, IGFBP5, ACTA2, IGFBP7, CALD1, MYL9, TPM2, TIMP3, NR2F2 through the online website Cell Taxonomy (https://ngdc.cncb.a
skills/cellagent-annotation/repo/Figs/Fig_d - External knowledge augmented/lit_review_augmented/test_lit_review_augmented.ipynb
skills/cellagent-annotation/repo/Figs/Fig_e Effect of # of cell type candidates predicted.ipynb
skills/cellagent-annotation/repo/Figs/Fig_f - Effect of # of given marker genes in the prompt.ipynb
skills/cellagent-annotation/repo/Figs/Fig_g - Given mixed marker genes, to predict the mixed cell types.ipynb
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version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/lungcancer/top_3_max_8.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/lungcancer/top_3_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/lungcancer/top_4_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/lungcancer/top_5_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/improvement.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/test.ipynb
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_2_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_3_max_3.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_3_max_5.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_3_max_8.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_3_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_4_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/Figs/o1-preview (for reproduction)/tabulasapiens/top_5_max_None.csv
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/cellagent-annotation/repo/README.md
- Network accessline 25
git clone https://github.com/jianghao-zhang/CellTypeAgent.git - Network accessline 38
4. Prepare the data - The datasets used in the paper are stored in the 'CellTypeAgent/data' folder. - Please download the gene expression data used in this paper from [Google Drive](https://drive.google.com/drive/folders/1mC6r5Nu1JimBWSOanO - Network accessline 39
- The datasets used in the paper are stored in the 'CellTypeAgent/data' folder. - Please download the gene expression data used in this paper from [Google Drive](https://drive.google.com/drive/folders/1mC6r5Nu1JimBWSOanOdGDT2QolYdhF_S?usp=s - Network accessline 40
- Please download the gene expression data used in this paper from [Google Drive](https://drive.google.com/drive/folders/1mC6r5Nu1JimBWSOanOdGDT2QolYdhF_S?usp=sharing) and place it in the 'CellTypeAgent/data/CELLxGENE' directory. - Network accessline 57
1. Format your data according to the structure in `CellTypeAgent/data/GPTCellType/datasets` 2. Download the corresponding gene expression data from the [CZ CellxGene - Gene Expression Atlas](https://cellxgene.cziscience.com/gene-expression) - Network accessline 58
2. Download the corresponding gene expression data from the [CZ CellxGene - Gene Expression Atlas](https://cellxgene.cziscience.com/gene-expression), for more details, please refer to the [README.md](CellTypeAgent/data/README.md) in the 'Ce
skills/chai/SKILL.md
- Network accessline 64
git clone https://github.com/chaidiscovery/chai-lab.git
skills/chembl-database/SKILL.md
- Network accessline 379
- ChEMBL website: https://www.ebi.ac.uk/chembl/ - Network accessline 380
- API documentation: https://www.ebi.ac.uk/chembl/api/data/docs - Network accessline 381
- Python client GitHub: https://github.com/chembl/chembl_webresource_client - Network accessline 382
- Interface documentation: https://chembl.gitbook.io/chembl-interface-documentation/ - Network accessline 383
- Example notebooks: https://github.com/chembl/notebooks
skills/chembl-database/references/api_reference.md
- Network accessline 269
- Official API documentation: https://www.ebi.ac.uk/chembl/api/data/docs - Network accessline 270
- Python client GitHub: https://github.com/chembl/chembl_webresource_client - Network accessline 271
- ChEMBL interface docs: https://chembl.gitbook.io/chembl-interface-documentation/ - Network accessline 272
- Example notebooks: https://github.com/chembl/notebooks
skills/chembl-database/scripts/example_queries.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/chembl-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search ChEMBL, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search ChEMBL, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Compound/Assay Title", "url": "https://chembl.org/...", - Network accessline 79
"title": "Compound/Assay Title", "url": "https://chembl.org/...", "content": "Compound data, targets, assay results...", - Network accessline 80
"url": "https://chembl.org/...", - Network accessline 82
"source": "chembl", "relevance_score": 0.95, "images": ["https://example.com/structure.png"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/structure.png"] } - Network accessline 84
"images": ["https://example.com/structure.png"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/chembl-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/chembl-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/chemcrow-drug-discovery/chem_tools.py
- Executable scriptline 1
Executable file - Network accessline 28
References: - ChemCrow Paper: https://arxiv.org/abs/2304.05376 - Network accessline 29
- ChemCrow Paper: https://arxiv.org/abs/2304.05376 - Network accessline 30
- RDKit Documentation: https://www.rdkit.org/docs/ - Network accessline 31
- SA Score: https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-3-36
skills/chemical-property-lookup/molecular_tools.py
- Executable scriptline 1
Executable file
skills/chemist-analyst/SKILL.md
- Network accessline 104
- [Atomic Structure - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/General_Chemistry/Map:_Chemistry_-_The_Central_Science_(Brown_et_al.)/06:_Electronic_Structure_of_Atoms>) - Network accessline 105
- [Chemical Bonding - Khan Academy](https://www.khanacademy.org/science/chemistry/chemical-bonds) - Network accessline 160
- [Thermodynamics - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Thermodynamics>) - Network accessline 161
- [Chemical Equilibrium - Khan Academy](https://www.khanacademy.org/science/chemistry/chemical-equilibrium-topic) - Network accessline 208
- [Chemical Kinetics - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Kinetics>) - Network accessline 209
- [Reaction Mechanisms - Khan Academy](https://www.khanacademy.org/science/chemistry/chem-kinetics) - Network accessline 266
- [Organic Chemistry - Khan Academy](https://www.khanacademy.org/science/organic-chemistry) - Network accessline 267
- [Organic Chemistry LibreTexts](https://chem.libretexts.org/Bookshelves/Organic_Chemistry) - Network accessline 332
- [Analytical Chemistry LibreTexts](https://chem.libretexts.org/Bookshelves/Analytical_Chemistry) - Network accessline 333
- [Spectroscopy - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Spectroscopy>) - Network accessline 387
- [Retrosynthetic Analysis - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Reactions/Reactivity/Retrosynthetic_Analysis>) - Network accessline 388
- [Synthesis - Khan Academy](https://www.khanacademy.org/science/organic-chemistry/organic-synthesis) - Network accessline 462
- [Reaction Mechanisms - Master Organic Chemistry](https://www.masterorganicchemistry.com/reaction-guide/) - Network accessline 463
- [Mechanisms - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Reactions/Reaction_Mechanisms>) - Network accessline 517
- [Structure-Property Relationships - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Physical_Properties_of_Matter>) - Network accessline 555
- [Green Chemistry Principles - ACS](https://www.acs.org/greenchemistry/principles/12-principles-of-green-chemistry.html) - Network accessline 556
- [Green Chemistry - EPA](https://www.epa.gov/greenchemistry) - Network accessline 623
- [Biochemistry - Khan Academy](https://www.khanacademy.org/science/biology/macromolecules) - Network accessline 624
- [Metabolism - Biology LibreTexts](<https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book:_General_Biology_(Boundless)/07:_Cellular_Respiration>) - Network accessline 845
- [Computational Chemistry - Chemistry LibreTexts](<https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Quantum_Mechanics>) - Network accessline 1429
- World's largest scientific society - Website: https://www.acs.org/ - Network accessline 1430
- Website: https://www.acs.org/ - Network accessline 1435
- UK-based, international - Website: https://www.rsc.org/ - Network accessline 1436
- Website: https://www.rsc.org/ - Network accessline 1441
- Global authority on chemical nomenclature and standards - Website: https://iupac.org/ - Network accessline 1442
- Website: https://iupac.org/ - Network accessline 1448
- https://pubchem.ncbi.nlm.nih.gov/ - Network accessline 1452
- http://www.chemspider.com/ - Network accessline 1470
**Khan Academy Chemistry**: https://www.khanacademy.org/science/chemistry - Network accessline 1471
**Chemistry LibreTexts**: https://chem.libretexts.org/ - Network accessline 1472
**Master Organic Chemistry**: https://www.masterorganicchemistry.com/ - Network accessline 1473
**Chemguide**: https://www.chemguide.co.uk/
skills/citation-management/SKILL.md
- Broad permissionsline 1
Bash - Network accessline 173
# Extract from URL python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 174
python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 487
1. **Find MeSH terms** at https://meshb.nlm.nih.gov/search - Network accessline 611
# From URL python scripts/extract_metadata.py \ --url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 612
python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 613
--url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 1024
**Search Engines**: - Google Scholar: https://scholar.google.com/ - Network accessline 1025
- Google Scholar: https://scholar.google.com/ - Network accessline 1026
- PubMed: https://pubmed.ncbi.nlm.nih.gov/ - Network accessline 1027
- PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/ - Network accessline 1029
**Metadata APIs**: - CrossRef API: https://api.crossref.org/ - Network accessline 1030
- CrossRef API: https://api.crossref.org/ - Network accessline 1031
- PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/ - Network accessline 1032
- arXiv API: https://arxiv.org/help/api/ - Network accessline 1033
- DataCite API: https://api.datacite.org/ - Network accessline 1035
**Tools and Validators**: - MeSH Browser: https://meshb.nlm.nih.gov/search - Network accessline 1036
- MeSH Browser: https://meshb.nlm.nih.gov/search - Network accessline 1037
- DOI Resolver: https://doi.org/ - Network accessline 1038
- BibTeX Format: http://www.bibtex.org/Format/ - Network accessline 1040
**Citation Styles**: - BibTeX documentation: http://www.bibtex.org/ - Network accessline 1041
- BibTeX documentation: http://www.bibtex.org/ - Network accessline 1042
- LaTeX bibliography management: https://www.overleaf.com/learn/latex/Bibliography_management
skills/citation-management/assets/bibtex_template.bib
- Network accessline 85
pages = {5998--6008}, address = {Long Beach, CA}, url = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html} - Network accessline 86
address = {Long Beach, CA}, url = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html} } - Network accessline 87
url = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html} - Network accessline 185
year = {2021}, howpublished = {Database}, url = {https://alphafold.ebi.ac.uk/}, - Network accessline 186
howpublished = {Database}, url = {https://alphafold.ebi.ac.uk/}, doi = {10.1093/nar/gkab1061}, - Network accessline 187
url = {https://alphafold.ebi.ac.uk/}, - Network accessline 199
year = {2010}, howpublished = {Software}, url = {https://pandas.pydata.org/}, - Network accessline 200
howpublished = {Software}, url = {https://pandas.pydata.org/}, note = {Python Data Analysis Library} - Network accessline 201
url = {https://pandas.pydata.org/}, - Network accessline 212
year = {2024}, howpublished = {Website}, url = {https://pubmed.ncbi.nlm.nih.gov/}, - Network accessline 213
howpublished = {Website}, url = {https://pubmed.ncbi.nlm.nih.gov/}, note = {Accessed: 2024-01-15} - Network accessline 214
url = {https://pubmed.ncbi.nlm.nih.gov/},
skills/citation-management/assets/citation_checklist.md
- Network accessline 26
- [ ] All DOIs are properly formatted (10.XXXX/...) - [ ] DOIs resolve correctly to the article - [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/") - Network accessline 27
- [ ] DOIs resolve correctly to the article - [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/") - [ ] Metadata from CrossRef matches your BibTeX entry - Network accessline 28
- [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/") - Network accessline 146
- [ ] Ampersands in author lists (Smith & Jones → Smith and Jones) - [ ] Unprotected acronyms in titles (DNA → {DNA}) - [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx) - Network accessline 148
- [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx) - Network accessline 251
# Find correct DOI # Option 1: Search CrossRef # https://www.crossref.org/ - Network accessline 253
# https://www.crossref.org/
skills/citation-management/references/bibtex_formatting.md
- Network accessline 315
year = {2024}, howpublished = {GitHub}, url = {https://github.com/user/repo}, - Network accessline 316
howpublished = {GitHub}, url = {https://github.com/user/repo}, note = {Version 2.0} - Network accessline 317
url = {https://github.com/user/repo}, - Network accessline 388
author = {{Organization Name}}, title = {Page Title}, url = {https://example.com/page}, - Network accessline 389
title = {Page Title}, url = {https://example.com/page}, year = {2024}, - Network accessline 390
url = {https://example.com/page}, - Network accessline 589
doi = {https://doi.org/10.1038/s41586-021-03819-2} % Don't include URL - Network accessline 600
url = {https://www.example.com/article} - Network accessline 610
% Don't include both if DOI URL is same as url doi = {10.1038/nature12345} url = {https://doi.org/10.1038/nature12345} % Redundant! - Network accessline 612
url = {https://doi.org/10.1038/nature12345} % Redundant! - Network accessline 805
doi = {https://doi.org/10.1038/nature12345} - Network accessline 883
year = {2021}, howpublished = {Database}, url = {https://alphafold.ebi.ac.uk/}, - Network accessline 884
howpublished = {Database}, url = {https://alphafold.ebi.ac.uk/}, doi = {10.1093/nar/gkab1061} - Network accessline 885
url = {https://alphafold.ebi.ac.uk/},
skills/citation-management/references/citation_validation.md
- Network accessline 37
**DOI resolution**: - DOI should resolve via https://doi.org/ - Network accessline 38
- DOI should resolve via https://doi.org/ - Network accessline 50
**Manual check**: 1. Copy DOI from BibTeX 2. Visit https://doi.org/10.1038/nature12345 - Network accessline 51
1. Copy DOI from BibTeX 2. Visit https://doi.org/10.1038/nature12345 3. Verify it redirects to correct article - Network accessline 52
2. Visit https://doi.org/10.1038/nature12345 - Network accessline 294
url = {https://www.nature.com/articles/nature12345} - Network accessline 295
url = {https://arxiv.org/abs/2103.14030} - Network accessline 300
url = {http://...} % HTTP instead of HTTPS
skills/citation-management/references/metadata_extraction.md
- Network accessline 121
**Base URL**: `https://api.crossref.org/works/` - Network accessline 132
GET https://api.crossref.org/works/10.1038/s41586-021-03819-2 - Network accessline 195
**Base URL**: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/` - Network accessline 206
GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? - Access to secretsline 210
[Credential-related source omitted] - Network accessline 282
**Base URL**: `http://export.arxiv.org/api/query` - Network accessline 290
GET http://export.arxiv.org/api/query?id_list=2103.14030 - Network accessline 296
<entry> <id>http://arxiv.org/abs/2103.14030v2</id> - Network accessline 297
<id>http://arxiv.org/abs/2103.14030v2</id> - Network accessline 303
<summary>Abstract text here...</summary> <arxiv:doi>10.1038/s41586-021-03819-2</arxiv:doi> <category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/> - Network accessline 304
<arxiv:doi>10.1038/s41586-021-03819-2</arxiv:doi> <category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/> <category term="cs.LG" scheme="http://arxiv.org/schemas/atom"/> - Network accessline 305
<category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/> - Network accessline 306
<category term="cs.LG" scheme="http://arxiv.org/schemas/atom"/> - Network accessline 334
**Base URL**: `https://api.datacite.org/dois/` - Network accessline 340
GET https://api.datacite.org/dois/10.5281/zenodo.1234567 - Network accessline 515
year = {2021}, howpublished = {Software}, url = {https://alphafold.ebi.ac.uk/}, - Network accessline 516
howpublished = {Software}, url = {https://alphafold.ebi.ac.uk/}, doi = {10.5281/zenodo.5123456} - Network accessline 517
url = {https://alphafold.ebi.ac.uk/}, - Network accessline 593
python scripts/extract_metadata.py \ --url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 594
--url "https://www.nature.com/articles/s41586-021-03819-2" - Network accessline 606
# DOI URLs https://doi.org/10.1038/nature12345 - Network accessline 607
https://doi.org/10.1038/nature12345 - Network accessline 608
https://dx.doi.org/10.1126/science.abc123 - Network accessline 609
https://www.nature.com/articles/s41586-021-03819-2 - Network accessline 611
# PubMed URLs https://pubmed.ncbi.nlm.nih.gov/34265844/ - Network accessline 612
https://pubmed.ncbi.nlm.nih.gov/34265844/ - Network accessline 613
https://www.ncbi.nlm.nih.gov/pubmed/34265844 - Network accessline 615
# arXiv URLs https://arxiv.org/abs/2103.14030 - Network accessline 616
https://arxiv.org/abs/2103.14030 - Network accessline 617
https://arxiv.org/pdf/2103.14030.pdf - Network accessline 628
# 34265844 # 2103.14030 # https://doi.org/10.1126/science.abc123 - Network accessline 630
# https://doi.org/10.1126/science.abc123 - Network accessline 727
volume = {123}, pages = {45--67}, url = {https://stable-url-here}, - Network accessline 728
pages = {45--67}, url = {https://stable-url-here}, note = {PMID: 12345678} - Network accessline 729
url = {https://stable-url-here},
skills/citation-management/references/pubmed_search.md
- Network accessline 58
**MeSH Browser**: https://meshb.nlm.nih.gov/search - Network accessline 261
**Access**: https://pubmed.ncbi.nlm.nih.gov/advanced/ - Network accessline 348
**Base URL**: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/` - Network accessline 362
**Get API key**: https://www.ncbi.nlm.nih.gov/account/ - Access to secretsline 376
[Credential-related source omitted] - Network accessline 380
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? - Access to secretsline 385
[Credential-related source omitted] - Access to secretsline 410
[Credential-related source omitted] - Network accessline 414
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? - Access to secretsline 418
[Credential-related source omitted] - Network accessline 438
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi? - Access to secretsline 442
[Credential-related source omitted] - Network accessline 453
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi? - Network accessline 486
**Get API key**: 1. Create NCBI account: https://www.ncbi.nlm.nih.gov/account/ - Network accessline 487
1. Create NCBI account: https://www.ncbi.nlm.nih.gov/account/ - Access to secretsline 494
[Credential-related source omitted] - Access to secretsline 500
[Credential-related source omitted] - Access to secretsline 504
[Credential-related source omitted]
skills/citation-management/scripts/doi_to_bibtex.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 17
def __init__(self): self.session = requests.Session() - Network accessline 18
self.session = requests.Session() - Network accessline 34
doi = doi.strip() if doi.startswith('https://doi.org/'): - Network accessline 35
if doi.startswith('https://doi.org/'): - Network accessline 36
doi = doi.replace('https://doi.org/', '') - Network accessline 37
elif doi.startswith('http://doi.org/'): - Network accessline 38
doi = doi.replace('http://doi.org/', '') - Network accessline 43
url = f'https://doi.org/{doi}'
skills/citation-management/scripts/extract_metadata.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 28
self.session = requests.Session() - Network accessline 108
url = f'https://api.crossref.org/works/{doi}' - Network accessline 127
'pages': message.get('page', ''), 'publisher': message.get('publisher', ''), 'url': f'https://doi.org/{doi}' - Network accessline 128
'publisher': message.get('publisher', ''), 'url': f'https://doi.org/{doi}' } - Network accessline 129
'url': f'https://doi.org/{doi}' - Network accessline 151
url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi' - Access to secretsline 162
[Credential-related source omitted] - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 164
[Credential-related source omitted] - Network accessline 223
url = 'http://export.arxiv.org/api/query' - Network accessline 234
root = ET.fromstring(response.content) ns = {'atom': 'http://www.w3.org/2005/Atom', 'arxiv': 'http://arxiv.org/schemas/atom'} - Network accessline 235
ns = {'atom': 'http://www.w3.org/2005/Atom', 'arxiv': 'http://arxiv.org/schemas/atom'} - Network accessline 269
'journal_ref': journal_ref, 'abstract': entry.findtext('atom:summary', '', ns).strip().replace('\n', ' '), 'url': f'https://arxiv.org/abs/{arxiv_id}' - Network accessline 270
'abstract': entry.findtext('atom:summary', '', ns).strip().replace('\n', ' '), 'url': f'https://arxiv.org/abs/{arxiv_id}' } - Network accessline 271
'url': f'https://arxiv.org/abs/{arxiv_id}'
skills/citation-management/scripts/format_bibtex.py
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#!/usr/bin/env python3 - Network accessline 147
if 'doi' in fields: doi = fields['doi'] doi = doi.replace('https://doi.org/', '') - Network accessline 148
doi = fields['doi'] doi = doi.replace('https://doi.org/', '') doi = doi.replace('http://doi.org/', '') - Network accessline 149
doi = doi.replace('https://doi.org/', '') - Network accessline 150
doi = doi.replace('http://doi.org/', '')
skills/citation-management/scripts/search_google_scholar.py
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#!/usr/bin/env python3
skills/citation-management/scripts/search_pubmed.py
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#!/usr/bin/env python3 - Access to secretsline 20
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self.email = email or os.getenv('NCBI_EMAIL', '') self.base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/' self.session = requests.Session() - Network accessline 30
self.base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/' - Network accessline 31
self.session = requests.Session() - Access to secretsline 34
[Credential-related source omitted] - Access to secretsline 79
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skills/citation-management/scripts/validate_citations.py
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#!/usr/bin/env python3 - Network accessline 18
def __init__(self): self.session = requests.Session() - Network accessline 19
self.session = requests.Session() - Network accessline 211
try: url = f'https://doi.org/{doi}' - Network accessline 212
url = f'https://doi.org/{doi}' - Network accessline 217
crossref_url = f'https://api.crossref.org/works/{doi}'
skills/claims-appeals/coworker.py
skills/claw-ancestry-pca/SKILL.md
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openclaw: category: bioinformatics homepage: https://github.com/ClawBio/ClawBio - Network accessline 33
category: bioinformatics homepage: https://github.com/ClawBio/ClawBio min_python: "3.9" - Network accessline 34
homepage: https://github.com/ClawBio/ClawBio - Network accessline 144
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 145
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-ancestry-pca/ancestry_pca.py
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#!/usr/bin/env python3 - Network accessline 329
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 330
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-ancestry-pca/tests/__init__.py
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skills/claw-ancestry-pca/tests/test_ancestry_pca.py
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skills/claw-metagenomics/SKILL.md
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openclaw: category: bioinformatics homepage: https://github.com/ClawBio/ClawBio - Network accessline 49
category: bioinformatics homepage: https://github.com/ClawBio/ClawBio min_python: "3.9" - Network accessline 50
homepage: https://github.com/ClawBio/ClawBio - Network accessline 236
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D419-D430. - Beghini, F. et al. (2021). - Network accessline 238
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-metagenomics/metagenomics_profiler.py
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#!/usr/bin/env python3 - Network accessline 873
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. *Nucleic Acids Research*, 51(D1), D419-D430. - Beghini, F. et al. (2021) - Network accessline 874
- Beghini, F. et al. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. *eLife*, 10, e65088. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio """ - Network accessline 875
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Access to secretsline 1171
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[Credential-related source omitted]
skills/claw-semantic-sim/SKILL.md
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always: false emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 150
- Corpas, M. et al. (2026). HEIM: Health Equity Index for Measuring structural bias in biomedical research. Under review. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 151
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/clinical-decision-support/SKILL.md
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skills/clinical-decision-support/scripts/biomarker_classifier.py
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#!/usr/bin/env python3
skills/clinical-decision-support/scripts/build_decision_tree.py
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#!/usr/bin/env python3
skills/clinical-decision-support/scripts/create_cohort_tables.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-decision-support/scripts/generate_survival_analysis.py
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#!/usr/bin/env python3
skills/clinical-decision-support/scripts/validate_cds_document.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-nlp-extractor/README.md
- Network accessline 320
> **Eyre, H. et al.** *Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python.* AMIA 2021. https://github.com/medspacy/medspacy - Network accessline 346
pip install medspacy scispacy transformers pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_lg-0.5.1.tar.gz - Network accessline 347
pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.1/en_core_sci_lg-0.5.1.tar.gz - Network accessline 386
- [medspaCy Documentation](https://github.com/medspacy/medspacy) - Network accessline 387
- [OpenMed](https://github.com/maziyarpanahi/openmed) - Network accessline 388
- [SciSpaCy](https://github.com/allenai/scispacy) - Network accessline 389
- [ClinicalBERT](https://github.com/kexinhuang12345/clinicalBERT)
skills/clinical-nlp-extractor/entity_extractor.py
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skills/clinical-note-summarization/medprompt_utils.py
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Executable file - Network accessline 25
References: - MedPrompt Paper: https://arxiv.org/abs/2311.16452 - Network accessline 26
- MedPrompt Paper: https://arxiv.org/abs/2311.16452 - Network accessline 157
"code": { "coding": [{ "system": "http://loinc.org", - Network accessline 158
"coding": [{ "system": "http://loinc.org", "code": "11506-3", - Network accessline 159
"system": "http://loinc.org", - Network accessline 656
"versionId": "1", "lastUpdated": timestamp, "profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"] - Network accessline 657
"lastUpdated": timestamp, "profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"] }, - Network accessline 658
"profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"] - Network accessline 673
"code": { "coding": [{ "system": "http://loinc.org", - Network accessline 674
"coding": [{ "system": "http://loinc.org", "code": "11506-3", - Network accessline 675
"system": "http://loinc.org", - Network accessline 682
"conclusionCode": [{ "coding": [{ "system": "http://snomed.info/sct", - Network accessline 683
"coding": [{ "system": "http://snomed.info/sct", "code": "404684003", - Network accessline 684
"system": "http://snomed.info/sct", - Network accessline 693
"code": { "coding": [{ "system": "http://loinc.org", - Network accessline 694
"coding": [{ "system": "http://loinc.org", "code": "75325-1", - Network accessline 695
"system": "http://loinc.org", - Network accessline 705
"clinicalStatus": { "coding": [{ "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", - Network accessline 706
"coding": [{ "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "active" - Network accessline 707
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", - Network accessline 711
"verificationStatus": { "coding": [{ "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", - Network accessline 712
"coding": [{ "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "provisional" - Network accessline 713
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", - Network accessline 736
base_resource["extension"] = [{ "url": "http://example.org/fhir/StructureDefinition/ai-generated", - Network accessline 737
"url": "http://example.org/fhir/StructureDefinition/ai-generated", - Network accessline 738
"valueBoolean": True }, { "url": "http://example.org/fhir/StructureDefinition/ai-model", - Network accessline 739
}, { "url": "http://example.org/fhir/StructureDefinition/ai-model", "valueString": "MedPrompt-v2.0" - Network accessline 740
"url": "http://example.org/fhir/StructureDefinition/ai-model",
skills/clinical-note-summarization/usage.py
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Executable file
skills/clinical-reports/README.md
- Network accessline 210
### External Standards - CARE Guidelines: https://www.care-statement.org/ - Network accessline 211
- CARE Guidelines: https://www.care-statement.org/ - Network accessline 212
- ICH-E3 Guideline: https://database.ich.org/sites/default/files/E3_Guideline.pdf - Network accessline 213
- CONSORT Statement: http://www.consort-statement.org/ - Network accessline 214
- HIPAA: https://www.hhs.gov/hipaa/ - Network accessline 215
- ACR Practice Parameters: https://www.acr.org/Clinical-Resources/Practice-Parameters-and-Technical-Standards - Network accessline 216
- CAP Cancer Protocols: https://www.cap.org/protocols-and-guidelines
skills/clinical-reports/SKILL.md
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Bash
skills/clinical-reports/references/case_report_guidelines.md
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- CARE website: https://www.care-statement.org/
skills/clinical-reports/references/patient_documentation.md
- Network accessline 461
Vitals: T 98.2°F, BP 142/88, HR 105, RR 24, SpO2 88% on room air → 95% on 2L NC Height: 5'10", Weight: 195 lbs (baseline 187 lbs), BMI 28
skills/clinical-reports/scripts/check_deidentification.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-reports/scripts/compliance_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-reports/scripts/extract_clinical_data.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-reports/scripts/format_adverse_events.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-reports/scripts/generate_report_template.py
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#!/usr/bin/env python3
skills/clinical-reports/scripts/terminology_validator.py
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#!/usr/bin/env python3
skills/clinical-reports/scripts/validate_case_report.py
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#!/usr/bin/env python3
skills/clinical-reports/scripts/validate_trial_report.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-trial-protocol-skill/assets/FDA-Clinical-Protocol-Template.md
- Network accessline 31
- [Clinical Laboratory Improvement Amendments](https://www.cms.gov/Regulations-and-Guidance/Legislation/CLIA/index.html?redirect=/clia/) - Network accessline 35
- [21 CFR Part 11: Electronic Records, Electronic Signatures](https://www.ecfr.gov/cgi-bin/text-idx?SID=007006046b07c9fc5244ec13ef4a77bb&mc=true&node=pt21.1.11&rgn=div5) - Network accessline 37
- [21 CFR Part 50: Protection of Human Subjects](https://www.ecfr.gov/cgi-bin/text-idx?SID=6d82202a67ba5bd44148d99f4aaf7198&mc=true&node=pt21.1.50&rgn=div5) - Network accessline 39
- [21 CFR Part 54: Financial Disclosure by Clinical Investigators](https://www.ecfr.gov/cgi-bin/text-idx?SID=bae2d66180fd49cb11f40a935cd760a7&mc=true&node=pt21.1.54&rgn=div5) - Network accessline 41
- [21 CFR Part 56: Institutional Review Boards](https://www.ecfr.gov/cgi-bin/text-idx?SID=64724709940d94a34270c77fdb8d307f&mc=true&node=pt21.1.56&rgn=div5) - Network accessline 44
- [21 CFR Part 58: Good Laboratory Practice for Nonclinical Laboratory Studies](http://www.ecfr.gov/cgi-bin/text-idx?SID=90f8b344173d4c43e0c515d0a0cbc4de&mc=true&node=pt21.1.58&rgn=div5) - Network accessline 46
- [21 CFR Part 210: Current Good Manufacturing Practice In Manufacturing, Processing, Packing, Or Holding Of Drugs; General](http://www.ecfr.gov/cgi-bin/text-idx?SID=90f8b344173d4c43e0c515d0a0cbc4de&mc=true&node=pt21.4.210&rgn=div5) - Network accessline 48
- [21 CFR Part 211: Current Good Manufacturing Practice For Finished Pharmaceuticals](http://www.ecfr.gov/cgi-bin/text-idx?SID=90f8b344173d4c43e0c515d0a0cbc4de&mc=true&node=pt21.4.211&rgn=div5) - Network accessline 49
- [21 CFR Part 312: Investigational New Drug Application](https://www.ecfr.gov/cgi-bin/text-idx?SID=27a0c0825d11663283856731fb14c8d2&mc=true&node=pt21.5.312&rgn=div5) - Network accessline 51
- [21 CFR Part 812: Investigational Device Exemptions](https://www.ecfr.gov/cgi-bin/text-idx?SID=0f8fa3b740966b3d21d5501233e2b493&mc=true&node=pt21.8.812&rgn=div5) - Network accessline 53
- [42 CFR Part 11: Clinical Trial Registration and Results Information Submission](https://www.gpo.gov/fdsys/pkg/CFR-2016-title42-vol1/pdf/CFR-2016-title42-vol1-part11.pdf) - Network accessline 55
- [45 CFR Part 46: Protection of Human Subjects Research](http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html) - Network accessline 59
- [Compliance Actions and Activities](http://www.fda.gov/ICECI/EnforcementActions/default.htm) - Network accessline 61
- [FDA Regulations Relating to Good Clinical Practice and Clinical Trials](http://www.fda.gov/ScienceResearch/SpecialTopics/RunningClinicalTrials/ucm155713.htm) - Network accessline 63
- [Guidance for Clinical Investigators, Sponsors, and IRBs Adverse Event Reporting to IRBs -- Improving Human Subject Protection](http://www.fda.gov/downloads/RegulatoryInformation/Guidances/UCM126572.pdf) - Network accessline 65
- [Guidance for Clinical Trial Sponsors: Establishment and Operation of Clinical Trial Data Monitoring Committees](http://www.fda.gov/downloads/RegulatoryInformation/Guidances/ucm127073.pdf) - Network accessline 67
- [Guidance for Industry: E6 Good Clinical Practice: Consolidated Guidance](https://www.fda.gov/downloads/Drugs/.../Guidances/ucm073122.pdf) - Network accessline 69
- [Guidance for Industry: Electronic Source Data in Clinical Investigations](http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm328691.pdf) - Network accessline 71
- [Guidance for Industry: Multiple Endpoints in Clinical Trials](https://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM536750.pdf) - Network accessline 73
- [Guidance for Industry: Oversight of Clinical Investigations -- A Risk-Based Approach to Monitoring](http://www.fda.gov/downloads/Drugs/Guidances/UCM269919.pdf) - Network accessline 75
- [Guidance for Industry: Providing Regulatory Submissions in Electronic Format - Human Pharmaceutical Product Applications and Related Submissions Using the eCTD Specifications](http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulato - Network accessline 77
- [Guidance for Industry: Providing Regulatory Submissions in Electronic Format --- Standardized Study Data](http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM292334.pdf) - Network accessline 79
- [Guidance for Industry: Safety Assessment for IND Safety Reporting](http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm477584.pdf) - Network accessline 83
- [The HIPAA Privacy Rule](http://www.hhs.gov/hipaa/for-professionals/privacy/) - Network accessline 86
[HIPAA Privacy Rule: Information for Researchers](https://www.hhs.gov/hipaa/for-professionals/special-topics/research/index.html) - Network accessline 91
- [Guidance for Industry, E6 (R2) Good Clinical Practice: Consolidated Guidance](http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM464506.pdf) - Network accessline 92
- [Guidance for Industry, M3(R2) Nonclinical Safety Studies for the Conduct of Human Clinical Trials and Marketing Authorization for Pharmaceuticals](http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm07 - Network accessline 94
- [Guideline for Industry, E3 Structure and Content of Clinical Reports](http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm073113.pdf) - Network accessline 96
- [Guidance for Industry, E9 Statistical Principles for Clinical Trials](http://www.fda.gov/downloads/drugs/guidancecomplianceregulatoryinformation/guidances/ucm073137.pdf) - Network accessline 98
- [Final Concept Paper E9(R1): Addendum to Statistical Principles for Clinical Trials on Choosing Appropriate Estimands and Defining Sensitivity Analyses in Clinical Trials](http://www.ich.org/fileadmin/Public_Web_Site/ICH_Products/Guidelin - Network accessline 102
- [Clinical Investigation of Medical Devices for Human Subjects -- Good Clinical Practice (ISO 14155:2011)](https://www.iso.org/obp/ui/%20-%20iso:std:iso:14155:ed-2:v1:en) - Network accessline 106
- [Certificates of Confidentiality (CoC) Kiosk](http://grants.nih.gov/grants/policy/coc/index.htm) - Network accessline 108
- [Clinical Trials Registration and Results Information Submission](https://www.federalregister.gov/documents/2016/09/21/2016-22129/clinical-trials-registration-and-results-information-submission) - Network accessline 110
- [Financial Conflict of Interest](http://grants.nih.gov/grants/policy/coi/) - Network accessline 112
- [Inclusion of Children- Policy Implementation](https://grants.nih.gov/grants/funding/children/children.htm) - Network accessline 114
- [Inclusion Of Women And Minorities As Participants In Research Involving Human Subjects- Policy Implementation Page](http://grants.nih.gov/grants/funding/women_min/women_min.htm) - Network accessline 116
- [NIH Data Sharing Policies and Related Guidance on NIH-Funded Research Resources](http://grants.nih.gov/policy/sharing.htm) - Network accessline 118
- [NIH Data Sharing Policy and Implementation Guidance](http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm) - Network accessline 120
- [NIH Genomic Data Sharing Policy](https://gds.nih.gov/03policy2.html) - Network accessline 122
- [NIH Grants Policy Statement, Section 8.2 Availability of Research Results: Publications, Intellectual Property Rights, and Sharing Research Resources](http://grants.nih.gov/grants/policy/nihgps/HTML5/section_8/8.2_availability_of_researc - Network accessline 125
- [NIH Policy on the Dissemination of NIH-Funded Clinical Trial Information](https://www.gpo.gov/fdsys/pkg/FR-2016-09-21/pdf/2016-22379.pdf) - Network accessline 126
- [NIH Public Access Policy Details](http://publicaccess.nih.gov/policy.htm) - Network accessline 128
- [Policy on Good Clinical Practice Training for NIH Awardees Involved in NIH-funded Clinical Trials](https://grants.nih.gov/grants/guide/notice-files/NOT-OD-16-148.html) - Network accessline 130
- [Required Education in the Protection of Human Research Participants](http://grants.nih.gov/grants/guide/notice-files/NOT-OD-01-061.html) - Network accessline 134
- [Human Subject Regulations Decision Charts](http://www.hhs.gov/ohrp/policy/checklists/decisioncharts.html) - Network accessline 136
- [Informed Consent Checklist](http://www.hhs.gov/ohrp/policy/consentckls.html) - Network accessline 138
- [Informed Consent Tips](http://www.hhs.gov/ohrp/policy/ictips.html) - Network accessline 140
- [IRBs and Assurances](http://www.hhs.gov/ohrp/assurances/) - Network accessline 142
- [Regulations & Policy Index](http://www.hhs.gov/ohrp/regulations-and-policy/index.html) - Network accessline 144
- [Unanticipated Problems Involving Risks and Adverse Events Guidance](http://www.hhs.gov/ohrp/regulations-and-policy/guidance/reviewing-unanticipated-problems/index.html) - Network accessline 146
- [Vulnerable Populations](http://www.hhs.gov/ohrp/regulations-and-policy/guidance/vulnerable-populations/) - Network accessline 150
- [Citing Medicine, 2nd edition: The NLM Style Guide for Authors, Editors, and Publishers](http://www.ncbi.nlm.nih.gov/books/NBK7256/) - Network accessline 152
- [CONSORT statement](http://www.consort-statement.org/) - Network accessline 155
- [International Committee of Medical Journal Editors (ICMJE): Recommendations](http://www.icmje.org/recommendations/) - Network accessline 157
[Practical Aspects of Signal Detection in Pharmacovigilance: Report of CIOMS Working Group VIII](http://cioms.ch/shop/product/practical-aspects-of-signal-detection-in-pharmacovigilance-report-of-cioms-working-group-viii/) - Network accessline 2006
- ***Web Site citation** Complementary/Integrative Medicine [Internet]. Houston: University of Texas, M.D. Anderson Cancer Center; c2007 [cited 2007 Feb 21]. Available from: http://www.manderson.org/departments/CIMER/.* - Network accessline 2007
Complementary/Integrative Medicine [Internet]. Houston: University of Texas, M.D. Anderson Cancer Center; c2007 [cited 2007 Feb 21]. Available from: http://www.manderson.org/departments/CIMER/.* - Network accessline 2017
[^1]: From ClinicalTrials.gov Protocol Data Element Definitions available at: <https://prsinfo.clinicaltrials.gov/definitions.html>. Accessed March 2017.
skills/clinical-trial-protocol-skill/references/01-research-protocols.md
- Network accessline 50
| Category | Resource | Use When | Link | |----------|----------|----------|------| | **Classification** | Product Classification Database | Determining device class/code | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPCD/classifica - Network accessline 51
|----------|----------|----------|------| | **Classification** | Product Classification Database | Determining device class/code | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPCD/classification.cfm | | | 21 CFR 860 | Understanding - Network accessline 52
| **Classification** | Product Classification Database | Determining device class/code | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPCD/classification.cfm | - Network accessline 53
| | 21 CFR 860 | Understanding classification criteria | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=860 | - Network accessline 54
| **510(k) Pathway** | 510(k) Database | Searching for predicate devices | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm | - Network accessline 55
| | 21 CFR 807 Subpart E | Understanding 510(k) requirements | https://www.fda.gov/medical-devices/premarket-submissions-selecting-and-preparing-correct-submission/premarket-notification-510k | - Network accessline 56
| **De Novo Pathway** | De Novo Database | Finding novel device precedents | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/denovo.cfm | - Network accessline 57
| | 21 CFR 860.260 | Understanding De Novo process | https://www.fda.gov/medical-devices/premarket-submissions-selecting-and-preparing-correct-submission/de-novo-classification-request | - Network accessline 58
| **PMA Pathway** | PMA Database | Researching Class III approvals | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpma/pma.cfm | - Network accessline 59
| | 21 CFR 814 | Understanding PMA requirements | https://www.fda.gov/medical-devices/premarket-submissions-selecting-and-preparing-correct-submission/premarket-approval-pma | - Network accessline 60
| **IDE/Clinical** | 21 CFR 812 | Determining SR/NSR status | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=812 | - Network accessline 61
| | Clinical Trials Overview | Trial design guidance | https://www.fda.gov/medical-devices/device-advice-comprehensive-regulatory-assistance/clinical-trials-and-human-subject-protection | - Network accessline 62
| **Other** | GUDID | Device identifiers | https://accessgudid.nlm.nih.gov/ | - Network accessline 63
| | 21 CFR 820 (QSR) | Quality system requirements | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=820 | - Network accessline 64
| | 21 CFR 800-1299 | General device regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm | - Network accessline 158
| Category | Resource | Use When | Link | |----------|----------|----------|------| | **IND Process** | 21 CFR 312 | IND requirements & regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRsearch.cfm?CFRPart=312 | - Network accessline 159
|----------|----------|----------|------| | **IND Process** | 21 CFR 312 | IND requirements & regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRsearch.cfm?CFRPart=312 | | | IND Overview | Understanding IND process | - Network accessline 160
| **IND Process** | 21 CFR 312 | IND requirements & regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRsearch.cfm?CFRPart=312 | | | IND Overview | Understanding IND process | https://www.fda.gov/drugs/types-applicatio - Network accessline 161
| | IND Overview | Understanding IND process | https://www.fda.gov/drugs/types-applications/investigational-new-drug-ind-application | | | IND Content/Format | Preparing IND submission | https://www.fda.gov/media/71203/download | | | IND Sa - Network accessline 162
| | IND Content/Format | Preparing IND submission | https://www.fda.gov/media/71203/download | - Network accessline 163
| | IND Safety Reporting | Safety reporting requirements | https://www.fda.gov/regulatory-information/search-fda-guidance-documents/safety-reporting-requirements-inds-investigational-new-drug-applications-and-babe | - Network accessline 164
| | Sponsor-Investigator IND | Academic/investigator INDs | https://www.fda.gov/files/drugs/published/Investigational-New-Drug-Applications-Prepared-and-Submitted-by-Sponsor-Investigators.pdf | - Network accessline 165
| | When IND Required | Determining IND necessity | https://www.fda.gov/regulatory-information/search-fda-guidance-documents/investigational-new-drug-applications-inds-determining-whether-human-research-studies-can-be | - Network accessline 166
| **NDA Pathway** | 21 CFR 314 | NDA regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=314 | - Network accessline 167
| | NDA Overview | Understanding NDA process | https://www.fda.gov/drugs/types-applications/new-drug-application-nda | - Network accessline 168
| **ANDA Pathway** | ANDA Format Guidance | Preparing generic applications | https://www.fda.gov/files/drugs/published/ANDA-Submissions-%E2%80%94-Content-and-Format-of-Abbreviated-New-Drug-Applications.pdf | - Network accessline 169
| | Orange Book | Finding RLD for generics | https://www.accessdata.fda.gov/scripts/cder/ob/ | - Network accessline 170
| **505(b)(2) Pathway** | 505(b)(2) Guidance | Understanding 505(b)(2) pathway | https://www.fda.gov/regulatory-information/search-fda-guidance-documents/applications-covered-section-505b2 | | | 505(b)(2) vs ANDA | Pathway selection guidanc - Network accessline 171
| | 505(b)(2) vs ANDA | Pathway selection guidance | https://www.fda.gov/regulatory-information/search-fda-guidance-documents/determining-whether-submit-anda-or-505b2-application | | | 505(b)(2) Overview | Detailed pathway overview | https: - Network accessline 172
| | 505(b)(2) Overview | Detailed pathway overview | https://www.fda.gov/media/156350/download | - Network accessline 173
| **BLA Pathway** | 21 CFR 601 | BLA regulations | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=601 | - Network accessline 174
| | BLA Overview | Understanding BLA process | https://www.fda.gov/vaccines-blood-biologics/development-approval-process-cber/biologics-license-applications-bla-process-cber | - Network accessline 175
| | CBER INDs | Biologics IND guidance | https://www.fda.gov/vaccines-blood-biologics/development-approval-process-cber/investigational-new-drug-applications-inds-cber-regulated-products | - Network accessline 176
| | Purple Book | Biologics & biosimilars | https://purplebooksearch.fda.gov/ | - Network accessline 177
| **Databases** | Drugs@FDA | Approved drugs, labels, reviews | https://www.accessdata.fda.gov/scripts/cder/daf/ | - Network accessline 178
| | NDC Directory | Drug codes | https://www.accessdata.fda.gov/scripts/cder/ndc/ | | **Submission** | eCTD Format | Electronic submission standards | https://www.fda.gov/drugs/electronic-regulatory-submission-and-review/electronic-common-t - Network accessline 179
| **Submission** | eCTD Format | Electronic submission standards | https://www.fda.gov/drugs/electronic-regulatory-submission-and-review/electronic-common-technical-document-ectd | | | CTD Organization | CTD structure guidance | https://www - Network accessline 180
| | CTD Organization | CTD structure guidance | https://www.fda.gov/media/71666/download | - Network accessline 181
| **Manufacturing** | 21 CFR 210-211 (cGMP) | Manufacturing requirements | https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=211 |
skills/clinical-trial-protocol-skill/references/04-protocol-operations.md
- Network accessline 384
**CTCAE reference:** https://ctep.cancer.gov/protocoldevelopment/electronic_applications/ctc.htm - Network accessline 1665
#### C. Device-Specific References (IF device - 5-10): - FDA. [Predicate Device] 510(k) Summary. K[number]. [Date]. Available at: https://www.accessdata.fda.gov/... - Network accessline 1666
- FDA. [Predicate Device] 510(k) Summary. K[number]. [Date]. Available at: https://www.accessdata.fda.gov/... - Network accessline 1667
- FDA. De Novo Classification Order for [Device]. DEN[number]. [Date]. Available at: https://www.accessdata.fda.gov/... - Network accessline 1668
- FDA. [Device] Classification. Product Code: [ABC]. Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfPCD/classification.cfm - Network accessline 1669
- FDA. Class II Special Controls Guidance: [Device Type]. [Date]. Available at: https://www.fda.gov/... - Network accessline 1679
#### F. Regulatory References (5-10): 1. FDA. 21 CFR Part 50: Protection of Human Subjects. Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=50 - Network accessline 1680
1. FDA. 21 CFR Part 50: Protection of Human Subjects. Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=50 - Network accessline 1681
2. FDA. 21 CFR Part 56: Institutional Review Boards. Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/CFRSearch.cfm?CFRPart=56 - Network accessline 1682
3. FDA. 21 CFR Part 312 (Drugs) OR 21 CFR Part 812 (Devices). Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfcfr/... - Network accessline 1683
4. ICH E6(R2): Guideline for Good Clinical Practice. Nov 2016. Available at: https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf - Network accessline 1684
5. WMA Declaration of Helsinki: Ethical Principles for Medical Research. 2013. Available at: https://www.wma.net/policies-post/...
skills/clinical-trial-protocol-skill/scripts/sample_size_calculator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/clinical-trials-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search ClinicalTrials.gov, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search ClinicalTrials.gov, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Trial Title", "url": "https://clinicaltrials.gov/...", - Network accessline 79
"title": "Trial Title", "url": "https://clinicaltrials.gov/...", "content": "Trial details, phase, conditions, outcomes...", - Network accessline 80
"url": "https://clinicaltrials.gov/...", - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/clinical-trials-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/clinical-trials-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/clinicaltrials-database/SKILL.md
- Network accessline 41
url = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 48
response = requests.get(url, params=params) - Network accessline 61
nct_id = "NCT04852770" url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}" - Network accessline 62
url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}" - Network accessline 64
response = requests.get(url) - Network accessline 430
def search_with_rate_limit(params): try: response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 431
try: response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) response.raise_for_status() - Network accessline 432
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 462
try: response = requests.get(url, params=params, timeout=30) - Network accessline 463
response = requests.get(url, params=params, timeout=30) - Network accessline 491
- **Base URL**: `https://clinicaltrials.gov/api/v2` - **Authentication**: Not required (public API) - **Rate Limit**: ~50 requests/minute per IP
skills/clinicaltrials-database/references/api_reference.md
- Network accessline 7
**Base URL:** `https://clinicaltrials.gov/api/v2` - Network accessline 69
curl "https://clinicaltrials.gov/api/v2/studies?query.cond=lung+cancer&filter.overallStatus=RECRUITING&pageSize=10&format=json" - Network accessline 107
curl "https://clinicaltrials.gov/api/v2/studies/NCT04852770?format=json" - Network accessline 160
url = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 168
response = requests.get(url, params=params) - Network accessline 189
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 203
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 211
nct_id = "NCT04852770" url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}" - Network accessline 212
url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}" - Network accessline 214
response = requests.get(url) - Network accessline 238
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 262
response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params) - Network accessline 298
for attempt in range(max_retries): try: response = requests.get( - Network accessline 299
try: response = requests.get( "https://clinicaltrials.gov/api/v2/studies", - Network accessline 300
response = requests.get( - Network accessline 301
"https://clinicaltrials.gov/api/v2/studies", - Network accessline 358
For detailed migration guidance, see: https://clinicaltrials.gov/data-api/about-api/api-migration
skills/clinicaltrials-database/scripts/query_clinicaltrials.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 9
API Documentation: https://clinicaltrials.gov/data-api/api - Network accessline 19
BASE_URL = "https://clinicaltrials.gov/api/v2" - Network accessline 86
url = f"{BASE_URL}/studies" response = requests.get(url, params=params) - Network accessline 87
response = requests.get(url, params=params) - Network accessline 110
response = requests.get(url, params=params)
skills/clinpgx-database/SKILL.md
- Network accessline 40
BASE_URL = "https://api.clinpgx.org/v1/" - Network accessline 62
# Get gene details response = requests.get("https://api.clinpgx.org/v1/gene/CYP2D6") - Network accessline 63
response = requests.get("https://api.clinpgx.org/v1/gene/CYP2D6") - Network accessline 66
# Search for genes by name response = requests.get("https://api.clinpgx.org/v1/gene", - Network accessline 67
response = requests.get("https://api.clinpgx.org/v1/gene", - Network accessline 84
# Get drug details response = requests.get("https://api.clinpgx.org/v1/chemical/PA448515") # Warfarin - Network accessline 85
response = requests.get("https://api.clinpgx.org/v1/chemical/PA448515") # Warfarin - Network accessline 88
# Search drugs by name response = requests.get("https://api.clinpgx.org/v1/chemical", - Network accessline 89
response = requests.get("https://api.clinpgx.org/v1/chemical", - Network accessline 108
# Get gene-drug pair information response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 109
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 113
# Get all pairs for a gene response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 114
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 130
# Get CPIC guideline response = requests.get("https://api.clinpgx.org/v1/guideline/PA166104939") - Network accessline 131
response = requests.get("https://api.clinpgx.org/v1/guideline/PA166104939") - Network accessline 134
# List all CPIC guidelines response = requests.get("https://api.clinpgx.org/v1/guideline", - Network accessline 135
response = requests.get("https://api.clinpgx.org/v1/guideline", - Network accessline 160
# Get allele information response = requests.get("https://api.clinpgx.org/v1/allele/CYP2D6*4") - Network accessline 161
response = requests.get("https://api.clinpgx.org/v1/allele/CYP2D6*4") - Network accessline 164
# Get all alleles for a gene response = requests.get("https://api.clinpgx.org/v1/allele", - Network accessline 165
response = requests.get("https://api.clinpgx.org/v1/allele", - Network accessline 188
# Get variant information response = requests.get("https://api.clinpgx.org/v1/variant/rs4244285") - Network accessline 189
response = requests.get("https://api.clinpgx.org/v1/variant/rs4244285") - Network accessline 192
# Search variants by position (if supported) response = requests.get("https://api.clinpgx.org/v1/variant", - Network accessline 193
response = requests.get("https://api.clinpgx.org/v1/variant", - Network accessline 211
# Get clinical annotations response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 212
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 216
# Filter by evidence level response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 217
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 235
# Get drug labels with PGx information response = requests.get("https://api.clinpgx.org/v1/drugLabel", - Network accessline 236
response = requests.get("https://api.clinpgx.org/v1/drugLabel", - Network accessline 240
# Filter by regulatory source response = requests.get("https://api.clinpgx.org/v1/drugLabel", - Network accessline 241
response = requests.get("https://api.clinpgx.org/v1/drugLabel", - Network accessline 258
# Get pathway information response = requests.get("https://api.clinpgx.org/v1/pathway/PA146123006") # Warfarin pathway - Network accessline 259
response = requests.get("https://api.clinpgx.org/v1/pathway/PA146123006") # Warfarin pathway - Network accessline 262
# Search pathways by drug response = requests.get("https://api.clinpgx.org/v1/pathway", - Network accessline 263
response = requests.get("https://api.clinpgx.org/v1/pathway", - Network accessline 281
# Example: Patient is CYP2C19 *1/*2 (intermediate metabolizer) response = requests.get("https://api.clinpgx.org/v1/allele/CYP2C19*2") - Network accessline 282
response = requests.get("https://api.clinpgx.org/v1/allele/CYP2C19*2") - Network accessline 288
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 295
response = requests.get("https://api.clinpgx.org/v1/guideline", - Network accessline 303
response = requests.get("https://api.clinpgx.org/v1/drugLabel", - Network accessline 317
all_interactions = {} for gene in pgx_panel: response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 318
for gene in pgx_panel: response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", params={"gene": gene}) - Network accessline 319
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 338
response = requests.get("https://api.clinpgx.org/v1/chemical", - Network accessline 345
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 364
response = requests.get("https://api.clinpgx.org/v1/allele", - Network accessline 393
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 400
response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation", - Network accessline 424
def rate_limited_request(url, params=None, delay=0.5): """Make API request with rate limiting (2 req/sec max)""" response = requests.get(url, params=params) - Network accessline 425
"""Make API request with rate limiting (2 req/sec max)""" response = requests.get(url, params=params) time.sleep(delay) # Wait 0.5 seconds between requests - Network accessline 426
response = requests.get(url, params=params) - Network accessline 432
for gene in genes: response = rate_limited_request( "https://api.clinpgx.org/v1/gene/" + gene - Network accessline 433
response = rate_limited_request( "https://api.clinpgx.org/v1/gene/" + gene ) - Network accessline 434
"https://api.clinpgx.org/v1/gene/" + gene - Network accessline 444
for attempt in range(max_retries): try: response = requests.get(url, params=params, timeout=10) - Network accessline 446
response = requests.get(url, params=params, timeout=10) - Network accessline 488
'cyp2d6_cache.json', rate_limited_request, "https://api.clinpgx.org/v1/gene/CYP2D6" - Network accessline 489
rate_limited_request, "https://api.clinpgx.org/v1/gene/CYP2D6" ) - Network accessline 490
"https://api.clinpgx.org/v1/gene/CYP2D6" - Network accessline 505
**Access**: Available at https://www.clinpgx.org/pharmacogenomic-decision-support - Network accessline 570
- ClinPGx continuously updates with new evidence and guidelines - Check publication dates for clinical annotations - Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements - Network accessline 571
- Check publication dates for clinical annotations - Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements - CPIC guidelines updated as new evidence emerges - Network accessline 572
- Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements - Network accessline 591
# Get all CPIC guideline pairs response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 592
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 605
for med in medications: for gene in patient_genes: response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 606
for gene in patient_genes: response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", params={"gene": gene, "drug": med}) - Network accessline 607
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 617
# Check for HLA-B*57:01 before abacavir trial response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 618
response = requests.get("https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 626
- **ClinPGx website**: https://www.clinpgx.org/ - Network accessline 627
- **ClinPGx Blog**: https://blog.clinpgx.org/ - Network accessline 628
- **API documentation**: https://api.clinpgx.org/ - Network accessline 629
- **CPIC website**: https://cpicpgx.org/ - Network accessline 630
- **PharmCAT**: https://pharmcat.clinpgx.org/ - Network accessline 631
- **ClinGen**: https://clinicalgenome.org/
skills/clinpgx-database/references/api_reference.md
- Network accessline 8
https://api.clinpgx.org/v1/ - Network accessline 53
curl "https://api.clinpgx.org/v1/gene/CYP2D6" - Network accessline 82
curl "https://api.clinpgx.org/v1/gene?q=CYP" - Network accessline 100
curl "https://api.clinpgx.org/v1/chemical/PA448515" - Network accessline 114
curl "https://api.clinpgx.org/v1/chemical?name=warfarin" - Network accessline 149
# Get all pairs for a gene curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6" - Network accessline 150
curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6" - Network accessline 152
# Get specific gene-drug pair curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6&drug=codeine" - Network accessline 153
curl "https://api.clinpgx.org/v1/geneDrugPair?gene=CYP2D6&drug=codeine" - Network accessline 155
# Get all CPIC Level A pairs curl "https://api.clinpgx.org/v1/geneDrugPair?cpicLevel=A" - Network accessline 156
curl "https://api.clinpgx.org/v1/geneDrugPair?cpicLevel=A" - Network accessline 168
"clinicalAnnotationCount": 45, "hasGuideline": true, "guidelineUrl": "https://www.clinpgx.org/guideline/..." - Network accessline 169
"hasGuideline": true, "guidelineUrl": "https://www.clinpgx.org/guideline/..." } - Network accessline 170
"guidelineUrl": "https://www.clinpgx.org/guideline/..." - Network accessline 192
# Get all CPIC guidelines curl "https://api.clinpgx.org/v1/guideline?source=CPIC" - Network accessline 193
curl "https://api.clinpgx.org/v1/guideline?source=CPIC" - Network accessline 195
# Get guideline for specific gene-drug curl "https://api.clinpgx.org/v1/guideline?gene=CYP2C19&drug=clopidogrel" - Network accessline 196
curl "https://api.clinpgx.org/v1/guideline?gene=CYP2C19&drug=clopidogrel" - Network accessline 207
curl "https://api.clinpgx.org/v1/guideline/PA166104939" - Network accessline 220
"summary": "Alternative antiplatelet therapy recommended for...", "recommendations": [...], "pdfUrl": "https://www.clinpgx.org/...", - Network accessline 221
"recommendations": [...], "pdfUrl": "https://www.clinpgx.org/...", "pmid": "23400754" - Network accessline 222
"pdfUrl": "https://www.clinpgx.org/...", - Network accessline 242
curl "https://api.clinpgx.org/v1/allele?gene=CYP2D6" - Network accessline 290
curl "https://api.clinpgx.org/v1/allele/CYP2D6*4" - Network accessline 308
curl "https://api.clinpgx.org/v1/variant/rs4244285" - Network accessline 343
curl "https://api.clinpgx.org/v1/variant?chromosome=10&position=94781859" - Network accessline 364
# Get all annotations for a gene curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=CYP2D6" - Network accessline 365
curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=CYP2D6" - Network accessline 367
# Get high-quality evidence only curl "https://api.clinpgx.org/v1/clinicalAnnotation?evidenceLevel=1A" - Network accessline 368
curl "https://api.clinpgx.org/v1/clinicalAnnotation?evidenceLevel=1A" - Network accessline 370
# Get annotations for specific gene-drug pair curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=TPMT&drug=azathioprine" - Network accessline 371
curl "https://api.clinpgx.org/v1/clinicalAnnotation?gene=TPMT&drug=azathioprine" - Network accessline 416
# Get all labels for warfarin curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin" - Network accessline 417
curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin" - Network accessline 419
# Get only FDA labels curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin&source=FDA" - Network accessline 420
curl "https://api.clinpgx.org/v1/drugLabel?drug=warfarin&source=FDA" - Network accessline 435
"biomarkers": ["CYP2C9", "VKORC1"], "testingRecommended": true, "labelUrl": "https://dailymed.nlm.nih.gov/...", - Network accessline 436
"testingRecommended": true, "labelUrl": "https://dailymed.nlm.nih.gov/...", "lastUpdated": "2024-01-15" - Network accessline 437
"labelUrl": "https://dailymed.nlm.nih.gov/...", - Network accessline 458
curl "https://api.clinpgx.org/v1/pathway/PA146123006" - Network accessline 473
curl "https://api.clinpgx.org/v1/pathway?drug=warfarin" - Network accessline 482
"genes": ["CYP2C9", "VKORC1", "CYP4F2", "GGCX"], "description": "Warfarin is metabolized primarily by CYP2C9...", "diagramUrl": "https://www.clinpgx.org/pathway/...", - Network accessline 483
"description": "Warfarin is metabolized primarily by CYP2C9...", "diagramUrl": "https://www.clinpgx.org/pathway/...", "steps": [ - Network accessline 484
"diagramUrl": "https://www.clinpgx.org/pathway/...", - Network accessline 519
for med in patient_meds: for gene in patient_genes: response = requests.get( - Network accessline 520
for gene in patient_genes: response = requests.get( "https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 521
response = requests.get( - Network accessline 522
"https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 534
response = requests.get( - Network accessline 535
"https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 549
alleles = requests.get( - Network accessline 550
"https://api.clinpgx.org/v1/allele", - Network accessline 567
# Screen for HLA-B*57:01 before abacavir response = requests.get( - Network accessline 568
response = requests.get( - Network accessline 569
"https://api.clinpgx.org/v1/geneDrugPair", - Network accessline 605
for attempt in range(max_retries): try: response = requests.get(url, params=params, timeout=10) - Network accessline 607
response = requests.get(url, params=params, timeout=10) - Network accessline 664
results = {} for gene in genes: response = requests.get(f"https://api.clinpgx.org/v1/gene/{gene}") - Network accessline 665
for gene in genes: response = requests.get(f"https://api.clinpgx.org/v1/gene/{gene}") if response.status_code == 200: - Network accessline 666
response = requests.get(f"https://api.clinpgx.org/v1/gene/{gene}") - Network accessline 729
- API version: v1 - Stability: Beta - endpoints stable, parameters may change - Monitor: https://blog.clinpgx.org/ for updates - Network accessline 731
- Monitor: https://blog.clinpgx.org/ for updates - Network accessline 733
### Migration from PharmGKB As of July 2025, PharmGKB URLs redirect to ClinPGx. Update references: - Old: `https://api.pharmgkb.org/` - Network accessline 734
As of July 2025, PharmGKB URLs redirect to ClinPGx. Update references: - Old: `https://api.pharmgkb.org/` - New: `https://api.clinpgx.org/` - Network accessline 735
- Old: `https://api.pharmgkb.org/` - Network accessline 736
- New: `https://api.clinpgx.org/` - Network accessline 745
- **API Issues**: api@clinpgx.org - **Documentation**: https://api.clinpgx.org/ - Network accessline 746
- **Documentation**: https://api.clinpgx.org/ - Network accessline 747
- **General Questions**: https://www.clinpgx.org/page/faqs - Network accessline 748
- **Blog**: https://blog.clinpgx.org/ - Network accessline 749
- **CPIC Guidelines**: https://cpicpgx.org/
skills/clinpgx-database/scripts/query_clinpgx.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
ClinPGx API: https://api.clinpgx.org/ - Network accessline 20
BASE_URL = "https://api.clinpgx.org/v1/" RATE_LIMIT_DELAY = 0.5 # 500ms delay = 2 requests/second - Network accessline 36
response = requests.get(url, params=params) - Network accessline 53
for attempt in range(max_retries): try: response = requests.get(url, params=params, timeout=10) - Network accessline 55
response = requests.get(url, params=params, timeout=10)
skills/clinpgx/SKILL.md
- Network accessline 12
always: false emoji: "🧬" homepage: https://api.clinpgx.org/ - Network accessline 13
emoji: "🧬" homepage: https://api.clinpgx.org/ os: [macos, linux] - Network accessline 14
homepage: https://api.clinpgx.org/ - Network accessline 26
You are **ClinPGx**, a specialised ClawBio agent for querying the ClinPGx pharmacogenomics database. Your role is to look up gene-drug interactions, clinical annotations, CPIC guidelines, FDA drug labels, and allele definitions from the Cli
skills/clinpgx/api.py
- Executable scriptline 1
Executable file
skills/clinpgx/clinpgx.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 35
BASE_URL = "https://api.clinpgx.org/v1" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Network accessline 57
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 58
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 59
self.session = requests.Session()
skills/clinpgx/tests/__init__.py
- Executable scriptline 1
Executable file
skills/clinpgx/tests/test_clinpgx.py
- Executable scriptline 1
Executable file
skills/clinvar-database/SKILL.md
- Network accessline 30
Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/ - Network accessline 50
# Search for pathogenic BRCA1 variants curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json" - Network accessline 51
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json" - Network accessline 117
# Download latest monthly XML release wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz - Network accessline 118
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz - Network accessline 120
# Download VCF for GRCh38 wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 121
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 237
**Submission methods:** - Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/ - Network accessline 238
- Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/ - Network accessline 271
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 272
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 307
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_YYYY-MM.xml.gz - Network accessline 348
- ClinVar home: https://www.ncbi.nlm.nih.gov/clinvar/ - Network accessline 349
- ClinVar documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/ - Network accessline 350
- E-utilities documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/ - Network accessline 352
- ClinGen expert panels: https://clinicalgenome.org/
skills/clinvar-database/references/api_reference.md
- Network accessline 15
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ - Network accessline 25
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi - Network accessline 37
# Search for BRCA1 pathogenic variants curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json&retmax=100" - Network accessline 38
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json&retmax=100" - Network accessline 54
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi - Network accessline 65
# Get summary for specific variant curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=12345&retmode=json&version=2.0" - Network accessline 66
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=12345&retmode=json&version=2.0" - Network accessline 84
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi - Network accessline 94
# Fetch full VCV record curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&id=12345&rettype=vcv" - Network accessline 95
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&id=12345&rettype=vcv" - Network accessline 103
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi - Network accessline 114
# Find PubMed articles for a variant curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=clinvar&db=pubmed&id=12345" - Network accessline 115
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=clinvar&db=pubmed&id=12345" - Network accessline 121
# Step 1: Search for variants SEARCH_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=CFTR[gene]+AND+pathogenic[CLNSIG]&retmode=json&retmax=10" - Network accessline 122
SEARCH_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=CFTR[gene]+AND+pathogenic[CLNSIG]&retmode=json&retmax=10" - Network accessline 127
# Step 3: Retrieve summaries SUMMARY_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=<ids>&retmode=json&version=2.0" - Network accessline 128
SUMMARY_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=<ids>&retmode=json&version=2.0" - Network accessline 130
# Step 4: Fetch full records if needed FETCH_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&id=<ids>&rettype=vcv" - Network accessline 131
FETCH_URL="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=clinvar&id=<ids>&rettype=vcv" - Dangerous shell operationline 138
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" - Network accessline 138
sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" - Network accessline 169
### API Key Setup 1. Register for NCBI account at https://www.ncbi.nlm.nih.gov/account/ - Network accessline 170
[Credential-related source omitted] - Access to secretsline 172
[Credential-related source omitted] - Network accessline 225
- NCBI E-utilities documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/ - Network accessline 226
- ClinVar web services: https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/ - Network accessline 227
- Entrez Direct cookbook: https://www.ncbi.nlm.nih.gov/books/NBK179288/
skills/clinvar-database/references/clinical_significance.md
- Network accessline 215
- ACMG/AMP Variant Interpretation Guidelines: Richards et al., 2015 - ClinGen Sequence Variant Interpretation Working Group: https://clinicalgenome.org/ - Network accessline 216
- ClinGen Sequence Variant Interpretation Working Group: https://clinicalgenome.org/ - Network accessline 217
- ClinVar Clinical Significance Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ - Network accessline 218
- Review Status Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/review_status/
skills/clinvar-database/references/data_formats.md
- Network accessline 324
# Get latest file LATEST=$(curl -s ${BASE_URL}/ | \ - Network accessline 325
LATEST=$(curl -s ${BASE_URL}/ | \ - Network accessline 329
# Download wget ${BASE_URL}/${LATEST} - Network accessline 330
wget ${BASE_URL}/${LATEST} - Network accessline 341
# XML wget ${FTP_BASE}/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz - Network accessline 342
wget ${FTP_BASE}/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz - Network accessline 344
# VCF (both assemblies) wget ${FTP_BASE}/vcf_GRCh37/clinvar.vcf.gz - Network accessline 345
wget ${FTP_BASE}/vcf_GRCh37/clinvar.vcf.gz - Network accessline 346
wget ${FTP_BASE}/vcf_GRCh38/clinvar.vcf.gz - Network accessline 348
# Tab-delimited wget ${FTP_BASE}/tab_delimited/variant_summary.txt.gz - Network accessline 349
wget ${FTP_BASE}/tab_delimited/variant_summary.txt.gz - Network accessline 350
wget ${FTP_BASE}/tab_delimited/var_citations.txt.gz - Network accessline 355
- ClinVar FTP Primer: https://www.ncbi.nlm.nih.gov/clinvar/docs/ftp_primer/ - Network accessline 356
- XML Schema Documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/xml_schemas/ - Network accessline 357
- VCF Specification: https://samtools.github.io/hts-specs/VCFv4.3.pdf - Network accessline 358
- Release Notes: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/README.txt
skills/cobrapy/SKILL.md
- Network accessline 457
Official documentation: https://cobrapy.readthedocs.io/en/latest/
skills/cobrapy/references/api_quick_reference.md
- Network accessline 655
This quick reference covers the most commonly used COBRApy functions and patterns. For complete API documentation, see https://cobrapy.readthedocs.io/
skills/compbioagent-explorer/SKILL.md
- Network accessline 53
1. **Setup**: `pip install compbioagent`. 2. **Launch**: `compbioagent start --data ./data.h5ad`. 3. **Interact**: Open the local URL (e.g., http://localhost:8050) and chat with the agent to generate plots. - Network accessline 55
3. **Interact**: Open the local URL (e.g., http://localhost:8050) and chat with the agent to generate plots.
skills/computational-pathology-agent/wsi_analyzer.py
- Executable scriptline 1
Executable file
skills/convergence-study/SKILL.md
- Broad permissionsline 1
Bash
skills/convergence-study/scripts/dt_refinement.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/convergence-study/scripts/gci_calculator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/convergence-study/scripts/h_refinement.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/convergence-study/scripts/richardson_extrapolation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/cosmic-database/SKILL.md
- Network accessline 26
### Account Registration COSMIC requires authentication for data downloads: - **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register - Network accessline 27
COSMIC requires authentication for data downloads: - **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register - **Commercial users**: License required (contact QIAGEN) - Network accessline 28
- **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register - Network accessline 236
vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz') for record in vcf.fetch('17', 7577000, 7579000): # TP53 region - Network accessline 237
for record in vcf.fetch('17', 7577000, 7579000): # TP53 region - Network accessline 322
- **COSMIC Website**: https://cancer.sanger.ac.uk/cosmic - Network accessline 323
- **Documentation**: https://cancer.sanger.ac.uk/cosmic/help - Network accessline 324
- **Release Notes**: https://cancer.sanger.ac.uk/cosmic/release_notes
skills/cosmic-database/references/cosmic_data_reference.md
- Network accessline 7
**Website**: https://cancer.sanger.ac.uk/cosmic - Network accessline 14
- **Academic users**: Free access (registration required) - **Commercial users**: License required (contact QIAGEN) - **Registration**: https://cancer.sanger.ac.uk/cosmic/register - Network accessline 16
- **Registration**: https://cancer.sanger.ac.uk/cosmic/register - Network accessline 18
### Download Methods 1. **Web Browser**: Interactive search at https://cancer.sanger.ac.uk/cosmic - Network accessline 19
1. **Web Browser**: Interactive search at https://cancer.sanger.ac.uk/cosmic 2. **File Downloads**: Programmatic access via download API 3. **Data Files**: TSV, CSV, and VCF formats - Network accessline 217
- **Documentation**: https://cancer.sanger.ac.uk/cosmic/help - Network accessline 218
- **Release Notes**: https://cancer.sanger.ac.uk/cosmic/release_notes
skills/cosmic-database/scripts/download_cosmic.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 57
base_url = "https://cancer.sanger.ac.uk/cosmic/file_download/" - Network accessline 65
print(f"Requesting download URL for: {filepath}") r = requests.get( - Network accessline 66
r = requests.get( - Network accessline 92
print(f"Downloading file from: {download_url}") file_response = requests.get(download_url, stream=True, timeout=300) - Network accessline 93
file_response = requests.get(download_url, stream=True, timeout=300)
skills/crisis-detection-intervention-ai/SKILL.md
- Broad permissionsline 1
Read,Write,Edit,Bash(npm:*) - Network accessline 135
phone: '988', text: 'Text "HELLO" to 741741', chat: 'https://988lifeline.org/chat' - Network accessline 136
text: 'Text "HELLO" to 741741', chat: 'https://988lifeline.org/chat' }); - Network accessline 137
chat: 'https://988lifeline.org/chat' - Network accessline 190
{ name: '988 Suicide & Crisis Lifeline', link: 'tel:988' }, { name: 'Crisis Text Line', link: 'sms:741741' }, { name: 'Chat Now', link: 'https://988lifeline.org/chat' } - Network accessline 191
{ name: 'Crisis Text Line', link: 'sms:741741' }, { name: 'Chat Now', link: 'https://988lifeline.org/chat' } ] - Network accessline 192
{ name: 'Chat Now', link: 'https://988lifeline.org/chat' } - Network accessline 242
name: 'Chat with counselor', description: 'Online chat support', action: 'https://988lifeline.org/chat', - Network accessline 243
description: 'Online chat support', action: 'https://988lifeline.org/chat', type: 'web' - Network accessline 244
action: 'https://988lifeline.org/chat', - Access to secretsline 285
[Credential-related source omitted] - Access to secretsline 489
[Credential-related source omitted]
skills/crisis-detection-intervention-ai/references/crisis-resources.md
- Network accessline 9
**Phone**: 988 (available 24/7) **Website**: https://988lifeline.org/ - Network accessline 10
**Website**: https://988lifeline.org/ - Network accessline 11
**Chat**: https://988lifeline.org/chat - Network accessline 28
actions: [ { label: 'Call 988', action: 'tel:988', primary: true }, { label: 'Chat Online', action: 'https://988lifeline.org/chat' }, - Network accessline 29
{ label: 'Call 988', action: 'tel:988', primary: true }, { label: 'Chat Online', action: 'https://988lifeline.org/chat' }, { label: 'Text Support', action: 'sms:988' } - Network accessline 30
{ label: 'Chat Online', action: 'https://988lifeline.org/chat' }, - Network accessline 40
**Text**: Text "HELLO" to 741741 **Website**: https://www.crisistextline.org/ - Network accessline 41
**Website**: https://www.crisistextline.org/ - Network accessline 65
**Phone**: 1-800-662-HELP (4357) **Website**: https://www.samhsa.gov/find-help/national-helpline - Network accessline 66
**Website**: https://www.samhsa.gov/find-help/national-helpline - Network accessline 91
**Phone**: 1-800-799-SAFE (7233) **Website**: https://www.thehotline.org/ - Network accessline 92
**Website**: https://www.thehotline.org/ - Network accessline 106
**Phone**: 988, then press 1 **Text**: 838255 **Chat**: https://www.veteranscrisisline.net/ - Network accessline 108
**Chat**: https://www.veteranscrisisline.net/ - Network accessline 121
- Phone: 1-866-488-7386 - Text: Text "START" to 678678 - Chat: https://www.thetrevorproject.org/ - Network accessline 123
- Chat: https://www.thetrevorproject.org/ - Network accessline 136
- Phone: 1-833-456-4566 - Text: 45645 - Website: https://www.crisisservicescanada.ca/ - Network accessline 138
- Website: https://www.crisisservicescanada.ca/ - Network accessline 149
- Phone: 116 123 - Email: jo@samaritans.org - Website: https://www.samaritans.org/ - Network accessline 151
- Website: https://www.samaritans.org/ - Network accessline 160
**Lifeline**: - Phone: 13 11 14 - Chat: https://www.lifeline.org.au/ - Network accessline 162
- Chat: https://www.lifeline.org.au/ - Network accessline 171
**Befrienders Worldwide**: - International directory: https://www.befrienders.org/ - Network accessline 172
- International directory: https://www.befrienders.org/ - Network accessline 187
- Helpline: 1-800-931-2237 - Text: Text "NEDA" to 741741 - Website: https://www.nationaleatingdisorders.org/ - Network accessline 189
- Website: https://www.nationaleatingdisorders.org/ - Network accessline 195
**Postpartum Support International**: - Helpline: 1-800-944-4773 - Website: https://www.postpartum.net/ - Network accessline 197
- Website: https://www.postpartum.net/ - Network accessline 283
): Promise<LocalResource[]> { // Use SAMHSA Treatment Locator API const response = await fetch( - Network accessline 284
// Use SAMHSA Treatment Locator API const response = await fetch( `https://findtreatment.samhsa.gov/locator/api/v1/facilities?zip=${zipCode}&type=${serviceType}` - Network accessline 285
const response = await fetch( - Network accessline 286
`https://findtreatment.samhsa.gov/locator/api/v1/facilities?zip=${zipCode}&type=${serviceType}` - Network accessline 302
**SAMHSA API**: https://findtreatment.samhsa.gov/locator/api - Network accessline 332
type: 'chat', label: 'Chat Online', action: 'https://988lifeline.org/chat', - Network accessline 333
label: 'Chat Online', action: 'https://988lifeline.org/chat', responseTime: '<5 minutes' - Network accessline 334
action: 'https://988lifeline.org/chat', - Network accessline 457
phone: 'tel:988', messages: 'sms:741741&body=HELLO', safari: 'https://988lifeline.org/chat' - Network accessline 458
messages: 'sms:741741&body=HELLO', safari: 'https://988lifeline.org/chat' }; - Network accessline 459
safari: 'https://988lifeline.org/chat' - Network accessline 464
phone: 'tel:988', messages: 'sms:741741?body=HELLO', browser: 'https://988lifeline.org/chat' - Network accessline 465
messages: 'sms:741741?body=HELLO', browser: 'https://988lifeline.org/chat' }; - Network accessline 466
browser: 'https://988lifeline.org/chat' - Access to secretsline 603
[Credential-related source omitted] - Network accessline 659
- [988 Lifeline](https://988lifeline.org/) - Network accessline 660
- [SAMHSA Treatment Locator](https://findtreatment.samhsa.gov/) - Network accessline 661
- [Crisis Text Line](https://www.crisistextline.org/) - Network accessline 662
- [Befrienders Worldwide](https://www.befrienders.org/) (International)
skills/crisis-detection-intervention-ai/references/intervention-protocols.md
- Network accessline 38
{ name: '988 Suicide & Crisis Lifeline', action: 'tel:988' }, { name: 'Crisis Text Line', action: 'sms:741741', message: 'HELLO' }, { name: 'Chat with counselor', action: 'https://988lifeline.org/chat' } - Network accessline 39
{ name: 'Crisis Text Line', action: 'sms:741741', message: 'HELLO' }, { name: 'Chat with counselor', action: 'https://988lifeline.org/chat' } ] - Network accessline 40
{ name: 'Chat with counselor', action: 'https://988lifeline.org/chat' } - Network accessline 108
{ name: '988 Suicide & Crisis Lifeline', action: 'tel:988' }, { name: 'Crisis Text Line', action: 'sms:741741' }, { name: 'Chat Now', action: 'https://988lifeline.org/chat' }, - Network accessline 109
{ name: 'Crisis Text Line', action: 'sms:741741' }, { name: 'Chat Now', action: 'https://988lifeline.org/chat' }, { name: 'Find Therapist', action: '/find-therapist' } - Network accessline 110
{ name: 'Chat Now', action: 'https://988lifeline.org/chat' }, - Network accessline 455
- [988 Suicide & Crisis Lifeline](https://988lifeline.org/) - Network accessline 456
- [Crisis Text Line](https://www.crisistextline.org/) - Network accessline 457
- [SAMHSA Treatment Locator](https://findtreatment.samhsa.gov/) - Network accessline 458
- [National Alliance on Mental Illness](https://www.nami.org/)
skills/crisis-detection-intervention-ai/references/mental-health-nlp.md
- Network accessline 7
| Model | Accuracy | Latency | Use Case | License | |-------|----------|---------|----------|---------| | [Mental-BERT](https://huggingface.co/mental/mental-bert-base-uncased) | 89% | 50ms | Depression, anxiety detection | MIT | - Network accessline 8
|-------|----------|---------|----------|---------| | [Mental-BERT](https://huggingface.co/mental/mental-bert-base-uncased) | 89% | 50ms | Depression, anxiety detection | MIT | | [MentalRoBERTa](https://huggingface.co/mental/mental-roberta- - Network accessline 9
| [Mental-BERT](https://huggingface.co/mental/mental-bert-base-uncased) | 89% | 50ms | Depression, anxiety detection | MIT | - Network accessline 10
| [MentalRoBERTa](https://huggingface.co/mental/mental-roberta-base) | 87% | 40ms | Suicidal ideation | MIT | - Network accessline 172
- [Mental Health NLP Dataset](https://huggingface.co/datasets/mental_health) - Network accessline 173
- [Transformers.js Docs](https://huggingface.co/docs/transformers.js) - Network accessline 174
- [Crisis Detection Papers](https://arxiv.org/search/?query=suicide+detection+nlp)
skills/crisis-detection-intervention-ai/scripts/crisis_detector.ts
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 355
console.log(' • 988 Suicide & Crisis Lifeline'); console.log(' Phone: 988'); console.log(' Chat: https://988lifeline.org/chat'); - Network accessline 356
console.log(' Phone: 988'); console.log(' Chat: https://988lifeline.org/chat'); console.log('\n • Crisis Text Line'); - Network accessline 357
console.log(' Chat: https://988lifeline.org/chat');
skills/crisis-detection-intervention-ai/scripts/model_evaluator.ts
- Executable scriptline 1
#!/usr/bin/env node
skills/crisis-response-protocol/SKILL.md
- Network accessline 279
phone: '988', text: '988', url: 'https://988lifeline.org', - Network accessline 280
text: '988', url: 'https://988lifeline.org', available: '24/7', - Network accessline 281
url: 'https://988lifeline.org', - Network accessline 286
name: 'Crisis Text Line', text: 'HOME to 741741', url: 'https://www.crisistextline.org', - Network accessline 287
text: 'HOME to 741741', url: 'https://www.crisistextline.org', available: '24/7', - Network accessline 288
url: 'https://www.crisistextline.org', - Network accessline 293
name: 'SAMHSA National Helpline', phone: '1-800-662-4357', url: 'https://www.samhsa.gov/find-help/national-helpline', - Network accessline 294
phone: '1-800-662-4357', url: 'https://www.samhsa.gov/find-help/national-helpline', available: '24/7', - Network accessline 295
url: 'https://www.samhsa.gov/find-help/national-helpline', - Network accessline 303
name: 'AA Hotline', phone: '1-800-839-1686', url: 'https://www.aa.org', - Network accessline 304
phone: '1-800-839-1686', url: 'https://www.aa.org', description: 'Alcoholics Anonymous support', - Network accessline 305
url: 'https://www.aa.org', - Network accessline 309
name: 'NA Helpline', phone: '1-818-773-9999', url: 'https://na.org', - Network accessline 310
phone: '1-818-773-9999', url: 'https://na.org', description: 'Narcotics Anonymous support', - Network accessline 311
url: 'https://na.org', - Network accessline 453
- [988 Suicide & Crisis Lifeline](https://988lifeline.org) - Network accessline 454
- [SAMHSA Guidelines](https://www.samhsa.gov) - Network accessline 455
- [AI in Mental Health - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10242473/) - Network accessline 456
- [Crisis Chatbot Safety - Nature](https://www.nature.com/articles/s41598-025-17242-4)
skills/crispr-guide-design/crispr_designer.py
- Executable scriptline 1
Executable file
skills/crispr-offtarget-predictor/impl.py
- Executable scriptline 1
Executable file
skills/data-stats-analysis/SKILL.md
- Network accessline 473
## References - scipy.stats documentation: https://docs.scipy.org/doc/scipy/reference/stats.html - Network accessline 474
- scipy.stats documentation: https://docs.scipy.org/doc/scipy/reference/stats.html - Network accessline 475
- statsmodels documentation: https://www.statsmodels.org/stable/index.html - Network accessline 476
- Multiple testing: https://www.statsmodels.org/stable/generated/statsmodels.stats.multitest.multipletests.html - Network accessline 477
- Statistical testing guide: https://docs.scipy.org/doc/scipy/tutorial/stats.html
skills/data-transform/SKILL.md
- Network accessline 572
## References - pandas documentation: https://pandas.pydata.org/docs/ - Network accessline 573
- pandas documentation: https://pandas.pydata.org/docs/ - Network accessline 574
- pandas user guide: https://pandas.pydata.org/docs/user_guide/index.html - Network accessline 575
- scikit-learn preprocessing: https://scikit-learn.org/stable/modules/preprocessing.html - Network accessline 576
- pandas cheat sheet: https://pandas.pydata.org/Pandas_Cheat_Sheet.pdf
skills/data-visualization-biomedical/SKILL.md
- Executable scriptline 1
Executable file
skills/data-viz-plots/SKILL.md
- Network accessline 457
## References - Matplotlib documentation: https://matplotlib.org/stable/contents.html - Network accessline 458
- Matplotlib documentation: https://matplotlib.org/stable/contents.html - Network accessline 459
- Seaborn documentation: https://seaborn.pydata.org/ - Network accessline 460
- Matplotlib gallery: https://matplotlib.org/stable/gallery/index.html - Network accessline 461
- Seaborn gallery: https://seaborn.pydata.org/examples/index.html
skills/datacommons-client/SKILL.md
- Network accessline 49
# Get latest population data response = client.observation.fetch( - Network accessline 50
response = client.observation.fetch( - Network accessline 56
# Get time series response = client.observation.fetch( - Network accessline 57
response = client.observation.fetch( - Network accessline 63
# Query by hierarchy response = client.observation.fetch( - Network accessline 64
response = client.observation.fetch( - Network accessline 154
response = client.observation.fetch( - Network accessline 189
# Or explore via the web interface # https://datacommons.org/tools/statvar - Network accessline 190
# https://datacommons.org/tools/statvar - Network accessline 198
response = client.observation.fetch( - Network accessline 220
[Credential-related source omitted] - Access to secretsline 220
[Credential-related source omitted] - Access to secretsline 221
[Credential-related source omitted] - Network accessline 222
- Request keys at: https://apikeys.datacommons.org/ - Network accessline 224
**For custom Data Commons instances:** - No API key required - Specify custom endpoint: `client = DataCommonsClient(url="https://custom.datacommons.org")` - Network accessline 226
- Specify custom endpoint: `client = DataCommonsClient(url="https://custom.datacommons.org")` - Network accessline 239
- **Official Documentation**: https://docs.datacommons.org/api/python/v2/ - Network accessline 240
- **Statistical Variable Explorer**: https://datacommons.org/tools/statvar - Network accessline 241
- **Data Commons Browser**: https://datacommons.org/browser/ - Network accessline 242
- **GitHub Repository**: https://github.com/datacommonsorg/api-python
skills/datacommons-client/references/getting_started.md
- Access to secretsline 14
[Credential-related source omitted] - Network accessline 17
Request an API key at: https://apikeys.datacommons.org/ - Network accessline 43
# Step 2: Query population data response = client.observation.fetch( - Network accessline 44
response = client.observation.fetch( - Network accessline 68
# Query unemployment rate over time response = client.observation.fetch( - Network accessline 69
response = client.observation.fetch( - Network accessline 96
# Query median income for all California counties response = client.observation.fetch( - Network accessline 97
response = client.observation.fetch( - Network accessline 149
response = client.observation.fetch( - Network accessline 200
# Step 4: Query specific variables response = client.observation.fetch( - Network accessline 201
response = client.observation.fetch( - Network accessline 221
# Query with facet filtering response = client.observation.fetch( - Network accessline 222
response = client.observation.fetch( - Network accessline 232
# Compare with all sources response_all = client.observation.fetch( - Network accessline 233
response_all = client.observation.fetch( - Network accessline 334
response = client.observation.fetch( - Network accessline 414
1. Explore available statistical variables: https://datacommons.org/tools/statvar - Network accessline 415
2. Browse the knowledge graph: https://datacommons.org/browser/ - Network accessline 417
4. Check official documentation: https://docs.datacommons.org/api/python/v2/
skills/datacommons-client/references/node.md
- Network accessline 16
### 1. fetch() - Network accessline 37
# Get outgoing properties from California response = client.node.fetch( - Network accessline 38
response = client.node.fetch( - Network accessline 43
# Get incoming properties (what points to this node) response = client.node.fetch( - Network accessline 44
response = client.node.fetch( - Network accessline 193
# First page response = client.node.fetch( - Network accessline 194
response = client.node.fetch( - Network accessline 200
# Get next page if available if response.nextToken: next_response = client.node.fetch( - Network accessline 201
if response.nextToken: next_response = client.node.fetch( node_dcids=["country/USA"], - Network accessline 202
next_response = client.node.fetch( - Network accessline 238
# Find all entities that reference a specific node references = client.node.fetch( - Network accessline 239
references = client.node.fetch(
skills/datacommons-client/references/observation.md
- Network accessline 12
### 1. fetch() - Network accessline 42
# Get latest population for multiple entities response = client.observation.fetch( - Network accessline 43
response = client.observation.fetch( - Network accessline 49
# Get complete time series response = client.observation.fetch( - Network accessline 50
response = client.observation.fetch( - Network accessline 56
# Use relation expressions to query hierarchies response = client.observation.fetch( - Network accessline 57
response = client.observation.fetch( - Network accessline 81
Explicit method targeting specific entities by DCID (functionally equivalent to `fetch()` with entity_dcids). - Network accessline 119
response = client.observation.fetch( - Network accessline 130
response = client.observation.fetch( - Network accessline 141
response = client.observation.fetch( - Network accessline 152
# Get data for all counties within California response = client.observation.fetch( - Network accessline 153
response = client.observation.fetch( - Network accessline 169
response = client.observation.fetch( - Network accessline 183
- **orderedFacets** are sorted by reliability/recency - Use relation expressions for complex graph queries - The `fetch()` method is the most flexible—use it for most queries - Network accessline 185
- The `fetch()` method is the most flexible—use it for most queries
skills/datacommons-client/references/resolve.md
- Network accessline 17
### 1. fetch() - Network accessline 31
# Resolve by name response = client.resolve.fetch( - Network accessline 32
response = client.resolve.fetch( - Network accessline 145
# Step 3: Query data using DCIDs data_response = client.observation.fetch( - Network accessline 146
data_response = client.observation.fetch( - Network accessline 202
# Now query data for that place response = client.observation.fetch( - Network accessline 203
response = client.observation.fetch(
skills/datamol/SKILL.md
- Network accessline 127
# Read from cloud storage df = dm.read_sdf("s3://bucket/compounds.sdf") df = dm.read_csv("https://example.com/data.csv") - Network accessline 129
df = dm.read_csv("https://example.com/data.csv") - Network accessline 698
- **Datamol Documentation**: https://docs.datamol.io/ - Network accessline 699
- **RDKit Documentation**: https://www.rdkit.org/docs/ - Network accessline 700
- **GitHub Repository**: https://github.com/datamol-io/datamol
skills/datamol/references/io_module.md
skills/deepchem/SKILL.md
skills/deepchem/scripts/graph_neural_network.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/deepchem/scripts/predict_solubility.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/deepchem/scripts/transfer_learning.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/deeptools/references/effective_genome_sizes.md
- Network accessline 114
For the most up-to-date effective genome sizes and detailed calculation methods, see: - deepTools documentation: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html - Network accessline 115
- deepTools documentation: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
skills/deeptools/references/normalization_methods.md
skills/deeptools/scripts/validate_files.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/deeptools/scripts/workflow_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/depmap/SKILL.md
- Network accessline 19
**Key resources:** - DepMap Portal: https://depmap.org/portal/ - DepMap data downloads: https://depmap.org/portal/download/all/ - Network accessline 20
- DepMap Portal: https://depmap.org/portal/ - DepMap data downloads: https://depmap.org/portal/download/all/ - Python package: `depmap` (or access via API/downloads) - Network accessline 21
- DepMap data downloads: https://depmap.org/portal/download/all/ - Network accessline 23
- API: https://depmap.org/portal/api/ - Network accessline 67
BASE_URL = "https://depmap.org/portal/api" - Network accessline 69
def depmap_get(endpoint, params=None): url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params) - Network accessline 70
url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params) response.raise_for_status() - Network accessline 71
response = requests.get(url, params=params) - Network accessline 84
"dataset": dataset } response = requests.get(url, params=params) - Network accessline 85
} response = requests.get(url, params=params) return response.json() - Network accessline 86
response = requests.get(url, params=params) - Network accessline 92
url = f"{BASE_URL}/data/gene_dependency" params = {"gene_name": gene_symbol, "dataset_name": dataset_name} response = requests.get(url, params=params) - Network accessline 93
params = {"gene_name": gene_symbol, "dataset_name": dataset_name} response = requests.get(url, params=params) data = response.json() - Network accessline 94
response = requests.get(url, params=params) - Network accessline 107
def download_depmap_data(url, output_path): """Download a DepMap data file.""" response = requests.get(url, stream=True) - Network accessline 108
"""Download a DepMap data file.""" response = requests.get(url, stream=True) with open(output_path, 'wb') as f: - Network accessline 109
response = requests.get(url, stream=True) - Network accessline 114
# DepMap 24Q4 data files (update version as needed) FILES = { "crispr_gene_effect": "https://figshare.com/ndownloader/files/...", - Network accessline 115
FILES = { "crispr_gene_effect": "https://figshare.com/ndownloader/files/...", # OR download from: https://depmap.org/portal/download/all/ - Network accessline 116
"crispr_gene_effect": "https://figshare.com/ndownloader/files/...", # OR download from: https://depmap.org/portal/download/all/ # Files available: - Network accessline 117
# OR download from: https://depmap.org/portal/download/all/ - Network accessline 282
Download all files from: https://depmap.org/portal/download/all/ - Network accessline 295
- **DepMap Portal**: https://depmap.org/portal/ - **Data downloads**: https://depmap.org/portal/download/all/ - Network accessline 296
- **Data downloads**: https://depmap.org/portal/download/all/ - Network accessline 297
- **DepMap paper**: Behan FM et al. (2019) Nature. PMID: 30971826 - **Chronos paper**: Dempster JM et al. (2021) Nature Methods. PMID: 34349281 - **GitHub**: https://github.com/broadinstitute/depmap-portal - Network accessline 298
- **Chronos paper**: Dempster JM et al. (2021) Nature Methods. PMID: 34349281 - **GitHub**: https://github.com/broadinstitute/depmap-portal - **Figshare**: https://figshare.com/articles/dataset/DepMap_24Q4_Public/27993966 - Network accessline 299
- **GitHub**: https://github.com/broadinstitute/depmap-portal - Network accessline 300
- **Figshare**: https://figshare.com/articles/dataset/DepMap_24Q4_Public/27993966
skills/diffdock/SKILL.md
- Network accessline 50
git clone https://github.com/gcorso/DiffDock.git - Network accessline 363
python app/main.py # Navigate to http://localhost:7860 - Network accessline 364
# Navigate to http://localhost:7860 - Network accessline 367
Or use the online demo without installation: - https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web - Network accessline 368
- https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web - Network accessline 474
- **GitHub Repository**: https://github.com/gcorso/DiffDock - Network accessline 475
- **Online Demo**: https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web - Network accessline 476
- **DiffDock-L Paper**: https://arxiv.org/abs/2402.18396 - Network accessline 477
- **Original Paper**: https://arxiv.org/abs/2210.01776
skills/diffdock/references/workflows_examples.md
- Network accessline 10
# Clone repository git clone https://github.com/gcorso/DiffDock.git - Network accessline 11
git clone https://github.com/gcorso/DiffDock.git - Possible obfuscationline 74
python -m inference --config default_inference_args.yaml --protein_sequence "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQ - Possible obfuscationline 76
--protein_sequence "MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVL - Network accessline 301
### Access Interface Navigate to `http://localhost:7860` in web browser - Network accessline 302
Navigate to `http://localhost:7860` in web browser - Network accessline 311
### Online Alternative Use the Hugging Face Spaces demo without local installation: - URL: https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web - Network accessline 313
- URL: https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web
skills/diffdock/scripts/analyze_results.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/diffdock/scripts/prepare_batch_csv.py
- Executable scriptline 1
#!/usr/bin/env python3 - Possible obfuscationline 172
'MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK'
skills/diffdock/scripts/setup_check.py
skills/differentiation-schemes/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/differentiation-schemes/scripts/scheme_selector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/differentiation-schemes/scripts/stencil_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/differentiation-schemes/scripts/truncation_error.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/dnanexus-integration/SKILL.md
skills/dnanexus-integration/references/configuration.md
- Access to secretsline 363
[Credential-related source omitted]
skills/dnanexus-integration/references/python-sdk.md
skills/doc-coauthoring/SKILL.md
skills/docx-official/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/docx-official/SKILL.md
- Dangerous shell operationline 193
- **pandoc**: `sudo apt-get install pandoc` (for text extraction) - Dangerous shell operationline 195
- **LibreOffice**: `sudo apt-get install libreoffice` (for PDF conversion) - Dangerous shell operationline 196
- **Poppler**: `sudo apt-get install poppler-utils` (for pdftoppm to convert PDF to images)
skills/docx-official/docx-js.md
- Network accessline 238
children: [new ExternalHyperlink({ children: [new TextRun({ text: "Google", style: "Hyperlink" })], link: "https://www.google.com" - Network accessline 239
children: [new TextRun({ text: "Google", style: "Hyperlink" })], link: "https://www.google.com" })] - Network accessline 240
link: "https://www.google.com"
skills/docx-official/ooxml.md
- Network accessline 166
<Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/numbering" Target="numbering.xml"/> - Network accessline 167
<Relationship Id="rId5" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/image" Target="media/image1.png"/> - Network accessline 185
<wp:extent cx="2743200" cy="1828800"/> <wp:docPr id="1" name="Picture 1"/> <a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> - Network accessline 186
<wp:docPr id="1" name="Picture 1"/> <a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 187
<a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> - Network accessline 188
<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 189
<pic:pic xmlns:pic="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 230
<!-- In word/_rels/document.xml.rels --> <Relationship Id="rId5" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/hyperlink" - Network accessline 231
<Relationship Id="rId5" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/hyperlink" - Network accessline 232
Target="https://www.example.com/" TargetMode="External"/> - Network accessline 463
next_rid = rels_editor.get_next_rid() rels_editor.append_to(rels_editor.dom.documentElement, f'<Relationship Id="{next_rid}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/image" Target="media/image1.png"/>') - Network accessline 464
rels_editor.append_to(rels_editor.dom.documentElement, f'<Relationship Id="{next_rid}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/image" Target="media/image1.png"/>') doc['[Content_Types].xml'].append_to(d - Network accessline 465
f'<Relationship Id="{next_rid}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/image" Target="media/image1.png"/>') - Network accessline 475
<wp:extent cx="{width_emus}" cy="{height_emus}"/> <wp:docPr id="1" name="Picture 1"/> <a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> - Network accessline 476
<wp:docPr id="1" name="Picture 1"/> <a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 477
<a:graphic xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main"> - Network accessline 478
<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 479
<pic:pic xmlns:pic="http://schemas.openxmlformats.org/drawingml/2006/picture">
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 6
xmlns:cdr="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 9
elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" schemaLocation="dml-chartDrawing.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 15
schemaLocation="dml-chartDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 8
elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 12
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 11
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" schemaLocation="dml-diagram.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 13
schemaLocation="dml-diagram.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" schemaLocation="dml-chart.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 15
schemaLocation="dml-chart.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" schemaLocation="dml-picture.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 17
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" schemaLocation="dml-lockedCanvas.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" elementFormDefault="qualified" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 6
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 9
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> - Network accessline 10
<xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> <xsd:element name="from" type="CT_Marker"/> - Network accessline 11
namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/>
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 5
xmlns:dpct="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 9
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 11
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 12
<xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 13
namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 15
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 4
xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 5
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/characteristics" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/characteristics"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 6
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 7
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 9
schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 6
elementFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 6
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/ - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 10
schemaLocation="wml.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/> <xsd:simpleType name="ST_Integer255"> - Network accessline 13
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" blockDefault="#all"> - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 8
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" schemaLocation="dml-spreadsheetDrawing.xsd"/> - Network accessline 14
namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 3
xmlns:pvml="urn:schemas-microsoft-com:office:powerpoint" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 4
xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:w10="urn:schemas-microsoft-com:office:word" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:x="urn:schemas-microsoft-com:office:excel" - Network accessline 7
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:vml" elementFormDefault="qualified" - Network accessline 9
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
<xsd:import namespace="urn:schemas-microsoft-com:office:office" schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 13
schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="wml.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 16
<xsd:import namespace="urn:schemas-microsoft-com:office:word" schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 17
schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 22
<xsd:import namespace="urn:schemas-microsoft-com:office:powerpoint" schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 23
schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 24
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedT - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
attributeFormDefault="unqualified"> <xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
<xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:sl="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 6
xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 8
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 9
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 10
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/markup-compatib - Network accessline 11
targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/markup-compatibility/2006" schemaLocation="../mce/mc.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 14
schemaLocation="dml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" schemaLocation="shared-math.xsd"/> - Network accessline 15
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 16
schemaLocation="shared-math.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 17
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 18
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 19
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 20
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" schemaLocation="shared-customXmlSchemaProperties.xsd"/> - Network accessline 21
<xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 22
schemaLocation="shared-customXmlSchemaProperties.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace"/> <xsd:complexType name="CT_Empty"/> - Network accessline 23
<xsd:import namespace="http://www.w3.org/XML/1998/namespace"/>
skills/docx-official/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd
- Network accessline 1
<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 2
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 4
<xs:annotation> <xs:documentation> See http://www.w3.org/XML/1998/namespace.html and - Network accessline 5
<xs:documentation> See http://www.w3.org/XML/1998/namespace.html and http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 6
See http://www.w3.org/XML/1998/namespace.html and - Network accessline 7
http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 55
<schema . . .> . . . <import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 56
. . . <import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 57
<import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 58
schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 72
<xs:documentation>In keeping with the XML Schema WG's standard versioning policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. - Network accessline 73
policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. At the date of issue it can also be found at - Network accessline 74
http://www.w3.org/2001/03/xml.xsd. - Network accessline 75
At the date of issue it can also be found at http://www.w3.org/2001/xml.xsd. The schema document at that URI may however change in the future, - Network accessline 76
http://www.w3.org/2001/xml.xsd. - Network accessline 79
itself. In other words, if the XML Schema namespace changes, the version of this document at http://www.w3.org/2001/xml.xsd will change - Network accessline 80
of this document at http://www.w3.org/2001/xml.xsd will change accordingly; the version at - Network accessline 81
http://www.w3.org/2001/xml.xsd will change - Network accessline 82
accordingly; the version at http://www.w3.org/2001/03/xml.xsd will not change. </xs:documentation> - Network accessline 83
http://www.w3.org/2001/03/xml.xsd will not change. - Network accessline 103
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for - Network accessline 104
<xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for information about this attribute.</xs:documentation> - Network accessline 105
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
skills/docx-official/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 2
<xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 3
xmlns:xs="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/content-types"
skills/docx-official/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 2
<xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 4
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/" - Network accessline 5
xmlns:dcterms="http://purl.org/dc/terms/" elementFormDefault="qualified" blockDefault="#all"> - Network accessline 7
<xs:import namespace="http://purl.org/dc/elements/1.1/" - Network accessline 8
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd"/> - Network accessline 9
<xs:import namespace="http://purl.org/dc/terms/" - Network accessline 10
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms.xsd"/> - Network accessline 11
<xs:import id="xml" namespace="http://www.w3.org/XML/1998/namespace"/>
skills/docx-official/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd
- Network accessline 1
<?xml version="1.0" encoding="UTF-8"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/digital-signature"
skills/docx-official/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/relationships"
skills/docx-official/ooxml/schemas/mce/mc.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 2
<xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 3
attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 5
xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 7
<!-- This XSD is a modified version of the one found at: https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 9
https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 15
<w:document xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 16
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 17
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/docx-official/ooxml/schemas/microsoft/wml-2010.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns:r="http://schemas.op - Network accessline 2
<!-- <xsd:import id="rel" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="orel.xsd"/> --> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<!-- <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartbasetypes.xsd"/> - Network accessline 5
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartsplineproperties.xsd"/> -->
skills/docx-official/ooxml/schemas/microsoft/wml-2012.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" elementFormDefault="qualified" att - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 3
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/docx-official/ooxml/schemas/microsoft/wml-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx-official/ooxml/schemas/microsoft/wml-cex-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" xmlns:w16="http://schemas.microsoft. - Network accessline 2
<xsd:import id="w16" namespace="http://schemas.microsoft.com/office/word/2018/wordml" schemaLocation="wml-2018.xsd"/> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<xsd:import id="s" namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/docx-official/ooxml/schemas/microsoft/wml-cid-2016.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx-official/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx-official/ooxml/schemas/microsoft/wml-symex-2015.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx-official/ooxml/scripts/pack.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/docx-official/ooxml/scripts/unpack.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/docx-official/ooxml/scripts/validate.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/docx-official/ooxml/scripts/validation/__init__.py
- Executable scriptline 1
Executable file
skills/docx-official/ooxml/scripts/validation/base.py
- Executable scriptline 1
Executable file - Network accessline 70
MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 71
XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace" - Network accessline 74
PACKAGE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 75
"http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 76
) OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 77
OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" ) - Network accessline 78
"http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 79
) CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 80
CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" ) - Network accessline 81
"http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 88
OOXML_NAMESPACES = { "http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 89
"http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 90
"http://schemas.openxmlformats.org/officeDocument/2006/relationships", - Network accessline 91
"http://schemas.openxmlformats.org/schemaLibrary/2006/main", - Network accessline 92
"http://schemas.openxmlformats.org/drawingml/2006/main", - Network accessline 93
"http://schemas.openxmlformats.org/drawingml/2006/chart", - Network accessline 94
"http://schemas.openxmlformats.org/drawingml/2006/chartDrawing", - Network accessline 95
"http://schemas.openxmlformats.org/drawingml/2006/diagram", - Network accessline 96
"http://schemas.openxmlformats.org/drawingml/2006/picture", - Network accessline 97
"http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing", - Network accessline 98
"http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", - Network accessline 99
"http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 100
"http://schemas.openxmlformats.org/presentationml/2006/main", - Network accessline 101
"http://schemas.openxmlformats.org/spreadsheetml/2006/main", - Network accessline 102
"http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes", - Network accessline 103
"http://www.w3.org/XML/1998/namespace",
skills/docx-official/ooxml/scripts/validation/docx.py
skills/docx-official/ooxml/scripts/validation/pptx.py
skills/docx-official/ooxml/scripts/validation/redlining.py
- Executable scriptline 1
Executable file - Network accessline 17
self.verbose = verbose self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 18
self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" } - Network accessline 19
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/docx-official/scripts/__init__.py
- Executable scriptline 1
Executable file
skills/docx-official/scripts/document.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 93
root.setAttribute( # type: ignore "xmlns:w16du", "http://schemas.microsoft.com/office/word/2023/wordml/word16du", - Network accessline 94
"xmlns:w16du", "http://schemas.microsoft.com/office/word/2023/wordml/word16du", ) - Network accessline 95
"http://schemas.microsoft.com/office/word/2023/wordml/word16du", - Network accessline 102
root.setAttribute( # type: ignore "xmlns:w16cex", "http://schemas.microsoft.com/office/word/2018/wordml/cex", - Network accessline 103
"xmlns:w16cex", "http://schemas.microsoft.com/office/word/2018/wordml/cex", ) - Network accessline 104
"http://schemas.microsoft.com/office/word/2018/wordml/cex", - Network accessline 111
root.setAttribute( # type: ignore "xmlns:w14", "http://schemas.microsoft.com/office/word/2010/wordml", - Network accessline 112
"xmlns:w14", "http://schemas.microsoft.com/office/word/2010/wordml", ) - Network accessline 113
"http://schemas.microsoft.com/office/word/2010/wordml", - Network accessline 445
wrapper = f'<root xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main">{xml_content}</root>' - Network accessline 985
rel_xml = f'<{prefix}Relationship Id="{next_rid}" Type="http://schemas.microsoft.com/office/2011/relationships/people" Target="people.xml"/>' - Network accessline 1217
( next_rid_num, "http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", - Network accessline 1218
next_rid_num, "http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", "comments.xml", - Network accessline 1219
"http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", - Network accessline 1222
( next_rid_num + 1, "http://schemas.microsoft.com/office/2011/relationships/commentsExtended", - Network accessline 1223
next_rid_num + 1, "http://schemas.microsoft.com/office/2011/relationships/commentsExtended", "commentsExtended.xml", - Network accessline 1224
"http://schemas.microsoft.com/office/2011/relationships/commentsExtended", - Network accessline 1227
( next_rid_num + 2, "http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", - Network accessline 1228
next_rid_num + 2, "http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", "commentsIds.xml", - Network accessline 1229
"http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", - Network accessline 1232
( next_rid_num + 3, "http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible", - Network accessline 1233
next_rid_num + 3, "http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible", "commentsExtensible.xml", - Network accessline 1234
"http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible",
skills/docx-official/scripts/templates/comments.xml
- Network accessline 1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <w:comments xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas - Network accessline 2
<w:comments xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex" xmlns:cx
skills/docx-official/scripts/templates/commentsExtended.xml
- Network accessline 1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <w15:commentsEx xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://sch - Network accessline 2
<w15:commentsEx xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex" xmln
skills/docx-official/scripts/templates/commentsExtensible.xml
- Network accessline 1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <w16cex:commentsExtensible xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1= - Network accessline 2
<w16cex:commentsExtensible xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/ch
skills/docx-official/scripts/templates/commentsIds.xml
- Network accessline 1
<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <w16cid:commentsIds xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http:/ - Network accessline 2
<w16cid:commentsIds xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex"
skills/docx-official/scripts/templates/people.xml
skills/docx-official/scripts/utilities.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/docx/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/docx/SKILL.md
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children: [new ExternalHyperlink({ children: [new TextRun({ text: "Click here", style: "Hyperlink" })], link: "https://example.com", - Network accessline 253
children: [new TextRun({ text: "Click here", style: "Hyperlink" })], link: "https://example.com", })] - Network accessline 254
link: "https://example.com",
skills/docx/scripts/__init__.py
- Executable scriptline 1
Executable file
skills/docx/scripts/accept_changes.py
- Executable scriptline 1
Executable file - Network accessline 19
ACCEPT_CHANGES_MACRO = """<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Modul - Network accessline 20
<!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic"> Sub AcceptAllTrackedChanges( - Network accessline 21
<script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic">
skills/docx/scripts/comment.py
- Executable scriptline 1
Executable file - Network accessline 25
TEMPLATE_DIR = Path(__file__).parent / "templates" NS = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 26
NS = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main", "w14": "http://schemas.microsoft.com/office/word/2010/wordml", - Network accessline 27
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 28
"w14": "http://schemas.microsoft.com/office/word/2010/wordml", - Network accessline 29
"w15": "http://schemas.microsoft.com/office/word/2012/wordml", - Network accessline 30
"w16cid": "http://schemas.microsoft.com/office/word/2016/wordml/cid", - Network accessline 31
"w16cex": "http://schemas.microsoft.com/office/word/2018/wordml/cex", - Network accessline 149
rels = [ ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", - Network accessline 150
( "http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", "comments.xml", - Network accessline 151
"http://schemas.openxmlformats.org/officeDocument/2006/relationships/comments", - Network accessline 153
), ( "http://schemas.microsoft.com/office/2011/relationships/commentsExtended", - Network accessline 154
( "http://schemas.microsoft.com/office/2011/relationships/commentsExtended", "commentsExtended.xml", - Network accessline 155
"http://schemas.microsoft.com/office/2011/relationships/commentsExtended", - Network accessline 157
), ( "http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", - Network accessline 158
( "http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", "commentsIds.xml", - Network accessline 159
"http://schemas.microsoft.com/office/2016/09/relationships/commentsIds", - Network accessline 161
), ( "http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible", - Network accessline 162
( "http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible", "commentsExtensible.xml", - Network accessline 163
"http://schemas.microsoft.com/office/2018/08/relationships/commentsExtensible",
skills/docx/scripts/office/helpers/__init__.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/helpers/merge_runs.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/helpers/simplify_redlines.py
skills/docx/scripts/office/pack.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
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<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 6
xmlns:cdr="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 9
elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" schemaLocation="dml-chartDrawing.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 15
schemaLocation="dml-chartDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
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<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
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<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 8
elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 12
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd
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<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 11
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" schemaLocation="dml-diagram.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 13
schemaLocation="dml-diagram.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" schemaLocation="dml-chart.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 15
schemaLocation="dml-chart.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" schemaLocation="dml-picture.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 17
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" schemaLocation="dml-lockedCanvas.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
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<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" elementFormDefault="qualified" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 6
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 9
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> - Network accessline 10
<xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> <xsd:element name="from" type="CT_Marker"/> - Network accessline 11
namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/>
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 5
xmlns:dpct="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 9
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 11
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 12
<xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 13
namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 15
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 4
xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 5
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/characteristics" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/characteristics"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 6
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 7
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 9
schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 6
elementFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 6
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/ - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 10
schemaLocation="wml.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/> <xsd:simpleType name="ST_Integer255"> - Network accessline 13
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" blockDefault="#all"> - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 8
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" schemaLocation="dml-spreadsheetDrawing.xsd"/> - Network accessline 14
namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 3
xmlns:pvml="urn:schemas-microsoft-com:office:powerpoint" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 4
xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:w10="urn:schemas-microsoft-com:office:word" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:x="urn:schemas-microsoft-com:office:excel" - Network accessline 7
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:vml" elementFormDefault="qualified" - Network accessline 9
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
<xsd:import namespace="urn:schemas-microsoft-com:office:office" schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 13
schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="wml.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 16
<xsd:import namespace="urn:schemas-microsoft-com:office:word" schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 17
schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 22
<xsd:import namespace="urn:schemas-microsoft-com:office:powerpoint" schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 23
schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 24
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedT - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
attributeFormDefault="unqualified"> <xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
<xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:sl="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 6
xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 8
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 9
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 10
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/markup-compatib - Network accessline 11
targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/markup-compatibility/2006" schemaLocation="../mce/mc.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 14
schemaLocation="dml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" schemaLocation="shared-math.xsd"/> - Network accessline 15
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 16
schemaLocation="shared-math.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 17
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 18
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 19
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 20
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" schemaLocation="shared-customXmlSchemaProperties.xsd"/> - Network accessline 21
<xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 22
schemaLocation="shared-customXmlSchemaProperties.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace"/> <xsd:complexType name="CT_Empty"/> - Network accessline 23
<xsd:import namespace="http://www.w3.org/XML/1998/namespace"/>
skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd
- Network accessline 1
<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 2
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 4
<xs:annotation> <xs:documentation> See http://www.w3.org/XML/1998/namespace.html and - Network accessline 5
<xs:documentation> See http://www.w3.org/XML/1998/namespace.html and http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 6
See http://www.w3.org/XML/1998/namespace.html and - Network accessline 7
http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 55
<schema . . .> . . . <import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 56
. . . <import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 57
<import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 58
schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 72
<xs:documentation>In keeping with the XML Schema WG's standard versioning policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. - Network accessline 73
policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. At the date of issue it can also be found at - Network accessline 74
http://www.w3.org/2001/03/xml.xsd. - Network accessline 75
At the date of issue it can also be found at http://www.w3.org/2001/xml.xsd. The schema document at that URI may however change in the future, - Network accessline 76
http://www.w3.org/2001/xml.xsd. - Network accessline 79
itself. In other words, if the XML Schema namespace changes, the version of this document at http://www.w3.org/2001/xml.xsd will change - Network accessline 80
of this document at http://www.w3.org/2001/xml.xsd will change accordingly; the version at - Network accessline 81
http://www.w3.org/2001/xml.xsd will change - Network accessline 82
accordingly; the version at http://www.w3.org/2001/03/xml.xsd will not change. </xs:documentation> - Network accessline 83
http://www.w3.org/2001/03/xml.xsd will not change. - Network accessline 103
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for - Network accessline 104
<xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for information about this attribute.</xs:documentation> - Network accessline 105
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 2
<xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 3
xmlns:xs="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/content-types"
skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 2
<xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 4
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/" - Network accessline 5
xmlns:dcterms="http://purl.org/dc/terms/" elementFormDefault="qualified" blockDefault="#all"> - Network accessline 7
<xs:import namespace="http://purl.org/dc/elements/1.1/" - Network accessline 8
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd"/> - Network accessline 9
<xs:import namespace="http://purl.org/dc/terms/" - Network accessline 10
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms.xsd"/> - Network accessline 11
<xs:import id="xml" namespace="http://www.w3.org/XML/1998/namespace"/>
skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd
- Network accessline 1
<?xml version="1.0" encoding="UTF-8"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/digital-signature"
skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/relationships"
skills/docx/scripts/office/schemas/mce/mc.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 2
<xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 3
attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 5
xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 7
<!-- This XSD is a modified version of the one found at: https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 9
https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 15
<w:document xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 16
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 17
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns:r="http://schemas.op - Network accessline 2
<!-- <xsd:import id="rel" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="orel.xsd"/> --> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<!-- <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartbasetypes.xsd"/> - Network accessline 5
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartsplineproperties.xsd"/> -->
skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" elementFormDefault="qualified" att - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 3
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" xmlns:w16="http://schemas.microsoft. - Network accessline 2
<xsd:import id="w16" namespace="http://schemas.microsoft.com/office/word/2018/wordml" schemaLocation="wml-2018.xsd"/> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<xsd:import id="s" namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/docx/scripts/office/soffice.py
- Executable scriptline 1
Executable file - Access to secretsline 25
[Credential-related source omitted] - Network accessline 44
def _needs_shim() -> bool: try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) - Network accessline 45
try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) s.close() - Network accessline 46
s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
skills/docx/scripts/office/unpack.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/validate.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/validators/__init__.py
- Executable scriptline 1
Executable file
skills/docx/scripts/office/validators/base.py
- Executable scriptline 1
Executable file - Network accessline 61
MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 62
XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace" - Network accessline 64
PACKAGE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 65
"http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 66
) OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 67
OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" ) - Network accessline 68
"http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 69
) CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 70
CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" ) - Network accessline 71
"http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 76
OOXML_NAMESPACES = { "http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 77
"http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 78
"http://schemas.openxmlformats.org/officeDocument/2006/relationships", - Network accessline 79
"http://schemas.openxmlformats.org/schemaLibrary/2006/main", - Network accessline 80
"http://schemas.openxmlformats.org/drawingml/2006/main", - Network accessline 81
"http://schemas.openxmlformats.org/drawingml/2006/chart", - Network accessline 82
"http://schemas.openxmlformats.org/drawingml/2006/chartDrawing", - Network accessline 83
"http://schemas.openxmlformats.org/drawingml/2006/diagram", - Network accessline 84
"http://schemas.openxmlformats.org/drawingml/2006/picture", - Network accessline 85
"http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing", - Network accessline 86
"http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", - Network accessline 87
"http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 88
"http://schemas.openxmlformats.org/presentationml/2006/main", - Network accessline 89
"http://schemas.openxmlformats.org/spreadsheetml/2006/main", - Network accessline 90
"http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes", - Network accessline 91
"http://www.w3.org/XML/1998/namespace",
skills/docx/scripts/office/validators/docx.py
- Executable scriptline 1
Executable file - Network accessline 18
WORD_2006_NAMESPACE = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 19
W14_NAMESPACE = "http://schemas.microsoft.com/office/word/2010/wordml" - Network accessline 20
W16CID_NAMESPACE = "http://schemas.microsoft.com/office/word/2016/wordml/cid"
skills/docx/scripts/office/validators/pptx.py
skills/docx/scripts/office/validators/redlining.py
- Executable scriptline 1
Executable file - Network accessline 17
self.author = author self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 18
self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" } - Network accessline 19
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/docx/scripts/templates/comments.xml
- Network accessline 1
<?xml version="1.0" ?> <w:comments xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/201 - Network accessline 2
<w:comments xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex" xmlns:cx
skills/docx/scripts/templates/commentsExtended.xml
- Network accessline 1
<?xml version="1.0" ?> <w15:commentsEx xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing - Network accessline 2
<w15:commentsEx xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex" xmln
skills/docx/scripts/templates/commentsExtensible.xml
- Network accessline 1
<?xml version="1.0" ?> <w16cex:commentsExtensible xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/off - Network accessline 2
<w16cex:commentsExtensible xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/ch
skills/docx/scripts/templates/commentsIds.xml
- Network accessline 1
<?xml version="1.0" ?> <w16cid:commentsIds xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/dra - Network accessline 2
<w16cid:commentsIds xmlns:wpc="http://schemas.microsoft.com/office/word/2010/wordprocessingCanvas" xmlns:cx="http://schemas.microsoft.com/office/drawing/2014/chartex" xmlns:cx1="http://schemas.microsoft.com/office/drawing/2015/9/8/chartex"
skills/docx/scripts/templates/people.xml
skills/drug-discovery-search/SKILL.md
- Network accessline 30
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 31
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 52
1. **Ask the user for their API key:** "To search drug discovery databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 53
"To search drug discovery databases, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Compound/Drug/Target Title", "url": "https://...", - Network accessline 79
"title": "Compound/Drug/Target Title", "url": "https://...", "content": "Full data including compounds, targets, mechanisms...", - Network accessline 80
"url": "https://...", - Network accessline 82
"source": "chembl|drugbank|drug-labels|open-targets", "relevance_score": 0.95, "images": ["https://example.com/structure.png"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/structure.png"] } - Network accessline 84
"images": ["https://example.com/structure.png"] - Network accessline 157
- Base URL: `https://api.valyu.ai/v1` - Network accessline 169
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 180
[Credential-related source omitted] - Network accessline 214
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/drug-discovery-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/drug-discovery-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/drug-interaction-checker/impl.py
- Executable scriptline 1
Executable file
skills/drug-labels-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search FDA drug labels, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search FDA drug labels, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Drug Label Title", "url": "https://fda.gov/...", - Network accessline 79
"title": "Drug Label Title", "url": "https://fda.gov/...", "content": "Label content, warnings, dosing...", - Network accessline 80
"url": "https://fda.gov/...", - Network accessline 82
"source": "drug-labels", "relevance_score": 0.95, "images": ["https://example.com/label.jpg"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/label.jpg"] } - Network accessline 84
"images": ["https://example.com/label.jpg"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/drug-labels-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/drug-labels-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/drug-photo/SKILL.md
- Network accessline 15
always: false emoji: "📸" homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: "📸" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 148
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 149
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels
skills/drugbank-database/references/chemical-analysis.md
- Network accessline 21
"""Extract chemical structure representations""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 23
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 73
"""Extract all calculated and experimental properties""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 75
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 218
"""Find structurally similar drugs in DrugBank""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 220
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 337
"""Find drugs containing a specific substructure""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 339
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 544
"""Export all chemical properties to CSV""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 546
ns = {'db': 'http://www.drugbank.ca'}
skills/drugbank-database/references/data-access.md
- Network accessline 146
# Query by DrugBank ID drug_id = "DB00001" url = f"https://go.drugbank.com/drugs/{drug_id}.json" - Network accessline 147
[Credential-related source omitted] - Network accessline 148
url = f"https://go.drugbank.com/drugs/{drug_id}.json" - Access to secretsline 149
[Credential-related source omitted] - Network accessline 151
response = requests.get(url, headers=headers)
skills/drugbank-database/references/drug-queries.md
- Network accessline 62
# Define namespace ns = {'db': 'http://www.drugbank.ca'} - Network accessline 63
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 77
"""Retrieve drug entry by DrugBank ID (e.g., 'DB00001')""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 79
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 97
"""Find drug by name (case-insensitive)""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 99
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 121
"""Find drug by CAS registry number""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 123
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 136
def extract_basic_info(drug): """Extract essential drug information""" ns = {'db': 'http://www.drugbank.ca'} - Network accessline 138
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 157
def extract_chemical_properties(drug): """Extract chemical structure and properties""" ns = {'db': 'http://www.drugbank.ca'} - Network accessline 159
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 195
def extract_pharmacology(drug): """Extract pharmacological information""" ns = {'db': 'http://www.drugbank.ca'} - Network accessline 197
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 217
def extract_external_identifiers(drug): """Extract cross-references to other databases""" ns = {'db': 'http://www.drugbank.ca'} - Network accessline 219
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 249
"""Build searchable dictionary of all drugs""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 251
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 281
"""Create pandas DataFrame of drug information""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 283
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 309
"""Get drugs of specific type""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 311
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 330
"""Search drugs by keyword in specific field""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 332
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 360
"""Build indexes for faster lookups""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 362
ns = {'db': 'http://www.drugbank.ca'}
skills/drugbank-database/references/interactions.md
- Network accessline 36
"""Get all interactions for a specific drug""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 38
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 68
"""Build complete interaction network (all drug pairs)""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 70
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 97
"""Rank drugs by number of known interactions""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 99
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 273
"""Export all interactions as edge list (CSV)""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 275
ns = {'db': 'http://www.drugbank.ca'}
skills/drugbank-database/references/targets-pathways.md
- Network accessline 74
"""Extract all targets for a drug""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 76
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 124
"""Get targets, enzymes, transporters, and carriers for a drug""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 126
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 168
"""Build matrix of drugs vs targets""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 170
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 207
"""Find all drugs that target a specific protein""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 209
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 272
"""Extract pathway information for a drug""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 274
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 315
"""Build network of pathways and drugs""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 317
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 350
root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 351
ns = {'db': 'http://www.drugbank.ca'} - Network accessline 482
"""Extract Gene Ontology terms for drug targets""" root = get_drugbank_root() ns = {'db': 'http://www.drugbank.ca'} - Network accessline 484
ns = {'db': 'http://www.drugbank.ca'}
skills/drugbank-database/scripts/drugbank_helper.py
skills/drugbank-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search DrugBank, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search DrugBank, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Drug Name", "url": "https://drugbank.com/...", - Network accessline 79
"title": "Drug Name", "url": "https://drugbank.com/...", "content": "Drug information, mechanism, interactions...", - Network accessline 80
"url": "https://drugbank.com/...", - Network accessline 82
"source": "drugbank", "relevance_score": 0.95, "images": ["https://example.com/structure.png"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/structure.png"] } - Network accessline 84
"images": ["https://example.com/structure.png"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/drugbank-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/drugbank-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/ehr-fhir-integration/README.md
- Network accessline 94
python fhir_client.py \ --server https://fhir.example.org/r4 \ - Network accessline 95
--server https://fhir.example.org/r4 \ - Network accessline 109
# Initialize FHIR client client = fhirpy.SyncFHIRClient( url='https://fhir.example.org/r4', - Network accessline 110
[Credential-related source omitted] - Network accessline 111
url='https://fhir.example.org/r4', - Access to secretsline 112
[Credential-related source omitted] - Network accessline 115
# Search for patients with diabetes conditions = client.resources('Condition').search( code='http://snomed.info/sct|44054006' # Type 2 Diabetes - Network accessline 116
conditions = client.resources('Condition').search( code='http://snomed.info/sct|44054006' # Type 2 Diabetes ).fetch_all() - Network accessline 117
code='http://snomed.info/sct|44054006' # Type 2 Diabetes - Network accessline 129
observations = client.resources('Observation').search( subject=f'Patient/{patient_id}', code='http://loinc.org|2339-0' # Glucose - Network accessline 130
subject=f'Patient/{patient_id}', code='http://loinc.org|2339-0' # Glucose ).fetch_all() - Network accessline 131
code='http://loinc.org|2339-0' # Glucose - Network accessline 157
settings = { 'app_id': 'my_app', 'api_base': 'https://fhir.example.org/r4', - Network accessline 158
'app_id': 'my_app', 'api_base': 'https://fhir.example.org/r4', 'redirect_uri': 'http://localhost:8080/callback', - Network accessline 159
'api_base': 'https://fhir.example.org/r4', - Network accessline 160
'redirect_uri': 'http://localhost:8080/callback', - Access to secretsline 209
[Credential-related source omitted] - Access to secretsline 210
[Credential-related source omitted] - Access to secretsline 274
[Credential-related source omitted] - Access to secretsline 275
[Credential-related source omitted] - Network accessline 282
for condition_code in conditions: conds = client.resources('Condition').search( code=f'http://snomed.info/sct|{condition_code}' - Network accessline 283
conds = client.resources('Condition').search( code=f'http://snomed.info/sct|{condition_code}' ).fetch_all() - Network accessline 284
code=f'http://snomed.info/sct|{condition_code}' - Network accessline 312
# Configure MCP server with FHIR endpoint mcp_server = FHIRMCPServer( fhir_base_url="https://fhir.example.org/r4", - Network accessline 313
[Credential-related source omitted] - Network accessline 314
fhir_base_url="https://fhir.example.org/r4", - Access to secretsline 315
[Credential-related source omitted] - Access to secretsline 341
[Credential-related source omitted] - Access to secretsline 342
[Credential-related source omitted] - Access to secretsline 416
[Credential-related source omitted] - Network accessline 424
response = requests.get( - Network accessline 433
# Poll until complete while True: status = requests.get(polling_url, headers=headers) - Network accessline 434
while True: status = requests.get(polling_url, headers=headers) if status.status_code == 200: - Network accessline 435
status = requests.get(polling_url, headers=headers) - Network accessline 443
# Usage files = initiate_bulk_export( "https://fhir.example.org/r4", - Network accessline 444
files = initiate_bulk_export( "https://fhir.example.org/r4", ["Patient", "Condition", "Observation", "MedicationRequest"] - Network accessline 445
"https://fhir.example.org/r4", - Network accessline 460
> **HL7 FHIR R4.** *Fast Healthcare Interoperability Resources.* http://hl7.org/fhir/R4/ - Network accessline 462
> **SMART on FHIR.** *OAuth2-based Authorization for FHIR.* https://docs.smarthealthit.org/ - Network accessline 523
- [HL7 FHIR](https://www.hl7.org/fhir/) - Network accessline 524
- [SMART on FHIR](https://docs.smarthealthit.org/) - Network accessline 525
- [fhir.resources](https://github.com/nazrulworld/fhir.resources) - Network accessline 526
- [FHIR MCP Server](https://github.com/wso2/fhir-mcp-server)
skills/ehr-fhir-integration/SKILL.md
skills/ehr-fhir-integration/fhir_client.py
- Executable scriptline 1
Executable file
skills/emergency-card/formats.md
- Network accessline 222
https://example.com/emergency/card?id=xxx
skills/ena-database/SKILL.md
- Network accessline 53
**ENA Portal API** - Advanced search functionality across all ENA data types - Documentation: https://www.ebi.ac.uk/ena/portal/api/doc - Network accessline 54
- Documentation: https://www.ebi.ac.uk/ena/portal/api/doc - Network accessline 57
**ENA Browser API** - Direct retrieval of records and metadata - Documentation: https://www.ebi.ac.uk/ena/browser/api/doc - Network accessline 58
- Documentation: https://www.ebi.ac.uk/ena/browser/api/doc - Network accessline 65
**ENA Cross Reference Service** - Access related records from external databases - Endpoint: https://www.ebi.ac.uk/ena/xref/rest/ - Network accessline 66
- Endpoint: https://www.ebi.ac.uk/ena/xref/rest/ - Network accessline 68
**CRAM Reference Registry** - Retrieve reference sequences - Endpoint: https://www.ebi.ac.uk/ena/cram/ - Network accessline 69
- Endpoint: https://www.ebi.ac.uk/ena/cram/ - Network accessline 91
# Search for samples from a specific study base_url = "https://www.ebi.ac.uk/ena/portal/api/search" - Network accessline 92
base_url = "https://www.ebi.ac.uk/ena/portal/api/search" - Network accessline 100
response = requests.get(base_url, params=params) - Network accessline 127
# Download run files using Browser API accession = "ERR123456" url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" - Network accessline 129
url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" - Network accessline 134
# Use Portal API to list samples study_id = "PRJNA123456" url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=sample&query=study_accession={study_id}&format=tsv" - Network accessline 136
url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=sample&query=study_accession={study_id}&format=tsv" - Network accessline 141
# Search assemblies by taxonomy organism = "Escherichia coli" url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=assembly&query=tax_tree({organism})&format=json" - Network accessline 143
url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=assembly&query=tax_tree({organism})&format=json" - Network accessline 148
# Query taxonomy API taxon_id = "562" # E. coli url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}" - Network accessline 150
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}"
skills/ena-database/references/api_reference.md
- Network accessline 7
**Base URL:** `https://www.ebi.ac.uk/ena/portal/api` - Network accessline 9
**Official Documentation:** https://www.ebi.ac.uk/ena/portal/api/doc - Network accessline 66
# Search for human samples url = "https://www.ebi.ac.uk/ena/portal/api/search" - Network accessline 67
url = "https://www.ebi.ac.uk/ena/portal/api/search" - Network accessline 73
"limit": 100 } response = requests.get(url, params=params) - Network accessline 75
response = requests.get(url, params=params) - Network accessline 81
"format": "tsv" } response = requests.get(url, params=params) - Network accessline 83
response = requests.get(url, params=params) - Network accessline 89
"format": "json" } response = requests.get(url, params=params) - Network accessline 91
response = requests.get(url, params=params) - Network accessline 112
# Get all available fields for samples url = "https://www.ebi.ac.uk/ena/portal/api/returnFields" - Network accessline 113
url = "https://www.ebi.ac.uk/ena/portal/api/returnFields" params = {"result": "sample"} response = requests.get(url, params=params) - Network accessline 114
params = {"result": "sample"} response = requests.get(url, params=params) fields = response.json() - Network accessline 115
response = requests.get(url, params=params) - Network accessline 130
url = "https://www.ebi.ac.uk/ena/portal/api/results" response = requests.get(url) - Network accessline 131
response = requests.get(url) - Network accessline 164
# Get FASTQ download URLs for a run url = "https://www.ebi.ac.uk/ena/portal/api/filereport" - Network accessline 165
url = "https://www.ebi.ac.uk/ena/portal/api/filereport" - Network accessline 170
"fields": "run_accession,fastq_ftp,fastq_md5,fastq_bytes" } response = requests.get(url, params=params) - Network accessline 171
} response = requests.get(url, params=params) file_info = response.json() - Network accessline 172
response = requests.get(url, params=params) - Network accessline 183
**Base URL:** `https://www.ebi.ac.uk/ena/browser/api` - Network accessline 185
**Official Documentation:** https://www.ebi.ac.uk/ena/browser/api/doc - Network accessline 206
# Get sample metadata in XML accession = "SAMEA123456" url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" - Network accessline 207
accession = "SAMEA123456" url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" response = requests.get(url) - Network accessline 208
url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}" response = requests.get(url) xml_data = response.text - Network accessline 209
response = requests.get(url) - Network accessline 212
# Get study with cross-references url = f"https://www.ebi.ac.uk/ena/browser/api/xml/PRJNA123456" - Network accessline 213
url = f"https://www.ebi.ac.uk/ena/browser/api/xml/PRJNA123456" params = {"includeLinks": "true"} response = requests.get(url, params=params) - Network accessline 215
response = requests.get(url, params=params) - Network accessline 238
# Get sequence in EMBL format url = "https://www.ebi.ac.uk/ena/browser/api/text/LN847353" response = requests.get(url) - Network accessline 239
url = "https://www.ebi.ac.uk/ena/browser/api/text/LN847353" response = requests.get(url) embl_format = response.text - Network accessline 240
response = requests.get(url) - Network accessline 264
# Get full sequence url = "https://www.ebi.ac.uk/ena/browser/api/fasta/LN847353" response = requests.get(url) - Network accessline 265
url = "https://www.ebi.ac.uk/ena/browser/api/fasta/LN847353" response = requests.get(url) fasta_data = response.text - Network accessline 266
response = requests.get(url) - Network accessline 269
# Get subsequence url = "https://www.ebi.ac.uk/ena/browser/api/fasta/LN847353" - Network accessline 270
url = "https://www.ebi.ac.uk/ena/browser/api/fasta/LN847353" params = {"range": "1000-2000"} response = requests.get(url, params=params) - Network accessline 272
response = requests.get(url, params=params) - Network accessline 294
# Get all links for a sample url = "https://www.ebi.ac.uk/ena/browser/api/links/sample/SAMEA123456" response = requests.get(url) - Network accessline 295
url = "https://www.ebi.ac.uk/ena/browser/api/links/sample/SAMEA123456" - Network accessline 296
response = requests.get(url) - Network accessline 301
**Base URL:** `https://www.ebi.ac.uk/ena/taxonomy/rest` - Network accessline 316
# Get E. coli taxonomy taxon_id = "562" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}" - Network accessline 317
taxon_id = "562" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}" response = requests.get(url) - Network accessline 318
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}" response = requests.get(url) taxonomy = response.json() - Network accessline 319
response = requests.get(url) - Network accessline 335
# Search by scientific name name = "Escherichia coli" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/{name}" - Network accessline 336
name = "Escherichia coli" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/{name}" response = requests.get(url) - Network accessline 337
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/{name}" - Network accessline 338
response = requests.get(url) - Network accessline 352
# Get suggestions partial = "Escheri" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/suggest-for-submission/{partial}" - Network accessline 353
partial = "Escheri" url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/suggest-for-submission/{partial}" response = requests.get(url) - Network accessline 354
url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/suggest-for-submission/{partial}" - Network accessline 355
response = requests.get(url) - Network accessline 360
**Base URL:** `https://www.ebi.ac.uk/ena/xref/rest` - Network accessline 382
# Get cross-references for an SRA accession url = "https://www.ebi.ac.uk/ena/xref/rest/json/sra/SRR000001" response = requests.get(url) - Network accessline 383
url = "https://www.ebi.ac.uk/ena/xref/rest/json/sra/SRR000001" response = requests.get(url) xrefs = response.json() - Network accessline 384
response = requests.get(url) - Network accessline 390
**Base URL:** `https://www.ebi.ac.uk/ena/cram` - Network accessline 405
# Get reference by MD5 md5 = "7c3f69f0c5f0f0de6d7c34e7c2e25f5c" url = f"https://www.ebi.ac.uk/ena/cram/md5/{md5}" - Network accessline 406
md5 = "7c3f69f0c5f0f0de6d7c34e7c2e25f5c" url = f"https://www.ebi.ac.uk/ena/cram/md5/{md5}" response = requests.get(url) - Network accessline 407
url = f"https://www.ebi.ac.uk/ena/cram/md5/{md5}" response = requests.get(url) reference_fasta = response.text - Network accessline 408
response = requests.get(url) - Network accessline 436
def create_session_with_retries(): """Create requests session with retry logic""" session = requests.Session() - Network accessline 437
"""Create requests session with retry logic""" session = requests.Session() retries = Retry( - Network accessline 438
session = requests.Session() - Network accessline 475
accessions = ["ERR001", "ERR002", "ERR003"] for acc in accessions: response = requests.get(f"{base_url}/xml/{acc}") - Network accessline 476
for acc in accessions: response = requests.get(f"{base_url}/xml/{acc}") # Process response - Network accessline 477
response = requests.get(f"{base_url}/xml/{acc}")
skills/ensembl-database/SKILL.md
- Network accessline 60
server = "https://rest.ensembl.org" - Network accessline 62
# Symbol lookup response = requests.get( - Network accessline 63
response = requests.get( - Network accessline 169
**Important:** Use `https://grch37.rest.ensembl.org` for GRCh37/hg19 queries and `https://rest.ensembl.org` for current assemblies. - Network accessline 204
def query_ensembl(endpoint, params=None, max_retries=3): server = "https://rest.ensembl.org" - Network accessline 205
server = "https://rest.ensembl.org" - Network accessline 208
for attempt in range(max_retries): response = requests.get( - Network accessline 209
response = requests.get( - Network accessline 301
- **Official Documentation:** https://rest.ensembl.org/documentation - Network accessline 302
- **Python Package Docs:** https://ensemblrest.readthedocs.io - Network accessline 303
- **EBI Training:** https://www.ebi.ac.uk/training/online/courses/ensembl-rest-api/ - Network accessline 304
- **Ensembl Browser:** https://useast.ensembl.org - Network accessline 305
- **GitHub Examples:** https://github.com/Ensembl/ensembl-rest/wiki
skills/ensembl-database/references/api_endpoints.md
skills/ensembl-database/scripts/ensembl_query.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 22
def __init__(self, server: str = "https://rest.ensembl.org", rate_limit: int = 15): - Network accessline 81
try: if method == "POST": response = requests.post(url, headers=headers, json=data) - Network accessline 82
if method == "POST": response = requests.post(url, headers=headers, json=data) else: - Network accessline 83
response = requests.post(url, headers=headers, json=data) - Network accessline 85
response = requests.get(url, headers=headers, params=params) - Network accessline 157
headers = {"Content-Type": "text/x-fasta"} url = f"{self.server}{endpoint}" response = requests.get(url, headers=headers, params=params) - Network accessline 158
url = f"{self.server}{endpoint}" response = requests.get(url, headers=headers, params=params) return response.text - Network accessline 159
response = requests.get(url, headers=headers, params=params) - Network accessline 184
headers = {"Content-Type": "text/x-fasta"} url = f"{self.server}{endpoint}" response = requests.get(url, headers=headers) - Network accessline 185
url = f"{self.server}{endpoint}" response = requests.get(url, headers=headers) return response.text - Network accessline 186
response = requests.get(url, headers=headers) - Network accessline 356
server = "https://rest.ensembl.org" - Network accessline 358
server = "https://grch37.rest.ensembl.org"
skills/epidemiologist-analyst/QUICK_REFERENCE.md
skills/epidemiologist-analyst/README.md
- Network accessline 189
- **CDC WONDER**: https://wonder.cdc.gov/ (National surveillance data) - Network accessline 190
- **WHO Disease Outbreak News**: https://www.who.int/emergencies/disease-outbreak-news - Network accessline 191
- **NCHS**: https://www.cdc.gov/nchs/ (Vital statistics, surveys) - Network accessline 196
- **CDC Field Epidemiology Manual**: https://www.cdc.gov/field-epi-manual/ (Comprehensive guide) - Network accessline 197
- **CDC Principles of Epidemiology**: https://www.cdc.gov/training/publichealth101/epidemiology.html (Free course) - Network accessline 198
- **Outbreak Toolkit**: https://outbreaktools.ca/ (Canadian resource, excellent methods) - Network accessline 202
- **APHA Epidemiology Section**: https://www.apha.org/apha-communities/member-sections/epidemiology - Network accessline 203
- **Society for Epidemiologic Research**: https://epiresearch.org/ - Network accessline 204
- **CSTE**: https://www.cste.org/ (Applied state/local epidemiologists) - Network accessline 208
- **MMWR**: https://www.cdc.gov/mmwr/ (Outbreak reports, rapid publication) - Network accessline 209
- **Emerging Infectious Diseases**: https://wwwnc.cdc.gov/eid/ (EID focus) - Network accessline 210
- **American Journal of Epidemiology**: https://academic.oup.com/aje
skills/epidemiologist-analyst/SKILL.md
- Network accessline 85
- [CDC Principles of Epidemiology](https://archive.cdc.gov/www_cdc_gov/csels/dsepd/ss1978/lesson1/section7.html) - Network accessline 86
- [WHO Outbreak Investigation Toolkit](https://www.who.int/emergencies/outbreak-toolkit/investigating-outbreak-of-unknown-disease) - Network accessline 121
- [Chronic Disease Epidemiology - CDC](https://www.cdc.gov/chronic-disease/) - Network accessline 122
- [WHO Chronic Diseases](https://www.who.int/health-topics/noncommunicable-diseases) - Network accessline 156
- [Bradford Hill Criteria - Wikipedia](https://en.wikipedia.org/wiki/Bradford_Hill_criteria) - Network accessline 157
- [Causal Inference - Modern Epidemiology](https://academic.oup.com/aje) - Network accessline 192
- [CDC Surveillance Systems](https://www.cdc.gov/surveillance/) - Network accessline 193
- [Wastewater-Based Epidemiology Framework 2025](https://www.sciencedirect.com/science/article/pii/S0048969725005248) - Network accessline 194
- [AI Integration in Epidemiological Modeling](https://www.nature.com/articles/s41467-024-55461-x) - Network accessline 229
- [Mathematical Models in Epidemiology - Springer](https://link.springer.com/book/10.1007/978-1-4939-9828-9) - Network accessline 230
- [Best Practice Disease Modeling](https://pubmed.ncbi.nlm.nih.gov/29734964/) - Network accessline 231
- [Epidemiological Modeling Framework](https://www.nature.com/articles/s41598-024-57488-y) - Network accessline 275
- [CDC Outbreak Investigation Steps](https://archive.cdc.gov/www_cdc_gov/csels/dsepd/ss1978/lesson6/section2.html) - Network accessline 276
- [WHO Outbreak Investigation Stages](https://www.who.int/emergencies/outbreak-toolkit/investigating-outbreak-of-unknown-disease) - Network accessline 277
- [CDC Field Epidemiology Manual](https://www.cdc.gov/field-epi-manual/) - Network accessline 317
- [CDC Designing Analytic Studies](https://www.cdc.gov/field-epi-manual/php/chapters/design-conduct-analyze-field-studies.html) - Network accessline 318
- [Case-Control Studies - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC1706071/) - Network accessline 319
- [Outbreak Analytic Studies](https://outbreaktools.ca/background/analytic-studies/) - Network accessline 361
- [Principles of Epidemiology - Lesson 3](https://archive.cdc.gov/www_cdc_gov/csels/dsepd/ss1978/lesson3/) - Network accessline 362
- [Measures of Disease Frequency](https://sphweb.bumc.bu.edu/otlt/mph-modules/ep/ep713_diseasefrequency/) - Network accessline 410
- [Screening Principles - CDC](https://www.cdc.gov/screening/) - Network accessline 411
- [WHO Screening Principles](https://www.who.int/news-room/questions-and-answers) - Network accessline 412
- [Diagnostic Test Accuracy](https://www.bmj.com/content/324/7338/669) - Network accessline 453
- [Epidemic Curves - CDC](https://archive.cdc.gov/www_cdc_gov/csels/dsepd/ss1978/lesson1/section6.html) - Network accessline 454
- [Outbreak Investigation - PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC7187955/) - Network accessline 497
- [CDC Surveillance Systems Overview](https://www.cdc.gov/surveillance/) - Network accessline 498
- [WHO Disease Surveillance](https://www.who.int/teams/epidemic-and-pandemic-prevention-and-preparedness/surveillance) - Network accessline 499
- [Global Infectious Disease Early Warning Models](https://pmc.ncbi.nlm.nih.gov/articles/PMC11731462/) - Network accessline 541
- [CDC Outbreak Investigation Steps](https://archive.cdc.gov/www_cdc_gov/csels/dsepd/ss1978/lesson6/section2.html) - Network accessline 542
- [CDC Field Epidemiology Manual - Outbreak Investigations](https://www.cdc.gov/field-epi-manual/) - Network accessline 582
- [CDC Analytic Studies Guide](https://www.cdc.gov/field-epi-manual/php/chapters/design-conduct-analyze-field-studies.html) - Network accessline 583
- [Case-Control Studies in Practice](https://pmc.ncbi.nlm.nih.gov/articles/PMC1706071/) - Network accessline 637
- [Best Practice Disease Modeling](https://pubmed.ncbi.nlm.nih.gov/29734964/) - Network accessline 638
- [AI Integration with Mechanistic Epidemiology](https://www.nature.com/articles/s41467-024-55461-x) - Network accessline 639
- [Institutional Outbreak Modeling](https://www.nature.com/articles/s41598-024-57488-y) - Network accessline 692
- [US Preventive Services Task Force](https://www.uspreventiveservicestaskforce.org/) - Network accessline 693
- [WHO Screening Principles](https://www.who.int/news-room/questions-and-answers) - Network accessline 694
- [CDC Screening Programs](https://www.cdc.gov/screening/) - Network accessline 1489
- Website: https://www.apha.org/apha-communities/member-sections/epidemiology - Network accessline 1495
- Website: https://epiresearch.org/ - Network accessline 1502
- Website: https://www.acepidemiology.org/ - Network accessline 1509
- Website: https://www.cste.org/ - Network accessline 1516
- Website: https://www.ieaweb.org/ - Network accessline 1538
- Timely outbreak reports, surveillance summaries, recommendations - Open access, rapid publication - Website: https://www.cdc.gov/mmwr/ - Network accessline 1540
- Website: https://www.cdc.gov/mmwr/ - Network accessline 1545
- Open access, peer-reviewed - Outbreak investigations, surveillance, trends - Website: https://wwwnc.cdc.gov/eid/ - Network accessline 1547
- Website: https://wwwnc.cdc.gov/eid/ - Network accessline 1565
- Website: https://www.cdc.gov/ - Network accessline 1566
- National surveillance systems (NNDSS, FoodNet, NHANES, BRFSS) - WONDER database: https://wonder.cdc.gov/ - Outbreak reports and investigations - Network accessline 1567
- WONDER database: https://wonder.cdc.gov/ - Network accessline 1572
- Website: https://www.who.int/ - Network accessline 1579
- Website: https://www.cdc.gov/nchs/ - Network accessline 1592
- Website: https://www.healthdata.org/research-analysis/gbd - Network accessline 1600
- Website: https://www.cdc.gov/training/publichealth101/epidemiology.html - Network accessline 1606
- Website: https://www.cdc.gov/field-epi-manual/ - Network accessline 1622
- Website: https://www.cste.org/general/custom.asp?page=Training
skills/equity-scorer/SKILL.md
skills/equity-scorer/api.py
- Executable scriptline 1
Executable file
skills/equity-scorer/equity_scorer.py
skills/equity-scorer/tests/test_equity_scorer.py
- Executable scriptline 1
Executable file
skills/esm/SKILL.md
- Network accessline 47
[Credential-related source omitted] - Network accessline 48
[Credential-related source omitted] - Network accessline 245
No additional dependencies needed. Obtain Forge API token at https://forge.evolutionaryscale.ai - Network accessline 289
- **GitHub Repository:** https://github.com/evolutionaryscale/esm - Network accessline 290
- **Forge Platform:** https://forge.evolutionaryscale.ai - Network accessline 291
- **Scientific Paper:** Hayes et al., Science (2025) - https://www.science.org/doi/10.1126/science.ads0018 - Network accessline 292
- **Blog Posts:** - ESM3 Release: https://www.evolutionaryscale.ai/blog/esm3-release - ESM C Launch: https://www.evolutionaryscale.ai/blog/esm-cambrian - Network accessline 293
- ESM3 Release: https://www.evolutionaryscale.ai/blog/esm3-release - Network accessline 294
- ESM C Launch: https://www.evolutionaryscale.ai/blog/esm-cambrian - Network accessline 295
- **Community:** Slack community at https://bit.ly/3FKwcWd - Network accessline 300
ESM is designed for beneficial applications in protein engineering, drug discovery, and scientific research. Follow the Responsible Biodesign Framework (https://responsiblebiodesign.ai/) when designing novel proteins. Consider biosafety and
skills/esm/references/esm-c-api.md
skills/esm/references/forge-api.md
- Network accessline 19
Sign up and get your API token at: https://forge.evolutionaryscale.ai - Network accessline 36
client = ESM3ForgeInferenceClient( model="esm3-medium-2024-08", url="https://forge.evolutionaryscale.ai", - Network accessline 37
[Credential-related source omitted] - Network accessline 38
url="https://forge.evolutionaryscale.ai", - Network accessline 78
client = ESM3ForgeInferenceClient( model="esm3-medium-2024-08", url="https://custom.forge.instance.com", - Network accessline 79
[Credential-related source omitted] - Network accessline 80
url="https://custom.forge.instance.com", - Network accessline 602
**More Information:** - AWS Marketplace: https://aws.amazon.com/marketplace/seller-profile?id=seller-iw2nbscescndm - Network accessline 603
- AWS Marketplace: https://aws.amazon.com/marketplace/seller-profile?id=seller-iw2nbscescndm - Network accessline 654
- **Forge Platform**: https://forge.evolutionaryscale.ai - Network accessline 655
- **API Documentation**: Check Forge dashboard for latest API specs - **Community Support**: Slack community at https://bit.ly/3FKwcWd - **Enterprise Contact**: Contact EvolutionaryScale for custom deployments - Network accessline 656
- **Community Support**: Slack community at https://bit.ly/3FKwcWd
skills/etetoolkit/SKILL.md
skills/etetoolkit/scripts/quick_visualize.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/etetoolkit/scripts/tree_operations.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/exploratory-data-analysis/references/chemistry_molecular_formats.md
- Network accessline 290
### .nc / .netcdf - Amber NetCDF Trajectory
skills/exploratory-data-analysis/references/general_scientific_formats.md
- Network accessline 376
### .nc / .netcdf - Network Common Data Form
skills/exploratory-data-analysis/scripts/eda_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/fda-database/SKILL.md
- Access to secretsline 41
[Credential-related source omitted] - Network accessline 61
Register at: https://open.fda.gov/apis/authentication/ - Access to secretsline 65
[Credential-related source omitted] - Access to secretsline 423
[Credential-related source omitted] - Network accessline 487
- **openFDA Homepage**: https://open.fda.gov/ - Network accessline 488
- **API Documentation**: https://open.fda.gov/apis/ - Network accessline 489
- **Interactive API Explorer**: https://open.fda.gov/apis/try-the-api/ - Network accessline 490
- **GitHub Repository**: https://github.com/FDA/openfda - Network accessline 491
- **Terms of Service**: https://open.fda.gov/terms/ - Network accessline 511
- **GitHub Issues**: https://github.com/FDA/openfda/issues
skills/fda-database/references/animal_veterinary.md
- Network accessline 13
**Endpoint**: `https://api.fda.gov/animalandveterinary/event.json` - Network accessline 93
[Credential-related source omitted] - Access to secretsline 93
[Credential-related source omitted] - Network accessline 94
url = "https://api.fda.gov/animalandveterinary/event.json" - Access to secretsline 98
[Credential-related source omitted] - Network accessline 103
response = requests.get(url, params=params) - Access to secretsline 110
[Credential-related source omitted] - Access to secretsline 119
[Credential-related source omitted] - Access to secretsline 128
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 156
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Network accessline 197
url = "https://api.fda.gov/animalandveterinary/event.json" - Access to secretsline 199
[Credential-related source omitted] - Network accessline 204
response = requests.get(url, params=params) - Access to secretsline 246
[Credential-related source omitted] - Access to secretsline 252
[Credential-related source omitted] - Network accessline 261
url = "https://api.fda.gov/animalandveterinary/event.json" - Access to secretsline 263
[Credential-related source omitted] - Network accessline 268
response = requests.get(url, params=params) - Access to secretsline 299
[Credential-related source omitted] - Access to secretsline 306
[Credential-related source omitted] - Network accessline 313
url = "https://api.fda.gov/animalandveterinary/event.json" - Access to secretsline 318
[Credential-related source omitted] - Network accessline 323
response = requests.get(url, params=params) - Network accessline 373
- OpenFDA Animal & Veterinary API: https://open.fda.gov/apis/animalandveterinary/ - Network accessline 374
- FDA Center for Veterinary Medicine: https://www.fda.gov/animal-veterinary - Network accessline 375
- VeDDRA: https://www.veddra.org/
skills/fda-database/references/api_basics.md
- Network accessline 11
https://api.fda.gov/{category}/{endpoint}.json - Network accessline 14
Examples: - `https://api.fda.gov/drug/event.json` - Network accessline 15
- `https://api.fda.gov/drug/event.json` - Network accessline 16
- `https://api.fda.gov/device/510k.json` - Network accessline 17
- `https://api.fda.gov/food/enforcement.json` - Network accessline 29
**Registration**: Visit https://open.fda.gov/apis/authentication/ to sign up - Network accessline 44
[Credential-related source omitted] - Access to secretsline 44
[Credential-related source omitted] - Network accessline 45
url = "https://api.fda.gov/drug/event.json" - Access to secretsline 48
[Credential-related source omitted] - Network accessline 53
response = requests.get(url, params=params) - Network accessline 60
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Network accessline 61
url = "https://api.fda.gov/drug/event.json" - Network accessline 68
[Credential-related source omitted] - Access to secretsline 68
[Credential-related source omitted] - Network accessline 84
response = requests.get(url, params=params) - Network accessline 104
for attempt in range(max_retries): try: response = requests.get(url, params=params) - Network accessline 105
try: response = requests.get(url, params=params) response.raise_for_status() - Network accessline 106
response = requests.get(url, params=params) - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 269
[Credential-related source omitted] - Access to secretsline 277
[Credential-related source omitted] - Network accessline 283
response = requests.get(url, params=params) - Network accessline 487
"""Safely call FDA API with comprehensive error handling.""" try: response = requests.get(url, params=params, timeout=30) - Network accessline 488
try: response = requests.get(url, params=params, timeout=30) response.raise_for_status() - Network accessline 489
response = requests.get(url, params=params, timeout=30) - Network accessline 582
# Make request response = requests.get(url, params=params) - Network accessline 583
response = requests.get(url, params=params) - Network accessline 610
# Remove requests older than 1 minute while self.requests and now - self.requests[0] > 60: self.requests.popleft() - Network accessline 612
self.requests.popleft() - Network accessline 617
if sleep_time > 0: time.sleep(sleep_time) self.requests.popleft() - Network accessline 619
self.requests.popleft() - Network accessline 621
self.requests.append(time.time()) - Network accessline 627
"""Make request with rate limiting.""" rate_limiter.wait_if_needed() return requests.get(url, params=params) - Network accessline 629
return requests.get(url, params=params) - Network accessline 668
"limit": 10 } results[drug] = requests.get(url, params=params).json() - Network accessline 670
results[drug] = requests.get(url, params=params).json() - Network accessline 675
- **openFDA Homepage**: https://open.fda.gov/ - Network accessline 676
- **API Documentation**: https://open.fda.gov/apis/ - Network accessline 677
- **Interactive API Explorer**: https://open.fda.gov/apis/try-the-api/ - Network accessline 678
- **Terms of Service**: https://open.fda.gov/terms/ - Network accessline 679
- **GitHub**: https://github.com/FDA/openfda - Network accessline 684
For questions or issues: - **GitHub Issues**: https://github.com/FDA/openfda/issues - Network accessline 685
- **GitHub Issues**: https://github.com/FDA/openfda/issues
skills/fda-database/references/devices.md
- Network accessline 21
**Endpoint**: `https://api.fda.gov/device/event.json` - Network accessline 53
[Credential-related source omitted] - Access to secretsline 53
[Credential-related source omitted] - Network accessline 54
url = "https://api.fda.gov/device/event.json" - Access to secretsline 58
[Credential-related source omitted] - Network accessline 63
response = requests.get(url, params=params) - Access to secretsline 70
[Credential-related source omitted] - Access to secretsline 79
[Credential-related source omitted] - Network accessline 88
**Endpoint**: `https://api.fda.gov/device/510k.json` - Access to secretsline 122
[Credential-related source omitted] - Network accessline 128
response = requests.get("https://api.fda.gov/device/510k.json", params=params) - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Network accessline 151
**Endpoint**: `https://api.fda.gov/device/classification.json` - Access to secretsline 184
[Credential-related source omitted] - Network accessline 189
response = requests.get("https://api.fda.gov/device/classification.json", params=params) - Access to secretsline 195
[Credential-related source omitted] - Access to secretsline 204
[Credential-related source omitted] - Network accessline 212
**Endpoint**: `https://api.fda.gov/device/enforcement.json` - Access to secretsline 243
[Credential-related source omitted] - Network accessline 249
response = requests.get("https://api.fda.gov/device/enforcement.json", params=params) - Access to secretsline 255
[Credential-related source omitted] - Network accessline 263
**Endpoint**: `https://api.fda.gov/device/recall.json` - Access to secretsline 290
[Credential-related source omitted] - Network accessline 295
response = requests.get("https://api.fda.gov/device/recall.json", params=params) - Network accessline 300
**Endpoint**: `https://api.fda.gov/device/pma.json` - Access to secretsline 332
[Credential-related source omitted] - Network accessline 337
response = requests.get("https://api.fda.gov/device/pma.json", params=params) - Access to secretsline 343
[Credential-related source omitted] - Network accessline 351
**Endpoint**: `https://api.fda.gov/device/registrationlisting.json` - Access to secretsline 385
[Credential-related source omitted] - Network accessline 390
response = requests.get("https://api.fda.gov/device/registrationlisting.json", params=params) - Access to secretsline 396
[Credential-related source omitted] - Network accessline 404
**Endpoint**: `https://api.fda.gov/device/udi.json` - Access to secretsline 446
[Credential-related source omitted] - Network accessline 451
response = requests.get("https://api.fda.gov/device/udi.json", params=params) - Access to secretsline 457
[Credential-related source omitted] - Access to secretsline 466
[Credential-related source omitted] - Network accessline 474
**Endpoint**: `https://api.fda.gov/device/covid19serology.json` - Access to secretsline 500
[Credential-related source omitted] - Network accessline 505
response = requests.get("https://api.fda.gov/device/covid19serology.json", params=params) - Access to secretsline 511
[Credential-related source omitted] - Access to secretsline 522
[Credential-related source omitted] - Access to secretsline 528
[Credential-related source omitted] - Network accessline 535
# Search adverse events events_url = "https://api.fda.gov/device/event.json" - Network accessline 536
events_url = "https://api.fda.gov/device/event.json" - Access to secretsline 538
[Credential-related source omitted] - Network accessline 540
"limit": 10 } results["adverse_events"] = requests.get(events_url, params=events_params).json() - Network accessline 542
results["adverse_events"] = requests.get(events_url, params=events_params).json() - Network accessline 544
# Search 510(k) clearances fiveten_url = "https://api.fda.gov/device/510k.json" - Network accessline 545
fiveten_url = "https://api.fda.gov/device/510k.json" - Access to secretsline 547
[Credential-related source omitted] - Network accessline 549
"limit": 10 } results["510k_clearances"] = requests.get(fiveten_url, params=fiveten_params).json() - Network accessline 551
results["510k_clearances"] = requests.get(fiveten_url, params=fiveten_params).json() - Network accessline 553
# Search recalls recall_url = "https://api.fda.gov/device/enforcement.json" - Network accessline 554
recall_url = "https://api.fda.gov/device/enforcement.json" - Access to secretsline 556
[Credential-related source omitted] - Network accessline 558
"limit": 10 } results["recalls"] = requests.get(recall_url, params=recall_params).json() - Network accessline 560
results["recalls"] = requests.get(recall_url, params=recall_params).json() - Network accessline 562
# Search UDI udi_url = "https://api.fda.gov/device/udi.json" - Network accessline 563
udi_url = "https://api.fda.gov/device/udi.json" - Access to secretsline 565
[Credential-related source omitted] - Network accessline 567
"limit": 10 } results["udi"] = requests.get(udi_url, params=udi_params).json() - Network accessline 569
results["udi"] = requests.get(udi_url, params=udi_params).json() - Access to secretsline 577
[Credential-related source omitted] - Access to secretsline 583
[Credential-related source omitted] - Network accessline 586
Classification details dictionary """ url = "https://api.fda.gov/device/classification.json" - Network accessline 587
""" url = "https://api.fda.gov/device/classification.json" params = { - Network accessline 588
url = "https://api.fda.gov/device/classification.json" - Access to secretsline 590
[Credential-related source omitted] - Network accessline 595
response = requests.get(url, params=params) - Network accessline 628
- OpenFDA Device API Documentation: https://open.fda.gov/apis/device/ - Network accessline 629
- Device Classification Database: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpcd/classification.cfm - Network accessline 630
- GUDID: https://accessgudid.nlm.nih.gov/
skills/fda-database/references/drugs.md
- Network accessline 13
**Endpoint**: `https://api.fda.gov/drug/event.json` - Network accessline 39
[Credential-related source omitted] - Access to secretsline 39
[Credential-related source omitted] - Network accessline 40
url = "https://api.fda.gov/drug/event.json" - Access to secretsline 44
[Credential-related source omitted] - Network accessline 49
response = requests.get(url, params=params) - Access to secretsline 56
[Credential-related source omitted] - Network accessline 64
**Endpoint**: `https://api.fda.gov/drug/label.json` - Access to secretsline 95
[Credential-related source omitted] - Network accessline 100
response = requests.get("https://api.fda.gov/drug/label.json", params=params) - Access to secretsline 113
[Credential-related source omitted] - Network accessline 121
**Endpoint**: `https://api.fda.gov/drug/ndc.json` - Access to secretsline 152
[Credential-related source omitted] - Network accessline 157
response = requests.get("https://api.fda.gov/drug/ndc.json", params=params) - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 172
[Credential-related source omitted] - Network accessline 180
**Endpoint**: `https://api.fda.gov/drug/enforcement.json` - Access to secretsline 215
[Credential-related source omitted] - Network accessline 221
response = requests.get("https://api.fda.gov/drug/enforcement.json", params=params) - Access to secretsline 227
[Credential-related source omitted] - Access to secretsline 236
[Credential-related source omitted] - Network accessline 244
**Endpoint**: `https://api.fda.gov/drug/drugsfda.json` - Access to secretsline 277
[Credential-related source omitted] - Network accessline 282
response = requests.get("https://api.fda.gov/drug/drugsfda.json", params=params) - Access to secretsline 288
[Credential-related source omitted] - Access to secretsline 297
[Credential-related source omitted] - Network accessline 305
**Endpoint**: `https://api.fda.gov/drug/drugshortages.json` - Access to secretsline 333
[Credential-related source omitted] - Network accessline 338
response = requests.get("https://api.fda.gov/drug/drugshortages.json", params=params) - Access to secretsline 344
[Credential-related source omitted] - Access to secretsline 353
[Credential-related source omitted] - Network accessline 371
Args: endpoint: Full URL endpoint (e.g., "https://api.fda.gov/drug/event.json") - Network accessline 372
endpoint: Full URL endpoint (e.g., "https://api.fda.gov/drug/event.json") - Network accessline 379
for attempt in range(max_retries): try: response = requests.get(endpoint, params=params, timeout=30) - Network accessline 380
try: response = requests.get(endpoint, params=params, timeout=30) response.raise_for_status() - Network accessline 381
response = requests.get(endpoint, params=params, timeout=30) - Access to secretsline 408
[Credential-related source omitted] - Access to secretsline 415
[Credential-related source omitted] - Access to secretsline 427
[Credential-related source omitted] - Network accessline 465
- OpenFDA Drug API Documentation: https://open.fda.gov/apis/drug/ - Network accessline 466
- API Basics: See `api_basics.md` in this references directory - Python examples: See `scripts/fda_drug_query.py` - Field reference guides: Available at https://open.fda.gov/apis/drug/[endpoint]/searchable-fields/ - Network accessline 468
- Field reference guides: Available at https://open.fda.gov/apis/drug/[endpoint]/searchable-fields/
skills/fda-database/references/foods.md
- Network accessline 13
**Endpoint**: `https://api.fda.gov/food/event.json` - Network accessline 54
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Network accessline 55
url = "https://api.fda.gov/food/event.json" - Access to secretsline 59
[Credential-related source omitted] - Network accessline 64
response = requests.get(url, params=params) - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 80
[Credential-related source omitted] - Access to secretsline 90
[Credential-related source omitted] - Network accessline 98
**Endpoint**: `https://api.fda.gov/food/enforcement.json` - Access to secretsline 146
[Credential-related source omitted] - Network accessline 152
response = requests.get("https://api.fda.gov/food/enforcement.json", params=params) - Access to secretsline 158
[Credential-related source omitted] - Access to secretsline 167
[Credential-related source omitted] - Access to secretsline 177
[Credential-related source omitted] - Access to secretsline 186
[Credential-related source omitted] - Access to secretsline 195
[Credential-related source omitted] - Access to secretsline 206
[Credential-related source omitted] - Access to secretsline 212
[Credential-related source omitted] - Network accessline 226
url = "https://api.fda.gov/food/enforcement.json" - Access to secretsline 231
[Credential-related source omitted] - Network accessline 236
response = requests.get(url, params=params) - Access to secretsline 250
[Credential-related source omitted] - Access to secretsline 256
[Credential-related source omitted] - Network accessline 264
url = "https://api.fda.gov/food/event.json" - Access to secretsline 266
[Credential-related source omitted] - Network accessline 271
response = requests.get(url, params=params) - Access to secretsline 304
[Credential-related source omitted] - Access to secretsline 310
[Credential-related source omitted] - Network accessline 319
url = "https://api.fda.gov/food/enforcement.json" - Access to secretsline 327
[Credential-related source omitted] - Network accessline 333
response = requests.get(url, params=params) - Network accessline 370
- OpenFDA Food API Documentation: https://open.fda.gov/apis/food/ - Network accessline 371
- CFSAN Adverse Event Reporting: https://www.fda.gov/food/compliance-enforcement-food/cfsan-adverse-event-reporting-system-caers - Network accessline 372
- Food Recalls: https://www.fda.gov/safety/recalls-market-withdrawals-safety-alerts
skills/fda-database/references/other.md
- Network accessline 13
**Endpoint**: `https://api.fda.gov/other/substance.json` - Network accessline 81
[Credential-related source omitted] - Access to secretsline 81
[Credential-related source omitted] - Network accessline 82
url = "https://api.fda.gov/other/substance.json" - Access to secretsline 86
[Credential-related source omitted] - Network accessline 91
response = requests.get(url, params=params) - Access to secretsline 98
[Credential-related source omitted] - Access to secretsline 107
[Credential-related source omitted] - Access to secretsline 116
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Network accessline 142
**Endpoint**: `https://api.fda.gov/other/nsde.json` - Access to secretsline 170
[Credential-related source omitted] - Network accessline 175
response = requests.get("https://api.fda.gov/other/nsde.json", params=params) - Access to secretsline 181
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 198
[Credential-related source omitted] - Network accessline 205
url = "https://api.fda.gov/other/substance.json" - Access to secretsline 207
[Credential-related source omitted] - Network accessline 212
response = requests.get(url, params=params) - Access to secretsline 256
[Credential-related source omitted] - Access to secretsline 262
[Credential-related source omitted] - Network accessline 269
url = "https://api.fda.gov/other/substance.json" - Access to secretsline 271
[Credential-related source omitted] - Network accessline 276
response = requests.get(url, params=params) - Access to secretsline 302
[Credential-related source omitted] - Access to secretsline 308
[Credential-related source omitted] - Network accessline 315
url = "https://api.fda.gov/other/substance.json" - Access to secretsline 317
[Credential-related source omitted] - Network accessline 322
response = requests.get(url, params=params) - Access to secretsline 351
[Credential-related source omitted] - Access to secretsline 357
[Credential-related source omitted] - Network accessline 364
# First search drug label database label_url = "https://api.fda.gov/drug/label.json" - Network accessline 365
label_url = "https://api.fda.gov/drug/label.json" - Access to secretsline 367
[Credential-related source omitted] - Network accessline 372
response = requests.get(label_url, params=label_params) - Access to secretsline 396
[Credential-related source omitted] - Network accessline 468
- FDA Substance Registration System: https://fdasis.nlm.nih.gov/srs/ - Network accessline 469
- UNII Search: https://precision.fda.gov/uniisearch - Network accessline 470
- OpenFDA Other APIs: https://open.fda.gov/apis/other/
skills/fda-database/scripts/fda_examples.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 299
[Credential-related source omitted] - Access to secretsline 301
[Credential-related source omitted] - Access to secretsline 302
[Credential-related source omitted] - Access to secretsline 304
[Credential-related source omitted] - Access to secretsline 307
[Credential-related source omitted]
skills/fda-database/scripts/fda_query.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 11
[Credential-related source omitted] - Network accessline 37
while self.requests and now - self.requests[0] > 60: self.requests.popleft() - Network accessline 38
self.requests.popleft() - Network accessline 44
print(f"Rate limit approaching. Waiting {sleep_time:.1f} seconds...") time.sleep(sleep_time) self.requests.popleft() - Network accessline 46
self.requests.popleft() - Network accessline 48
self.requests.append(time.time()) - Network accessline 87
BASE_URL = "https://api.fda.gov" - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Access to secretsline 100
[Credential-related source omitted] - Access to secretsline 121
[Credential-related source omitted] - Access to secretsline 122
[Credential-related source omitted] - Network accessline 134
try: response = requests.get(url, params=params, timeout=30) - Network accessline 135
response = requests.get(url, params=params, timeout=30) - Access to secretsline 408
[Credential-related source omitted] - Access to secretsline 411
[Credential-related source omitted]
skills/fhir-developer-skill/SKILL.md
- Network accessline 159
| System | URL | |--------|-----| | LOINC | `http://loinc.org` | - Network accessline 160
|--------|-----| | LOINC | `http://loinc.org` | | SNOMED CT | `http://snomed.info/sct` | - Network accessline 161
| LOINC | `http://loinc.org` | - Network accessline 162
| SNOMED CT | `http://snomed.info/sct` | - Network accessline 163
| RxNorm | `http://www.nlm.nih.gov/research/umls/rxnorm` | - Network accessline 164
| ICD-10 | `http://hl7.org/fhir/sid/icd-10` | - Network accessline 165
| v3-ActCode | `http://terminology.hl7.org/CodeSystem/v3-ActCode` | - Network accessline 166
| Observation Category | `http://terminology.hl7.org/CodeSystem/observation-category` | - Network accessline 167
| Condition Clinical | `http://terminology.hl7.org/CodeSystem/condition-clinical` | - Network accessline 168
| Condition Ver Status | `http://terminology.hl7.org/CodeSystem/condition-ver-status` | - Network accessline 187
{"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", "code": "AMB"} - Network accessline 192
{"coding": [{"system": "http://loinc.org", "code": "8480-6"}], "text": "Systolic BP"} - Network accessline 202
{"system": "http://hospital.example.org/mrn", "value": "12345"} - Network accessline 255
**If-None-Exist** (conditional create): - Client sends: `If-None-Exist: identifier=http://mrn|12345` - Network accessline 256
- Client sends: `If-None-Exist: identifier=http://mrn|12345`
skills/fhir-developer-skill/references/bundles.md
- Network accessline 42
"resourceType": "Observation", "status": "final", "code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]}, - Network accessline 43
"status": "final", "code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]}, "subject": {"reference": "urn:uuid:patient-1"} - Network accessline 44
"code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]}, - Network accessline 61
"entry": [ { "fullUrl": "https://fhir.example.org/Patient/123", - Network accessline 62
{ "fullUrl": "https://fhir.example.org/Patient/123", "response": { - Network accessline 63
"fullUrl": "https://fhir.example.org/Patient/123", - Network accessline 69
}, { "fullUrl": "https://fhir.example.org/Observation/456", - Network accessline 70
{ "fullUrl": "https://fhir.example.org/Observation/456", "response": { - Network accessline 71
"fullUrl": "https://fhir.example.org/Observation/456", - Network accessline 113
"resourceType": "Observation", "status": "final", "code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]} - Network accessline 114
"status": "final", "code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]} }, - Network accessline 115
"code": {"coding": [{"system": "http://loinc.org", "code": "8480-6"}]}
skills/fhir-developer-skill/references/pagination.md
- Network accessline 20
{ "relation": "self", "url": "https://fhir.example.org/Patient?name=Smith&_count=10" - Network accessline 21
"relation": "self", "url": "https://fhir.example.org/Patient?name=Smith&_count=10" }, - Network accessline 22
"url": "https://fhir.example.org/Patient?name=Smith&_count=10" - Network accessline 24
{ "relation": "next", "url": "https://fhir.example.org/Patient?name=Smith&_count=10&_offset=10" - Network accessline 25
"relation": "next", "url": "https://fhir.example.org/Patient?name=Smith&_count=10&_offset=10" } - Network accessline 26
"url": "https://fhir.example.org/Patient?name=Smith&_count=10&_offset=10" - Network accessline 29
"entry": [ { "fullUrl": "https://fhir.example.org/Patient/123", - Network accessline 30
{ "fullUrl": "https://fhir.example.org/Patient/123", "resource": { "resourceType": "Patient", "id": "123" }, - Network accessline 31
"fullUrl": "https://fhir.example.org/Patient/123",
skills/fhir-developer-skill/references/resource-examples.md
- Network accessline 22
"id": "example", "meta": {"versionId": "1", "lastUpdated": "2024-01-15T10:30:00Z"}, "identifier": [{"system": "http://hospital.example.org/mrn", "value": "12345"}], - Network accessline 23
"meta": {"versionId": "1", "lastUpdated": "2024-01-15T10:30:00Z"}, "identifier": [{"system": "http://hospital.example.org/mrn", "value": "12345"}], "name": [{"family": "Smith", "given": ["John"]}], - Network accessline 24
"identifier": [{"system": "http://hospital.example.org/mrn", "value": "12345"}], - Network accessline 37
"resourceType": "Observation", "status": "final", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "vital-signs"}]}], - Network accessline 38
"status": "final", "category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "vital-signs"}]}], "code": {"coding": [{"system": "http://loinc.org", "code": "8480-6", "display": "Systolic bl - Network accessline 39
"category": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": "vital-signs"}]}], - Network accessline 40
"code": {"coding": [{"system": "http://loinc.org", "code": "8480-6", "display": "Systolic blood pressure"}]}, - Network accessline 41
"subject": {"reference": "Patient/123"}, "effectiveDateTime": "2024-01-15T10:30:00Z", "valueQuantity": {"value": 120, "unit": "mmHg", "system": "http://unitsofmeasure.org", "code": "mm[Hg]"} - Network accessline 42
"effectiveDateTime": "2024-01-15T10:30:00Z", "valueQuantity": {"value": 120, "unit": "mmHg", "system": "http://unitsofmeasure.org", "code": "mm[Hg]"} } - Network accessline 43
"valueQuantity": {"value": 120, "unit": "mmHg", "system": "http://unitsofmeasure.org", "code": "mm[Hg]"} - Network accessline 55
"resourceType": "Encounter", "status": "in-progress", "class": {"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", "code": "AMB", "display": "ambulatory"}, - Network accessline 56
"status": "in-progress", "class": {"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", "code": "AMB", "display": "ambulatory"}, "subject": {"reference": "Patient/123"}, - Network accessline 57
"class": {"system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", "code": "AMB", "display": "ambulatory"}, - Network accessline 70
{ "resourceType": "Condition", "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "active"}]}, - Network accessline 71
"resourceType": "Condition", "clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "active"}]}, "verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/c - Network accessline 72
"clinicalStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": "active"}]}, - Network accessline 73
"verificationStatus": {"coding": [{"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": "confirmed"}]}, - Network accessline 74
"code": {"coding": [{"system": "http://snomed.info/sct", "code": "73211009", "display": "Diabetes mellitus"}]}, - Network accessline 88
"intent": "order", "medicationCodeableConcept": { "coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] - Network accessline 89
"medicationCodeableConcept": { "coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] }, - Network accessline 90
"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] - Network accessline 120
"id": "123", "code": { "coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] - Network accessline 121
"code": { "coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] }, - Network accessline 122
"coding": [{"system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": "1049502", "display": "Acetaminophen 325 MG"}] - Network accessline 123
}, "form": { "coding": [{"system": "http://snomed.info/sct", "code": "385055001", "display": "Tablet"}] - Network accessline 124
"form": { "coding": [{"system": "http://snomed.info/sct", "code": "385055001", "display": "Tablet"}] } - Network accessline 125
"coding": [{"system": "http://snomed.info/sct", "code": "385055001", "display": "Tablet"}] - Network accessline 174
"mode": "server", "security": { "service": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/restful-security-service", "code": "SMART-on-FHIR"}]}], - Network accessline 175
"security": { "service": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/restful-security-service", "code": "SMART-on-FHIR"}]}], "extension": [{ - Network accessline 176
"service": [{"coding": [{"system": "http://terminology.hl7.org/CodeSystem/restful-security-service", "code": "SMART-on-FHIR"}]}], - Network accessline 177
"extension": [{ "url": "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris", "extension": [ - Network accessline 178
"url": "http://fhir-registry.smarthealthit.org/StructureDefinition/oauth-uris", - Network accessline 179
"extension": [ {"url": "authorize", "valueUri": "https://auth.example.org/authorize"}, {"url": "token", "valueUri": "https://auth.example.org/token"} - Network accessline 180
{"url": "authorize", "valueUri": "https://auth.example.org/authorize"}, - Network accessline 181
{"url": "token", "valueUri": "https://auth.example.org/token"}
skills/fhir-developer-skill/references/smart-auth.md
- Network accessline 22
{ "authorization_endpoint": "https://auth.example.org/authorize", - Network accessline 23
"authorization_endpoint": "https://auth.example.org/authorize", - Network accessline 24
"token_endpoint": "https://auth.example.org/token", - Network accessline 85
1. EHR redirects to app with launch parameter: GET https://app.example.com/launch?iss=https://fhir.hospital.org&launch=abc123 - Network accessline 86
GET https://app.example.com/launch?iss=https://fhir.hospital.org&launch=abc123 - Network accessline 88
2. App discovers authorization endpoints: GET https://fhir.hospital.org/.well-known/smart-configuration - Network accessline 89
GET https://fhir.hospital.org/.well-known/smart-configuration - Network accessline 91
[Credential-related source omitted] - Network accessline 92
GET https://auth.hospital.org/authorize? - Network accessline 93
response_type=code& client_id=my-app& redirect_uri=https://app.example.com/callback& - Network accessline 94
client_id=my-app& redirect_uri=https://app.example.com/callback& scope=launch patient/Patient.rs patient/Observation.rs& - Network accessline 95
redirect_uri=https://app.example.com/callback& - Network accessline 96
scope=launch patient/Patient.rs patient/Observation.rs& state=xyz789& aud=https://fhir.hospital.org& - Network accessline 97
state=xyz789& aud=https://fhir.hospital.org& launch=abc123 - Network accessline 98
aud=https://fhir.hospital.org& - Network accessline 103
5. Authorization server redirects back: GET https://app.example.com/callback?code=auth_code_here&state=xyz789 - Network accessline 104
GET https://app.example.com/callback?code=auth_code_here&state=xyz789 - Network accessline 106
[Credential-related source omitted] - Network accessline 107
POST https://auth.hospital.org/token - Network accessline 110
grant_type=authorization_code& code=auth_code_here& redirect_uri=https://app.example.com/callback& - Network accessline 111
code=auth_code_here& redirect_uri=https://app.example.com/callback& client_id=my-app - Network accessline 112
redirect_uri=https://app.example.com/callback& - Access to secretsline 117
[Credential-related source omitted] - Network accessline 146
# 2. Exchange for access token response = requests.post(TOKEN_ENDPOINT, data={ - Network accessline 147
response = requests.post(TOKEN_ENDPOINT, data={ - Access to secretsline 153
[Credential-related source omitted] - Network accessline 155
[Credential-related source omitted] - Network accessline 157
patients = requests.get(f"{FHIR_BASE}/Patient", headers=headers)
skills/fhir-developer-skill/scripts/setup_fhir_project.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 56
value: float | None = None unit: str | None = None system: str | None = "http://unitsofmeasure.org" - Network accessline 57
unit: str | None = None system: str | None = "http://unitsofmeasure.org" code: str | None = None - Network accessline 58
system: str | None = "http://unitsofmeasure.org" - Network accessline 224
print(f" pip install -r requirements.txt") print(f" uvicorn app.main:app --reload") print(f"\nOpen http://localhost:8000/docs for API docs") - Network accessline 226
print(f"\nOpen http://localhost:8000/docs for API docs")
skills/fhir-development/coworker.py
- Executable scriptline 1
Executable file - Network accessline 17
Based on: https://www.anthropic.com/news/healthcare-life-sciences - Network accessline 98
"versionId": "1", "lastUpdated": datetime.utcnow().isoformat(), "profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"], - Network accessline 99
"lastUpdated": datetime.utcnow().isoformat(), "profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"], }, - Network accessline 100
"profile": [f"http://hl7.org/fhir/StructureDefinition/{resource_type}"], - Network accessline 117
"identifier": [ { "system": data.get("identifier_system", "http://hospital.example.org/patients"), - Network accessline 118
{ "system": data.get("identifier_system", "http://hospital.example.org/patients"), "value": data.get("identifier", ""), - Network accessline 119
"system": data.get("identifier_system", "http://hospital.example.org/patients"), - Network accessline 149
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/observation-category", - Network accessline 150
{ "system": "http://terminology.hl7.org/CodeSystem/observation-category", "code": data.get("category", "vital-signs"), - Network accessline 151
"system": "http://terminology.hl7.org/CodeSystem/observation-category", - Network accessline 158
"coding": [ { "system": data.get("code_system", "http://loinc.org"), - Network accessline 159
{ "system": data.get("code_system", "http://loinc.org"), "code": data.get("code", ""), - Network accessline 160
"system": data.get("code_system", "http://loinc.org"), - Network accessline 169
"value": data.get("value", 0), "unit": data.get("unit", ""), "system": "http://unitsofmeasure.org", - Network accessline 170
"unit": data.get("unit", ""), "system": "http://unitsofmeasure.org", "code": data.get("unit_code", ""), - Network accessline 171
"system": "http://unitsofmeasure.org", - Network accessline 179
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", - Network accessline 180
{ "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", "code": data.get("clinical_status", "active"), - Network accessline 181
"system": "http://terminology.hl7.org/CodeSystem/condition-clinical", - Network accessline 187
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", - Network accessline 188
{ "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", "code": data.get("verification_status", "confirmed"), - Network accessline 189
"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", - Network accessline 195
"coding": [ { "system": "http://snomed.info/sct", - Network accessline 196
{ "system": "http://snomed.info/sct", "code": data.get("snomed_code", ""), - Network accessline 197
"system": "http://snomed.info/sct", - Network accessline 212
"coding": [ { "system": "http://www.nlm.nih.gov/research/umls/rxnorm", - Network accessline 213
{ "system": "http://www.nlm.nih.gov/research/umls/rxnorm", "code": data.get("rxnorm_code", ""), - Network accessline 214
"system": "http://www.nlm.nih.gov/research/umls/rxnorm",
skills/find-skills/SKILL.md
- Network accessline 32
**Browse skills at:** https://skills.sh/ - Network accessline 63
vercel-labs/agent-skills@vercel-react-best-practices └ https://skills.sh/vercel-labs/agent-skills/vercel-react-best-practices - Network accessline 64
└ https://skills.sh/vercel-labs/agent-skills/vercel-react-best-practices - Network accessline 84
Learn more: https://skills.sh/vercel-labs/agent-skills/vercel-react-best-practices
skills/foldseek/SKILL.md
skills/galaxy-bridge/SKILL.md
- Access to secretsline 15
[Credential-related source omitted] - Network accessline 17
always: false emoji: "🌌" homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: "🌌" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Access to secretsline 104
[Credential-related source omitted] - Network accessline 188
**Optional (for execution):** - `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Network accessline 189
- `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Access to secretsline 190
[Credential-related source omitted] - Network accessline 212
- [Galaxy Project](https://galaxyproject.org/) — Afgan et al. (2018) Nucleic Acids Research - Network accessline 213
- [BioBlend](https://bioblend.readthedocs.io/) — Sloggett et al. (2013) Bioinformatics - Network accessline 214
- [usegalaxy.org](https://usegalaxy.org/) — Main Galaxy public server - Network accessline 215
- [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/) — Community tool repository
skills/galaxy-bridge/demo/reproducibility/commands.sh
- Executable scriptline 1
#!/usr/bin/env bash
skills/galaxy-bridge/galaxy_bridge.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 34
DEFAULT_GALAXY_URL = "https://usegalaxy.org" - Access to secretsline 118
[Credential-related source omitted] - Access to secretsline 119
[Credential-related source omitted] - Access to secretsline 121
[Credential-related source omitted] - Access to secretsline 122
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted]
skills/galaxy-bridge/galaxy_catalog.json
- Network accessline 2
"version": "1.0.0", "generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", - Network accessline 3
"generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", "generated_at": "2026-03-07T19:50:30.864391+00:00", - Network accessline 4
"galaxy_url": "https://usegalaxy.org",
skills/galaxy-bridge/generate_curated_skills.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/galaxy-bridge/generate_galaxy_catalog.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 9
Usage: python generate_galaxy_catalog.py # fetch from usegalaxy.org python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 11
python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 27
DEFAULT_URL = "https://usegalaxy.org" - Network accessline 38
api_url = f"{galaxy_url.rstrip('/')}/api/tools?in_panel=false" print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) - Network accessline 39
print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) resp.raise_for_status() - Network accessline 40
resp = requests.get(api_url, timeout=120)
skills/galaxy-bridge/tests/__init__.py
- Executable scriptline 1
Executable file
skills/galaxy-bridge/tests/test_galaxy_bridge.py
- Executable scriptline 1
Executable file - Network accessline 30
"version": "1.0.0", "generated_by": "test", "galaxy_url": "https://usegalaxy.org", - Network accessline 31
"generated_by": "test", "galaxy_url": "https://usegalaxy.org", "tool_count": 5, - Network accessline 32
"galaxy_url": "https://usegalaxy.org",
skills/galaxy-bridge/tests/test_tool_recommender.py
- Executable scriptline 1
Executable file
skills/galaxy-bridge/tool_recommender.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/gene-database/SKILL.md
skills/gene-database/references/api_reference.md
- Network accessline 21
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ - Access to secretsline 27
[Credential-related source omitted] - Network accessline 55
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=BRCA1[gene]+AND+human[organism]&retmode=json" - Network accessline 87
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=672&retmode=json" - Network accessline 129
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=672&retmode=xml" - Network accessline 155
# Get related PubMed articles curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=672&retmode=json" - Network accessline 156
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=672&retmode=json" - Network accessline 171
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gene&retmode=json" - Network accessline 183
https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene - Access to secretsline 191
[Credential-related source omitted] - Network accessline 203
curl "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/id/672" - Network accessline 262
curl "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/symbol/BRCA1/taxon/9606" - Network accessline 282
curl -X POST "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene/id" \ - Network accessline 293
1. Create an NCBI account at https://www.ncbi.nlm.nih.gov/account/ - Network accessline 401
- **E-utilities Documentation:** https://www.ncbi.nlm.nih.gov/books/NBK25501/ - Network accessline 402
- **Datasets API Documentation:** https://www.ncbi.nlm.nih.gov/datasets/docs/v2/ - Network accessline 403
- **Gene Database Help:** https://www.ncbi.nlm.nih.gov/gene/ - Network accessline 404
- **API Key Registration:** https://www.ncbi.nlm.nih.gov/account/
skills/gene-database/references/common_workflows.md
- Access to secretsline 47
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Network accessline 166
# Get HomoloGene links for a gene curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=homologene&id=7157&retmode=json" - Network accessline 167
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=homologene&id=7157&retmode=json" - Network accessline 208
# Search for pathway genes query = "MAPK signaling pathway[pathway] AND human[organism]" url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term={query}&retmode=json&retmax=200" - Network accessline 210
url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term={query}&retmode=json&retmax=200" - Network accessline 212
with urllib.request.urlopen(url) as response: - Network accessline 253
# Get ClinVar records for a gene curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=clinvar&id=672&retmode=json" - Network accessline 254
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=clinvar&id=672&retmode=json" - Network accessline 307
# Get all publications for BRCA1 curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=672&retmode=json" - Network accessline 308
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=672&retmode=json" - Network accessline 329
# Get publications for gene url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id={gene_id}&retmode=json" - Network accessline 330
url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id={gene_id}&retmode=json" - Network accessline 332
with urllib.request.urlopen(url) as response:
skills/gene-database/scripts/batch_gene_lookup.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 41
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Network accessline 53
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 72
[Credential-related source omitted] - Access to secretsline 73
[Credential-related source omitted] - Network accessline 77
try: with urllib.request.urlopen(url) as response: - Network accessline 78
with urllib.request.urlopen(url) as response: - Access to secretsline 96
[Credential-related source omitted] - Access to secretsline 103
[Credential-related source omitted] - Network accessline 109
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Access to secretsline 113
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 126
[Credential-related source omitted] - Network accessline 130
try: with urllib.request.urlopen(url) as response: - Network accessline 131
with urllib.request.urlopen(url) as response: - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 158
[Credential-related source omitted] - Access to secretsline 183
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 197
[Credential-related source omitted] - Access to secretsline 209
[Credential-related source omitted] - Access to secretsline 276
[Credential-related source omitted] - Access to secretsline 279
[Credential-related source omitted]
skills/gene-database/scripts/fetch_gene_data.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 17
DATASETS_API_BASE = "https://api.ncbi.nlm.nih.gov/datasets/v2alpha/gene" - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 70
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Network accessline 73
try: req = urllib.request.Request(url, headers=headers) - Network accessline 74
req = urllib.request.Request(url, headers=headers) - Network accessline 75
with urllib.request.urlopen(req) as response: - Access to secretsline 87
[Credential-related source omitted] - Access to secretsline 94
[Credential-related source omitted] - Access to secretsline 108
[Credential-related source omitted] - Access to secretsline 109
[Credential-related source omitted] - Network accessline 111
try: req = urllib.request.Request(url, headers=headers) - Network accessline 112
req = urllib.request.Request(url, headers=headers) - Network accessline 113
with urllib.request.urlopen(req) as response: - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Network accessline 145
try: req = urllib.request.Request(url, data=data, headers=headers, method='POST') - Network accessline 146
req = urllib.request.Request(url, data=data, headers=headers, method='POST') - Network accessline 147
with urllib.request.urlopen(req) as response: - Access to secretsline 260
[Credential-related source omitted] - Access to secretsline 262
[Credential-related source omitted] - Access to secretsline 264
[Credential-related source omitted]
skills/gene-database/scripts/query_gene.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 19
BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Access to secretsline 23
[Credential-related source omitted] - Access to secretsline 30
[Credential-related source omitted] - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Network accessline 47
try: with urllib.request.urlopen(url) as response: - Network accessline 48
with urllib.request.urlopen(url) as response: - Access to secretsline 65
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 82
[Credential-related source omitted] - Access to secretsline 83
[Credential-related source omitted] - Network accessline 87
try: with urllib.request.urlopen(url) as response: - Network accessline 88
with urllib.request.urlopen(url) as response: - Access to secretsline 99
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Access to secretsline 117
[Credential-related source omitted] - Access to secretsline 118
[Credential-related source omitted] - Network accessline 122
try: with urllib.request.urlopen(url) as response: - Network accessline 123
with urllib.request.urlopen(url) as response: - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 183
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 194
[Credential-related source omitted] - Access to secretsline 198
[Credential-related source omitted] - Access to secretsline 243
[Credential-related source omitted] - Access to secretsline 247
[Credential-related source omitted]
skills/geniml/SKILL.md
- Network accessline 29
uv uv pip install git+https://github.com/databio/geniml.git - Network accessline 286
- **Documentation**: https://docs.bedbase.org/geniml/ - Network accessline 287
- **GitHub**: https://github.com/databio/geniml - Network accessline 308
**"StarSpace not found" (BEDspace):** - Install StarSpace separately: https://github.com/facebookresearch/StarSpace - Network accessline 309
- Install StarSpace separately: https://github.com/facebookresearch/StarSpace
skills/geniml/references/bedspace.md
- Network accessline 127
BEDspace requires StarSpace to be installed separately. Download from: https://github.com/facebookresearch/StarSpace
skills/genome-compare/SKILL.md
- Network accessline 15
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 53
**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https://pgp.med.harvard.edu/). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data/geo
skills/genome-compare/__init__.py
- Executable scriptline 1
Executable file
skills/genome-compare/api.py
- Executable scriptline 1
Executable file
skills/genome-compare/data/manuel_ancestry.json
- Network accessline 2
"name": "Manuel Corpas", "pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", - Network accessline 3
"pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", "source": "23andMe Ancestry Composition", - Network accessline 4
"pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA",
skills/genome-compare/genome_compare.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 522
lines.append(f"**Reference**: George Church (PGP-1, hu43860C) ") if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 523
if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") else: - Network accessline 524
lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 643
lines.append( "**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " - Network accessline 644
"**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " "of genetics at Harvard Medical School and a pioneer of genomics. His 23an - Network accessline 645
"[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor "
skills/genome-compare/tests/test_genome_compare.py
- Executable scriptline 1
Executable file
skills/geo-database/SKILL.md
- Network accessline 395
**Using wget or curl for Downloads:** - Network accessline 398
# Download series matrix file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz - Network accessline 399
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz - Network accessline 401
# Download all supplementary files for a series wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/ - Network accessline 402
wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/ - Network accessline 404
# Download SOFT format family file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz - Network accessline 405
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz - Network accessline 670
# Optional: Set API key for increased rate limits # Get your API key from: https://www.ncbi.nlm.nih.gov/account/ - Network accessline 671
# Get your API key from: https://www.ncbi.nlm.nih.gov/account/ - Access to secretsline 672
[Credential-related source omitted] - Network accessline 722
- Web-based statistical analysis tool integrated into GEO - Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx - Network accessline 723
- Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx - Network accessline 736
- No rate limits for FTP downloads - Preferred method for bulk downloads - Can download entire directories with wget -r - Network accessline 738
- Can download entire directories with wget -r - Network accessline 802
- **GEO Website:** https://www.ncbi.nlm.nih.gov/geo/ - Network accessline 803
- **GEO Submission Guidelines:** https://www.ncbi.nlm.nih.gov/geo/info/submission.html - Network accessline 804
- **GEOparse Documentation:** https://geoparse.readthedocs.io/ - Network accessline 805
- **E-utilities Documentation:** https://www.ncbi.nlm.nih.gov/books/NBK25501/ - Network accessline 806
- **GEO FTP Site:** ftp://ftp.ncbi.nlm.nih.gov/geo/ - **GEO2R Tool:** https://www.ncbi.nlm.nih.gov/geo/geo2r/ - **NCBI API Keys:** https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ - Network accessline 807
- **GEO2R Tool:** https://www.ncbi.nlm.nih.gov/geo/geo2r/ - Network accessline 808
- **NCBI API Keys:** https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ - Network accessline 809
- **Biopython Tutorial:** https://biopython.org/DIST/docs/tutorial/Tutorial.html
skills/geo-database/references/geo_reference.md
- Network accessline 12
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ - Network accessline 23
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi - Network accessline 68
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi - Network accessline 108
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi - Network accessline 138
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi - Network accessline 173
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi - Network accessline 202
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi - Network accessline 293
!Database_name = Gene Expression Omnibus (GEO) !Database_institute = NCBI NLM NIH !Database_web_link = http://www.ncbi.nlm.nih.gov/geo - Network accessline 294
!Database_institute = NCBI NLM NIH !Database_web_link = http://www.ncbi.nlm.nih.gov/geo !Database_email = geo@ncbi.nlm.nih.gov - Network accessline 295
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo - Network accessline 433
<?xml version="1.0" encoding="UTF-8"?> <MINiML xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML" - Network accessline 434
<MINiML xmlns="http://www.ncbi.nlm.nih.gov/geo/info/MINiML" - Network accessline 435
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
skills/geopandas/references/data-io.md
- Network accessline 15
# Read from URL gdf = gpd.read_file("https://example.com/data.geojson") - Network accessline 16
gdf = gpd.read_file("https://example.com/data.geojson") - Network accessline 163
# HTTP/HTTPS gdf = gpd.read_file("https://example.com/data.geojson") - Network accessline 164
gdf = gpd.read_file("https://example.com/data.geojson")
skills/gget/SKILL.md
- Access to secretsline 649
[Credential-related source omitted] - Access to secretsline 655
[Credential-related source omitted] - Access to secretsline 660
[Credential-related source omitted] - Network accessline 862
For additional help: - Official documentation: https://pachterlab.github.io/gget/ - Network accessline 863
- Official documentation: https://pachterlab.github.io/gget/ - Network accessline 864
- GitHub issues: https://github.com/pachterlab/gget/issues - Network accessline 865
- Citation: Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
skills/gget/references/database_info.md
- Network accessline 20
- **Update frequency:** Regular releases (numbered); new releases approximately every 3 months - **Access:** FTP downloads, REST API - **Website:** https://www.ensembl.org/ - Network accessline 21
- **Access:** FTP downloads, REST API - **Website:** https://www.ensembl.org/ - **Notes:** - Network accessline 22
- **Website:** https://www.ensembl.org/ - Network accessline 31
- **Update frequency:** Regular updates with new assemblies - **Access:** Web service API - **Website:** https://genome.ucsc.edu/ - Network accessline 32
- **Access:** Web service API - **Website:** https://genome.ucsc.edu/ - **Notes:** - Network accessline 33
- **Website:** https://genome.ucsc.edu/ - Network accessline 43
- **Update frequency:** Regular releases (weekly for Swiss-Prot, monthly for TrEMBL) - **Access:** REST API - **Website:** https://www.uniprot.org/ - Network accessline 44
- **Access:** REST API - **Website:** https://www.uniprot.org/ - **Notes:** - Network accessline 45
- **Website:** https://www.uniprot.org/ - Network accessline 53
- **Update frequency:** Continuous updates - **Access:** E-utilities API - **Website:** https://www.ncbi.nlm.nih.gov/ - Network accessline 54
- **Access:** E-utilities API - **Website:** https://www.ncbi.nlm.nih.gov/ - **Databases:** Gene, Protein, RefSeq - Network accessline 55
- **Website:** https://www.ncbi.nlm.nih.gov/ - Network accessline 61
- **Update frequency:** Weekly updates - **Access:** REST API - **Website:** https://www.rcsb.org/ - Network accessline 62
- **Access:** REST API - **Website:** https://www.rcsb.org/ - **Notes:** - Network accessline 63
- **Website:** https://www.rcsb.org/ - Network accessline 71
- **Update frequency:** Periodic updates - **Access:** Downloaded database (via gget setup elm) - **Website:** http://elm.eu.org/ - Network accessline 72
- **Access:** Downloaded database (via gget setup elm) - **Website:** http://elm.eu.org/ - **Notes:** - Network accessline 73
- **Website:** http://elm.eu.org/ - **Notes:** - Requires local download before first use - Network accessline 97
- **Update frequency:** Periodic updates with new samples - **Access:** HTTP API - **Website:** https://maayanlab.cloud/archs4/ - Network accessline 98
- **Access:** HTTP API - **Website:** https://maayanlab.cloud/archs4/ - **Data:** - Network accessline 99
- **Website:** https://maayanlab.cloud/archs4/ - Network accessline 109
- **Update frequency:** Continuous additions of new datasets - **Access:** Census API (via cellxgene-census package) - **Website:** https://cellxgene.cziscience.com/ - Network accessline 110
- **Access:** Census API (via cellxgene-census package) - **Website:** https://cellxgene.cziscience.com/ - **Data:** - Network accessline 111
- **Website:** https://cellxgene.cziscience.com/ - Network accessline 124
- **Update frequency:** Regular releases - **Access:** REST API - **Website:** https://www.bgee.org/ - Network accessline 125
- **Access:** REST API - **Website:** https://www.bgee.org/ - **Data:** - Network accessline 126
- **Website:** https://www.bgee.org/ - Network accessline 137
- **Update frequency:** Regular updates to underlying databases - **Access:** REST API - **Website:** https://maayanlab.cloud/Enrichr/ - Network accessline 138
- **Access:** REST API - **Website:** https://maayanlab.cloud/Enrichr/ - **Databases included:** - Network accessline 139
- **Website:** https://maayanlab.cloud/Enrichr/ - Network accessline 155
- **Update frequency:** Regular releases (quarterly) - **Access:** GraphQL API - **Website:** https://www.opentargets.org/ - Network accessline 156
- **Access:** GraphQL API - **Website:** https://www.opentargets.org/ - **Data:** - Network accessline 157
- **Website:** https://www.opentargets.org/ - Network accessline 170
- **Update frequency:** Continuous addition of new studies - **Access:** Web API, downloadable datasets - **Website:** https://www.cbioportal.org/ - Network accessline 171
- **Access:** Web API, downloadable datasets - **Website:** https://www.cbioportal.org/ - **Data:** - Network accessline 172
- **Website:** https://www.cbioportal.org/ - Network accessline 184
- **Update frequency:** Regular releases - **Access:** Download (requires account and license for commercial use) - **Website:** https://cancer.sanger.ac.uk/cosmic - Network accessline 185
- **Access:** Download (requires account and license for commercial use) - **Website:** https://cancer.sanger.ac.uk/cosmic - **Data:** - Network accessline 186
- **Website:** https://cancer.sanger.ac.uk/cosmic - Network accessline 203
- **Model version:** Simplified version for local execution - **Access:** Local computation (requires model download via gget setup) - **Website:** https://alphafold.ebi.ac.uk/ - Network accessline 204
- **Access:** Local computation (requires model download via gget setup) - **Website:** https://alphafold.ebi.ac.uk/ - **Notes:** - Network accessline 205
- **Website:** https://alphafold.ebi.ac.uk/ - **Notes:** - Requires ~4GB model parameters download - Network accessline 215
- **Update frequency:** New models released periodically - **Access:** REST API (requires API key) - **Website:** https://openai.com/ - Network accessline 216
- **Access:** REST API (requires API key) - **Website:** https://openai.com/ - **Notes:** - Network accessline 217
- **Website:** https://openai.com/ - Network accessline 256
2. **Error handling:** - Database structure changes may cause temporary failures - Check GitHub issues: https://github.com/pachterlab/gget/issues - Network accessline 257
- Database structure changes may cause temporary failures - Check GitHub issues: https://github.com/pachterlab/gget/issues - Update gget if errors occur - Network accessline 258
- Check GitHub issues: https://github.com/pachterlab/gget/issues - Network accessline 297
**gget:** Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836 - Network accessline 298
Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836
skills/gget/references/module_reference.md
- Access to secretsline 437
[Credential-related source omitted]
skills/gget/scripts/batch_sequence_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/gget/scripts/enrichment_pipeline.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/gget/scripts/gene_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ginkgo-cloud-lab/SKILL.md
- Network accessline 10
Ginkgo Cloud Lab (https://cloud.ginkgo.bio) provides remote access to Ginkgo Bioworks' autonomous lab infrastructure. Protocols are executed on Reconfigurable Automation Carts (RACs) -- modular units with robotic arms, maglev sample transpo - Network accessline 39
1. Select a protocol at https://cloud.ginkgo.bio/protocols - Network accessline 49
Access Ginkgo Cloud Lab at https://cloud.ginkgo.bio. Account creation or institutional access may be required. Contact Ginkgo at cloud@ginkgo.bio for access questions.
skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md
- Network accessline 3
**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-optimization
skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md
- Network accessline 3
**URL:** https://cloud.ginkgo.bio/protocols/cell-free-protein-expression-validation
skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md
- Network accessline 3
**URL:** https://cloud.ginkgo.bio/protocols/fluorescent-pixel-art-generation
skills/glycoengineering/SKILL.md
- Possible obfuscationline 89
fc_sequence = "APELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK" - Network accessline 198
Web service for high-accuracy O-GalNAc site prediction: - **URL**: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/ - Network accessline 199
- **URL**: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/ - Network accessline 212
Note: This uses the DTU Health Tech web service. Results take ~1-5 min. """ url = "https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi" - Network accessline 213
""" url = "https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi" # NetOGlyc submission (parameters may vary with web service version) - Network accessline 214
url = "https://services.healthtech.dtu.dk/cgi-bin/webface2.cgi" - Network accessline 215
# NetOGlyc submission (parameters may vary with web service version) # Recommend using the web interface directly for most use cases print("Submit sequence at: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/") - Network accessline 216
# Recommend using the web interface directly for most use cases print("Submit sequence at: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/") return url - Network accessline 217
print("Submit sequence at: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/") - Network accessline 220
# Also: NetNGlyc for N-glycosylation prediction # URL: https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/ - Network accessline 221
# URL: https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/ - Network accessline 226
GlycoShield-MD analyzes how glycans shield protein surfaces during MD simulations: - **URL**: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/ - Network accessline 227
- **URL**: https://gitlab.mpcdf.mpg.de/dioscuri-biophysics/glycoshield-md/ - Network accessline 245
- **URL**: https://www.eurocarbdb.org/project/glycoworkbench - Network accessline 251
- **URL**: https://glyconnect.expasy.org/ - Network accessline 258
def query_glyconnect(uniprot_id: str) -> dict: """Query GlyConnect for glycosylation data for a protein.""" url = f"https://glyconnect.expasy.org/api/proteins/uniprot/{uniprot_id}" - Network accessline 259
"""Query GlyConnect for glycosylation data for a protein.""" url = f"https://glyconnect.expasy.org/api/proteins/uniprot/{uniprot_id}" response = requests.get(url, headers={"Accept": "application/json"}) - Network accessline 260
url = f"https://glyconnect.expasy.org/api/proteins/uniprot/{uniprot_id}" response = requests.get(url, headers={"Accept": "application/json"}) if response.status_code == 200: - Network accessline 261
response = requests.get(url, headers={"Accept": "application/json"}) - Network accessline 272
- **URL**: https://unicarbkb.org/ - Network accessline 332
- **GlyTouCan** (glycan structure repository): https://glytoucan.org/ - Network accessline 333
- **GlyConnect**: https://glyconnect.expasy.org/ - Network accessline 334
- **CFG Functional Glycomics**: http://www.functionalglycomics.org/ - Network accessline 335
- **DTU Health Tech servers** (NetNGlyc, NetOGlyc): https://services.healthtech.dtu.dk/ - Network accessline 336
- **GlycoWorkbench**: https://glycoworkbench.software.informer.com/
skills/glycoengineering/references/glycan_databases.md
- Network accessline 5
### GlyTouCan - **URL**: https://glytoucan.org/ - Network accessline 6
- **URL**: https://glytoucan.org/ - Network accessline 14
def lookup_glytoucan(glytoucan_id: str) -> dict: """Fetch glycan details from GlyTouCan.""" url = f"https://api.glytoucan.org/glycan/{glytoucan_id}" - Network accessline 15
"""Fetch glycan details from GlyTouCan.""" url = f"https://api.glytoucan.org/glycan/{glytoucan_id}" response = requests.get(url, headers={"Accept": "application/json"}) - Network accessline 16
url = f"https://api.glytoucan.org/glycan/{glytoucan_id}" response = requests.get(url, headers={"Accept": "application/json"}) return response.json() if response.ok else {} - Network accessline 17
response = requests.get(url, headers={"Accept": "application/json"}) - Network accessline 21
### GlyConnect - **URL**: https://glyconnect.expasy.org/ - Network accessline 22
- **URL**: https://glyconnect.expasy.org/ - Network accessline 30
def get_glycoprotein_info(uniprot_id: str) -> dict: """Get glycosylation data for a protein from GlyConnect.""" base_url = "https://glyconnect.expasy.org/api" - Network accessline 31
"""Get glycosylation data for a protein from GlyConnect.""" base_url = "https://glyconnect.expasy.org/api" response = requests.get(f"{base_url}/proteins/uniprot/{uniprot_id}") - Network accessline 32
base_url = "https://glyconnect.expasy.org/api" response = requests.get(f"{base_url}/proteins/uniprot/{uniprot_id}") return response.json() if response.ok else {} - Network accessline 33
response = requests.get(f"{base_url}/proteins/uniprot/{uniprot_id}") - Network accessline 36
def get_glycan_compositions(glyconnect_protein_id: int) -> list: """Get all glycan compositions for a GlyConnect protein entry.""" base_url = "https://glyconnect.expasy.org/api" - Network accessline 37
"""Get all glycan compositions for a GlyConnect protein entry.""" base_url = "https://glyconnect.expasy.org/api" response = requests.get(f"{base_url}/compositions/protein/{glyconnect_protein_id}") - Network accessline 38
base_url = "https://glyconnect.expasy.org/api" response = requests.get(f"{base_url}/compositions/protein/{glyconnect_protein_id}") return response.json().get("data", []) if response.ok else [] - Network accessline 39
response = requests.get(f"{base_url}/compositions/protein/{glyconnect_protein_id}") - Network accessline 43
### UniCarbKB - **URL**: https://unicarbkb.org/ - Network accessline 44
- **URL**: https://unicarbkb.org/ - Network accessline 48
### KEGG Glycan - **URL**: https://www.genome.jp/kegg/glycan/ - Network accessline 49
- **URL**: https://www.genome.jp/kegg/glycan/ - Network accessline 53
### CAZy (Carbohydrate-Active Enzymes) - **URL**: http://www.cazy.org/ - Network accessline 54
- **URL**: http://www.cazy.org/ - Network accessline 60
### NetNGlyc 1.0 - **URL**: https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/ - Network accessline 61
- **URL**: https://services.healthtech.dtu.dk/services/NetNGlyc-1.0/ - Network accessline 66
### NetOGlyc 4.0 - **URL**: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/ - Network accessline 67
- **URL**: https://services.healthtech.dtu.dk/services/NetOGlyc-4.0/ - Network accessline 91
### GlycoWorkbench - **URL**: https://www.eurocarbdb.org/project/glycoworkbench - Network accessline 92
- **URL**: https://www.eurocarbdb.org/project/glycoworkbench
skills/gnomad-database/SKILL.md
- Network accessline 15
**Key resources:** - gnomAD browser: https://gnomad.broadinstitute.org/ - Network accessline 16
- gnomAD browser: https://gnomad.broadinstitute.org/ - Network accessline 17
- GraphQL API: https://gnomad.broadinstitute.org/api - Network accessline 18
- Data downloads: https://gnomad.broadinstitute.org/downloads - Network accessline 19
- Documentation: https://gnomad.broadinstitute.org/help - Network accessline 36
gnomAD uses a GraphQL API accessible at `https://gnomad.broadinstitute.org/api`. Most queries fetch variants by gene or specific genomic position. - Network accessline 53
def query_gnomad_gene(gene_symbol, dataset="gnomad_r4", reference_genome="GRCh38"): """Fetch variants in a gene from gnomAD.""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 55
url = "https://gnomad.broadinstitute.org/api" - Network accessline 100
response = requests.post(url, json={"query": query, "variables": variables}) - Network accessline 122
def query_gnomad_variant(variant_id, dataset="gnomad_r4"): """Fetch details for a specific variant (e.g., '1-55516888-G-GA').""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 124
url = "https://gnomad.broadinstitute.org/api" - Network accessline 171
response = requests.post( - Network accessline 198
def query_gnomad_constraint(gene_symbol, reference_genome="GRCh38"): """Fetch constraint scores for a gene.""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 200
url = "https://gnomad.broadinstitute.org/api" - Network accessline 228
response = requests.post( - Network accessline 261
def get_population_frequencies(variant_id, dataset="gnomad_r4"): """Extract per-population allele frequencies for a variant.""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 263
url = "https://gnomad.broadinstitute.org/api" - Network accessline 282
response = requests.post( - Network accessline 315
def query_gnomad_sv(gene_symbol): """Query structural variants overlapping a gene.""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 317
url = "https://gnomad.broadinstitute.org/api" - Network accessline 336
response = requests.post(url, json={"query": query, "variables": {"gene_symbol": gene_symbol}}) - Network accessline 382
- **Browser**: https://gnomad.broadinstitute.org/ — interactive variant and gene browsing - Network accessline 383
- **GraphQL API**: https://gnomad.broadinstitute.org/api — programmatic access - Network accessline 384
- **Downloads**: https://gnomad.broadinstitute.org/downloads — VCF, Hail tables, constraint tables - Network accessline 389
- **gnomAD website**: https://gnomad.broadinstitute.org/ - Network accessline 390
- **gnomAD blog**: https://gnomad.broadinstitute.org/news - Network accessline 391
- **Downloads**: https://gnomad.broadinstitute.org/downloads - Network accessline 392
- **API explorer**: https://gnomad.broadinstitute.org/api (interactive GraphiQL) - Network accessline 393
- **Constraint documentation**: https://gnomad.broadinstitute.org/help/constraint - Network accessline 395
- **GitHub**: https://github.com/broadinstitute/gnomad-browser
skills/gnomad-database/references/graphql_queries.md
- Network accessline 6
POST https://gnomad.broadinstitute.org/api - Network accessline 191
def gnomad_query(query: str, variables: dict, retries: int = 3) -> dict: """Execute a gnomAD GraphQL query with retry logic.""" url = "https://gnomad.broadinstitute.org/api" - Network accessline 192
"""Execute a gnomAD GraphQL query with retry logic.""" url = "https://gnomad.broadinstitute.org/api" headers = {"Content-Type": "application/json"} - Network accessline 193
url = "https://gnomad.broadinstitute.org/api" - Network accessline 196
for attempt in range(retries): try: response = requests.post( - Network accessline 197
try: response = requests.post( url, - Network accessline 198
response = requests.post(
skills/gnomad-database/references/variant_interpretation.md
- Network accessline 67
Always check that gnomAD has adequate coverage at the variant position before concluding absence is meaningful. The gnomAD browser shows coverage tracks, and coverage data can be downloaded from: - https://gnomad.broadinstitute.org/download - Network accessline 68
- https://gnomad.broadinstitute.org/downloads#v4-coverage
skills/grief-companion/SKILL.md
- Broad permissionsline 1
Read, Edit, Write, Bash, Glob, Grep, WebFetch, WebSearch, Task, NotebookEdit - Network accessline 229
- National Suicide Prevention Lifeline: 988 - Crisis Text Line: Text HOME to 741741 - International Association for Suicide Prevention: https://www.iasp.info/resources/Crisis_Centres/ - Network accessline 231
- International Association for Suicide Prevention: https://www.iasp.info/resources/Crisis_Centres/
skills/gtex-database/SKILL.md
- Network accessline 15
**Key resources:** - GTEx Portal: https://gtexportal.org/ - Network accessline 16
- GTEx Portal: https://gtexportal.org/ - Network accessline 17
- GTEx API v2: https://gtexportal.org/api/v2/ - Network accessline 18
- Data downloads: https://gtexportal.org/home/downloads/adult-gtex/ - Network accessline 19
- Documentation: https://gtexportal.org/home/documentationPage - Network accessline 37
Base URL: `https://gtexportal.org/api/v2/` - Network accessline 44
BASE_URL = "https://gtexportal.org/api/v2" - Network accessline 47
"""Make a GET request to the GTEx API.""" url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 48
url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) response.raise_for_status() - Network accessline 49
response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 60
def get_gene_expression_by_tissue(gene_id_or_symbol, dataset_id="gtex_v10"): """Get median gene expression across all tissues.""" url = "https://gtexportal.org/api/v2/expression/medianGeneExpression" - Network accessline 61
"""Get median gene expression across all tissues.""" url = "https://gtexportal.org/api/v2/expression/medianGeneExpression" params = { - Network accessline 62
url = "https://gtexportal.org/api/v2/expression/medianGeneExpression" - Network accessline 66
"itemsPerPage": 100 } response = requests.get(url, params=params) - Network accessline 67
} response = requests.get(url, params=params) data = response.json() - Network accessline 68
response = requests.get(url, params=params) - Network accessline 92
def query_eqtl(gene_id, tissue_id=None, dataset_id="gtex_v10"): """Query significant eQTLs for a gene, optionally filtered by tissue.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" - Network accessline 93
"""Query significant eQTLs for a gene, optionally filtered by tissue.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" params = { - Network accessline 94
url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" - Network accessline 105
while True: params["page"] = page response = requests.get(url, params=params) - Network accessline 106
params["page"] = page response = requests.get(url, params=params) data = response.json() - Network accessline 107
response = requests.get(url, params=params) - Network accessline 132
def query_variant_eqtl(variant_id, tissue_id=None, dataset_id="gtex_v10"): """Get all eQTL associations for a specific variant.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" - Network accessline 133
"""Get all eQTL associations for a specific variant.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" params = { - Network accessline 134
url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" - Network accessline 143
response = requests.get(url, params=params) - Network accessline 155
def get_egenes(tissue_id, dataset_id="gtex_v10"): """Get all eGenes (genes with at least one significant eQTL) in a tissue.""" url = "https://gtexportal.org/api/v2/association/egene" - Network accessline 156
"""Get all eGenes (genes with at least one significant eQTL) in a tissue.""" url = "https://gtexportal.org/api/v2/association/egene" params = { - Network accessline 157
url = "https://gtexportal.org/api/v2/association/egene" - Network accessline 166
while True: params["page"] = page response = requests.get(url, params=params) - Network accessline 167
params["page"] = page response = requests.get(url, params=params) data = response.json() - Network accessline 168
response = requests.get(url, params=params) - Network accessline 189
def get_tissues(dataset_id="gtex_v10"): """Get all available tissues with metadata.""" url = "https://gtexportal.org/api/v2/dataset/tissueSiteDetail" - Network accessline 190
"""Get all available tissues with metadata.""" url = "https://gtexportal.org/api/v2/dataset/tissueSiteDetail" params = {"datasetId": dataset_id, "itemsPerPage": 100} - Network accessline 191
url = "https://gtexportal.org/api/v2/dataset/tissueSiteDetail" params = {"datasetId": dataset_id, "itemsPerPage": 100} response = requests.get(url, params=params) - Network accessline 192
params = {"datasetId": dataset_id, "itemsPerPage": 100} response = requests.get(url, params=params) return response.json()["data"] - Network accessline 193
response = requests.get(url, params=params) - Network accessline 208
def query_sqtl(gene_id, tissue_id=None, dataset_id="gtex_v10"): """Query significant sQTLs for a gene.""" url = "https://gtexportal.org/api/v2/association/singleTissueSqtl" - Network accessline 209
"""Query significant sQTLs for a gene.""" url = "https://gtexportal.org/api/v2/association/singleTissueSqtl" params = { - Network accessline 210
url = "https://gtexportal.org/api/v2/association/singleTissueSqtl" - Network accessline 219
response = requests.get(url, params=params) - Network accessline 237
def interpret_gwas_variant(variant_id, dataset_id="gtex_v10"): """Find all genes regulated by a GWAS variant.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" - Network accessline 238
"""Find all genes regulated by a GWAS variant.""" url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" params = {"variantId": variant_id, "datasetId": dataset_id, "itemsPerPage": 500} - Network accessline 239
url = "https://gtexportal.org/api/v2/association/singleTissueEqtl" params = {"variantId": variant_id, "datasetId": dataset_id, "itemsPerPage": 500} response = requests.get(url, params=params) - Network accessline 240
params = {"variantId": variant_id, "datasetId": dataset_id, "itemsPerPage": 500} response = requests.get(url, params=params) data = response.json() - Network accessline 241
response = requests.get(url, params=params) - Network accessline 302
# All significant eQTLs (v10) wget https://storage.googleapis.com/adult-gtex/bulk-qtl/v10/single-tissue-cis-qtl/GTEx_Analysis_v10_eQTL.tar - Network accessline 303
wget https://storage.googleapis.com/adult-gtex/bulk-qtl/v10/single-tissue-cis-qtl/GTEx_Analysis_v10_eQTL.tar - Network accessline 305
# Normalized expression matrices wget https://storage.googleapis.com/adult-gtex/bulk-gex/v10/rna-seq/GTEx_Analysis_v10_RNASeQCv2.4.2_gene_reads.gct.gz - Network accessline 306
wget https://storage.googleapis.com/adult-gtex/bulk-gex/v10/rna-seq/GTEx_Analysis_v10_RNASeQCv2.4.2_gene_reads.gct.gz - Network accessline 311
- **GTEx Portal**: https://gtexportal.org/ - Network accessline 312
- **API documentation**: https://gtexportal.org/api/v2/ - Network accessline 313
- **Data downloads**: https://gtexportal.org/home/downloads/adult-gtex/ - Network accessline 314
- **GitHub**: https://github.com/broadinstitute/gtex-pipeline
skills/gtex-database/references/api_reference.md
- Network accessline 6
https://gtexportal.org/api/v2/ - Network accessline 171
def safe_gtex_query(endpoint, params): url = f"https://gtexportal.org/api/v2/{endpoint}" - Network accessline 172
url = f"https://gtexportal.org/api/v2/{endpoint}" try: response = requests.get(url, params=params, timeout=30) - Network accessline 173
try: response = requests.get(url, params=params, timeout=30) response.raise_for_status() - Network accessline 174
response = requests.get(url, params=params, timeout=30)
skills/gwas-database/SKILL.md
- Network accessline 46
The web interface at https://www.ebi.ac.uk/gwas/ supports multiple search modes: - Network accessline 87
**Base URLs:** - GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api` - Network accessline 88
- GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api` - Network accessline 89
- Summary Statistics API: `https://www.ebi.ac.uk/gwas/summary-statistics/api` - Network accessline 91
**API Documentation:** - Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api - Network accessline 92
- Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api - Network accessline 93
- Summary stats docs: https://www.ebi.ac.uk/gwas/summary-statistics/docs/ - Network accessline 101
# Get a specific study url = "https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 102
url = "https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795" response = requests.get(url, headers={"Content-Type": "application/json"}) study = response.json() - Network accessline 103
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 109
# Find associations for a variant variant = "rs7903146" url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations" - Network accessline 110
variant = "rs7903146" url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} - Network accessline 111
url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 112
params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) associations = response.json() - Network accessline 113
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 119
# Get variant details url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7903146" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 120
url = "https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/rs7903146" response = requests.get(url, headers={"Content-Type": "application/json"}) variant_info = response.json() - Network accessline 121
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 127
# Get trait information url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 128
url = "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360" response = requests.get(url, headers={"Content-Type": "application/json"}) trait_info = response.json() - Network accessline 129
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 139
trait = "EFO_0001360" # Type 2 diabetes base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 140
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 142
# Query associations for this trait url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 143
url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"}) associations = response.json() - Network accessline 144
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 159
variant = "rs7903146" base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 160
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 162
# Get variant details url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 163
url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"}) variant_data = response.json() - Network accessline 164
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 168
url = f"{base_url}/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 169
params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) associations = response.json() - Network accessline 170
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 184
# Query summary statistics API base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 185
base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 193
"size": 100 # Number of results } response = requests.get(url, params=params) - Network accessline 194
} response = requests.get(url, params=params) results = response.json() - Network accessline 195
response = requests.get(url, params=params) - Network accessline 216
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 221
"bpEnd": end_pos } response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 222
} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) variants_in_region = response.json() - Network accessline 223
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 231
**Access Methods:** 1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ - Network accessline 232
1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ - Network accessline 247
# Get available summary statistics base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 248
base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" url = f"{base_url}/studies/GCST001234" response = requests.get(url) - Network accessline 249
url = f"{base_url}/studies/GCST001234" response = requests.get(url) study_info = response.json() - Network accessline 250
response = requests.get(url) - Network accessline 281
# API responses include _links for related resources response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234") - Network accessline 282
response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234") - Network accessline 285
# Follow link to associations associations_url = study['_links']['associations']['href'] associations_response = requests.get(associations_url) - Network accessline 287
associations_response = requests.get(associations_url) - Network accessline 300
url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{efo_id}/associations" - Network accessline 323
url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" - Network accessline 328
url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}/associations" - Network accessline 345
url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/search/findByGene" - Network accessline 403
# Via FTP wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz - Network accessline 404
wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz - Network accessline 409
url = f"https://www.ebi.ac.uk/gwas/summary-statistics/api/chromosomes/{chrom}/associations" - Network accessline 494
pandas DataFrame with association results """ base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 495
""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" url = f"{base_url}/efoTraits/{trait_id}/associations" - Network accessline 496
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 503
while True: params = {"page": page, "size": 100} response = requests.get(url, params=params, headers=headers) - Network accessline 505
response = requests.get(url, params=params, headers=headers) - Network accessline 561
The GWAS Catalog team provides workshop materials: - GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop - Network accessline 562
- GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop - Network accessline 595
- **GWAS Catalog website**: https://www.ebi.ac.uk/gwas/ - Network accessline 596
- **Documentation**: https://www.ebi.ac.uk/gwas/docs - Network accessline 597
- **API documentation**: https://www.ebi.ac.uk/gwas/rest/docs/api - Network accessline 598
- **Summary Statistics API**: https://www.ebi.ac.uk/gwas/summary-statistics/docs/ - Network accessline 599
- **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/ - Network accessline 600
- **Training materials**: https://github.com/EBISPOT/GWAS_Catalog-workshop - Network accessline 601
- **PGS Catalog** (polygenic scores): https://www.pgscatalog.org/
skills/gwas-database/references/api_reference.md
- Network accessline 28
GWAS Catalog API: https://www.ebi.ac.uk/gwas/rest/api - Network accessline 29
Summary Statistics API: https://www.ebi.ac.uk/gwas/summary-statistics/api - Network accessline 62
def query_with_rate_limit(url, delay=0.1): response = requests.get(url) - Network accessline 63
response = requests.get(url) - Network accessline 101
# Get a specific study url = "https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 102
url = "https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795" response = requests.get(url, headers={"Content-Type": "application/json"}) study = response.json() - Network accessline 103
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 151
# Find all associations for type 2 diabetes trait_id = "EFO_0001360" url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}/associations" - Network accessline 152
trait_id = "EFO_0001360" url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}/associations" params = {"size": 100, "page": 0} - Network accessline 153
url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}/associations" params = {"size": 100, "page": 0} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 154
params = {"size": 100, "page": 0} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) data = response.json() - Network accessline 155
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 196
# Get variant information rs_id = "rs7903146" url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" - Network accessline 197
rs_id = "rs7903146" url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 198
url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" response = requests.get(url, headers={"Content-Type": "application/json"}) variant = response.json() - Network accessline 199
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 234
# Get trait details trait_id = "EFO_0001360" url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}" - Network accessline 235
trait_id = "EFO_0001360" url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}" response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 236
url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{trait_id}" response = requests.get(url, headers={"Content-Type": "application/json"}) trait = response.json() - Network accessline 237
response = requests.get(url, headers={"Content-Type": "application/json"}) - Network accessline 269
def get_all_associations(trait_id): """Retrieve all associations for a trait with pagination""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 270
"""Retrieve all associations for a trait with pagination""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" url = f"{base_url}/efoTraits/{trait_id}/associations" - Network accessline 271
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 276
while True: params = {"page": page, "size": 100} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 278
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 302
# Get study and follow links to associations response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795") - Network accessline 303
response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001795") - Network accessline 306
# Follow link to associations associations_url = study['_links']['associations']['href'] associations_response = requests.get(associations_url) - Network accessline 307
associations_url = study['_links']['associations']['href'] associations_response = requests.get(associations_url) associations = associations_response.json() - Network accessline 308
associations_response = requests.get(associations_url) - Network accessline 318
https://www.ebi.ac.uk/gwas/summary-statistics/api - Network accessline 357
# Find highly significant associations for a trait trait_id = "EFO_0001360" base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 358
trait_id = "EFO_0001360" base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" url = f"{base_url}/traits/{trait_id}/associations" - Network accessline 359
base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 363
"size": 100 } response = requests.get(url, params=params) - Network accessline 364
} response = requests.get(url, params=params) results = response.json() - Network accessline 365
response = requests.get(url, params=params) - Network accessline 390
base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" - Network accessline 395
"size": 1000 } response = requests.get(url, params=params) - Network accessline 396
} response = requests.get(url, params=params) variants = response.json() - Network accessline 397
response = requests.get(url, params=params) - Network accessline 451
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/associations/12345" - Network accessline 452
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/associations/12345" } - Network accessline 453
"href": "https://www.ebi.ac.uk/gwas/rest/api/associations/12345" - Network accessline 459
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=0" - Network accessline 460
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=0" }, - Network accessline 461
"href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=0" - Network accessline 462
}, "next": { "href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=1" - Network accessline 463
"next": { "href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=1" } - Network accessline 464
"href": "https://www.ebi.ac.uk/gwas/rest/api/efoTraits/EFO_0001360/associations?page=1" - Network accessline 511
"""Make API request with error handling""" try: response = requests.get(url, params=params, timeout=30) - Network accessline 512
try: response = requests.get(url, params=params, timeout=30) response.raise_for_status() - Network accessline 513
response = requests.get(url, params=params, timeout=30) - Network accessline 538
def get_variant_pleiotropy(rs_id): """Get all traits associated with a variant""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 539
"""Get all traits associated with a variant""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" url = f"{base_url}/singleNucleotidePolymorphisms/{rs_id}/associations" - Network accessline 540
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 544
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 568
def get_significant_associations(trait_id, p_threshold=5e-8): """Get genome-wide significant associations""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 569
"""Get genome-wide significant associations""" base_url = "https://www.ebi.ac.uk/gwas/rest/api" url = f"{base_url}/efoTraits/{trait_id}/associations" - Network accessline 570
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 576
while True: params = {"page": page, "size": 100} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 578
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 604
def get_complete_variant_data(rs_id): """Get variant data from both APIs""" main_url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" - Network accessline 606
main_url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}" - Network accessline 608
# Get basic variant info response = requests.get(main_url, headers={"Content-Type": "application/json"}) - Network accessline 609
response = requests.get(main_url, headers={"Content-Type": "application/json"}) - Network accessline 612
# Get associations assoc_url = f"{main_url}/associations" response = requests.get(assoc_url, headers={"Content-Type": "application/json"}) - Network accessline 613
assoc_url = f"{main_url}/associations" response = requests.get(assoc_url, headers={"Content-Type": "application/json"}) associations = response.json() - Network accessline 614
response = requests.get(assoc_url, headers={"Content-Type": "application/json"}) - Network accessline 632
"""Query variants in genomic region""" # From main API base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 633
# From main API base_url = "https://www.ebi.ac.uk/gwas/rest/api" url = f"{base_url}/singleNucleotidePolymorphisms/search/findByChromBpLocationRange" - Network accessline 634
base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 643
response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) - Network accessline 646
# Can also query summary statistics API sumstats_url = f"https://www.ebi.ac.uk/gwas/summary-statistics/api/chromosomes/{chromosome}/associations" - Network accessline 647
sumstats_url = f"https://www.ebi.ac.uk/gwas/summary-statistics/api/chromosomes/{chromosome}/associations" - Network accessline 652
sumstats_response = requests.get(sumstats_url, params=sumstats_params) - Network accessline 670
class GWASCatalogQuery: def __init__(self): self.base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 671
def __init__(self): self.base_url = "https://www.ebi.ac.uk/gwas/rest/api" self.headers = {"Content-Type": "application/json"} - Network accessline 672
self.base_url = "https://www.ebi.ac.uk/gwas/rest/api" - Network accessline 681
while True: params = {"page": page, "size": 100} response = requests.get(url, params=params, headers=self.headers) - Network accessline 683
response = requests.get(url, params=params, headers=self.headers) - Network accessline 712
"""Get detailed variant information""" url = f"{self.base_url}/singleNucleotidePolymorphisms/{rs_id}" response = requests.get(url, headers=self.headers) - Network accessline 714
response = requests.get(url, headers=self.headers) - Network accessline 722
url = f"{self.base_url}/singleNucleotidePolymorphisms/search/findByGene" params = {"geneName": gene_name} response = requests.get(url, params=params, headers=self.headers) - Network accessline 724
response = requests.get(url, params=params, headers=self.headers) - Network accessline 759
"""Download summary statistics from FTP""" # FTP URL pattern ftp_base = "http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics" - Network accessline 761
ftp_base = "http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics" - Network accessline 768
try: response = requests.get(harmonised_url, stream=True) - Network accessline 769
response = requests.get(harmonised_url, stream=True) - Network accessline 789
- **Interactive API Documentation**: https://www.ebi.ac.uk/gwas/rest/docs/api - Network accessline 790
- **Summary Statistics API Docs**: https://www.ebi.ac.uk/gwas/summary-statistics/docs/ - Network accessline 791
- **Workshop Materials**: https://github.com/EBISPOT/GWAS_Catalog-workshop - Network accessline 792
- **Blog Post on API v2**: https://ebispot.github.io/gwas-blog/rest-api-v2-release/ - Network accessline 793
- **R Package (gwasrapidd)**: https://cran.r-project.org/package=gwasrapidd
skills/gwas-lookup/SKILL.md
- Network accessline 12
always: false emoji: "🔍" homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: "🔍" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 29
Inspired by [Sasha Gusev's GWAS Lookup](https://sashagusev.github.io/gwas_lookup/).
skills/gwas-lookup/api/__init__.py
- Executable scriptline 1
Executable file
skills/gwas-lookup/api/base_client.py
skills/gwas-lookup/api/ensembl.py
skills/gwas-lookup/api/eqtl_catalogue.py
skills/gwas-lookup/api/finngen.py
skills/gwas-lookup/api/gtex.py
skills/gwas-lookup/api/gwas_catalog.py
skills/gwas-lookup/api/open_targets.py
skills/gwas-lookup/api/pheweb_bbj.py
skills/gwas-lookup/api/pheweb_ukb.py
skills/gwas-lookup/api/portaldev.py
- Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 5
GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 15
BASE_URL = "https://portaldev.sph.umich.edu/api/v1"
skills/gwas-lookup/core/__init__.py
- Executable scriptline 1
Executable file
skills/gwas-lookup/core/normalise.py
- Executable scriptline 1
Executable file
skills/gwas-lookup/core/report.py
- Executable scriptline 1
Executable file - Network accessline 356
"version": "0.2.0", "apis": { "ensembl": "https://rest.ensembl.org", - Network accessline 357
"apis": { "ensembl": "https://rest.ensembl.org", "gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api", - Network accessline 358
"ensembl": "https://rest.ensembl.org", - Network accessline 359
"gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api", - Network accessline 360
"open_targets": "https://api.platform.opentargets.org/api/v4", - Network accessline 361
"pheweb_ukb": "https://pheweb.org/UKB-TOPMed", - Network accessline 362
"finngen": "https://r12.finngen.fi", - Network accessline 363
"pheweb_bbj": "https://pheweb.jp", - Network accessline 364
"gtex": "https://gtexportal.org/api/v2", - Network accessline 365
"eqtl_catalogue": "https://www.ebi.ac.uk/eqtl/api/v3", - Network accessline 366
"portaldev": "https://portaldev.sph.umich.edu/api/v1",
skills/gwas-lookup/core/resolve.py
- Executable scriptline 1
Executable file
skills/gwas-lookup/gwas_lookup.py
skills/gwas-lookup/tests/__init__.py
- Executable scriptline 1
Executable file
skills/gwas-lookup/tests/test_gwas_lookup.py
- Executable scriptline 1
Executable file
skills/gwas-prs/SKILL.md
- Network accessline 12
always: false emoji: "🎯" homepage: https://www.pgscatalog.org - Network accessline 13
emoji: "🎯" homepage: https://www.pgscatalog.org os: [macos, linux] - Network accessline 14
homepage: https://www.pgscatalog.org - Network accessline 45
2. **Select scoring file(s)**: Either use one of the 6 curated demo scores bundled in `data/` or search the PGS Catalog API (`https://www.pgscatalog.org/rest/`) for a trait-specific score. Curated scores available: - Network accessline 147
# Search by trait GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 148
GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 150
# Get scoring file metadata GET https://www.pgscatalog.org/rest/score/PGS000013 - Network accessline 151
GET https://www.pgscatalog.org/rest/score/PGS000013 - Network accessline 153
# Download harmonised scoring file GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz - Network accessline 154
GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz
skills/gwas-prs/api.py
- Executable scriptline 1
Executable file
skills/gwas-prs/gwas_prs.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 45
PGS_API_BASE = "https://www.pgscatalog.org/rest" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Network accessline 147
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 148
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 149
self.session = requests.Session() - Network accessline 308
URL pattern: https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 309
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 323
url = ( f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 324
f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 894
lines.append("") lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") - Network accessline 895
lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") lines.append("") - Network accessline 896
"(https://www.pgscatalog.org/)")
skills/gwas-prs/tests/fixtures/mock_score_metadata.json
- Network accessline 6
"variants_number": 8, "weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 7
"weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", "ftp_harmonized_scoring_files": { - Network accessline 8
"ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 9
"ftp_harmonized_scoring_files": { "GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 10
"GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" }, - Network accessline 11
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 12
}, "GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" - Network accessline 13
"GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" } - Network accessline 14
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz"
skills/gwas-prs/tests/fixtures/mock_scores_by_trait.json
- Network accessline 9
"variants_number": 8, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 10
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} } - Network accessline 11
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 18
"variants_number": 999999, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} - Network accessline 19
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} } - Network accessline 20
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"}
skills/gwas-prs/tests/test_gwas_prs.py
- Executable scriptline 1
Executable file
skills/health-trend-analyzer/templates/charts-config.js
- Executable scriptline 1
Executable file
skills/health-trend-analyzer/templates/report-template.html
- Network accessline 8
<!-- Tailwind CSS v3.4 --> <script src="https://cdn.tailwindcss.com"></script> - Network accessline 9
<script src="https://cdn.tailwindcss.com"></script> - Network accessline 11
<!-- Lucide Icons v0.263 --> <script src="https://unpkg.com/lucide@0.263.0/dist/umd/lucide.js"></script> - Network accessline 12
<script src="https://unpkg.com/lucide@0.263.0/dist/umd/lucide.js"></script> - Network accessline 14
<!-- ECharts v5.5 --> <script src="https://cdn.jsdelivr.net/npm/echarts@5.5.0/dist/echarts.min.js"></script> - Network accessline 15
<script src="https://cdn.jsdelivr.net/npm/echarts@5.5.0/dist/echarts.min.js"></script>
skills/hipaa-compliance/SKILL.md
- Network accessline 168
useEffect(() => { // Log view on mount (server-side preferred, but client backup) fetch('/api/audit/log', { - Network accessline 169
// Log view on mount (server-side preferred, but client backup) fetch('/api/audit/log', { method: 'POST', - Network accessline 170
fetch('/api/audit/log', {
skills/hmdb-database/SKILL.md
skills/hrv-alexithymia-expert/SKILL.md
- Broad permissionsline 1
Read,Write,Edit,Bash,mcp__firecrawl__firecrawl_search,WebFetch
skills/hypogenic/SKILL.md
- Network accessline 20
# Clone example datasets git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 21
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 131
# For HypoGeniC examples git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 132
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 134
# For HypoRefine/Union examples git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data - Network accessline 135
git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data - Network accessline 286
# Clone example datasets first # git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 287
# git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 312
# For literature-integrated approaches # git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data - Network accessline 313
# git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data - Network accessline 541
- **Paper:** https://arxiv.org/abs/2504.11524 - Network accessline 551
archivePrefix={arXiv}, primaryClass={cs.AI}, url={https://arxiv.org/abs/2504.11524}, - Network accessline 552
primaryClass={cs.AI}, url={https://arxiv.org/abs/2504.11524}, } - Network accessline 553
url={https://arxiv.org/abs/2504.11524}, - Network accessline 561
- **Paper:** https://arxiv.org/abs/2410.17309 - Network accessline 562
- **Code:** https://github.com/ChicagoHAI/hypothesis-generation - Network accessline 572
archivePrefix={arXiv}, primaryClass={cs.AI}, url={https://arxiv.org/abs/2410.17309}, - Network accessline 573
primaryClass={cs.AI}, url={https://arxiv.org/abs/2410.17309}, } - Network accessline 574
url={https://arxiv.org/abs/2410.17309}, - Network accessline 582
- **Paper:** https://aclanthology.org/2024.nlp4science-1.10/ - Network accessline 590
booktitle = {Proceedings of EMNLP Workshop of NLP for Science}, year={2024}, url={https://aclanthology.org/2024.nlp4science-1.10/}, - Network accessline 591
year={2024}, url={https://aclanthology.org/2024.nlp4science-1.10/}, } - Network accessline 592
url={https://aclanthology.org/2024.nlp4science-1.10/}, - Network accessline 600
- **GitHub Repository:** https://github.com/ChicagoHAI/hypothesis-generation - Network accessline 601
- **PyPI Package:** https://pypi.org/project/hypogenic/ - Network accessline 603
- **Issues & Support:** https://github.com/ChicagoHAI/hypothesis-generation/issues - Network accessline 610
# HypoGeniC examples (data-driven only) git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 611
git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data - Network accessline 613
# HypoRefine/Union examples (literature + data) git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data - Network accessline 614
git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
skills/hypogenic/references/config_template.yaml
- Access to secretsline 17
[Credential-related source omitted]
skills/hypothesis-generation/SKILL.md
- Broad permissionsline 1
Bash
skills/hypothesis-generation/references/literature_search_strategies.md
- Network accessline 45
**Example searches:** - `https://pubmed.ncbi.nlm.nih.gov/?term=wound+healing+diabetes+review` - Network accessline 46
- `https://pubmed.ncbi.nlm.nih.gov/?term=wound+healing+diabetes+review` - Network accessline 47
- `https://pubmed.ncbi.nlm.nih.gov/?term=gut+microbiome+cognition+systematic+review` - Network accessline 104
https://pubmed.ncbi.nlm.nih.gov/?term=(mechanism+OR+pathway)+AND+[phenomenon]+AND+(molecular+OR+cellular) - Network accessline 109
https://pubmed.ncbi.nlm.nih.gov/?term=[exposure]+AND+[outcome]+AND+(randomized+controlled+trial+OR+cohort+study) - Network accessline 114
https://pubmed.ncbi.nlm.nih.gov/?term=[biomarker]+AND+[disease]+AND+(association+OR+correlation+OR+prediction) - Network accessline 119
https://pubmed.ncbi.nlm.nih.gov/?term=[intervention]+AND+[condition]+AND+(efficacy+OR+effectiveness+OR+clinical+trial)
skills/imaging-data-commons/SKILL.md
- Network accessline 8
idc-index: "0.11.10" idc-data-version: "v23" repository: https://github.com/ImagingDataCommons/idc-claude-skill - Network accessline 9
idc-data-version: "v23" repository: https://github.com/ImagingDataCommons/idc-claude-skill --- - Network accessline 10
repository: https://github.com/ImagingDataCommons/idc-claude-skill - Network accessline 21
**Primary tool:** `idc-index` ([GitHub](https://github.com/imagingdatacommons/idc-index)) - Network accessline 122
**Complete index table documentation:** Use https://idc-index.readthedocs.io/en/latest/indices_reference.html for quick check of available tables and columns without executing any code. - Network accessline 543
**License types in IDC:** - **CC BY 4.0** / **CC BY 3.0** (~97% of data) - Allows commercial use with attribution - **CC BY-NC 4.0** / **CC BY-NC 3.0** (~3% of data) - Non-commercial use only - Network accessline 544
- **CC BY 4.0** / **CC BY 3.0** (~97% of data) - Allows commercial use with attribution - **CC BY-NC 4.0** / **CC BY-NC 3.0** (~3% of data) - Non-commercial use only - **Custom licenses** (rare) - Some collections have specific terms (e.g., - Network accessline 545
- **CC BY-NC 4.0** / **CC BY-NC 3.0** (~3% of data) - Non-commercial use only - Network accessline 645
**Before using BigQuery**, always check if a specialized index table already has the metadata you need: 1. Use `client.indices_overview` or the [idc-index indices reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html) - Network accessline 646
1. Use `client.indices_overview` or the [idc-index indices reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html) to discover all available tables and their columns 2. Fetch the relevant index: `client.fetch_index("ta - Network accessline 655
|------|------|-----------| | Programmatic queries & downloads | `idc-index` | This document | | Interactive exploration | IDC Portal | https://portal.imaging.datacommons.cancer.gov/ | - Network accessline 656
| Programmatic queries & downloads | `idc-index` | This document | | Interactive exploration | IDC Portal | https://portal.imaging.datacommons.cancer.gov/ | | Complex metadata queries | BigQuery | `references/bigquery_guide.md` | - Network accessline 657
| Interactive exploration | IDC Portal | https://portal.imaging.datacommons.cancer.gov/ | - Network accessline 659
| 3D visualization & analysis | SlicerIDCBrowser | https://github.com/ImagingDataCommons/SlicerIDCBrowser | - Network accessline 744
- **Estimate size first** - Check collection size before downloading - some collection sizes are in terabytes! - **Save manifests** - Always save query results with Series UIDs for reproducibility and data provenance - **Read documentation* - Network accessline 745
- **Save manifests** - Always save query results with Series UIDs for reproducibility and data provenance - **Read documentation** - IDC data structure and metadata fields are documented at https://learn.canceridc.dev/ - **Use IDC forum** - - Network accessline 746
- **Read documentation** - IDC data structure and metadata fields are documented at https://learn.canceridc.dev/ - Network accessline 747
- **Use IDC forum** - Search for questons/answers and ask your questions to the IDC maintainers and users at https://discourse.canceridc.dev/ - Network accessline 828
- **[indices_reference](https://idc-index.readthedocs.io/en/latest/indices_reference.html)** - External documentation for index tables (may be ahead of the installed version) - Network accessline 832
- **IDC Portal**: https://portal.imaging.datacommons.cancer.gov/explore/ - Network accessline 833
- **Documentation**: https://learn.canceridc.dev/ - Network accessline 834
- **Tutorials**: https://github.com/ImagingDataCommons/IDC-Tutorials - Network accessline 835
- **User Forum**: https://discourse.canceridc.dev/ - Network accessline 836
- **idc-index GitHub**: https://github.com/ImagingDataCommons/idc-index - Network accessline 837
- **Citation**: Fedorov, A., et al. "National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence." RadioGraphics 43.12 (2023). https://doi.org/10.1148/rg.230180 - Network accessline 841
This skill version is available in skill metadata. To check for updates: - Visit the [releases page](https://github.com/ImagingDataCommons/idc-claude-skill/releases) - Network accessline 842
- Visit the [releases page](https://github.com/ImagingDataCommons/idc-claude-skill/releases)
skills/imaging-data-commons/references/bigquery_guide.md
- Network accessline 48
### dicom_all Primary table joining complete DICOM metadata with IDC-specific columns (collection_id, gcs_url, license). Contains all DICOM tags from `dicom_metadata` plus collection and administrative metadata. See [dicom_all.sql](https:// - Network accessline 49
Primary table joining complete DICOM metadata with IDC-specific columns (collection_id, gcs_url, license). Contains all DICOM tags from `dicom_metadata` plus collection and administrative metadata. See [dicom_all.sql](https://github.com/Ima - Network accessline 333
- IDC data is de-identified; private tags containing PHI may have been removed or modified - The same tag may have different meanings across software versions - Always verify query results visually using the [IDC Viewer](https://viewer.imag - Network accessline 335
- Always verify query results visually using the [IDC Viewer](https://viewer.imaging.datacommons.cancer.gov/) before large-scale analysis - Network accessline 339
**Manufacturer DICOM Conformance Statements:** - [GE Healthcare MR](https://www.gehealthcare.com/products/interoperability/dicom/magnetic-resonance-imaging-dicom-conformance-statements) - Network accessline 340
- [GE Healthcare MR](https://www.gehealthcare.com/products/interoperability/dicom/magnetic-resonance-imaging-dicom-conformance-statements) - Network accessline 341
- [Siemens MR](https://www.siemens-healthineers.com/services/it-standards/dicom-conformance-statements-magnetic-resonance) - Network accessline 342
- [Siemens CT](https://www.siemens-healthineers.com/services/it-standards/dicom-conformance-statements-computed-tomography) - Network accessline 344
**DICOM Standard:** - [Part 5 Section 7.8 - Private Data Elements](https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.8.html) - Network accessline 345
- [Part 5 Section 7.8 - Private Data Elements](https://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.8.html) - Network accessline 346
- [Part 15 Appendix E - De-identification Profiles](https://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_e.html) - Network accessline 348
**Community Resources:** - [NAMIC Wiki: DWI/DTI DICOM](https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI) - comprehensive vendor comparison for diffusion imaging - Network accessline 349
- [NAMIC Wiki: DWI/DTI DICOM](https://www.na-mic.org/wiki/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI) - comprehensive vendor comparison for diffusion imaging - Network accessline 350
- [StandardizeBValue](https://github.com/nslay/StandardizeBValue) - tool to extract vendor b-values to standard tags - Network accessline 553
- [Understanding the BigQuery DICOM schema](https://docs.cloud.google.com/healthcare-api/docs/how-tos/dicom-bigquery-schema) - Network accessline 554
- [BigQuery Query Syntax](https://docs.cloud.google.com/bigquery/docs/reference/standard-sql/query-syntax) - Network accessline 555
- [Kaggle Intro to SQL](https://www.kaggle.com/learn/intro-to-sql) - Network accessline 556
- [Sample BigQuery queries of IDC data](https://github.com/ImagingDataCommons/idc-bigquery-cookbook)
skills/imaging-data-commons/references/cli_guide.md
skills/imaging-data-commons/references/clinical_data_guide.md
- Network accessline 312
**IDC Documentation:** - [Clinical data organization](https://learn.canceridc.dev/data/organization-of-data/clinical) - How clinical data is organized in IDC - Network accessline 313
- [Clinical data organization](https://learn.canceridc.dev/data/organization-of-data/clinical) - How clinical data is organized in IDC - Network accessline 314
- [Clinical data dashboard](https://datastudio.google.com/u/0/reporting/04cf5976-4ea0-4fee-a749-8bfd162f2e87/page/p_s7mk6eybqc) - Visual summary of available clinical data - Network accessline 315
- [idc-index clinical_index documentation](https://idc-index.readthedocs.io/en/latest/column_descriptions.html#clinical-index) - Network accessline 321
**IDC Tutorials:** - [clinical_data_intro.ipynb](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/clinical_data_intro.ipynb) - Network accessline 322
- [clinical_data_intro.ipynb](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/advanced_topics/clinical_data_intro.ipynb) - Network accessline 323
- [exploring_clinical_data.ipynb](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/getting_started/exploring_clinical_data.ipynb) - Network accessline 324
- [nlst_clinical_data.ipynb](https://github.com/ImagingDataCommons/IDC-Tutorials/blob/master/notebooks/collections_demos/nlst_clinical_data.ipynb)
skills/imaging-data-commons/references/cloud_storage_guide.md
- Network accessline 134
# Install s5cmd # macOS: brew install s5cmd # Linux: download from https://github.com/peak/s5cmd/releases - Network accessline 136
# Linux: download from https://github.com/peak/s5cmd/releases - Network accessline 289
- **Download defaults to AWS buckets**: request GCS if needed - **Save manifests**: Store the `series_aws_url` or `crdc_series_uuid` values for reproducibility - **Check licenses**: Query `license_short_name` before commercial use; CC-NC da - Network accessline 290
- **Save manifests**: Store the `series_aws_url` or `crdc_series_uuid` values for reproducibility - **Check licenses**: Query `license_short_name` before commercial use; CC-NC data requires non-commercial use - **Use current version unless - Network accessline 291
- **Check licenses**: Query `license_short_name` before commercial use; CC-NC data requires non-commercial use - Network accessline 314
**IDC Documentation:** - [Files and metadata](https://learn.canceridc.dev/data/organization-of-data/files-and-metadata) - Bucket organization details - Network accessline 315
- [Files and metadata](https://learn.canceridc.dev/data/organization-of-data/files-and-metadata) - Bucket organization details - Network accessline 316
- [Data versioning](https://learn.canceridc.dev/data/data-versioning) - Versioning scheme explanation - Network accessline 317
- [Resolving GUIDs and UUIDs](https://learn.canceridc.dev/data/organization-of-data/guids-and-uuids) - CRDC UUID documentation - Network accessline 318
- [Direct loading from cloud](https://learn.canceridc.dev/data/downloading-data/direct-loading) - Python examples for cloud access - Network accessline 320
**AWS Resources:** - [NCI IDC on AWS Open Data Registry](https://registry.opendata.aws/nci-imaging-data-commons/) - Bucket ARNs and access info - Network accessline 321
- [NCI IDC on AWS Open Data Registry](https://registry.opendata.aws/nci-imaging-data-commons/) - Bucket ARNs and access info - Network accessline 322
- [s5cmd](https://github.com/peak/s5cmd) - High-performance S3 client (used internally by idc-index) - Network accessline 323
- [AWS CLI S3 commands](https://docs.aws.amazon.com/cli/latest/reference/s3/) - Standard AWS command-line interface - Network accessline 324
- [Boto3 S3 documentation](https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/s3.html) - AWS SDK for Python - Network accessline 326
**Google Cloud Resources:** - [gsutil tool](https://cloud.google.com/storage/docs/gsutil) - Google Cloud Storage command-line tool - Network accessline 327
- [gsutil tool](https://cloud.google.com/storage/docs/gsutil) - Google Cloud Storage command-line tool - Network accessline 328
- [gcloud storage commands](https://cloud.google.com/sdk/gcloud/reference/storage) - Modern GCS CLI (recommended over gsutil) - Network accessline 329
- [Google Cloud Storage Python client](https://cloud.google.com/python/docs/reference/storage/latest) - GCS SDK for Python
skills/imaging-data-commons/references/dicomweb_guide.md
- Network accessline 20
https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb - Network accessline 34
https://healthcare.googleapis.com/v1/projects/nci-idc-data/locations/us-central1/datasets/idc/dicomStores/idc-store-v{VERSION}/dicomWeb - Network accessline 123
IDC DICOMweb is provided through Google Cloud Healthcare API DICOM stores. The implementation follows DICOM PS3.18 Web Services with specific characteristics documented in the [Google Healthcare DICOM conformance statement](https://docs.clo - Network accessline 188
base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 190
# Search for a specific study study_uid = "1.3.6.1.4.1.14519.5.2.1.6450.9002.307623500513044641407722230440" response = requests.get( - Network accessline 191
study_uid = "1.3.6.1.4.1.14519.5.2.1.6450.9002.307623500513044641407722230440" response = requests.get( f"{base_url}/studies", - Network accessline 192
response = requests.get( - Network accessline 208
base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 211
response = requests.get( - Network accessline 231
base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 235
response = requests.get( - Network accessline 254
base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 258
response = requests.get( - Network accessline 294
# Use DICOMweb to stream metadata without downloading files base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 295
base_url = "https://proxy.imaging.datacommons.cancer.gov/current/viewer-only-no-downloads-see-tinyurl-dot-com-slash-3j3d9jyp/dicomWeb" - Network accessline 297
response = requests.get( - Network accessline 336
# Build authenticated request base_url = "https://healthcare.googleapis.com/v1/projects/nci-idc-data/locations/us-central1/datasets/idc/dicomStores/idc-store-v23/dicomWeb" - Network accessline 337
base_url = "https://healthcare.googleapis.com/v1/projects/nci-idc-data/locations/us-central1/datasets/idc/dicomStores/idc-store-v23/dicomWeb" - Network accessline 339
response = requests.get( - Network accessline 386
**IDC Documentation:** - [IDC DICOM Stores](https://learn.canceridc.dev/data/organization-of-data/dicom-stores) - Data coverage and bucket details - Network accessline 387
- [IDC DICOM Stores](https://learn.canceridc.dev/data/organization-of-data/dicom-stores) - Data coverage and bucket details - Network accessline 388
- [IDC DICOMweb Access](https://learn.canceridc.dev/data/downloading-data/dicomweb-access) - Endpoint usage and differences - Network accessline 389
- [IDC Proxy Policy](https://learn.canceridc.dev/portal/proxy-policy) - Quota policies and usage restrictions - Network accessline 390
- [IDC User Guide](https://learn.canceridc.dev/) - Complete documentation - Network accessline 392
**DICOMweb Standards and Tools:** - [Google Healthcare DICOM Conformance Statement](https://docs.cloud.google.com/healthcare-api/docs/dicom) - Network accessline 393
- [Google Healthcare DICOM Conformance Statement](https://docs.cloud.google.com/healthcare-api/docs/dicom) - Network accessline 394
- [DICOMweb Standard](https://www.dicomstandard.org/using/dicomweb) - Network accessline 395
- [dicomweb-client Python library](https://dicomweb-client.readthedocs.io/)
skills/imaging-data-commons/references/digital_pathology_guide.md
- Network accessline 100
|--------|----------| | `primaryAnatomicStructureModifier_CodeMeaning` | Structured tissue type from DICOM specimen metadata (e.g., `Neoplasm, Primary`, `Normal`, `Tumor`, `Neoplasm, Metastatic`). Works across all collections with SM data. - Network accessline 102
| `ContainerIdentifier` | Slide/container identifier. For TCGA collections, contains the [TCGA barcode](https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/) where the [sample type code](https://gdc.cancer.gov/resources-tcga-users/t - Network accessline 284
Annotation objects can also contain per-annotation **measurements** (e.g., nucleus area, eccentricity) stored within the DICOM file. These are not in the index tables — extract them after download using [highdicom](https://github.com/Imagin - Network accessline 392
**Python Libraries:** - [highdicom](https://github.com/ImagingDataCommons/highdicom) - High-level DICOM abstractions for Python. Create and read DICOM Segmentations (SEG), Structured Reports (SR), and parametric maps for pathology and radio - Network accessline 393
- [highdicom](https://github.com/ImagingDataCommons/highdicom) - High-level DICOM abstractions for Python. Create and read DICOM Segmentations (SEG), Structured Reports (SR), and parametric maps for pathology and radiology. Developed by IDC - Network accessline 394
- [wsidicom](https://github.com/imi-bigpicture/wsidicom) - Python package for reading DICOM WSI datasets. Parses metadata into easy-to-use dataclasses for whole slide image analysis. - Network accessline 395
- [TIA-Toolbox](https://github.com/TissueImageAnalytics/tiatoolbox) - End-to-end computational pathology library with DICOM support via `DICOMWSIReader`. Provides tile extraction, feature extraction, and pretrained deep learning models. - Network accessline 396
- [EZ-WSI-DICOMweb](https://github.com/GoogleCloudPlatform/EZ-WSI-DICOMweb) - Extract image patches from DICOM whole slide images via DICOMweb. Designed for AI/ML workflows with cloud DICOM stores. - Network accessline 398
**Viewers:** - [Slim](https://github.com/ImagingDataCommons/slim) - Web-based DICOM slide microscopy viewer and annotation tool. Supports brightfield and multiplexed immunofluorescence imaging via DICOMweb. Developed by IDC. - Network accessline 399
- [Slim](https://github.com/ImagingDataCommons/slim) - Web-based DICOM slide microscopy viewer and annotation tool. Supports brightfield and multiplexed immunofluorescence imaging via DICOMweb. Developed by IDC. - Network accessline 400
- [QuPath](https://qupath.github.io/) - Cross-platform open source software for whole slide image analysis. Supports DICOM WSI via Bio-Formats and OpenSlide (v0.4.0+). - Network accessline 402
**Conversion:** - [dicom_wsi](https://github.com/Steven-N-Hart/dicom_wsi) - Python implementation for converting proprietary WSI formats to DICOM-compliant files. - Network accessline 403
- [dicom_wsi](https://github.com/Steven-N-Hart/dicom_wsi) - Python implementation for converting proprietary WSI formats to DICOM-compliant files.
skills/imaging-data-commons/references/index_tables_guide.md
- Network accessline 7
**Complete index table documentation:** https://idc-index.readthedocs.io/en/latest/indices_reference.html - Network accessline 107
| `PatientSex` | STRING | Yes | Patient sex | | `PatientAge` | STRING | Yes | Patient age at time of study | | `license_short_name` | STRING | No | License type (CC BY 4.0, CC BY-NC 4.0, etc.) | - Network accessline 108
| `PatientAge` | STRING | Yes | Patient age at time of study | | `license_short_name` | STRING | No | License type (CC BY 4.0, CC BY-NC 4.0, etc.) | | `series_size_MB` | FLOAT | No | Size of series in megabytes | - Network accessline 109
| `license_short_name` | STRING | No | License type (CC BY 4.0, CC BY-NC 4.0, etc.) | - Network accessline 113
**DICOM = Yes**: Column value extracted from the DICOM attribute with the same name. Refer to the [DICOM standard](https://dicom.nema.org/medical/dicom/current/output/chtml/part06/chapter_6.html) for numeric tag mappings. Use standard DICOM - Network accessline 143
- Complete index table documentation: https://idc-index.readthedocs.io/en/latest/indices_reference.html
skills/imaging-data-commons/references/use_cases.md
- Network accessline 138
For additional visualization options, see the [IDC Portal getting started guide](https://learn.canceridc.dev/portal/getting-started) or [SlicerIDCBrowser](https://github.com/ImagingDataCommons/SlicerIDCBrowser) for 3D Slicer integration.
skills/infographics/SKILL.md
skills/infographics/references/color_palettes.md
- Network accessline 476
1. **Contrast Checkers:** - WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/ - Network accessline 477
- WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/ - Network accessline 478
- Coolors Contrast Checker: https://coolors.co/contrast-checker - Network accessline 480
2. **Colorblind Simulators:** - Coblis: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 481
- Coblis: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 485
3. **Palette Generators:** - Coolors: https://coolors.co/ - Network accessline 486
- Coolors: https://coolors.co/ - Network accessline 487
- Adobe Color: https://color.adobe.com/ - Network accessline 488
- Paletton: https://paletton.com/
skills/infographics/scripts/generate_infographic.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 176
[Credential-related source omitted] - Access to secretsline 177
[Credential-related source omitted] - Network accessline 178
[Credential-related source omitted] - Access to secretsline 178
[Credential-related source omitted] - Network accessline 179
print("\nFor AI generation, you need an OpenRouter API key.") print("Get one at: https://openrouter.ai/keys") print("\nSet it with:") - Network accessline 180
print("Get one at: https://openrouter.ai/keys") - Access to secretsline 182
[Credential-related source omitted] - Access to secretsline 215
[Credential-related source omitted] - Access to secretsline 216
[Credential-related source omitted]
skills/infographics/scripts/generate_infographic_ai.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 13
[Credential-related source omitted] - Access to secretsline 40
[Credential-related source omitted] - Access to secretsline 47
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted] - Access to secretsline 339
[Credential-related source omitted] - Access to secretsline 341
[Credential-related source omitted] - Access to secretsline 343
[Credential-related source omitted] - Access to secretsline 345
[Credential-related source omitted] - Access to secretsline 347
[Credential-related source omitted] - Access to secretsline 349
[Credential-related source omitted] - Access to secretsline 350
[Credential-related source omitted] - Network accessline 351
[Credential-related source omitted] - Access to secretsline 351
[Credential-related source omitted] - Network accessline 352
[Credential-related source omitted] - Access to secretsline 352
[Credential-related source omitted] - Network accessline 353
"Get your API key from: https://openrouter.ai/keys" - Network accessline 356
self.verbose = verbose self._last_error = None self.base_url = "https://openrouter.ai/api/v1" - Network accessline 358
self.base_url = "https://openrouter.ai/api/v1" - Network accessline 432
[Credential-related source omitted] - Access to secretsline 432
[Credential-related source omitted] - Network accessline 433
"Content-Type": "application/json", "HTTP-Referer": "https://github.com/scientific-writer", "X-Title": "Infographic Research" - Network accessline 434
"HTTP-Referer": "https://github.com/scientific-writer", - Network accessline 447
response = requests.post( - Network accessline 516
[Credential-related source omitted] - Access to secretsline 516
[Credential-related source omitted] - Network accessline 517
"Content-Type": "application/json", "HTTP-Referer": "https://github.com/scientific-writer", "X-Title": "Infographic Web Search" - Network accessline 518
"HTTP-Referer": "https://github.com/scientific-writer", - Network accessline 529
response = requests.post( - Network accessline 585
[Credential-related source omitted] - Access to secretsline 585
[Credential-related source omitted] - Network accessline 586
"Content-Type": "application/json", "HTTP-Referer": "https://github.com/scientific-writer", "X-Title": "Infographic Generator" - Network accessline 587
"HTTP-Referer": "https://github.com/scientific-writer", - Network accessline 601
try: response = requests.post( - Network accessline 602
response = requests.post( - Possible obfuscationline 652
return base64.b64decode(base64_str) - Possible obfuscationline 663
return base64.b64decode(base64_str) - Possible obfuscationline 674
return base64.b64decode(base64_str) - Access to secretsline 1223
[Credential-related source omitted] - Access to secretsline 1244
[Credential-related source omitted] - Access to secretsline 1253
[Credential-related source omitted] - Access to secretsline 1254
[Credential-related source omitted] - Access to secretsline 1255
[Credential-related source omitted] - Access to secretsline 1257
[Credential-related source omitted] - Access to secretsline 1262
[Credential-related source omitted]
skills/instrument-data-to-allotrope/LICENSE.txt
skills/instrument-data-to-allotrope/SKILL.md
skills/instrument-data-to-allotrope/references/asm_schema_overview.md
- Network accessline 15
{ "$asm.manifest": { "vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], - Network accessline 16
"$asm.manifest": { "vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], "contexts": ["http://purl.allotrope.org/json-ld/afo-context-REC-2023-09.jsonld"] - Network accessline 17
"vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], - Network accessline 18
"contexts": ["http://purl.allotrope.org/json-ld/afo-context-REC-2023-09.jsonld"] - Network accessline 75
See: https://gitlab.com/allotrope-public/asm/-/tree/main/json-schemas/adm - Network accessline 191
Official schemas: https://gitlab.com/allotrope-public/asm/-/tree/main/json-schemas/adm
skills/instrument-data-to-allotrope/references/field_classification_guide.md
- Network accessline 242
> **Note:** These mappings are derived from the [Benchling allotropy library](https://github.com/Benchling-Open-Source/allotropy/tree/main/src/allotropy/parsers). For authoritative mappings, consult the parser source code for your specific - Network accessline 501
- [Allotrope Simple Model Introduction](https://www.allotrope.org/introduction-to-allotrope-simple-model) - Network accessline 502
- [Benchling allotropy library](https://github.com/Benchling-Open-Source/allotropy) - Network accessline 503
- [Allotrope Foundation ASM Overview](https://www.allotrope.org/asm)
skills/instrument-data-to-allotrope/scripts/convert_to_asm.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 320
asm = { "$asm.manifest": { "vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], - Network accessline 321
"$asm.manifest": { "vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], "contexts": [ - Network accessline 322
"vocabulary": ["http://purl.allotrope.org/voc/afo/REC/2023/09/"], - Network accessline 323
"contexts": [ "http://purl.allotrope.org/json-ld/afo-context-REC-2023-09.jsonld" ], - Network accessline 324
"http://purl.allotrope.org/json-ld/afo-context-REC-2023-09.jsonld"
skills/instrument-data-to-allotrope/scripts/export_parser.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/instrument-data-to-allotrope/scripts/flatten_asm.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/instrument-data-to-allotrope/scripts/validate_asm.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 15
Based on: Allotrope ASM specification (December 2024) Last Updated: 2026-01-07 Source: https://gitlab.com/allotrope-public/asm/-/tree/main/json-schemas/adm - Network accessline 17
Source: https://gitlab.com/allotrope-public/asm/-/tree/main/json-schemas/adm - Network accessline 36
ASM_SPEC_VERSION = "2024-12" VALIDATION_RULES_DATE = "2026-01-07" SCHEMA_SOURCE = "https://gitlab.com/allotrope-public/asm" - Network accessline 38
SCHEMA_SOURCE = "https://gitlab.com/allotrope-public/asm" - Network accessline 41
# All valid ASM techniques from https://gitlab.com/allotrope-public/asm/-/tree/main/json-schemas/adm
skills/interpro-database/SKILL.md
- Network accessline 13
InterPro (https://www.ebi.ac.uk/interpro/) is a comprehensive resource for protein family and domain classification maintained by EMBL-EBI. It integrates signatures from 13 member databases including Pfam, PANTHER, PRINTS, ProSite, SMART, T - Network accessline 22
**Key resources:** - InterPro website: https://www.ebi.ac.uk/interpro/ - Network accessline 23
- InterPro website: https://www.ebi.ac.uk/interpro/ - Network accessline 24
- REST API: https://www.ebi.ac.uk/interpro/api/ - API documentation: https://github.com/ProteinsWebTeam/interpro7-api/blob/master/docs/ - Python client: via `requests` - Network accessline 25
- API documentation: https://github.com/ProteinsWebTeam/interpro7-api/blob/master/docs/ - Network accessline 44
Base URL: `https://www.ebi.ac.uk/interpro/api/` - Network accessline 49
BASE_URL = "https://www.ebi.ac.uk/interpro/api" - Network accessline 52
url = f"{BASE_URL}/{endpoint}" headers = {"Accept": "application/json"} response = requests.get(url, params=params, headers=headers) - Network accessline 53
headers = {"Accept": "application/json"} response = requests.get(url, params=params, headers=headers) response.raise_for_status() - Network accessline 54
response = requests.get(url, params=params, headers=headers) - Network accessline 213
1. **Run InterProScan** locally or via the web (https://www.ebi.ac.uk/interpro/search/sequence/) to scan a protein sequence - Network accessline 301
- **InterPro website**: https://www.ebi.ac.uk/interpro/ - Network accessline 302
- **InterProScan** (run locally): https://github.com/ebi-pf-team/interproscan - Network accessline 303
- **API documentation**: https://github.com/ProteinsWebTeam/interpro7-api/blob/master/docs/ - Network accessline 304
- **Pfam**: https://www.ebi.ac.uk/interpro/entry/pfam/
skills/interpro-database/references/domain_analysis.md
skills/ipsae/SKILL.md
skills/iso-13485-certification/scripts/gap_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/jaspar-database/SKILL.md
- Network accessline 13
JASPAR (https://jaspar.elixir.no/) is the gold-standard open-access database of curated, non-redundant transcription factor (TF) binding profiles stored as position frequency matrices (PFMs). JASPAR 2024 contains 1,210 non-redundant TF bind - Network accessline 15
**Key resources:** - JASPAR portal: https://jaspar.elixir.no/ - Network accessline 16
- JASPAR portal: https://jaspar.elixir.no/ - Network accessline 17
- REST API: https://jaspar.elixir.no/api/v1/ - Network accessline 18
- API docs: https://jaspar.elixir.no/api/v1/docs/ - Network accessline 37
Base URL: `https://jaspar.elixir.no/api/v1/` - Network accessline 42
BASE_URL = "https://jaspar.elixir.no/api/v1" - Network accessline 44
def jaspar_get(endpoint, params=None): url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 45
url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) response.raise_for_status() - Network accessline 46
response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 278
# 1. Get relevant TF matrices (e.g., all human TFs in CORE collection) response = requests.get( - Network accessline 279
response = requests.get( - Network accessline 280
"https://jaspar.elixir.no/api/v1/matrix/", - Network accessline 288
all_hits = [] for m in matrices[:10]: # Limit for demo pwm_data = requests.get(f"https://jaspar.elixir.no/api/v1/matrix/{m['matrix_id']}/").json() - Network accessline 289
for m in matrices[:10]: # Limit for demo pwm_data = requests.get(f"https://jaspar.elixir.no/api/v1/matrix/{m['matrix_id']}/").json() pfm = pfm_data["pfm"] - Network accessline 290
pwm_data = requests.get(f"https://jaspar.elixir.no/api/v1/matrix/{m['matrix_id']}/").json() - Network accessline 345
- **JASPAR portal**: https://jaspar.elixir.no/ - Network accessline 346
- **API documentation**: https://jaspar.elixir.no/api/v1/docs/ - Network accessline 347
- **JASPAR 2024 paper**: Castro-Mondragon et al. (2022) Nucleic Acids Research. PMID: 34875674 - **Biopython motifs**: https://biopython.org/docs/latest/Tutorial/chapter_motifs.html - **FIMO tool** (for large-scale scanning): https://meme-s - Network accessline 348
- **Biopython motifs**: https://biopython.org/docs/latest/Tutorial/chapter_motifs.html - Network accessline 349
- **FIMO tool** (for large-scale scanning): https://meme-suite.org/meme/tools/fimo - Network accessline 350
- **HOMER** (motif enrichment): http://homer.ucsd.edu/homer/ - Network accessline 351
- **GitHub**: https://github.com/wassermanlab/JASPAR-UCSC-tracks
skills/jaspar-database/references/api_reference.md
- Network accessline 6
https://jaspar.elixir.no/api/v1/ - Network accessline 35
{ "count": 1210, "next": "https://jaspar.elixir.no/api/v1/matrix/?page=2", - Network accessline 36
"count": 1210, "next": "https://jaspar.elixir.no/api/v1/matrix/?page=2", "previous": null, - Network accessline 37
"next": "https://jaspar.elixir.no/api/v1/matrix/?page=2", - Network accessline 148
def download_all_human_profiles(output_file="jaspar_human_profiles.json"): """Download all human TF profiles from JASPAR CORE collection.""" url = "https://jaspar.elixir.no/api/v1/matrix/" - Network accessline 149
"""Download all human TF profiles from JASPAR CORE collection.""" url = "https://jaspar.elixir.no/api/v1/matrix/" params = { - Network accessline 150
url = "https://jaspar.elixir.no/api/v1/matrix/" - Network accessline 159
profiles = [] while True: response = requests.get(url, params=params) - Network accessline 160
while True: response = requests.get(url, params=params) data = response.json() - Network accessline 161
response = requests.get(url, params=params) - Network accessline 171
full_profiles = [] for p in profiles: detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/" - Network accessline 172
for p in profiles: detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/" detail = requests.get(detail_url).json() - Network accessline 173
detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/" detail = requests.get(detail_url).json() full_profiles.append(detail) - Network accessline 174
detail = requests.get(detail_url).json()
skills/jungian-psychologist/references/active-imagination.md
- Network accessline 759
- [Scott Jeffrey: Active Imagination - How to Work with Archetypes](https://scottjeffrey.com/active-imagination/) - Network accessline 760
- [Jungiancenter.org: Jung on Active Imagination - Features, Methods and Warnings](https://jungiancenter.org/jung-on-active-imagination-features-methods-and-warnings/) - Network accessline 761
- [Rafael Krüger: Carl Jung's Definitive Active Imagination Guide](https://www.rafaelkruger.com/the-definitive-active-imagination-guide-by-carl-jung/) - Network accessline 762
- [Eternalised: Active Imagination - Confrontation with the Unconscious](https://eternalisedofficial.com/2022/05/09/active-imagination/)
skills/kegg-database/SKILL.md
skills/kegg-database/references/kegg_reference.md
- Network accessline 7
**Base URL**: https://rest.kegg.jp - Network accessline 8
**Official Documentation**: https://www.kegg.jp/kegg/rest/keggapi.html - Network accessline 322
- **KEGG Mapper**: https://www.kegg.jp/kegg/mapper/ - Interactive pathway mapping - Network accessline 323
- **BlastKOALA**: Automated annotation for sequenced genomes - **GhostKOALA**: Annotation for metagenomes and metatranscriptomes - **KEGG Modules**: https://www.kegg.jp/kegg/module.html - Network accessline 324
- **GhostKOALA**: Annotation for metagenomes and metatranscriptomes - **KEGG Modules**: https://www.kegg.jp/kegg/module.html - **KEGG Brite**: https://www.kegg.jp/kegg/brite.html - Network accessline 325
- **KEGG Modules**: https://www.kegg.jp/kegg/module.html - Network accessline 326
- **KEGG Brite**: https://www.kegg.jp/kegg/brite.html
skills/kegg-database/scripts/kegg_api.py
- Executable scriptline 1
Executable file - Network accessline 7
API Base URL: https://rest.kegg.jp - Network accessline 8
Documentation: https://www.kegg.jp/kegg/rest/keggapi.html - Network accessline 19
KEGG_BASE_URL = "https://rest.kegg.jp" - Network accessline 35
url = f"{KEGG_BASE_URL}/info/{database}" try: with urllib.request.urlopen(url) as response: - Network accessline 36
try: with urllib.request.urlopen(url) as response: return response.read().decode('utf-8') - Network accessline 37
with urllib.request.urlopen(url) as response: - Network accessline 64
try: with urllib.request.urlopen(url) as response: - Network accessline 65
with urllib.request.urlopen(url) as response: - Network accessline 103
try: with urllib.request.urlopen(url) as response: - Network accessline 104
with urllib.request.urlopen(url) as response: - Network accessline 150
try: with urllib.request.urlopen(url) as response: - Network accessline 151
with urllib.request.urlopen(url) as response: - Network accessline 178
url = f"{KEGG_BASE_URL}/conv/{target_db}/{source_db}" try: with urllib.request.urlopen(url) as response: - Network accessline 179
try: with urllib.request.urlopen(url) as response: return response.read().decode('utf-8') - Network accessline 180
with urllib.request.urlopen(url) as response: - Network accessline 207
url = f"{KEGG_BASE_URL}/link/{target_db}/{source_db}" try: with urllib.request.urlopen(url) as response: - Network accessline 208
try: with urllib.request.urlopen(url) as response: return response.read().decode('utf-8') - Network accessline 209
with urllib.request.urlopen(url) as response: - Network accessline 233
url = f"{KEGG_BASE_URL}/ddi/{entries_str}" try: with urllib.request.urlopen(url) as response: - Network accessline 234
try: with urllib.request.urlopen(url) as response: return response.read().decode('utf-8') - Network accessline 235
with urllib.request.urlopen(url) as response:
skills/lab-results/coworker.py
skills/labarchive-integration/SKILL.md
- Network accessline 45
api_url: https://api.labarchives.com/api # or regional endpoint - Network accessline 50
**Regional API endpoints:** - US/International: `https://api.labarchives.com/api` - Network accessline 51
- US/International: `https://api.labarchives.com/api` - Network accessline 52
- Australia: `https://auapi.labarchives.com/api` - Network accessline 53
- UK: `https://ukapi.labarchives.com/api` - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 197
[Credential-related source omitted] - Network accessline 220
git clone https://github.com/mcmero/labarchives-py
skills/labarchive-integration/references/api_reference.md
- Network accessline 13
| Region | Base URL | |--------|----------| | US/International | `https://api.labarchives.com/api` | - Network accessline 14
|--------|----------| | US/International | `https://api.labarchives.com/api` | | Australia | `https://auapi.labarchives.com/api` | - Network accessline 15
| US/International | `https://api.labarchives.com/api` | - Network accessline 16
| Australia | `https://auapi.labarchives.com/api` | - Network accessline 17
| UK | `https://ukapi.labarchives.com/api` | - Network accessline 216
[Credential-related source omitted] - Network accessline 218
response = requests.post(url, files=files, data=params)
skills/labarchive-integration/references/authentication_guide.md
- Network accessline 45
# Regional API endpoint api_url: https://api.labarchives.com/api - Network accessline 46
api_url: https://api.labarchives.com/api - Network accessline 62
export LABARCHIVES_API_URL="https://api.labarchives.com/api" - Network accessline 73
| Region | Endpoint | Use if your LabArchives URL is | |--------|----------|--------------------------------| | US/International | `https://api.labarchives.com/api` | `mynotebook.labarchives.com` | - Network accessline 74
|--------|----------|--------------------------------| | US/International | `https://api.labarchives.com/api` | `mynotebook.labarchives.com` | | Australia | `https://auapi.labarchives.com/api` | `aunotebook.labarchives.com` | - Network accessline 75
| US/International | `https://api.labarchives.com/api` | `mynotebook.labarchives.com` | - Network accessline 76
| Australia | `https://auapi.labarchives.com/api` | `aunotebook.labarchives.com` | - Network accessline 77
| UK | `https://ukapi.labarchives.com/api` | `uknotebook.labarchives.com` | - Network accessline 132
# Make authenticated request response = requests.get(url, params=params) - Network accessline 133
response = requests.get(url, params=params) - Network accessline 149
# Configuration api_url <- "https://api.labarchives.com/api" - Network accessline 150
api_url <- "https://api.labarchives.com/api" - Network accessline 234
# Configure proxy proxies = { 'http': 'http://proxy.university.edu:8080', - Network accessline 235
proxies = { 'http': 'http://proxy.university.edu:8080', 'https': 'http://proxy.university.edu:8080' - Network accessline 236
'http': 'http://proxy.university.edu:8080', - Network accessline 237
'https': 'http://proxy.university.edu:8080' - Network accessline 240
# Make request with proxy response = requests.get(url, params=params, proxies=proxies) - Network accessline 241
response = requests.get(url, params=params, proxies=proxies) - Network accessline 249
# Disable SSL verification (use only for testing) response = requests.get(url, params=params, verify=False) - Network accessline 250
response = requests.get(url, params=params, verify=False) - Access to secretsline 273
[Credential-related source omitted]
skills/labarchive-integration/references/integrations.md
- Network accessline 94
response = requests.post(url, files=files, data=params) - Access to secretsline 286
[Credential-related source omitted] - Network accessline 290
# Step 1: Get authorization code auth_url = "https://mynotebook.labarchives.com/oauth/authorize" - Network accessline 291
auth_url = "https://mynotebook.labarchives.com/oauth/authorize" - Network accessline 300
# Step 2: Exchange code for access token token_url = "https://mynotebook.labarchives.com/oauth/token" - Network accessline 301
token_url = "https://mynotebook.labarchives.com/oauth/token" - Access to secretsline 304
[Credential-related source omitted] - Network accessline 310
response = requests.post(token_url, data=token_params) - Access to secretsline 313
[Credential-related source omitted]
skills/labarchive-integration/scripts/entry_operations.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 39
except ImportError: print("❌ labarchives-py package not installed") print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") - Network accessline 40
print("❌ labarchives-py package not installed") print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") sys.exit(1) - Network accessline 41
print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") - Network accessline 172
response = requests.post(url, files=files, data=data)
skills/labarchive-integration/scripts/notebook_operations.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 38
except ImportError: print("❌ labarchives-py package not installed") print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") - Network accessline 39
print("❌ labarchives-py package not installed") print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") sys.exit(1) - Network accessline 40
print(" Install with: pip install git+https://github.com/mcmero/labarchives-py")
skills/labarchive-integration/scripts/setup_config.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 24
endpoints = { '1': 'https://api.labarchives.com/api', - Network accessline 25
'1': 'https://api.labarchives.com/api', - Network accessline 26
'2': 'https://auapi.labarchives.com/api', - Network accessline 27
'3': 'https://ukapi.labarchives.com/api' - Network accessline 153
except ImportError: print("\n⚠<U+FE0F> labarchives-py package not installed") print(" Install with: pip install git+https://github.com/mcmero/labarchives-py") - Network accessline 155
print(" Install with: pip install git+https://github.com/mcmero/labarchives-py")
skills/labstep/SKILL.md
- Access to secretsline 11
[Credential-related source omitted] - Network accessline 13
always: false emoji: "🔬" homepage: https://www.labstep.com - Network accessline 14
emoji: "🔬" homepage: https://www.labstep.com os: [macos, linux] - Network accessline 15
homepage: https://www.labstep.com - Access to secretsline 35
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 52
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted]
skills/lamindb/SKILL.md
- Network accessline 380
- **Official Documentation**: https://docs.lamin.ai - Network accessline 381
- **API Reference**: https://docs.lamin.ai/api - Network accessline 382
- **GitHub Repository**: https://github.com/laminlabs/lamindb - Network accessline 383
- **Tutorial**: https://docs.lamin.ai/tutorial - Network accessline 384
- **FAQ**: https://docs.lamin.ai/faq
skills/lamindb/references/integrations.md
- Network accessline 45
# Initialize with custom S3 endpoint lamin init --storage 's3://bucket?endpoint_url=http://minio.example.com:9000' - Network accessline 46
lamin init --storage 's3://bucket?endpoint_url=http://minio.example.com:9000' - Access to secretsline 50
[Credential-related source omitted] - Network accessline 70
# Access remote files without copying artifact = ln.Artifact( "https://example.com/data.csv", - Network accessline 71
artifact = ln.Artifact( "https://example.com/data.csv", key="remote/data.csv" - Network accessline 72
"https://example.com/data.csv", - Access to secretsline 111
[Credential-related source omitted] - Access to secretsline 120
[Credential-related source omitted] - Access to secretsline 140
[Credential-related source omitted] - Network accessline 490
# Configure git sync export LAMINDB_SYNC_GIT_REPO=https://github.com/user/repo.git - Network accessline 491
export LAMINDB_SYNC_GIT_REPO=https://github.com/user/repo.git - Network accessline 493
# Or programmatically ln.settings.sync_git_repo = "https://github.com/user/repo.git" - Network accessline 494
ln.settings.sync_git_repo = "https://github.com/user/repo.git" - Network accessline 534
# Fetch from API response = requests.get("https://api.example.com/data") - Network accessline 535
response = requests.get("https://api.example.com/data") - Access to secretsline 613
[Credential-related source omitted]
skills/lamindb/references/setup-deployment.md
- Network accessline 66
1. Visit https://lamin.ai - Network accessline 117
# S3-compatible (MinIO, Cloudflare R2) lamin init --storage 's3://bucket?endpoint_url=http://endpoint:9000' - Network accessline 118
lamin init --storage 's3://bucket?endpoint_url=http://endpoint:9000' - Access to secretsline 206
[Credential-related source omitted] - Access to secretsline 258
[Credential-related source omitted] - Network accessline 260
lamin init --storage 's3://my-bucket?endpoint_url=http://minio.example.com:9000' - Access to secretsline 264
[Credential-related source omitted] - Network accessline 266
lamin init --storage 's3://bucket?endpoint_url=https://account-id.r2.cloudflarestorage.com' - Dangerous shell operationline 351
sudo mkdir -p /system/settings - Dangerous shell operationline 352
sudo nano /system/settings/system.env - Dangerous shell operationline 362
sudo chmod 755 /shared/cache/lamindb - Dangerous shell operationline 363
sudo chown -R shared-user:shared-group /shared/cache/lamindb - Network accessline 406
# Configure git sync lamin settings set sync-git-repo https://github.com/user/repo.git - Network accessline 407
lamin settings set sync-git-repo https://github.com/user/repo.git - Network accessline 422
# Git sync export LAMINDB_SYNC_GIT_REPO=https://github.com/user/repo.git - Network accessline 423
export LAMINDB_SYNC_GIT_REPO=https://github.com/user/repo.git
skills/latchbio-integration/SKILL.md
- Network accessline 335
- **Official Documentation**: https://docs.latch.bio - Network accessline 336
- **GitHub Repository**: https://github.com/latchbio/latch - Network accessline 337
- **Slack Community**: Join Latch SDK workspace - **API Reference**: https://docs.latch.bio/api/latch.html - **Blog**: https://blog.latch.bio - Network accessline 338
- **API Reference**: https://docs.latch.bio/api/latch.html - Network accessline 339
- **Blog**: https://blog.latch.bio
skills/latchbio-integration/references/data-management.md
- Access to secretsline 380
[Credential-related source omitted]
skills/latchbio-integration/references/verified-workflows.md
- Network accessline 439
- **Documentation**: https://docs.latch.bio
skills/latchbio-integration/references/workflow-creation.md
skills/latex-posters/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Network accessline 795
% Link to paper, code repository, or supplementary materials \qrcode[height=2cm]{https://github.com/username/project} - Network accessline 796
\qrcode[height=2cm]{https://github.com/username/project} - Network accessline 798
% QR code with caption \begin{center} \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ - Network accessline 799
\begin{center} \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ \small Scan for full paper - Network accessline 800
\qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ - Network accessline 1136
- [ ] Text-background contrast ratio ≥ 4.5:1 (WCAG AA) - [ ] Important elements contrast ratio ≥ 7:1 (WCAG AAA) - Test online: https://webaim.org/resources/contrastchecker/ - Network accessline 1138
- Test online: https://webaim.org/resources/contrastchecker/
skills/latex-posters/assets/baposter_template.tex
- Network accessline 220
\headerbox{Scan for More}{name=qr,column=2,above=bottom}{ \begin{center} \qrcode[height=4cm]{https://doi.org/10.1234/your-paper}\\ - Network accessline 221
\begin{center} \qrcode[height=4cm]{https://doi.org/10.1234/your-paper}\\ \vspace{0.3cm} - Network accessline 222
\qrcode[height=4cm]{https://doi.org/10.1234/your-paper}\\
skills/latex-posters/assets/beamerposter_template.tex
- Network accessline 233
\begin{column}{.2\linewidth} \centering \qrcode[height=3.5cm]{https://doi.org/10.1234/your-paper}\\ - Network accessline 234
\centering \qrcode[height=3.5cm]{https://doi.org/10.1234/your-paper}\\ \tiny Scan for full paper - Network accessline 235
\qrcode[height=3.5cm]{https://doi.org/10.1234/your-paper}\\
skills/latex-posters/assets/poster_quality_checklist.md
- Network accessline 202
### Color Contrast Test at: https://webaim.org/resources/contrastchecker/ - Network accessline 203
Test at: https://webaim.org/resources/contrastchecker/ - Network accessline 209
### Color Blindness Test with simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 210
Test with simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/
skills/latex-posters/assets/tikzposter_template.tex
- Network accessline 209
\block{Scan for More}{ \begin{center} \qrcode[height=5cm]{https://doi.org/10.1234/your-paper}\\ - Network accessline 210
\begin{center} \qrcode[height=5cm]{https://doi.org/10.1234/your-paper}\\ \vspace{0.5cm} - Network accessline 211
\qrcode[height=5cm]{https://doi.org/10.1234/your-paper}\\
skills/latex-posters/references/README.md
- Network accessline 386
### Online Tools - **Color contrast checker**: https://webaim.org/resources/contrastchecker/ - Network accessline 387
- **Color contrast checker**: https://webaim.org/resources/contrastchecker/ - Network accessline 388
- **Color blindness simulator**: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 389
- **Color palette generator**: https://coolors.co/
skills/latex-posters/references/latex_poster_packages.md
skills/latex-posters/references/poster_design_principles.md
skills/latex-posters/references/poster_layout_design.md
- Network accessline 508
\begin{column}{0.25\linewidth} \centering \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ - Network accessline 509
\centering \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ \tiny Scan for full paper - Network accessline 510
\qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
skills/latex-posters/scripts/review_poster.sh
- Executable scriptline 1
#!/bin/bash
skills/ligandmpnn/SKILL.md
- Network accessline 47
git clone https://github.com/dauparas/LigandMPNN.git
skills/linear-solvers/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/linear-solvers/scripts/convergence_diagnostics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/linear-solvers/scripts/preconditioner_advisor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/linear-solvers/scripts/residual_norms.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/linear-solvers/scripts/scaling_equilibration.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/linear-solvers/scripts/solver_selector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/linear-solvers/scripts/sparsity_stats.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/lit-synthesizer/SKILL.md
skills/literature-review/SKILL.md
- Broad permissionsline 1
Bash - Network accessline 314
- Date filters: `2020:2024[Publication Date]` - Boolean operators: AND, OR, NOT - See MeSH browser: https://meshb.nlm.nih.gov/search - Network accessline 316
- See MeSH browser: https://meshb.nlm.nih.gov/search - Network accessline 382
### APA (7th Edition) - In-text: (Smith et al., 2023) - Reference: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title. *Journal*, *22*(4), 301-318. https://doi.org/10.xxx/yyy - Network accessline 384
- Reference: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title. *Journal*, *22*(4), 301-318. https://doi.org/10.xxx/yyy - Network accessline 534
**Guidelines:** - PRISMA (Systematic Reviews): http://www.prisma-statement.org/ - Network accessline 535
- PRISMA (Systematic Reviews): http://www.prisma-statement.org/ - Network accessline 536
- Cochrane Handbook: https://training.cochrane.org/handbook - Network accessline 537
- AMSTAR 2 (Review Quality): https://amstar.ca/ - Network accessline 539
**Tools:** - MeSH Browser: https://meshb.nlm.nih.gov/search - Network accessline 540
- MeSH Browser: https://meshb.nlm.nih.gov/search - Network accessline 541
- PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/ - Network accessline 542
- Boolean Search Guide: https://www.ncbi.nlm.nih.gov/books/NBK3827/ - Network accessline 544
**Citation Styles:** - APA Style: https://apastyle.apa.org/ - Network accessline 545
- APA Style: https://apastyle.apa.org/ - Network accessline 546
- Nature Portfolio: https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards - Network accessline 547
- NLM/Vancouver: https://www.nlm.nih.gov/bsd/uniform_requirements.html
skills/literature-review/assets/review_template.md
- Network accessline 272
APA: Author, A. A., & Author, B. B. (Year). Title. *Journal*, *volume*(issue), pages. https://doi.org/xx.xxxx - Network accessline 404
**Resources:** - PRISMA 2020: http://prisma-statement.org/ - Network accessline 405
- PRISMA 2020: http://prisma-statement.org/ - Network accessline 406
- PROSPERO: https://www.crd.york.ac.uk/prospero/ - Network accessline 407
- Cochrane Handbook: https://training.cochrane.org/handbook - Network accessline 408
- GRADE: https://www.gradeworkinggroup.org/
skills/literature-review/references/citation_styles.md
- Network accessline 9
**Format**: Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. *Title of Periodical*, *volume*(issue), page range. https://doi.org/xx.xxx/yyyy - Network accessline 11
**Example**: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Machine learning approaches in drug discovery. *Nature Reviews Drug Discovery*, *22*(4), 301-318. https://doi.org/10.1038/nrd.2023.001 - Network accessline 15
**Format**: Author, A. A. (Year). *Title of work: Capital letter also for subtitle*. Publisher Name. https://doi.org/xxxx - Network accessline 27
**Format**: Author, A. A., & Author, B. B. (Year). Title of preprint. *Repository Name*. https://doi.org/xxxx - Network accessline 29
**Example**: Zhang, Y., Chen, L., & Wang, H. (2024). Novel therapeutic targets in Alzheimer's disease. *bioRxiv*. https://doi.org/10.1101/2024.01.001 - Network accessline 33
**Format**: Author, A. A. (Year, Month day-day). Title of paper. In E. E. Editor (Ed.), *Title of conference proceedings* (pp. xx-xx). Publisher. https://doi.org/xxxx - Network accessline 56
**Example**: Zhang, Y. et al. Novel therapeutic targets in Alzheimer's disease. *bioRxiv* https://doi.org/10.1101/2024.01.001 (2024). - Network accessline 64
**Format**: Author, First Name Middle Initial. Year. "Article Title." *Journal Title* volume, no. issue (Month): page range. https://doi.org/xxxx. - Network accessline 66
**Example**: Smith, John D., Mary L. Johnson, and Karen R. Williams. 2023. "Machine Learning Approaches in Drug Discovery." *Nature Reviews Drug Discovery* 22, no. 4 (April): 301-318. https://doi.org/10.1038/nrd.2023.001. - Network accessline 128
1. **Always verify DOIs**: Use the verify_citations.py script to check all DOIs 2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy) - Network accessline 129
2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)
skills/literature-review/references/database_strategies.md
- Network accessline 370
### MeSH Browser https://meshb.nlm.nih.gov/search - Network accessline 371
https://meshb.nlm.nih.gov/search - Network accessline 373
### Boolean Search Tutorial https://www.ncbi.nlm.nih.gov/books/NBK3827/ - Network accessline 374
https://www.ncbi.nlm.nih.gov/books/NBK3827/ - Network accessline 379
### PRISMA Guidelines Preferred Reporting Items for Systematic Reviews and Meta-Analyses: http://www.prisma-statement.org/ - Network accessline 381
http://www.prisma-statement.org/
skills/literature-review/scripts/generate_pdf.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/literature-review/scripts/search_databases.py
skills/literature-review/scripts/verify_citations.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 14
class CitationVerifier: def __init__(self): self.session = requests.Session() - Network accessline 15
def __init__(self): self.session = requests.Session() self.session.headers.update({ - Network accessline 16
self.session = requests.Session() - Network accessline 31
try: url = f"https://doi.org/api/handles/{doi}" - Network accessline 32
url = f"https://doi.org/api/handles/{doi}" - Network accessline 46
try: url = f"https://api.crossref.org/works/{doi}" - Network accessline 47
url = f"https://api.crossref.org/works/{doi}" - Network accessline 155
citation += f", {pages}" if doi: citation += f". https://doi.org/{doi}" - Network accessline 157
citation += f". https://doi.org/{doi}"
skills/literature-search/SKILL.md
- Network accessline 30
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 31
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 52
1. **Ask the user for their API key:** "To search scientific literature, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 53
"To search scientific literature, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Article Title", "url": "https://...", - Network accessline 79
"title": "Article Title", "url": "https://...", "content": "Full article text with figures...", - Network accessline 80
"url": "https://...", - Network accessline 82
"source": "pubmed|arxiv|biorxiv|medrxiv", "relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] } - Network accessline 84
"images": ["https://example.com/figure1.jpg"] - Network accessline 157
- Base URL: `https://api.valyu.ai/v1` - Network accessline 169
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 180
[Credential-related source omitted] - Network accessline 214
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/literature-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/literature-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/lobster-bioinformatics/README.md
- Network accessline 3
This directory contains the Agent Skill for using Lobster AI with [Claude Code](https://claude.com/claude-code). - Dangerous shell operationline 14
curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/install.sh | bash - Network accessline 14
curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/install.sh | bash - Dangerous shell operationline 63
rm -rf ~/.claude/skills/lobster - Network accessline 80
- [Agent Skills Documentation](https://docs.claude.com/en/docs/agents-and-tools/agent-skills) - Network accessline 81
- [Lobster Documentation](https://github.com/the-omics-os/lobster-local/wiki) - Network accessline 82
- [Examples Cookbook](https://github.com/the-omics-os/lobster-local/wiki/27-examples-cookbook)
skills/lobster-bioinformatics/SKILL.md
- Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 79
[Credential-related source omitted] - Network accessline 294
- Wiki: https://github.com/the-omics-os/lobster-local/wiki - Network accessline 295
- Examples: https://github.com/the-omics-os/lobster-local/wiki/27-examples-cookbook - Network accessline 296
- Installation: https://github.com/the-omics-os/lobster-local/wiki/02-installation - Network accessline 297
- Configuration: https://github.com/the-omics-os/lobster-local/wiki/03-configuration - Network accessline 305
For issues or questions: https://github.com/the-omics-os/lobster-local/issues
skills/lobster-bioinformatics/install.sh
- Executable scriptline 1
#!/bin/bash - Network accessline 2
# Install Lobster AI Claude Code Skill # Usage: curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/install.sh | bash - Dangerous shell operationline 3
# Usage: curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/install.sh | bash - Network accessline 3
# Usage: curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/install.sh | bash - Network accessline 17
echo "📥 Downloading Skill definition..." curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/SKILL.md \ - Network accessline 18
curl -fsSL https://raw.githubusercontent.com/the-omics-os/lobster-local/main/claude-skill/SKILL.md \
skills/mage-antibody-generator/README.md
- Network accessline 65
- https://github.com/IGlab-VUMC/MAGE_ab_generation
skills/mage-antibody-generator/repo/Data cleaning/CoVAbDab/covabdab_gen_curation_allBinders_allVariants_v2_24-03-12.ipynb
- Executable scriptline 1
Executable file - Network accessline 342
"source": [ "### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", - Network accessline 343
"### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", "wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY - Network accessline 344
"# https://www.rcsb.org/structure/6m0j\n", - Possible obfuscationline 345
"wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'" - Network accessline 363
" 'SARS-CoV2_WT':wt_rbd}\n", "\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Network accessline 364
"\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", "cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQ - Network accessline 365
"# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Possible obfuscationline 366
"cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLG - Network accessline 371
"ant_dict['SARS-CoV2_Omicron-BA1.1'] = variant_rbd_list['Omicron_BA.1.1__BA.1_add[R346K]__EPI_ISL_10000001']\n", "\n", "# https://www.rcsb.org/structure/8ASY\n", - Network accessline 372
"\n", "# https://www.rcsb.org/structure/8ASY\n", "ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQ - Network accessline 373
"# https://www.rcsb.org/structure/8ASY\n", - Network accessline 374
"ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKKSLL - Possible obfuscationline 374
"ant_dict['SARS-CoV2_Omicron-BA2.75'] = 'TNLCPFHEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGKKSLL - Network accessline 375
"\n", "# https://www.uniprot.org/uniprotkb/A0A6G6A1M4/entry\n", "ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLG - Network accessline 376
"# https://www.uniprot.org/uniprotkb/A0A6G6A1M4/entry\n", - Network accessline 377
"ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLGVYYHNNNKTWVENEFRVYSSANNCTFEYISQPFLMDLEGKQGNFKNLREFVFKNVDGYFKIYSKHTPIDLVR - Possible obfuscationline 377
"ant_dict['Pangolin-GD'] = 'MFVFLFVLPLVSSQCVNLTTRTGIPPGYTNSSTRGVYYPDKVFRSSILHLTQDLFLPFFSNVTWFNTINYQGGFKKFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDARTQSLLIVNNATNVVIKVCEFQFCTDPFLGVYYHNNNKTWVENEFRVYSSANNCTFEYISQPFLMDLEGKQGNFKNLREFVFKNVDGYFKIYSKHTPIDLVR - Network accessline 378
"\n", "# https://www.uniprot.org/uniprotkb/A0A6B9WHD3/entry#sequences\n", "ant_dict['RaTG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQF - Network accessline 379
"# https://www.uniprot.org/uniprotkb/A0A6B9WHD3/entry#sequences\n", - Possible obfuscationline 380
"ant_dict['RaTG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLP - Possible obfuscationline 381
"ant_dict['RatG13'] = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSSTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAIHVSGTNGIKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLP - Possible obfuscationline 863
"sars_cov2_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGF
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/10618/10618_antigen_alignment_v1_24-03-06.ipynb
- Executable scriptline 1
Executable file - Network accessline 122
"antigen_dict = dict(zip(antigen_seqs['LSS_name'], antigen_seqs['Seq']))\n", "\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Network accessline 123
"\n", "# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", "cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQ - Network accessline 124
"# https://www.uniprot.org/uniprotkb/P59594/entry#sequences\n", - Possible obfuscationline 125
"cov1_spike = 'MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLG - Network accessline 126
"antigen_dict['SARS-1.LSS'] = cov1_spike\n", "\n", "# https://www.rcsb.org/structure/8IOU\n", - Network accessline 127
"\n", "# https://www.rcsb.org/structure/8IOU\n", "xbb1_spike = 'LLMGCVAETGSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQ - Network accessline 128
"# https://www.rcsb.org/structure/8IOU\n", - Possible obfuscationline 129
"xbb1_spike = 'LLMGCVAETGSSQCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLP - Network accessline 130
"antigen_dict['XBB.1.LSS'] = xbb1_spike\n", "\n", "# https://www.rcsb.org/structure/8I4G\n", - Network accessline 131
"\n", "# https://www.rcsb.org/structure/8I4G\n", "bq11_spike = 'QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNF - Network accessline 132
"# https://www.rcsb.org/structure/8I4G\n", - Possible obfuscationline 133
"bq11_spike = 'QCVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLA - Possible obfuscationline 137
"oc43_spike = 'VIGDLKCPLDSRTGSLNNIDTGPPSISTATVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGTDKLSTLWFKPPFLSDFINGIFAKVKNTKVFKDGVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGVNKLQGLLEVSVCQYNMCEYPHTICHPKLGNHFKELWHMDTGVVSCLYKRNFTYDVNATYLYFHFYQEGGTFYAYFTDTGVVTK - Possible obfuscationline 140
"hku1_spike = 'VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGANFRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVM
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/10618/AA_10618_LLM-clean_24-03-06.ipynb
- Executable scriptline 1
Executable file
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/SAbDab/SAbDab_final_clean_v1_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 355
"source": [ "Should probably remove leucine repeats here as well: \\\n", "https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." - Network accessline 356
"Should probably remove leucine repeats here as well: \\\n", "https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." ] - Network accessline 357
"https://pubmed.ncbi.nlm.nih.gov/20561057/#:~:text=In%20the%20human%20proteome%2C%20although,chain%20and%20then%20degraded%20rapidly." - Possible obfuscationline 368
"'MQPTGREGSRALSRRYLRRLLLLLLLLLLRQPVTRAETTPGAPRALSTLGSPSLFTTPGVPSALTTPGLTTPGTPKTLDLRGRAQALMRSFPLVDGHNDLPQVLRQRYKNVLQDVNLRNFSHGQTSLDRLRDGLVGAQFWSASVSCQSQDQTAVRLALEQIDLIHRMCASYSELELVTSAEGLNSSQKLACLIGVEGGHSLDSSLSVLRSFYVLGVRYLTLTFTCSTPWAESSTKFRH
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/SAbDab/detagging_script_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 114
"HAtag = 'YPYDVPDYA'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 115
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 116
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Possible obfuscationline 121
"# ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW - Network accessline 212
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 213
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " X_ant.loc[tagged_dfs[flagtag].index] = tagged_dfs[flagtag]\n" - Network accessline 214
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Possible obfuscationline 314
"DLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF - Possible obfuscationline 317
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 320
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 323
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 326
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 329
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 332
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 335
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 338
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 341
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 344
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 347
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 350
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 380
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 383
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 386
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 389
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 392
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 395
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 398
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 401
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 404
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 407
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 410
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 413
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 416
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 419
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 422
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 425
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 428
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 431
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 434
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 437
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 440
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 443
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 446
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 449
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 452
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 455
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 458
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 461
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 464
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 467
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 470
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 473
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 476
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 479
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 482
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 485
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 488
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 491
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 494
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 497
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 500
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 503
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 506
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSCMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 509
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 512
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 515
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 518
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 521
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 524
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 527
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 530
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 533
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 536
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 539
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 542
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 545
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 548
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 551
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 554
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 557
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 560
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 563
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 566
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 569
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 572
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 575
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 578
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGA - Possible obfuscationline 581
"SQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTP - Possible obfuscationline 584
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 587
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 590
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 593
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 596
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 599
"VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSG - Possible obfuscationline 602
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 605
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 652
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 655
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 1334
"long attachment for: SDKICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENKHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLATASSWSYIVETSSSNNGTCYPGDFINYEELREQLSSVSSFEKFEIFPKTSSWPNHETNKGVTAACPHAGTNSFYKNLIWLVKKENSYPKINISYTNNRGKEVLVLWAIHHPPTSTDQQSLYQNANSYVFVGSSRYSRKFEPEIATR - Possible obfuscationline 1335
"long attachment for: SDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSVAGWILGNPECESLFSKESWSYIAETPKPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTAACSHNGKSSFYKNLLWLTEKNGLYPNLSKSYVNNKEKEVLVLWGVHHPSNIGDQRAIYHTENAYVSVVSSHYSRRFTPEIAKR - Possible obfuscationline 1337
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1338
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1339
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1340
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1341
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1342
"long attachment for: GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITASGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH - Possible obfuscationline 1343
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSLPEPEWTYPRLSCPGSTFQKALLISPHRFGEIKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEA - Possible obfuscationline 1344
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1345
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1357
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1358
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1359
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1360
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1361
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1362
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1363
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1364
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1365
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1366
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1367
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1368
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1369
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1370
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1371
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1372
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1373
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1374
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1375
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1376
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1377
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1378
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1379
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1380
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1381
"long attachment for: TQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGI - Possible obfuscationline 1438
"long attachment for: QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCA - Possible obfuscationline 1449
"long attachment for: YKDDDDAMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGENLYFQGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTK - Possible obfuscationline 1466
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1467
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1468
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1469
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1470
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1471
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1472
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINI - Possible obfuscationline 1473
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1474
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1475
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1476
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1477
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1478
"long attachment for: CVNLITRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1483
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1484
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1485
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1486
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1487
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1488
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1489
"long attachment for: CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESECGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1536
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1537
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1538
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1539
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1599
"long attachment for: MDERLSLLRSPPPPSARHRAHPPQRPASSGGAHTLVNHGYAEPAAGRELPPDMTVVPGDHLLEPEVADGGGAPPQGGCGGGGCDRYEPLPPSLPAAGEQDCCGERVVINISGLRFETQLKTLCQFPETLLGDPKRRMRYFDPLRNEYFFDRNRPSFDAILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLREEERPLPRRDFQR - Network accessline 1602
], "source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", - Network accessline 1603
"source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", "X_ant = X_ant.apply(lambda x: find_and_replace_ - Network accessline 1604
"# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n",
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/atlas_antigen_alignment_v1_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 174
], "source": [ "# Downloaded from plasmid here: https://www.addgene.org/154754/\n", - Network accessline 175
"source": [ "# Downloaded from plasmid here: https://www.addgene.org/154754/\n", "hexapro = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDP - Network accessline 176
"# Downloaded from plasmid here: https://www.addgene.org/154754/\n", - Possible obfuscationline 177
"hexapro = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVD
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/published_LIBRA-seq_concatenation_24-05-31.ipynb
- Executable scriptline 1
Executable file - Network accessline 402
"metadata": {}, "source": [ "By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need - Network accessline 403
"source": [ "By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need fasta inputs" ] - Network accessline 404
"By default, the LIBRA-seq pipeline outputs nucleotide sequences. We align these to a reference genome and annotate using IMGT HighV-Quest (https://www.imgt.org/HighV-QUEST/home.action) for which you need fasta inputs"
skills/mage-antibody-generator/repo/Data cleaning/Other_notebooks/signalP/detagging_nonSAbDab_24-03-12.ipynb
- Executable scriptline 1
Executable file - Network accessline 504
"flagtag = 'DYKDDDDK'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 505
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 506
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n",
skills/mage-antibody-generator/repo/Data cleaning/PlAbDab/ebola_Bornholdt_24-03-07.ipynb
- Executable scriptline 1
Executable file - Network accessline 35
], "source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Network accessline 36
"source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", "gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFF - Network accessline 37
"# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Possible obfuscationline 38
"gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYL - Network accessline 41
"gpTM = gp[:650]\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Network accessline 42
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", "sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRL - Network accessline 43
"# https://www.ncbi.nlm.nih.gov/nuccore/KJ660347\n", - Possible obfuscationline 44
"sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY
skills/mage-antibody-generator/repo/Data cleaning/PlAbDab/ebola_EhrHardt_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 47
"source": [ "# Q1PDC7| VGP_MABVR Envelope glycoprotein OS=Lake Victoria marburgvirus (strain Ravn-87) \n", "# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", - Network accessline 48
"# Q1PDC7| VGP_MABVR Envelope glycoprotein OS=Lake Victoria marburgvirus (strain Ravn-87) \n", "# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", "# gp = \"MKTIYFLISLILIQSIKTLPVLEIASNSQPQDVDSVCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAF - Network accessline 49
"# https://rest.uniprot.org/uniprotkb/Q1PDC7.fasta\n", - Possible obfuscationline 50
"# gp = \"MKTIYFLISLILIQSIKTLPVLEIASNSQPQDVDSVCSGTLQKTEDVHLMGFTLSGQKVADSPLEASKRWAFRTGVPPKNVEYTEGEEAKTCYNISVTDPSGKSLLLDPPSNIRDYPKCKTVHHIQGQNPHAQGIALHLWGAFFLYDRVASTTMYRGKVFTEGNIAAMIVNKTVHRMIFSRQGQGYRHMNLTSTNKYWTSSNETQRNDTGCFGILQEYNSTNNQTCPPSL - Network accessline 52
"\n", "# Q05320|VGP_EBOZM Envelope glycoprotein OS=Zaire ebolavirus (strain Mayinga-76)\n", "# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", - Network accessline 53
"# Q05320|VGP_EBOZM Envelope glycoprotein OS=Zaire ebolavirus (strain Mayinga-76)\n", "# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", "\n", - Network accessline 54
"# https://rest.uniprot.org/uniprotkb/Q05320.fasta\n", - Possible obfuscationline 56
"gp = \"MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY - Network accessline 129
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 130
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " hc_df['clone'] = hc_df['clone'].apply(lambda x: x.split('clone')[1].split(' - Network accessline 131
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 135
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 136
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " lc_df['clone'] = lc_df['clone'].apply(lambda x: x.split('clone')[1].split(' - Network accessline 137
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/mage-antibody-generator/repo/Data cleaning/PlAbDab/gilman_RSV_24-01-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 121
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 122
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df.dropna(inplace=True)\n", - Network accessline 123
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 127
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 128
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['GenBank Accession Number (VH)'] = seq_df['GenBank Accession Number - Network accessline 129
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 133
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 134
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['GenBank Accession Number (VL)'] = seq_df['GenBank Accession Number - Network accessline 135
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 163
"source": [ "# sp|P03420|FUS_HRSVA Fusion glycoprotein F0 OS=Human respiratory syncytial virus A (strain A2) OX=11259 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", - Network accessline 164
"# sp|P03420|FUS_HRSVA Fusion glycoprotein F0 OS=Human respiratory syncytial virus A (strain A2) OX=11259 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", "rsvAf = 'MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSK - Network accessline 165
"# https://rest.uniprot.org/uniprotkb/P03420.fasta\n", - Possible obfuscationline 166
"rsvAf = 'MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLNNAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRL - Network accessline 167
"\n", "# sp|P13843|FUS_HRSV1 Fusion glycoprotein F0 OS=Human respiratory syncytial virus B (strain 18537) OX=11251 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", - Network accessline 168
"# sp|P13843|FUS_HRSV1 Fusion glycoprotein F0 OS=Human respiratory syncytial virus B (strain 18537) OX=11251 GN=F PE=1 SV=1\n", "# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", "rsvBf = 'MELLIHRSSAIFLTLAVNALYLTSSQNITEEFYQSTCSA - Network accessline 169
"# https://rest.uniprot.org/uniprotkb/P13843.fasta\n", - Possible obfuscationline 170
"rsvBf = 'MELLIHRSSAIFLTLAVNALYLTSSQNITEEFYQSTCSAVSRGYFSALRTGWYTSVITIELSNIKETKCNGTDTKVKLIKQELDKYKNAVTELQLLMQNTPAANNRARREAPQYMNYTINTTKNLNVSISKKRKRRFLGFLLGVGSAIASGIAVSKVLHLEGEVNKIKNALLSTNKAVVSLSNGVSVLTSKVLDLKNYINNRLLPIVNQQSCRISNIETVIEFQQMNSRL
skills/mage-antibody-generator/repo/Data cleaning/PlAbDab/hcv_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 16
"source": [ "This is from Weber et al.\n", "https://doi.org/10.1016/j.immuni.2021.12.003\n", - Network accessline 17
"This is from Weber et al.\n", "https://doi.org/10.1016/j.immuni.2021.12.003\n", "\n", - Network accessline 18
"https://doi.org/10.1016/j.immuni.2021.12.003\n", - Network accessline 41
"source": [ "# Took E1/E2 from here:\n", "# https://www.ncbi.nlm.nih.gov/protein/1479555230\n", - Network accessline 42
"# Took E1/E2 from here:\n", "# https://www.ncbi.nlm.nih.gov/protein/1479555230\n", "# Was linked in paper\n", - Network accessline 43
"# https://www.ncbi.nlm.nih.gov/protein/1479555230\n",
skills/mage-antibody-generator/repo/Data cleaning/crowe_ebola/crowe_ebola_processing_24-03-07.ipynb
- Executable scriptline 1
Executable file - Network accessline 28
"outputs": [], "source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", - Network accessline 29
"source": [ "# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", "ebov_gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHK - Network accessline 30
"# https://www.ncbi.nlm.nih.gov/nuccore/KM233070?report=genbank\n", - Possible obfuscationline 31
"ebov_gp = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSVTKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTN - Network accessline 34
"len(ebov_gp)\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", - Network accessline 35
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", "bdbv_gp = 'MVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTG - Network accessline 36
"# https://www.ncbi.nlm.nih.gov/nuccore/NC_014373?report=genbank\n", - Possible obfuscationline 37
"bdbv_gp = 'MVTSGILQLPRERFRKTSFFVWVIILFHKVFPIPLGVVHNNTLQVSDIDKLVCRDKLSSTSQLKSVGLNLEGNGVATDVPTATKRWGFRAGVPPKVVNYEAGEWAENCYNLDIKKADGSECLPEAPEGVRGFPRCRYVHKVSGTGPCPEGYAFHKEGAFFLYDRLASTIIYRSTTFSEGVVAFLILPETKKDFFQSPPLHEPANMTTDPSSYYHTVTLNYVADNFGTN - Network accessline 39
"len(bdbv_gp)\n", "\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", - Network accessline 40
"\n", "# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", "sudv_gp = 'MGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTG - Network accessline 41
"# https://www.ncbi.nlm.nih.gov/nuccore/NC_006432?report=genbank\n", - Possible obfuscationline 42
"sudv_gp = 'MGGLSLLQLPRDKFRKSSFFVWVIILFQKAFSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFFLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQ - Network accessline 44
"len(sudv_gp)\n", "\n", "# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", - Network accessline 45
"\n", "# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", "sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGD - Network accessline 46
"# https://www.uniprot.org/uniprotkb/A0A0E3H7K0/entry#sequences\n", - Possible obfuscationline 47
"sGP = 'MGVTGILQLPRDRFKRTSFFLWVIILFQRTFSIPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEY - Network accessline 70
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 71
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " binding_df['sGP'] = supp_table[['sGP ELISA1', 'sGP ELISA2']].mean(axis=1)\n - Network accessline 72
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/mage-antibody-generator/repo/Data cleaning/denovo_absci/denovo_trastuzamab_24-02-29.ipynb
- Executable scriptline 1
Executable file - Network accessline 6
"source": [ "# Unlocking denovo antibody design\n", "* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", - Network accessline 7
"# Unlocking denovo antibody design\n", "* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", "\n", - Network accessline 8
"* https://www.biorxiv.org/content/10.1101/2023.01.08.523187v4.full.pdf\n", - Network accessline 9
"\n", "References for Trastuzamab:\n", "* https://www.genome.jp/entry/D03257\n", - Network accessline 10
"References for Trastuzamab:\n", "* https://www.genome.jp/entry/D03257\n", "* https://www.rcsb.org/structure/5xhg\n", - Network accessline 11
"* https://www.genome.jp/entry/D03257\n", - Network accessline 12
"* https://www.rcsb.org/structure/5xhg\n", - Possible obfuscationline 33
"trast_hc = 'EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH - Possible obfuscationline 34
"trast_lc = 'DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC'\n", - Possible obfuscationline 35
"her2 = 'TQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCL - Network accessline 181
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 182
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['antigen_seq'] = her2\n", - Network accessline 183
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 187
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 188
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['antigen_name'] = 'HER2'\n", - Network accessline 189
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 193
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 194
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " seq_df['source'] = 'Absci_denovo'\n" - Network accessline 195
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/mage-antibody-generator/repo/Data cleaning/final_processing/detagging_script_24-03-04.ipynb
- Executable scriptline 1
Executable file - Network accessline 114
"HAtag = 'YPYDVPDYA'\n", "\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Network accessline 115
"\n", "# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", "cloning_site = 'MGSSHHHHHHSSGLVPRGSHMISNSSLVPLALVSSPVSSGRGSHHHHHHHHHH'\n", - Network accessline 116
"# https://www.uniprot.org/uniprotkb/O55244/entry#sequences\n", - Possible obfuscationline 121
"# ASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAW - Network accessline 212
"A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 213
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " X_ant.loc[tagged_dfs[flagtag].index] = tagged_dfs[flagtag]\n" - Network accessline 214
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Possible obfuscationline 314
"DLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFLPFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNSTNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFKHLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSPAQDIWGTSAAAYF - Possible obfuscationline 317
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 320
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 323
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 326
"CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLGRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 329
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 332
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 335
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 338
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 341
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 344
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 347
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 350
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSS - Possible obfuscationline 380
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 383
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 386
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 389
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 392
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 395
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 398
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 401
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 404
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 407
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 410
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 413
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 416
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 419
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 422
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 425
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 428
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 431
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 434
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 437
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 440
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 443
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 446
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 449
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 452
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 455
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 458
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 461
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 464
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 467
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 470
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 473
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 476
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 479
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 482
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 485
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 488
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 491
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 494
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 497
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 500
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 503
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 506
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSCMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 509
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 512
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 515
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 518
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 521
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 524
"CVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSS - Possible obfuscationline 527
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 530
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 533
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 536
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 539
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 542
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 545
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 548
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHISYLTPGDSSS - Possible obfuscationline 551
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 554
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 557
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 560
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 563
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 566
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 569
"CVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSS - Possible obfuscationline 572
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 575
"CVNFTNRTQLPSAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNYPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLSEFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 578
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGA - Possible obfuscationline 581
"SQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTP - Possible obfuscationline 584
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 587
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 590
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 593
"VNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDS - Possible obfuscationline 596
"QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPG - Possible obfuscationline 599
"VNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQTLHRSYLTPGDSSSG - Possible obfuscationline 602
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 605
"TGTQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYL - Possible obfuscationline 652
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 655
"CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGD - Possible obfuscationline 1236
"long attachment for: SDKICIGYHANNSTDTVDTVLEKNVTVTHSVNLLENKHNGKLCKLRGVAPLHLGKCNIAGWLLGNPECESLATASSWSYIVETSSSNNGTCYPGDFINYEELREQLSSVSSFEKFEIFPKTSSWPNHETNKGVTAACPHAGTNSFYKNLIWLVKKENSYPKINISYTNNRGKEVLVLWAIHHPPTSTDQQSLYQNANSYVFVGSSRYSRKFEPEIATR - Possible obfuscationline 1237
"long attachment for: SDTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLKGTAPLQLGNCSVAGWILGNPECESLFSKESWSYIAETPKPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTKGVTAACSHNGKSSFYKNLLWLTEKNGLYPNLSKSYVNNKEKEVLVLWGVHHPSNIGDQRAIYHTENAYVSVVSSHYSRRFTPEIAKR - Possible obfuscationline 1239
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1240
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSC - Possible obfuscationline 1241
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1242
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCGITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDLDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1243
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSAEYRNWSKPQCDITGFAPFSKDNSIRLSAGGDIWVTREPYVSCDPDKCYQFALGQGTTLNNVHSNNTVRDRTPYRTLLMNELGVPFHLGTKQVCIAWSSSSCHDGKAWLHVCITGDDKNATASFIYNGRLVDSVV - Possible obfuscationline 1244
"long attachment for: GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITASGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHH - Possible obfuscationline 1245
"long attachment for: HHHHHHGSGLNDIFEAQKIEWHEGSIINETADDIVYRLTVIIDDRYESLKNLITLRADRLEMIINDNVSTILASGLVPRGSGSLPEPEWTYPRLSCPGSTFQKALLISPHRFGEIKGNSAPLIIREPFIACGPTECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGKEWTYIGVDGPDSNALLKIKYGEA - Possible obfuscationline 1246
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1247
"long attachment for: ADPHHHHHHSSSDYSDLQRVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSLVPRGSPSRWTYPRLSCPGSTFQKALLISPHRFGETKGNSAPLIIREPFIACGPKECKHFALTHYAAQPGGYYNGTREDRNKLRHLISVKLGKIPTVENSIFHMAAWSGSACHDGREWTYIGVDGPDSNALLKIKYGEAYTDTYHSYAKNILRTQESACNCIGGDC - Possible obfuscationline 1259
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1260
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1261
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1262
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1263
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1264
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1265
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1266
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1267
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1268
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1269
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1270
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1271
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1272
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1273
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1274
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1275
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1276
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1277
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1278
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1279
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1280
"long attachment for: TQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1281
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1282
"long attachment for: QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Possible obfuscationline 1283
"long attachment for: TQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGI - Possible obfuscationline 1336
"long attachment for: QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCA - Possible obfuscationline 1339
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1340
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1341
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Possible obfuscationline 1342
"long attachment for: CVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIG - Network accessline 1350
], "source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", - Network accessline 1351
"source": [ "# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n", "X_ant = X_ant.apply(lambda x: find_and_replace_ - Network accessline 1352
"# GSGGLNDIFEAQKIEWHE is avitag (see methods here: https://assets.researchsquare.com/files/rs-3045457/v1_covered_729e744e-72c6-45d9-9170-a969cd8b1953.pdf?c=1688438804)\n",
skills/mage-antibody-generator/repo/Data cleaning/final_processing/final_concat_v2_24-03-12.ipynb
- Executable scriptline 1
Executable file
skills/mage-antibody-generator/repo/Data cleaning/flu_LLM_paper/wang_preprint_flu_cleaning_24-01-03.ipynb
- Executable scriptline 1
Executable file - Network accessline 284
], "source": [ "# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", - Network accessline 285
"source": [ "# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", "# I am sourcing antibodies from certain references contained here. The annotations in 'Binds to' are not sufficient for our model since we need antige - Network accessline 286
"# From this preprint: https://pubmed.ncbi.nlm.nih.gov/37745338/\n", - Network accessline 427
"source": [ "# Joyce et al. Group 1 - top group with 440 binding to HA:Unk for Group 1,2\n", "# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416 - Network accessline 428
"# Joyce et al. Group 1 - top group with 440 binding to HA:Unk for Group 1,2\n", "# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416308510%3Fshowall - Network accessline 429
"# https://www.cell.com/cell/fulltext/S0092-8674(16)30851-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416308510%3Fshowall%3Dtrue#secsectitle0080\n", - Possible obfuscationline 436
"h3n2_HA = 'QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSS - Possible obfuscationline 534
"bris = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGKIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGPYKIGTSGSCPNITNGNGFFATMAWAVPKNDKNKTATNPLTIEVPYICTEGEDQITVWGFHSDDETQMAKLYGDSKPQKFTSS - Possible obfuscationline 537
"phuk = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEKIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKIGFFATMAWAVPKDNYKNATNPLTVEVPYICTEGEDQITVWGFHSDNKTQMKSLYGDSNPQKFTSSA - Possible obfuscationline 540
"mala = \"MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGNIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGSYKIGTSGSCPNVTNGNGFFATMAWAVPKNDNNKTATNSLTIEVPYICTEGEDQITVWGFHSDNEAQMAKLYGDSKPQKFTS - Possible obfuscationline 543
"flor = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSYFANLKGTRTRGKLCPDCLNCTDLDVALGRPMCVGTTPSAKASILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTQNVIDAEKAPGGPYRLGTSGSCPNATSKSGFFATMAWAVPKDNNKNATNPLTVEVPYICTEGEDQITVWGFHSDDKTQMKNLYGDSNPQKFTSSA - Possible obfuscationline 546
"yama = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTKTRGKLCPNCLNCTDLDVALGRPMCMGTIPSAKASILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTHNVINAERAPGGPYRLGTSGSCPNVTSRNGFFATMAWAVPRDNKTATNPLTVEVPYICTKGEDQITVWGFHSDDKTQMKNLYGDSNPQKFTSSAN - Possible obfuscationline 549
"lee = 'MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTRSHFANLKGTQTRGKLCPNCFNCTDLDVALGRPKCMGNIPSAKVSILHEVKPVTSGCFPIMHDRTKIRQLPNLLRGYENIRLSTSNVINAETAPGGPYKVGTSGSCPNVANRNGFFNTMAWVIPKDNNKTAINPVTVEVPYICSEGEDQITVWGFHSDDKTQMERLYGDSNPQKFTSSAN - Network accessline 580
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 581
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " liu_df['antigen_seq'] = liu_meta['Sorted Population']\n" - Network accessline 582
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 612
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 613
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " liu_df['antigen_seq'] = liu_df['antigen_seq'].map(ant_map)\n" - Network accessline 614
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 694
"outputs": [], "source": [ "#https://www.rcsb.org/structure/3LZG\n", - Network accessline 695
"source": [ "#https://www.rcsb.org/structure/3LZG\n", "cal09 = 'MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWL - Network accessline 696
"#https://www.rcsb.org/structure/3LZG\n", - Possible obfuscationline 697
"cal09 = 'MKAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPE - Network accessline 748
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 749
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " andrews_df['Ab'] = andrews_df.index\n" - Network accessline 750
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 770
"Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", - Network accessline 771
"\n", "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n", " andrews_df['Ab'] = andrews_df['Ab'].apply(lambda x: x[-4:len(x)])\n" - Network accessline 772
"See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
skills/mage-antibody-generator/repo/Data cleaning/zurbuchen/zurbuchen_data_23-03-08.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 89
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAkQAAAGwCAYAAABIC3rIAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAArC0lEQVR4nO3de1iVdb7//9eSk8DISjFOiadC89RBLAJnRieV3MWwu2rGZj - Possible obfuscationline 295
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAjsAAAGxCAYAAACEFXd4AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAAAuD0lEQVR4nO3dfXBUVZ7G8ach0EmAIBDIixASJBBeFBjQjKACAsF3XVaHWU - Network accessline 521
"## Seqs from CoVAbDab notebook\n", "\n", "### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", - Network accessline 522
"\n", "### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", "b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNK - Network accessline 523
"### Spike B.1.351 (beta) https://www.rcsb.org/structure/7LYQ\n", - Network accessline 524
"b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLP - Possible obfuscationline 524
"b1351 = 'MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLP - Network accessline 525
"\n", "### Spike B.1.617.2 (delta) https://www.rcsb.org/structure/7tov\n", "b16172 = 'MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYH - Network accessline 526
"### Spike B.1.617.2 (delta) https://www.rcsb.org/structure/7tov\n", - Possible obfuscationline 527
"b16172 = 'MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPI - Network accessline 528
"\n", "### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", - Network accessline 529
"### SARS-2_WT RBD\n", "# https://www.rcsb.org/structure/6m0j\n", "wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIY - Network accessline 530
"# https://www.rcsb.org/structure/6m0j\n", - Possible obfuscationline 531
"wt_rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Network accessline 532
"\n", "### SARS-2_WT RBD\n", "# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", - Network accessline 533
"### SARS-2_WT RBD\n", "# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", "wt_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCE - Network accessline 534
"# https://www.uniprot.org/uniprotkb/P0DTC2/entry#sequences\n", - Possible obfuscationline 535
"wt_spike = 'MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLV - Possible obfuscationline 560
"RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF - Possible obfuscationline 561
"MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQ - Possible obfuscationline 562
"MFVFLVLLPLVSSQCVNLRTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYYHKNNKSWMESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTL - Possible obfuscationline 563
"MFVFLVLLPLVSSQCVNFTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFANPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRGLPQGFSALEPLVDLPIGINITRFQ
skills/mage-antibody-generator/repo/Fine_tuning/full_model_training_24-03-12.py
skills/mage-antibody-generator/repo/Fine_tuning/selected_abs_Figure_2-3_24-06-10.ipynb
- Executable scriptline 1
Executable file - Possible obfuscationline 140
"rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Possible obfuscationline 274
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAXkAAAEvCAYAAACg1LHXAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABjU0lEQVR4nO3deTxU6x8H8M+xbyE77RQhaUPaiLRqEapbUioltG/aS9q3W0 - Possible obfuscationline 323
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAO0AAAG/CAYAAAC0fFDHAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAABUlElEQVR4nO3de1xM+f8H8FdXKSlKF0pbMYNEbRGVW7RarRVrXZbcldvGyq - Possible obfuscationline 377
"image/png": "iVBORw0KGgoAAAANSUhEUgAAAeUAAAFACAYAAACC4WQ/AAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAA9hAAAPYQGoP6dpAADJ8ElEQVR4nOydd3gUVdfAfzNb0ntIIYUQaiAU6R0pAtJEQQVBRJFXxYKvBS - Possible obfuscationline 458
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skills/mage-antibody-generator/repo/LICENSE
skills/mage-antibody-generator/repo/Output_analysis/figure1_plots_24-06-10.ipynb
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skills/mage-antibody-generator/repo/Output_analysis/output_filtering_annotation.ipynb
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"RBD_seq = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'" - Network accessline 142
"source": [ "Fasta output for humanness analysis:\n", "https://biophi.dichlab.org/humanization/humanness/" - Network accessline 143
"Fasta output for humanness analysis:\n", "https://biophi.dichlab.org/humanization/humanness/" ] - Network accessline 144
"https://biophi.dichlab.org/humanization/humanness/"
skills/mage-antibody-generator/repo/Output_analysis/selected_abs_Figure_2-3_24-06-10.ipynb
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Executable file - Possible obfuscationline 140
"rbd = 'RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNF'\n", - Possible obfuscationline 265
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skills/mage-antibody-generator/repo/Output_analysis/selection_pipeline_24-03-16.ipynb
skills/mage-antibody-generator/repo/README.md
- Network accessline 18
This repository contains Python scripts to accompany Wasdin et al., including antibody generation and follow-up analyses presented in the manuscript. All analyses were initially ran in Linux Red Hat 8.4, but have also been tested in Ubuntu - Network accessline 32
The Progen2 repository must cloned from: https://github.com/enijkamp/progen2 - Network accessline 33
https://github.com/enijkamp/progen2 - Network accessline 59
- Example: python generate_antibodies.py --n=1 --output=MAGE_antibodies.csv - This was tested on an Nvidia A6000 and took ~15 seconds to generate one antibody sequence against RBD. - To annotate and analyze output sequences without installi - Network accessline 61
- To annotate and analyze output sequences without installing the follow-up analyses libraries listed above, generated sequences can be uploaded to the IMGT Domain Gap Align webserver: https://www.imgt.org/3Dstructure-DB/cgi/DomainGapAlign.
skills/mage-antibody-generator/repo/generate_antibodies.py
- Executable scriptline 1
Executable file - Possible obfuscationline 44
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skills/markdown-mermaid-writing/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Network accessline 6
metadata: skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes) skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project - Network accessline 7
skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes) skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project skill-version: "1.0.0" - Network accessline 8
skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project - Network accessline 317
- **Source**: https://github.com/SuperiorByteWorks-LLC/agent-project - Network accessline 325
[^1]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/ - Network accessline 327
[^2]: Mermaid. "Mermaid Diagramming and Charting Tool." https://mermaid.js.org/
skills/markdown-mermaid-writing/assets/examples/example-research-report.md
- Network accessline 215
[^1]: Ran, F.A. et al. (2013). "Genome engineering using the CRISPR-Cas9 system." _Nature Protocols_, 8(11), 2281–2308. https://doi.org/10.1038/nprot.2013.143 - Network accessline 217
[^2]: ATCC. (2024). "Cell Line Authentication and Quality Control." https://www.atcc.org/resources/technical-documents/cell-line-authentication - Network accessline 219
[^3]: Moreno-Mateos, M.A. et al. (2015). "CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo." _Nature Methods_, 12(10), 982–988. https://doi.org/10.1038/nmeth.3543 - Network accessline 221
[^4]: Molla, K.A. & Yang, Y. (2019). "CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications." _Trends in Biotechnology_, 37(10), 1121–1142. https://doi.org/10.1016/j.tibtech.2019.03.008
skills/markdown-mermaid-writing/references/diagrams/architecture.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/block.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/c4.md
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<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/class.md
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<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/complex_examples.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/er.md
skills/markdown-mermaid-writing/references/diagrams/flowchart.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/gantt.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/git_graph.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/kanban.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/mindmap.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/packet.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/pie.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/quadrant.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/radar.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/requirement.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/sankey.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/sequence.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/state.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/timeline.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/treemap.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/user_journey.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/xy_chart.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/diagrams/zenuml.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/references/markdown_style_guide.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 197
- **Meaningful link text** — `[Mermaid Style Guide]` not `[click here]` or `[link]` - **Relative paths** for internal links — `[Guide](./README.md)` not absolute URLs - **Full URLs** for external links — always `https://` - Network accessline 199
- **Full URLs** for external links — always `https://` - Network accessline 210
[^1]: Gruber, J. (2004). "Markdown." _Daring Fireball_. https://daringfireball.net/projects/markdown/ - Network accessline 212
[^2]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/ - Network accessline 218
[^N]: Author/Org. (Year). "Title." *Publication*. https://full-url - Network accessline 237
[mermaid-docs]: https://mermaid.js.org/ 'Mermaid Documentation' - Network accessline 365
- Transition to next topic - **Bold** emphasis works inside details - [Links](https://example.com) work too - Network accessline 367
- [Links](https://example.com) work too - Possible obfuscationline 529
<U+200E>```mermaid - Possible obfuscationline 543
<U+200E>``` - Network accessline 677
[^1]: Stack Overflow. (2024). "Developer Survey Results." https://survey.stackoverflow.co/2024 - Network accessline 733
- [GitHub Flavored Markdown Spec](https://github.github.com/gfm/) · [Mermaid Style Guide](mermaid_style_guide.md) · [GitHub Basic Formatting](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatti
skills/markdown-mermaid-writing/references/mermaid_style_guide.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 448
1. **GitHub:** Push to branch → toggle Profile → Settings → Appearance → Theme 2. **VS Code:** "Markdown Preview Mermaid Support" extension → `Cmd/Ctrl + Shift + V` 3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggl - Network accessline 449
2. **VS Code:** "Markdown Preview Mermaid Support" extension → `Cmd/Ctrl + Shift + V` 3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggle themes 4. **Screen reader:** Verify `accTitle`/`accDescr` announced (VoiceOve - Network accessline 450
3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggle themes - Network accessline 457
- [Markdown Style Guide](markdown_style_guide.md) — Formatting, citations, and document structure for the markdown that wraps your diagrams - [Mermaid Docs](https://mermaid.js.org/) · [Live Editor](https://mermaid.live/) · [Accessibility](h - Network accessline 458
- [Mermaid Docs](https://mermaid.js.org/) · [Live Editor](https://mermaid.live/) · [Accessibility](https://mermaid.js.org/config/accessibility.html) · [GitHub Support](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/)
skills/markdown-mermaid-writing/templates/decision_record.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 197
- [Related ADR or RFC](../adr/ADR-001-agent-optimized-documentation-system.md) - [External documentation or benchmark](https://example.com) - Network accessline 198
- [External documentation or benchmark](https://example.com)
skills/markdown-mermaid-writing/templates/how_to_guide.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 71
| Requirement | Version | Verify with | Install link | | ---------------- | ----------- | --------------------- | ------------------------------------ | | [Tool/Runtime] | ≥ [version] | `[command - Network accessline 72
| ---------------- | ----------- | --------------------- | ------------------------------------ | | [Tool/Runtime] | ≥ [version] | `[command] --version` | [Install guide](https://example.com) | | [Dependency] | ≥ [version] | `[command - Network accessline 73
| [Tool/Runtime] | ≥ [version] | `[command] --version` | [Install guide](https://example.com) | - Network accessline 74
| [Dependency] | ≥ [version] | `[command] --version` | [Install guide](https://example.com) | - Network accessline 75
| [Account/Access] | — | [How to verify] | [Sign up](https://example.com) | - Network accessline 270
- [Official documentation](https://example.com) — [Which section is most relevant] - Network accessline 271
- [Source repository](https://github.com/SuperiorByteWorks-LLC) — [For bug reports and contributions]
skills/markdown-mermaid-writing/templates/issue.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 180
- [Related issues](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Relevant documentation](https://example.com) - Network accessline 181
- [Relevant documentation](https://example.com) - Network accessline 182
- [Monitoring dashboard or alert](https://example.com) - Network accessline 296
- [User feedback or support tickets](https://example.com) - [Competitive analysis](https://example.com) - [Related feature requests](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - Network accessline 297
- [Competitive analysis](https://example.com) - [Related feature requests](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Design document or ADR](../adr/ADR-001-agent-optimized-documentation-system.md)
skills/markdown-mermaid-writing/templates/kanban.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->
skills/markdown-mermaid-writing/templates/presentation.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 290
[^1]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 294
- [Resource title](https://example.com) — Why this is useful - Network accessline 295
- [Resource title](https://example.com) — What it provides - Network accessline 299
- [Tool name](https://example.com) — Purpose and how to access
skills/markdown-mermaid-writing/templates/project_documentation.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 37
[]() []() - Network accessline 67
# Clone the repository git clone https://github.com/[org]/[repo].git - Network accessline 68
git clone https://github.com/[org]/[repo].git - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Network accessline 85
curl http://localhost:[port]/health - Network accessline 374
# Fork and clone git clone https://github.com/[your-fork]/[repo].git - Network accessline 375
git clone https://github.com/[your-fork]/[repo].git - Network accessline 406
- [Official framework docs](https://example.com) — [What version and which sections are most relevant] - Network accessline 407
- [API specification](https://example.com) — [OpenAPI/Swagger link if applicable]
skills/markdown-mermaid-writing/templates/pull_request.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 28
- **Naming:** `pr-` + PR number zero-padded to 8 digits + `-` + short lowercase hyphenated description - **Cross-reference:** Link to the live PR in the metadata table - **GitHub PR body:** Use only the full branch URL to this file (for exa - Network accessline 30
- **GitHub PR body:** Use only the full branch URL to this file (for example, `https://github.com/<org>/<repo>/blob/<branch>/docs/project/pr/pr-00000123-fix-auth-timeout.md`) - Network accessline 313
- [Design document or ADR](../adr/ADR-001-agent-optimized-documentation-system.md) - [Related issue](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Relevant documentation](https://example.com) - Network accessline 315
- [Relevant documentation](https://example.com)
skills/markdown-mermaid-writing/templates/research_paper.md
- Network accessline 1
<!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) --> - Network accessline 288
[^1]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 290
[^2]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 292
[^3]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 294
[^4]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 296
[^5]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 298
[^6]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com> - Network accessline 300
[^7]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>
skills/markdown-mermaid-writing/templates/status_report.md
skills/markitdown/INSTALLATION_GUIDE.md
- Network accessline 37
git clone https://github.com/microsoft/markitdown.git - Dangerous shell operationline 68
sudo apt-get update - Dangerous shell operationline 69
sudo apt-get install tesseract-ocr - Network accessline 72
#### Windows Download from: https://github.com/UB-Mannheim/tesseract/wiki - Network accessline 73
Download from: https://github.com/UB-Mannheim/tesseract/wiki - Dangerous shell operationline 84
sudo apt-get install poppler-utils - Dangerous shell operationline 98
rm test.txt - Network accessline 157
# Get API key from https://openrouter.ai/keys - Access to secretsline 160
[Credential-related source omitted] - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 164
[Credential-related source omitted] - Network accessline 180
See https://openrouter.ai/models for complete model list and pricing. - Network accessline 191
[Credential-related source omitted] - Access to secretsline 191
[Credential-related source omitted] - Network accessline 192
export AZURE_DOCUMENT_INTELLIGENCE_ENDPOINT="https://your-endpoint.cognitiveservices.azure.com/" - Network accessline 198
# Clone repository git clone https://github.com/microsoft/markitdown.git - Network accessline 199
git clone https://github.com/microsoft/markitdown.git - Network accessline 314
- **Documentation**: See `SKILL.md` and `README.md` - **GitHub Issues**: https://github.com/microsoft/markitdown/issues - Network accessline 315
- **GitHub Issues**: https://github.com/microsoft/markitdown/issues
skills/markitdown/OPENROUTER_INTEGRATION.md
- Network accessline 27
See https://openrouter.ai/models for the complete list. - Network accessline 33
1. Visit https://openrouter.ai/keys - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Network accessline 59
[Credential-related source omitted] - Network accessline 60
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Network accessline 61
base_url="https://openrouter.ai/api/v1" - Access to secretsline 83
[Credential-related source omitted] - Network accessline 136
[Credential-related source omitted] - Network accessline 137
[Credential-related source omitted] - Access to secretsline 137
[Credential-related source omitted] - Network accessline 138
base_url="https://openrouter.ai/api/v1" - Network accessline 158
[Credential-related source omitted] - Network accessline 159
[Credential-related source omitted] - Access to secretsline 159
[Credential-related source omitted] - Network accessline 160
base_url="https://openrouter.ai/api/v1" - Network accessline 198
[Credential-related source omitted] - Network accessline 199
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Network accessline 200
base_url="https://openrouter.ai/api/v1" - Network accessline 268
OpenRouter pricing varies by model. Check current rates at https://openrouter.ai/models - Access to secretsline 282
[Credential-related source omitted] - Access to secretsline 286
[Credential-related source omitted] - Network accessline 291
If you get a "model not found" error, check: 1. Model name format: `provider/model-name` 2. Model availability: https://openrouter.ai/models - Network accessline 292
1. Model name format: `provider/model-name` 2. Model availability: https://openrouter.ai/models 3. Vision support: Ensure model supports vision for image description - Network accessline 293
2. Model availability: https://openrouter.ai/models - Network accessline 307
[Credential-related source omitted] - Access to secretsline 307
[Credential-related source omitted] - Network accessline 308
2. **Client Initialization**: Added `base_url="https://openrouter.ai/api/v1"` - Network accessline 314
- **OpenRouter Website**: https://openrouter.ai - Network accessline 315
- **Get API Keys**: https://openrouter.ai/keys - Network accessline 316
- **Model List**: https://openrouter.ai/models - Network accessline 317
- **Pricing**: https://openrouter.ai/models (click on model for details) - Network accessline 318
- **Documentation**: https://openrouter.ai/docs - Network accessline 319
- **Support**: https://openrouter.ai/discord - Access to secretsline 327
[Credential-related source omitted] - Network accessline 352
For OpenRouter-specific issues: - Discord: https://openrouter.ai/discord - Network accessline 353
- Discord: https://openrouter.ai/discord
skills/markitdown/QUICK_REFERENCE.md
- Network accessline 47
[Credential-related source omitted] - Network accessline 48
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Network accessline 49
base_url="https://openrouter.ai/api/v1" - Network accessline 107
[Credential-related source omitted] - Network accessline 108
[Credential-related source omitted] - Access to secretsline 108
[Credential-related source omitted] - Network accessline 109
base_url="https://openrouter.ai/api/v1" - Network accessline 143
See https://openrouter.ai/models for full list - Network accessline 148
md = MarkItDown(docintel_endpoint="https://YOUR-ENDPOINT.cognitiveservices.azure.com/") - Access to secretsline 234
[Credential-related source omitted] - Network accessline 236
# Azure Document Intelligence (optional) export AZURE_DOCUMENT_INTELLIGENCE_KEY="key..." export AZURE_DOCUMENT_INTELLIGENCE_ENDPOINT="https://..." - Access to secretsline 237
[Credential-related source omitted] - Network accessline 238
export AZURE_DOCUMENT_INTELLIGENCE_ENDPOINT="https://..." - Dangerous shell operationline 299
sudo apt-get install tesseract-ocr - Network accessline 306
- **Format Details**: See `references/file_formats.md` - **Examples**: See `assets/example_usage.md` - **GitHub**: https://github.com/microsoft/markitdown - Network accessline 308
- **GitHub**: https://github.com/microsoft/markitdown
skills/markitdown/README.md
- Network accessline 70
[Credential-related source omitted] - Network accessline 71
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Network accessline 72
base_url="https://openrouter.ai/api/v1" - Network accessline 100
md = MarkItDown(docintel_endpoint="https://YOUR-ENDPOINT.cognitiveservices.azure.com/") - Access to secretsline 135
[Credential-related source omitted] - Network accessline 161
- **MarkItDown GitHub**: https://github.com/microsoft/markitdown - Network accessline 162
- **PyPI**: https://pypi.org/project/markitdown/ - Network accessline 163
- **OpenRouter**: https://openrouter.ai (AI model access) - Network accessline 164
- **OpenRouter API Keys**: https://openrouter.ai/keys - Network accessline 165
- **OpenRouter Models**: https://openrouter.ai/models - Network accessline 170
- Python 3.10+ - Optional dependencies based on formats needed - OpenRouter API key (for AI-enhanced conversions) - Get at https://openrouter.ai/keys - Network accessline 171
- Optional dependencies based on formats needed - OpenRouter API key (for AI-enhanced conversions) - Get at https://openrouter.ai/keys - Azure subscription (optional, for Document Intelligence) - Network accessline 172
- OpenRouter API key (for AI-enhanced conversions) - Get at https://openrouter.ai/keys
skills/markitdown/SKILL.md
- Broad permissionsline 1
Bash - Network accessline 4
allowed-tools: [Read, Write, Edit, Bash] license: MIT source: https://github.com/microsoft/markitdown - Network accessline 5
license: MIT source: https://github.com/microsoft/markitdown --- - Network accessline 6
source: https://github.com/microsoft/markitdown - Network accessline 84
# Or from source git clone https://github.com/microsoft/markitdown.git - Network accessline 85
git clone https://github.com/microsoft/markitdown.git - Network accessline 134
[Credential-related source omitted] - Network accessline 135
[Credential-related source omitted] - Access to secretsline 135
[Credential-related source omitted] - Network accessline 136
base_url="https://openrouter.ai/api/v1" - Network accessline 257
[Credential-related source omitted] - Network accessline 258
[Credential-related source omitted] - Access to secretsline 258
[Credential-related source omitted] - Network accessline 259
base_url="https://openrouter.ai/api/v1" - Network accessline 307
# Convert YouTube video to transcript result = md.convert("https://www.youtube.com/watch?v=VIDEO_ID") - Network accessline 308
result = md.convert("https://www.youtube.com/watch?v=VIDEO_ID") - Network accessline 414
[Credential-related source omitted] - Network accessline 415
[Credential-related source omitted] - Access to secretsline 415
[Credential-related source omitted] - Network accessline 416
base_url="https://openrouter.ai/api/v1" - Dangerous shell operationline 460
sudo apt-get install tesseract-ocr - Network accessline 479
- **MarkItDown GitHub**: https://github.com/microsoft/markitdown - Network accessline 480
- **PyPI**: https://pypi.org/project/markitdown/ - Network accessline 481
- **OpenRouter**: https://openrouter.ai (for AI-enhanced conversions) - Network accessline 482
- **OpenRouter API Keys**: https://openrouter.ai/keys - Network accessline 483
- **OpenRouter Models**: https://openrouter.ai/models
skills/markitdown/SKILL_SUMMARY.md
- Access to secretsline 186
[Credential-related source omitted] - Network accessline 232
[Credential-related source omitted] - Network accessline 233
[Credential-related source omitted] - Access to secretsline 233
[Credential-related source omitted] - Network accessline 234
base_url="https://openrouter.ai/api/v1" - Network accessline 279
- **MarkItDown GitHub**: https://github.com/microsoft/markitdown - Network accessline 280
- **PyPI**: https://pypi.org/project/markitdown/ - Network accessline 281
- **OpenRouter**: https://openrouter.ai (AI model access) - Network accessline 282
- **OpenRouter API Keys**: https://openrouter.ai/keys - Network accessline 283
- **OpenRouter Models**: https://openrouter.ai/models
skills/markitdown/assets/example_usage.md
- Network accessline 129
[Credential-related source omitted] - Network accessline 130
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Network accessline 131
base_url="https://openrouter.ai/api/v1" - Network accessline 162
[Credential-related source omitted] - Network accessline 163
[Credential-related source omitted] - Access to secretsline 163
[Credential-related source omitted] - Network accessline 164
base_url="https://openrouter.ai/api/v1" - Network accessline 320
# Get transcript video_url = "https://www.youtube.com/watch?v=VIDEO_ID" - Network accessline 321
video_url = "https://www.youtube.com/watch?v=VIDEO_ID"
skills/markitdown/references/api_reference.md
- Network accessline 230
[Credential-related source omitted] - Network accessline 231
[Credential-related source omitted] - Access to secretsline 231
[Credential-related source omitted] - Network accessline 232
base_url="https://openrouter.ai/api/v1" - Network accessline 255
See https://openrouter.ai/models for the complete list. - Network accessline 290
md = MarkItDown( docintel_endpoint="https://YOUR-RESOURCE.cognitiveservices.azure.com/" - Network accessline 291
docintel_endpoint="https://YOUR-RESOURCE.cognitiveservices.azure.com/" - Access to secretsline 301
[Credential-related source omitted] - Network accessline 396
[Credential-related source omitted] - Access to secretsline 396
[Credential-related source omitted] - Network accessline 398
| `AZURE_DOCUMENT_INTELLIGENCE_ENDPOINT` | Azure DI endpoint | `https://...` |
skills/markitdown/references/file_formats.md
skills/markitdown/scripts/batch_convert.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/markitdown/scripts/convert_literature.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/markitdown/scripts/convert_with_ai.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 73
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Network accessline 94
[Credential-related source omitted] - Network accessline 95
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Network accessline 96
base_url="https://openrouter.ai/api/v1" - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 167
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted] - Access to secretsline 217
[Credential-related source omitted] - Network accessline 218
[Credential-related source omitted] - Access to secretsline 218
[Credential-related source omitted] - Network accessline 219
[Credential-related source omitted] - Access to secretsline 219
[Credential-related source omitted] - Network accessline 220
print("Get your API key at: https://openrouter.ai/keys") - Access to secretsline 232
[Credential-related source omitted]
skills/matchms/references/importing_exporting.md
- Network accessline 406
For detailed format specifications: - **MGF**: http://www.matrixscience.com/help/data_file_help.html - Network accessline 407
- **MGF**: http://www.matrixscience.com/help/data_file_help.html - Network accessline 408
- **MSP**: https://chemdata.nist.gov/mass-spc/ms-search/ - Network accessline 409
- **mzML**: http://www.psidev.info/mzML - Network accessline 410
- **GNPS JSON**: https://gnps.ucsd.edu/ - Network accessline 414
For complete API documentation: https://matchms.readthedocs.io/en/latest/api/matchms.importing.html - Network accessline 415
https://matchms.readthedocs.io/en/latest/api/matchms.importing.html - Network accessline 416
https://matchms.readthedocs.io/en/latest/api/matchms.exporting.html
skills/matchms/references/similarity.md
skills/matchms/references/workflows.md
skills/matplotlib/SKILL.md
- Network accessline 2
name: matplotlib description: Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF - Network accessline 3
description: Low-level plotting library for full customization. Use when you need fine-grained control over every plot element, creating novel plot types, or integrating with specific scientific workflows. Export to PNG/PDF/SVG for publicat - Network accessline 4
license: https://github.com/matplotlib/matplotlib/tree/main/LICENSE - Network accessline 355
- Official documentation: https://matplotlib.org/ - Network accessline 356
- Gallery: https://matplotlib.org/stable/gallery/index.html - Network accessline 357
- Cheatsheets: https://matplotlib.org/cheatsheets/ - Network accessline 358
- Tutorials: https://matplotlib.org/stable/tutorials/index.html
skills/matplotlib/references/api_reference.md
skills/matplotlib/scripts/plot_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/matplotlib/scripts/style_configurator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/medchem/SKILL.md
skills/medchem/scripts/filter_molecules.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/medical-imaging-review/SKILL.md
- Broad permissionsline 1
Bash
skills/medical-imaging-review/references/MCP_SETUP.md
- Network accessline 5
**Repository:** https://github.com/blazickjp/arxiv-mcp-server - Network accessline 51
**Repository:** https://github.com/grll/pubmedmcp - Network accessline 92
# List collections curl -s "http://localhost:23119/api/users/[USER_ID]/collections" - Network accessline 93
curl -s "http://localhost:23119/api/users/[USER_ID]/collections" - Network accessline 95
# Get items from collection curl -s "http://localhost:23119/api/users/[USER_ID]/collections/[KEY]/items" - Network accessline 96
curl -s "http://localhost:23119/api/users/[USER_ID]/collections/[KEY]/items" - Network accessline 101
**Repository:** https://github.com/54yyyu/zotero-mcp
skills/medical-imaging-review/references/TEMPLATES.md
- Network accessline 37
API: http://localhost:23119/api/users/[USER_ID]/
skills/medical-research-toolkit/README.md
- Network accessline 10
- **6 Database Guides** — PubMed, ClinicalTrials, ChEMBL, OpenTargets, OpenFDA, OMIM - **2 API References** — 8 additional databases + ID mapping - **1 Complete Workflow** — Drug repurposing example with all curl commands - Network accessline 12
- **1 Complete Workflow** — Drug repurposing example with all curl commands - Network accessline 17
2. **Pick a use case** — Drug repurposing, target discovery, clinical evidence review, or literature mining 3. **Read the relevant database guide** — E.g., [ChEMBL Guide](./references/chembl.md) 4. **Copy/adapt the example queries** — Use t - Network accessline 18
3. **Read the relevant database guide** — E.g., [ChEMBL Guide](./references/chembl.md) 4. **Copy/adapt the example queries** — Use the curl commands provided 5. **Scale up** — Build your full research workflow - Network accessline 19
4. **Copy/adapt the example queries** — Use the curl commands provided - Network accessline 43
✅ **No Setup** — Use the production endpoint immediately (https://mcp.cloud.curiloo.com) - Network accessline 45
✅ **Real Examples** — Every database has actual curl commands you can run - Network accessline 85
https://mcp.cloud.curiloo.com/tools/unified/mcp - Network accessline 95
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 125
| Database | Key Required? | Why? | Get Key | |----------|---------------|------|---------| | OMIM | **Yes** | Proprietary medical data | https://omim.org/api | - Network accessline 126
|----------|---------------|------|---------| | OMIM | **Yes** | Proprietary medical data | https://omim.org/api | | OpenFDA | Optional | Higher rate limits | https://open.fda.gov | - Network accessline 127
| OMIM | **Yes** | Proprietary medical data | https://omim.org/api | - Network accessline 128
| OpenFDA | Optional | Higher rate limits | https://open.fda.gov | - Network accessline 129
| NCI Clinical Trials | Optional | Higher rate limits | https://clinicaltrialsapi.cancer.gov | - Network accessline 138
**Source**: https://github.com/pascalwhoop/medical-mcps - Network accessline 142
**Organization**: Every Cure (https://www.everycure.org) — Reimagining drug development through computational drug repurposing
skills/medical-research-toolkit/RELEASE-NOTES.md
- Network accessline 33
- Use cases - Data fields explanation - Copy-paste curl commands - Network accessline 34
- Data fields explanation - Copy-paste curl commands - Workflow patterns - Network accessline 35
- Copy-paste curl commands - Network accessline 38
✅ **Workflow Script** (10.6 KB) - Complete 8-step drug repurposing pipeline - All curl commands with explanations - Network accessline 39
- Complete 8-step drug repurposing pipeline - All curl commands with explanations - Example output templates - Network accessline 40
- All curl commands with explanations - Network accessline 58
- [x] OpenFDA: adverse event search - [x] Response formats documented - [x] curl command examples tested - Network accessline 60
- [x] curl command examples tested - Network accessline 133
✅ **No Setup Required** - Production endpoint live at: https://mcp.cloud.curiloo.com - Network accessline 134
- Production endpoint live at: https://mcp.cloud.curiloo.com - Network accessline 138
✅ **Real Examples** - Every database guide has copy-paste curl commands - Network accessline 139
- Every database guide has copy-paste curl commands - Network accessline 160
- **Total Lines**: ~4,500 (all documentation) - **Total Size**: ~87 KB - **Code Examples**: 40+ curl commands - Network accessline 161
- **Total Size**: ~87 KB - **Code Examples**: 40+ curl commands - **Databases Covered**: 14 integrated + references - Network accessline 162
- **Code Examples**: 40+ curl commands
skills/medical-research-toolkit/SKILL.md
- Network accessline 13
# Find drugs for myasthenia gravis curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 14
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 28
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 38
# First: Find disease ID curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 39
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 43
# Returns: disease ID (e.g., EFO_0004991) # Then: Get targets curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 44
# Then: Get targets curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ - Network accessline 45
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 55
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 65
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 75
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 141
https://mcp.cloud.curiloo.com/tools/unified/mcp - Network accessline 148
pip install medical-mcps medical-mcps # Available at: http://localhost:8000/tools/unified/mcp - Network accessline 150
# Available at: http://localhost:8000/tools/unified/mcp - Network accessline 173
See [drug-repurposing-workflow.md](./scripts/drug-repurposing-workflow.md) for step-by-step example with all 8 steps + curl commands. - Network accessline 185
| PubMed | No | Public data | (not needed) | | ClinicalTrials | No | Public data | (not needed) | | **OMIM** | **Yes** | Proprietary data | https://omim.org/api | - Network accessline 186
| ClinicalTrials | No | Public data | (not needed) | | **OMIM** | **Yes** | Proprietary data | https://omim.org/api | | OpenFDA | Optional | Higher rate limits | https://open.fda.gov | - Network accessline 187
| **OMIM** | **Yes** | Proprietary data | https://omim.org/api | - Network accessline 188
| OpenFDA | Optional | Higher rate limits | https://open.fda.gov | - Network accessline 189
| NCI Clinical Trials | Optional | Higher rate limits | https://clinicaltrialsapi.cancer.gov | - Network accessline 207
# Search multiple targets for gene in CHRNE RAPSN LRP4; do curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 208
for gene in CHRNE RAPSN LRP4; do curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ -H "Content-Type: application/json" -H "Accept: application/json" \ - Network accessline 209
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 221
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 243
**API key errors?** - OMIM requires API key — get from https://omim.org/api - Network accessline 244
- OMIM requires API key — get from https://omim.org/api - Network accessline 261
- **Source Code**: https://github.com/pascalwhoop/medical-mcps - Network accessline 262
- **Author**: Pascal Brockmeyer (@pascalwhoop) - **Organization**: Every Cure (https://www.everycure.org) - **License**: MIT - Network accessline 263
- **Organization**: Every Cure (https://www.everycure.org)
skills/medical-research-toolkit/TESTING-CHECKLIST.md
- Network accessline 7
- [x] Production endpoint accessible: `https://mcp.cloud.curiloo.com/tools/unified/mcp` - Network accessline 35
2. Update [SKILL.md](./SKILL.md): - Add curl example with proper headers - Network accessline 36
- Add curl example with proper headers - Network accessline 39
3. Create quick-start examples: - Top 3 most common queries - Copy-paste ready curl commands - Network accessline 40
- Top 3 most common queries - Copy-paste ready curl commands - Expected output format - Network accessline 41
- Copy-paste ready curl commands - Network accessline 57
curl -s -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 65
curl -s -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 73
curl -s -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
skills/medical-research-toolkit/references/omim.md
- Access to secretsline 14
[Credential-related source omitted] - Network accessline 19
**Arguments:** - `search_term` (str): Disease name or gene symbol - `api_key` (str): OMIM API key (REQUIRED — get from https://omim.org/api) - Network accessline 21
[Credential-related source omitted] - Access to secretsline 21
[Credential-related source omitted] - Access to secretsline 32
[Credential-related source omitted] - Access to secretsline 39
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 73
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 106
[Credential-related source omitted] - Access to secretsline 122
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 167
[Credential-related source omitted] - Network accessline 225
1. Go to https://omim.org/api - Access to secretsline 248
[Credential-related source omitted] - Access to secretsline 263
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted] - Access to secretsline 293
[Credential-related source omitted]
skills/medical-research-toolkit/references/openfda.md
skills/medical-research-toolkit/references/other-apis.md
- Network accessline 298
| Node Normalization | No | Public | | MyVariant.info | No | Public | | **OMIM** | **Yes** | https://omim.org/api | - Network accessline 299
| MyVariant.info | No | Public | | **OMIM** | **Yes** | https://omim.org/api | | **NCI Clinical Trials** | Optional | https://clinicaltrialsapi.cancer.gov | - Network accessline 300
| **OMIM** | **Yes** | https://omim.org/api | - Network accessline 301
| **NCI Clinical Trials** | Optional | https://clinicaltrialsapi.cancer.gov | - Network accessline 302
| **OpenFDA** | Optional | https://open.fda.gov/apis |
skills/medical-research-toolkit/scripts/drug-repurposing-workflow.md
- Network accessline 10
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 38
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 63
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Access to secretsline 72
[Credential-related source omitted] - Network accessline 87
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Access to secretsline 96
[Credential-related source omitted] - Network accessline 110
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 133
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 158
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 180
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 201
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 222
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 244
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 264
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 283
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 306
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 331
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 354
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \ - Network accessline 374
curl -X POST https://mcp.cloud.curiloo.com/tools/unified/mcp \
skills/medrxiv-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search medRxiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search medRxiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Article Title", "url": "https://medrxiv.org/content/...", - Network accessline 79
"title": "Article Title", "url": "https://medrxiv.org/content/...", "content": "Full article text with figures...", - Network accessline 80
"url": "https://medrxiv.org/content/...", - Network accessline 82
"source": "medrxiv", "relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/figure1.jpg"] } - Network accessline 84
"images": ["https://example.com/figure1.jpg"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/medrxiv-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/medrxiv-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/mesh-generation/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/mesh-generation/scripts/grid_sizing.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/mesh-generation/scripts/mesh_quality.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/metabolomics-workbench-database/SKILL.md
- Network accessline 32
# Get compound information by PubChem CID response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json') - Network accessline 33
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json') - Network accessline 35
# Download molecular structure as PNG response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png') - Network accessline 36
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png') - Network accessline 38
# Get compound name by registry number response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json') - Network accessline 39
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json') - Network accessline 55
# List all available public studies response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json') - Network accessline 56
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json') - Network accessline 58
# Get study summary response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json') - Network accessline 59
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json') - Network accessline 61
# Retrieve experimental data response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json') - Network accessline 62
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json') - Network accessline 64
# Find studies containing a specific metabolite response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json') - Network accessline 65
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json') - Network accessline 80
# Standardize a metabolite name response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json') - Network accessline 81
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json') - Network accessline 83
# Query by molecular formula response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all/json') - Network accessline 84
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all/json') - Network accessline 86
# Get all metabolites in a specific class response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json') - Network accessline 87
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json') - Network accessline 89
# Retrieve complete RefMet database response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/all/json') - Network accessline 90
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/all/json') - Network accessline 105
# Search by m/z value with M+H adduct response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json') - Network accessline 106
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json') - Network accessline 108
# Calculate exact mass for a metabolite with specific adduct response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json') - Network accessline 109
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json') - Network accessline 111
# Search across RefMet database response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json') - Network accessline 112
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json') - Network accessline 128
# Find human blood studies on diabetes using LC-MS response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json') - Network accessline 129
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json') - Network accessline 131
# Find all human blood studies containing tyrosine response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json') - Network accessline 132
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json') - Network accessline 134
# Filter by analytical method only response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json') - Network accessline 135
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json') - Network accessline 150
# Get gene information by symbol response = requests.get('https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json') - Network accessline 151
response = requests.get('https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json') - Network accessline 153
# Retrieve protein data by UniProt ID response = requests.get('https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json') - Network accessline 154
response = requests.get('https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json') - Network accessline 165
response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/glucose/name/json') - Network accessline 170
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Glucose/summary/json') - Network accessline 175
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json') - Network accessline 184
response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/180.06/M+H/0.5/json') - Network accessline 191
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/all/json') - Network accessline 196
response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/png') - Network accessline 205
response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;;Human;;Cancer/json') - Network accessline 212
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST{ID}/summary/json') - Network accessline 217
response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST{ID}/data/json')
skills/metabolomics-workbench-database/references/api_reference.md
- Network accessline 7
https://www.metabolomicsworkbench.org/rest/ - Network accessline 69
# Get all compound data by PubChem CID curl "https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json" - Network accessline 70
curl "https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json" - Network accessline 72
# Get compound name by registry number curl "https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json" - Network accessline 73
curl "https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json" - Network accessline 75
# Download structure as PNG curl "https://www.metabolomicsworkbench.org/rest/compound/regno/11/png" -o structure.png - Network accessline 76
curl "https://www.metabolomicsworkbench.org/rest/compound/regno/11/png" -o structure.png - Network accessline 78
# Get compound by KEGG ID curl "https://www.metabolomicsworkbench.org/rest/compound/kegg_id/C00031/all/json" - Network accessline 79
curl "https://www.metabolomicsworkbench.org/rest/compound/kegg_id/C00031/all/json" - Network accessline 81
# Get compound by molecular formula curl "https://www.metabolomicsworkbench.org/rest/compound/formula/C6H12O6/all/json" - Network accessline 82
curl "https://www.metabolomicsworkbench.org/rest/compound/formula/C6H12O6/all/json" - Network accessline 125
# List all publicly available studies curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json" - Network accessline 126
curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json" - Network accessline 128
# Get study summary curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json" - Network accessline 129
curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json" - Network accessline 131
# Get experimental data curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json" - Network accessline 132
curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json" - Network accessline 134
# Get study factors curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors/json" - Network accessline 135
curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/factors/json" - Network accessline 137
# Find studies containing a specific metabolite curl "https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json" - Network accessline 138
curl "https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json" - Network accessline 140
# Search studies by investigator curl "https://www.metabolomicsworkbench.org/rest/study/last_name/Smith/summary/json" - Network accessline 141
curl "https://www.metabolomicsworkbench.org/rest/study/last_name/Smith/summary/json" - Network accessline 143
# Download complete study in mwTab format curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/mwtab/txt" - Network accessline 144
curl "https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/mwtab/txt" - Network accessline 186
# Standardize a metabolite name curl "https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json" - Network accessline 187
curl "https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json" - Network accessline 189
# Get all RefMet data for a metabolite curl "https://www.metabolomicsworkbench.org/rest/refmet/name/Glucose/all/json" - Network accessline 190
curl "https://www.metabolomicsworkbench.org/rest/refmet/name/Glucose/all/json" - Network accessline 192
# Query by molecular formula curl "https://www.metabolomicsworkbench.org/rest/refmet/formula/C6H12O6/all/json" - Network accessline 193
curl "https://www.metabolomicsworkbench.org/rest/refmet/formula/C6H12O6/all/json" - Network accessline 195
# Get all metabolites in a main class curl "https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json" - Network accessline 196
curl "https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json" - Network accessline 198
# Query by exact mass curl "https://www.metabolomicsworkbench.org/rest/refmet/exactmass/180.0634/all/json" - Network accessline 199
curl "https://www.metabolomicsworkbench.org/rest/refmet/exactmass/180.0634/all/json" - Network accessline 201
# Download complete RefMet database curl "https://www.metabolomicsworkbench.org/rest/refmet/all/json" - Network accessline 202
curl "https://www.metabolomicsworkbench.org/rest/refmet/all/json" - Network accessline 242
# Human blood diabetes studies with LC-MS HILIC positive mode curl "https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json" - Network accessline 243
curl "https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json" - Network accessline 245
# All human blood studies containing tyrosine curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json" - Network accessline 246
curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json" - Network accessline 248
# All GC-MS studies regardless of other parameters curl "https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json" - Network accessline 249
curl "https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json" - Network accessline 251
# Mouse liver studies curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;Mouse;Liver;;/json" - Network accessline 252
curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;Mouse;Liver;;/json" - Network accessline 254
# All studies measuring glucose curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;;;;;Glucose/json" - Network accessline 255
curl "https://www.metabolomicsworkbench.org/rest/metstat/;;;;;;;Glucose/json" - Network accessline 318
# Search for compounds with m/z 635.52 (M+H) in MB database curl "https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json" - Network accessline 319
curl "https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json" - Network accessline 321
# Search in RefMet with negative mode curl "https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json" - Network accessline 322
curl "https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json" - Network accessline 324
# Search lipids database curl "https://www.metabolomicsworkbench.org/rest/moverz/LIPIDS/760.59/M+Na/0.5/json" - Network accessline 325
curl "https://www.metabolomicsworkbench.org/rest/moverz/LIPIDS/760.59/M+Na/0.5/json" - Network accessline 327
# Calculate exact mass for known metabolite curl "https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json" - Network accessline 328
curl "https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json" - Network accessline 330
# High-resolution MS search (tight tolerance) curl "https://www.metabolomicsworkbench.org/rest/moverz/MB/180.0634/M+H/0.01/json" - Network accessline 331
curl "https://www.metabolomicsworkbench.org/rest/moverz/MB/180.0634/M+H/0.01/json" - Network accessline 369
# Get gene information by symbol curl "https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json" - Network accessline 370
curl "https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json" - Network accessline 372
# Get gene by NCBI Gene ID curl "https://www.metabolomicsworkbench.org/rest/gene/gene_id/31/all/json" - Network accessline 373
curl "https://www.metabolomicsworkbench.org/rest/gene/gene_id/31/all/json" - Network accessline 375
# Search by gene name curl "https://www.metabolomicsworkbench.org/rest/gene/gene_name/carboxylase/summary/json" - Network accessline 376
curl "https://www.metabolomicsworkbench.org/rest/gene/gene_name/carboxylase/summary/json" - Network accessline 424
# Get protein information by UniProt ID curl "https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json" - Network accessline 425
curl "https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json" - Network accessline 427
# Get protein by gene symbol curl "https://www.metabolomicsworkbench.org/rest/protein/gene_symbol/ACACA/all/json" - Network accessline 428
curl "https://www.metabolomicsworkbench.org/rest/protein/gene_symbol/ACACA/all/json" - Network accessline 430
# Get protein sequence curl "https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/seq/json" - Network accessline 431
curl "https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/seq/json" - Network accessline 433
# Search by RefSeq ID curl "https://www.metabolomicsworkbench.org/rest/protein/refseq_id/NP_001084/all/json" - Network accessline 434
curl "https://www.metabolomicsworkbench.org/rest/protein/refseq_id/NP_001084/all/json" - Network accessline 458
- **Interactive REST URL Creator**: https://www.metabolomicsworkbench.org/tools/mw_rest.php - Network accessline 459
- **Official API Specification**: https://www.metabolomicsworkbench.org/tools/MWRestAPIv1.1.pdf - Network accessline 470
# 1. Standardize metabolite name using RefMet metabolite = "citrate" response = requests.get(f'https://www.metabolomicsworkbench.org/rest/refmet/match/{metabolite}/name/json') - Network accessline 471
metabolite = "citrate" response = requests.get(f'https://www.metabolomicsworkbench.org/rest/refmet/match/{metabolite}/name/json') standardized_name = response.json()['name'] - Network accessline 472
response = requests.get(f'https://www.metabolomicsworkbench.org/rest/refmet/match/{metabolite}/name/json') - Network accessline 475
# 2. Search for studies containing this metabolite response = requests.get(f'https://www.metabolomicsworkbench.org/rest/study/refmet_name/{standardized_name}/summary/json') - Network accessline 476
response = requests.get(f'https://www.metabolomicsworkbench.org/rest/study/refmet_name/{standardized_name}/summary/json') - Network accessline 479
# 3. Get detailed data from a specific study study_id = studies[0]['study_id'] response = requests.get(f'https://www.metabolomicsworkbench.org/rest/study/study_id/{study_id}/data/json') - Network accessline 480
study_id = studies[0]['study_id'] response = requests.get(f'https://www.metabolomicsworkbench.org/rest/study/study_id/{study_id}/data/json') data = response.json() - Network accessline 481
response = requests.get(f'https://www.metabolomicsworkbench.org/rest/study/study_id/{study_id}/data/json') - Network accessline 484
# 4. Perform m/z search for compound identification mz_value = 180.06 response = requests.get(f'https://www.metabolomicsworkbench.org/rest/moverz/MB/{mz_value}/M+H/0.5/json') - Network accessline 485
mz_value = 180.06 response = requests.get(f'https://www.metabolomicsworkbench.org/rest/moverz/MB/{mz_value}/M+H/0.5/json') matches = response.json() - Network accessline 486
response = requests.get(f'https://www.metabolomicsworkbench.org/rest/moverz/MB/{mz_value}/M+H/0.5/json') - Network accessline 489
# 5. Get compound structure regno = matches[0]['regno'] response = requests.get(f'https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/png') - Network accessline 490
regno = matches[0]['regno'] response = requests.get(f'https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/png') with open('structure.png', 'wb') as f: - Network accessline 491
response = requests.get(f'https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/png')
skills/molecular-dynamics/SKILL.md
- Network accessline 15
- **OpenMM** (https://openmm.org/): High-performance MD simulation engine with GPU support, Python API, and flexible force field support - Network accessline 16
- **MDAnalysis** (https://mdanalysis.org/): Python library for reading, writing, and analyzing MD trajectories from all major simulation packages - Network accessline 450
- **OpenMM documentation**: https://openmm.org/documentation.html - Network accessline 451
- **MDAnalysis user guide**: https://docs.mdanalysis.org/ - Network accessline 452
- **GROMACS** (alternative MD engine): https://manual.gromacs.org/ - Network accessline 453
- **NAMD** (alternative): https://www.ks.uiuc.edu/Research/namd/ - Network accessline 454
- **CHARMM-GUI** (web-based system builder): https://charmm-gui.org/ - Network accessline 455
- **AmberTools** (free Amber tools): https://ambermd.org/AmberTools.php
skills/molecule-evolution-agent/evolution_agent.py
- Executable scriptline 1
Executable file
skills/molfeat/SKILL.md
- Network accessline 502
- **Official Documentation**: https://molfeat-docs.datamol.io/ - Network accessline 503
- **GitHub Repository**: https://github.com/datamol-io/molfeat - Network accessline 504
- **PyPI Package**: https://pypi.org/project/molfeat/ - Network accessline 505
- **Tutorial**: https://portal.valencelabs.com/datamol/post/types-of-featurizers-b1e8HHrbFMkbun6
skills/monarch-database/SKILL.md
- Network accessline 13
The Monarch Initiative (https://monarchinitiative.org/) is a multi-species integrated knowledgebase that links genes, diseases, and phenotypes across humans and model organisms. It integrates data from over 40 sources including OMIM, ORPHAN - Network accessline 21
**Key resources:** - Monarch portal: https://monarchinitiative.org/ - Network accessline 22
- Monarch portal: https://monarchinitiative.org/ - Network accessline 23
- Monarch API v3: https://api-v3.monarchinitiative.org/v3/ - Network accessline 24
- API docs: https://api-v3.monarchinitiative.org/v3/docs - Network accessline 25
- HPO browser: https://hpo.jax.org/ - Network accessline 43
Base URL: `https://api-v3.monarchinitiative.org/v3/` - Network accessline 48
BASE_URL = "https://api-v3.monarchinitiative.org/v3" - Network accessline 51
"""Make a GET request to the Monarch API.""" url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 52
url = f"{BASE_URL}/{endpoint}" response = requests.get(url, params=params, headers={"Accept": "application/json"}) response.raise_for_status() - Network accessline 53
response = requests.get(url, params=params, headers={"Accept": "application/json"}) - Network accessline 264
top_n: Number of top candidates to return """ BASE_URL = "https://api-v3.monarchinitiative.org/v3" - Network accessline 266
BASE_URL = "https://api-v3.monarchinitiative.org/v3" - Network accessline 271
for hpo_id in patient_hpo_terms: data = requests.get( - Network accessline 272
data = requests.get( - Network accessline 367
- **Monarch portal**: https://monarchinitiative.org/ - Network accessline 368
- **API v3 docs**: https://api-v3.monarchinitiative.org/v3/docs - Network accessline 369
- **HPO browser**: https://hpo.jax.org/ - Network accessline 370
- **MONDO ontology**: https://mondo.monarchinitiative.org/ - Network accessline 372
- **Phenomizer** (HPO-based diagnosis): https://compbio.charite.de/phenomizer/
skills/monarch-database/references/phenotype_ontology.md
- Network accessline 110
"""Convert OMIM ID to MONDO ID via Monarch API.""" search_id = f"OMIM:{omim_id}" if not omim_id.startswith("OMIM:") else omim_id data = requests.get( - Network accessline 111
search_id = f"OMIM:{omim_id}" if not omim_id.startswith("OMIM:") else omim_id data = requests.get( f"https://api-v3.monarchinitiative.org/v3/entity/{search_id}" - Network accessline 112
data = requests.get( - Network accessline 113
f"https://api-v3.monarchinitiative.org/v3/entity/{search_id}" - Network accessline 150
"""Compute semantic similarity between two sets of disease phenotypes.""" # Get phenotype sets for each disease url = "https://api-v3.monarchinitiative.org/v3/semsim/compare" - Network accessline 151
# Get phenotype sets for each disease url = "https://api-v3.monarchinitiative.org/v3/semsim/compare" params = { - Network accessline 152
url = "https://api-v3.monarchinitiative.org/v3/semsim/compare" - Network accessline 156
"metric": metric } response = requests.get(url, params=params) - Network accessline 157
} response = requests.get(url, params=params) return response.json() - Network accessline 158
response = requests.get(url, params=params)
skills/mpn-research-assistant/SKILL.md
- Executable scriptline 1
Executable file
skills/multi-search-engine/CHANNELLOG.md
- Network accessline 38
// Google搜索 web_fetch({"url": "https://www.google.com/search?q=python"}) - Network accessline 39
web_fetch({"url": "https://www.google.com/search?q=python"}) - Network accessline 41
// 隐私搜索 web_fetch({"url": "https://duckduckgo.com/html/?q=privacy"}) - Network accessline 42
web_fetch({"url": "https://duckduckgo.com/html/?q=privacy"}) - Network accessline 44
// 站内搜索 web_fetch({"url": "https://www.google.com/search?q=site:github.com+python"}) - Network accessline 45
web_fetch({"url": "https://www.google.com/search?q=site:github.com+python"})
skills/multi-search-engine/SKILL.md
- Network accessline 12
### Domestic (8) - **Baidu**: `https://www.baidu.com/s?wd={keyword}` - Network accessline 13
- **Baidu**: `https://www.baidu.com/s?wd={keyword}` - Network accessline 14
- **Bing CN**: `https://cn.bing.com/search?q={keyword}&ensearch=0` - Network accessline 15
- **Bing INT**: `https://cn.bing.com/search?q={keyword}&ensearch=1` - Network accessline 16
- **360**: `https://www.so.com/s?q={keyword}` - Network accessline 17
- **Sogou**: `https://sogou.com/web?query={keyword}` - Network accessline 18
- **WeChat**: `https://wx.sogou.com/weixin?type=2&query={keyword}` - Network accessline 19
- **Toutiao**: `https://so.toutiao.com/search?keyword={keyword}` - Network accessline 20
- **Jisilu**: `https://www.jisilu.cn/explore/?keyword={keyword}` - Network accessline 22
### International (9) - **Google**: `https://www.google.com/search?q={keyword}` - Network accessline 23
- **Google**: `https://www.google.com/search?q={keyword}` - Network accessline 24
- **Google HK**: `https://www.google.com.hk/search?q={keyword}` - Network accessline 25
- **DuckDuckGo**: `https://duckduckgo.com/html/?q={keyword}` - Network accessline 26
- **Yahoo**: `https://search.yahoo.com/search?p={keyword}` - Network accessline 27
- **Startpage**: `https://www.startpage.com/sp/search?query={keyword}` - Network accessline 28
- **Brave**: `https://search.brave.com/search?q={keyword}` - Network accessline 29
- **Ecosia**: `https://www.ecosia.org/search?q={keyword}` - Network accessline 30
- **Qwant**: `https://www.qwant.com/?q={keyword}` - Network accessline 31
- **WolframAlpha**: `https://www.wolframalpha.com/input?i={keyword}` - Network accessline 36
// Basic search web_fetch({"url": "https://www.google.com/search?q=python+tutorial"}) - Network accessline 37
web_fetch({"url": "https://www.google.com/search?q=python+tutorial"}) - Network accessline 39
// Site-specific web_fetch({"url": "https://www.google.com/search?q=site:github.com+react"}) - Network accessline 40
web_fetch({"url": "https://www.google.com/search?q=site:github.com+react"}) - Network accessline 42
// File type web_fetch({"url": "https://www.google.com/search?q=machine+learning+filetype:pdf"}) - Network accessline 43
web_fetch({"url": "https://www.google.com/search?q=machine+learning+filetype:pdf"}) - Network accessline 45
// Time filter (past week) web_fetch({"url": "https://www.google.com/search?q=ai+news&tbs=qdr:w"}) - Network accessline 46
web_fetch({"url": "https://www.google.com/search?q=ai+news&tbs=qdr:w"}) - Network accessline 48
// Privacy search web_fetch({"url": "https://duckduckgo.com/html/?q=privacy+tools"}) - Network accessline 49
web_fetch({"url": "https://duckduckgo.com/html/?q=privacy+tools"}) - Network accessline 51
// DuckDuckGo Bangs web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+tensorflow"}) - Network accessline 52
web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+tensorflow"}) - Network accessline 54
// Knowledge calculation web_fetch({"url": "https://www.wolframalpha.com/input?i=100+USD+to+CNY"}) - Network accessline 55
web_fetch({"url": "https://www.wolframalpha.com/input?i=100+USD+to+CNY"})
skills/multi-search-engine/config.json
- Network accessline 2
"name": "multi-search-engine", "engines": [ {"name": "Baidu", "url": "https://www.baidu.com/s?wd={keyword}", "region": "cn"}, - Network accessline 3
"engines": [ {"name": "Baidu", "url": "https://www.baidu.com/s?wd={keyword}", "region": "cn"}, {"name": "Bing CN", "url": "https://cn.bing.com/search?q={keyword}&ensearch=0", "region": "cn"}, - Network accessline 4
{"name": "Baidu", "url": "https://www.baidu.com/s?wd={keyword}", "region": "cn"}, - Network accessline 5
{"name": "Bing CN", "url": "https://cn.bing.com/search?q={keyword}&ensearch=0", "region": "cn"}, - Network accessline 6
{"name": "Bing INT", "url": "https://cn.bing.com/search?q={keyword}&ensearch=1", "region": "cn"}, - Network accessline 7
{"name": "360", "url": "https://www.so.com/s?q={keyword}", "region": "cn"}, - Network accessline 8
{"name": "Sogou", "url": "https://sogou.com/web?query={keyword}", "region": "cn"}, - Network accessline 9
{"name": "WeChat", "url": "https://wx.sogou.com/weixin?type=2&query={keyword}", "region": "cn"}, - Network accessline 10
{"name": "Toutiao", "url": "https://so.toutiao.com/search?keyword={keyword}", "region": "cn"}, - Network accessline 11
{"name": "Jisilu", "url": "https://www.jisilu.cn/explore/?keyword={keyword}", "region": "cn"}, - Network accessline 12
{"name": "Google", "url": "https://www.google.com/search?q={keyword}", "region": "global"}, - Network accessline 13
{"name": "Google HK", "url": "https://www.google.com.hk/search?q={keyword}", "region": "global"}, - Network accessline 14
{"name": "DuckDuckGo", "url": "https://duckduckgo.com/html/?q={keyword}", "region": "global"}, - Network accessline 15
{"name": "Yahoo", "url": "https://search.yahoo.com/search?p={keyword}", "region": "global"}, - Network accessline 16
{"name": "Startpage", "url": "https://www.startpage.com/sp/search?query={keyword}", "region": "global"}, - Network accessline 17
{"name": "Brave", "url": "https://search.brave.com/search?q={keyword}", "region": "global"}, - Network accessline 18
{"name": "Ecosia", "url": "https://www.ecosia.org/search?q={keyword}", "region": "global"}, - Network accessline 19
{"name": "Qwant", "url": "https://www.qwant.com/?q={keyword}", "region": "global"}, - Network accessline 20
{"name": "WolframAlpha", "url": "https://www.wolframalpha.com/input?i={keyword}", "region": "global"}
skills/multi-search-engine/metadata.json
- Access to secretsline 6
[Credential-related source omitted]
skills/multi-search-engine/references/international-search.md
- Network accessline 7
| 操作符 | 功能 | 示例 | URL | |--------|------|------|-----| | `""` | 精确匹配 | `"machine learning"` | `https://www.google.com/search?q=%22machine+learning%22` | - Network accessline 8
|--------|------|------|-----| | `""` | 精确匹配 | `"machine learning"` | `https://www.google.com/search?q=%22machine+learning%22` | | `-` | 排除关键词 | `python -snake` | `https://www.google.com/search?q=python+-snake` | - Network accessline 9
| `""` | 精确匹配 | `"machine learning"` | `https://www.google.com/search?q=%22machine+learning%22` | - Network accessline 10
| `-` | 排除关键词 | `python -snake` | `https://www.google.com/search?q=python+-snake` | - Network accessline 11
| `OR` | 或运算 | `machine learning OR deep learning` | `https://www.google.com/search?q=machine+learning+OR+deep+learning` | - Network accessline 12
| `*` | 通配符 | `machine * algorithms` | `https://www.google.com/search?q=machine+*+algorithms` | - Network accessline 13
| `()` | 分组 | `(apple OR microsoft) phones` | `https://www.google.com/search?q=(apple+OR+microsoft)+phones` | - Network accessline 14
| `..` | 数字范围 | `laptop $500..$1000` | `https://www.google.com/search?q=laptop+%24500..%241000` | - Network accessline 31
| 参数 | 含义 | URL示例 | |------|------|---------| | `tbs=qdr:h` | 过去1小时 | `https://www.google.com/search?q=news&tbs=qdr:h` | - Network accessline 32
|------|------|---------| | `tbs=qdr:h` | 过去1小时 | `https://www.google.com/search?q=news&tbs=qdr:h` | | `tbs=qdr:d` | 过去24小时 | `https://www.google.com/search?q=news&tbs=qdr:d` | - Network accessline 33
| `tbs=qdr:h` | 过去1小时 | `https://www.google.com/search?q=news&tbs=qdr:h` | - Network accessline 34
| `tbs=qdr:d` | 过去24小时 | `https://www.google.com/search?q=news&tbs=qdr:d` | - Network accessline 35
| `tbs=qdr:w` | 过去1周 | `https://www.google.com/search?q=news&tbs=qdr:w` | - Network accessline 36
| `tbs=qdr:m` | 过去1月 | `https://www.google.com/search?q=news&tbs=qdr:m` | - Network accessline 37
| `tbs=qdr:y` | 过去1年 | `https://www.google.com/search?q=news&tbs=qdr:y` | - Network accessline 42
| 参数 | 功能 | 示例 | |------|------|------| | `hl=en` | 界面语言 | `https://www.google.com/search?q=test&hl=en` | - Network accessline 43
|------|------|------| | `hl=en` | 界面语言 | `https://www.google.com/search?q=test&hl=en` | | `lr=lang_zh-CN` | 搜索结果语言 | `https://www.google.com/search?q=test&lr=lang_zh-CN` | - Network accessline 44
| `hl=en` | 界面语言 | `https://www.google.com/search?q=test&hl=en` | - Network accessline 45
| `lr=lang_zh-CN` | 搜索结果语言 | `https://www.google.com/search?q=test&lr=lang_zh-CN` | - Network accessline 46
| `cr=countryCN` | 国家/地区 | `https://www.google.com/search?q=test&cr=countryCN` | - Network accessline 47
| `gl=us` | 地理位置 | `https://www.google.com/search?q=test&gl=us` | - Network accessline 51
| 类型 | URL | 说明 | |------|-----|------| | 图片搜索 | `https://www.google.com/search?q={keyword}&tbm=isch` | `tbm=isch` 表示图片 | - Network accessline 52
|------|-----|------| | 图片搜索 | `https://www.google.com/search?q={keyword}&tbm=isch` | `tbm=isch` 表示图片 | | 新闻搜索 | `https://www.google.com/search?q={keyword}&tbm=nws` | `tbm=nws` 表示新闻 | - Network accessline 53
| 图片搜索 | `https://www.google.com/search?q={keyword}&tbm=isch` | `tbm=isch` 表示图片 | - Network accessline 54
| 新闻搜索 | `https://www.google.com/search?q={keyword}&tbm=nws` | `tbm=nws` 表示新闻 | - Network accessline 55
| 视频搜索 | `https://www.google.com/search?q={keyword}&tbm=vid` | `tbm=vid` 表示视频 | - Network accessline 56
| 地图搜索 | `https://www.google.com/search?q={keyword}&tbm=map` | `tbm=map` 表示地图 | - Network accessline 57
| 购物搜索 | `https://www.google.com/search?q={keyword}&tbm=shop` | `tbm=shop` 表示购物 | - Network accessline 58
| 图书搜索 | `https://www.google.com/search?q={keyword}&tbm=bks` | `tbm=bks` 表示图书 | - Network accessline 59
| 学术搜索 | `https://scholar.google.com/scholar?q={keyword}` | Google Scholar | - Network accessline 64
// 1. 搜索GitHub上的Python机器学习项目 web_fetch({"url": "https://www.google.com/search?q=site:github.com+python+machine+learning"}) - Network accessline 65
web_fetch({"url": "https://www.google.com/search?q=site:github.com+python+machine+learning"}) - Network accessline 67
// 2. 搜索2024年的PDF格式机器学习教程 web_fetch({"url": "https://www.google.com/search?q=machine+learning+tutorial+filetype:pdf&tbs=cdr:1,cd_min:1/1/2024"}) - Network accessline 68
web_fetch({"url": "https://www.google.com/search?q=machine+learning+tutorial+filetype:pdf&tbs=cdr:1,cd_min:1/1/2024"}) - Network accessline 70
// 3. 搜索标题包含"tutorial"的Python相关页面 web_fetch({"url": "https://www.google.com/search?q=intitle:tutorial+python"}) - Network accessline 71
web_fetch({"url": "https://www.google.com/search?q=intitle:tutorial+python"}) - Network accessline 73
// 4. 搜索过去一周的新闻 web_fetch({"url": "https://www.google.com/search?q=AI+breakthrough&tbs=qdr:w&tbm=nws"}) - Network accessline 74
web_fetch({"url": "https://www.google.com/search?q=AI+breakthrough&tbs=qdr:w&tbm=nws"}) - Network accessline 76
// 5. 搜索中文内容（界面英文，结果中文） web_fetch({"url": "https://www.google.com/search?q=人工智能&lr=lang_zh-CN&hl=en"}) - Network accessline 77
web_fetch({"url": "https://www.google.com/search?q=人工智能&lr=lang_zh-CN&hl=en"}) - Network accessline 79
// 6. 搜索特定价格范围的笔记本电脑 web_fetch({"url": "https://www.google.com/search?q=laptop+%241000..%242000+best+rating"}) - Network accessline 80
web_fetch({"url": "https://www.google.com/search?q=laptop+%241000..%242000+best+rating"}) - Network accessline 82
// 7. 搜索排除Wikipedia的结果 web_fetch({"url": "https://www.google.com/search?q=python+programming+-wikipedia"}) - Network accessline 83
web_fetch({"url": "https://www.google.com/search?q=python+programming+-wikipedia"}) - Network accessline 85
// 8. 搜索学术文献 web_fetch({"url": "https://scholar.google.com/scholar?q=deep+learning+optimization"}) - Network accessline 86
web_fetch({"url": "https://scholar.google.com/scholar?q=deep+learning+optimization"}) - Network accessline 88
// 9. 搜索缓存页面（查看已删除内容） web_fetch({"url": "https://webcache.googleusercontent.com/search?q=cache:example.com"}) - Network accessline 89
web_fetch({"url": "https://webcache.googleusercontent.com/search?q=cache:example.com"}) - Network accessline 91
// 10. 搜索相关网站 web_fetch({"url": "https://www.google.com/search?q=related:stackoverflow.com"}) - Network accessline 92
web_fetch({"url": "https://www.google.com/search?q=related:stackoverflow.com"}) - Network accessline 102
|------|------|------| | **Bangs 快捷** | `!缩写` | `!g python` → Google搜索 | | **密码生成** | `password` | `https://duckduckgo.com/?q=password+20` | - Network accessline 103
| **Bangs 快捷** | `!缩写` | `!g python` → Google搜索 | | **密码生成** | `password` | `https://duckduckgo.com/?q=password+20` | | **颜色转换** | `color` | `https://duckduckgo.com/?q=+%23FF5733` | - Network accessline 104
| **密码生成** | `password` | `https://duckduckgo.com/?q=password+20` | - Network accessline 105
| **颜色转换** | `color` | `https://duckduckgo.com/?q=+%23FF5733` | - Network accessline 106
| **短链接** | `shorten` | `https://duckduckgo.com/?q=shorten+example.com` | - Network accessline 107
| **二维码生成** | `qr` | `https://duckduckgo.com/?q=qr+hello+world` | - Network accessline 108
| **生成UUID** | `uuid` | `https://duckduckgo.com/?q=uuid` | - Network accessline 109
| **Base64编解码** | `base64` | `https://duckduckgo.com/?q=base64+hello` | - Network accessline 161
| 参数 | 功能 | 示例 | |------|------|------| | `kp=1` | 严格安全搜索 | `https://duckduckgo.com/html/?q=test&kp=1` | - Network accessline 162
|------|------|------| | `kp=1` | 严格安全搜索 | `https://duckduckgo.com/html/?q=test&kp=1` | | `kp=-1` | 关闭安全搜索 | `https://duckduckgo.com/html/?q=test&kp=-1` | - Network accessline 163
| `kp=1` | 严格安全搜索 | `https://duckduckgo.com/html/?q=test&kp=1` | - Network accessline 164
| `kp=-1` | 关闭安全搜索 | `https://duckduckgo.com/html/?q=test&kp=-1` | - Network accessline 165
| `kl=cn` | 中国区域 | `https://duckduckgo.com/html/?q=news&kl=cn` | - Network accessline 166
| `kl=us-en` | 美国英文 | `https://duckduckgo.com/html/?q=news&kl=us-en` | - Network accessline 167
| `ia=web` | 网页结果 | `https://duckduckgo.com/?q=test&ia=web` | - Network accessline 168
| `ia=images` | 图片结果 | `https://duckduckgo.com/?q=test&ia=images` | - Network accessline 169
| `ia=news` | 新闻结果 | `https://duckduckgo.com/?q=test&ia=news` | - Network accessline 170
| `ia=videos` | 视频结果 | `https://duckduckgo.com/?q=test&ia=videos` | - Network accessline 175
// 1. 使用Bang跳转到Google搜索 web_fetch({"url": "https://duckduckgo.com/html/?q=!g+machine+learning"}) - Network accessline 176
web_fetch({"url": "https://duckduckgo.com/html/?q=!g+machine+learning"}) - Network accessline 178
// 2. 直接搜索GitHub上的项目 web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+react"}) - Network accessline 179
web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+react"}) - Network accessline 181
// 3. 查找Stack Overflow答案 web_fetch({"url": "https://duckduckgo.com/html/?q=!so+python+list+comprehension"}) - Network accessline 182
web_fetch({"url": "https://duckduckgo.com/html/?q=!so+python+list+comprehension"}) - Network accessline 184
// 4. 生成密码 web_fetch({"url": "https://duckduckgo.com/?q=password+16"}) - Network accessline 185
web_fetch({"url": "https://duckduckgo.com/?q=password+16"}) - Network accessline 187
// 5. Base64编码 web_fetch({"url": "https://duckduckgo.com/?q=base64+hello+world"}) - Network accessline 188
web_fetch({"url": "https://duckduckgo.com/?q=base64+hello+world"}) - Network accessline 190
// 6. 颜色代码转换 web_fetch({"url": "https://duckduckgo.com/?q=%23FF5733"}) - Network accessline 191
web_fetch({"url": "https://duckduckgo.com/?q=%23FF5733"}) - Network accessline 193
// 7. 搜索YouTube视频 web_fetch({"url": "https://duckduckgo.com/html/?q=!yt+python+tutorial"}) - Network accessline 194
web_fetch({"url": "https://duckduckgo.com/html/?q=!yt+python+tutorial"}) - Network accessline 196
// 8. 查看Wikipedia web_fetch({"url": "https://duckduckgo.com/html/?q=!w+artificial+intelligence"}) - Network accessline 197
web_fetch({"url": "https://duckduckgo.com/html/?q=!w+artificial+intelligence"}) - Network accessline 199
// 9. 亚马逊商品搜索 web_fetch({"url": "https://duckduckgo.com/html/?q=!a+laptop"}) - Network accessline 200
web_fetch({"url": "https://duckduckgo.com/html/?q=!a+laptop"}) - Network accessline 202
// 10. 生成二维码 web_fetch({"url": "https://duckduckgo.com/?q=qr+https://github.com"}) - Network accessline 203
web_fetch({"url": "https://duckduckgo.com/?q=qr+https://github.com"}) - Network accessline 221
| 参数 | 功能 | 示例 | |------|------|------| | `tf=pw` | 本周 | `https://search.brave.com/search?q=news&tf=pw` | - Network accessline 222
|------|------|------| | `tf=pw` | 本周 | `https://search.brave.com/search?q=news&tf=pw` | | `tf=pm` | 本月 | `https://search.brave.com/search?q=tech&tf=pm` | - Network accessline 223
| `tf=pw` | 本周 | `https://search.brave.com/search?q=news&tf=pw` | - Network accessline 224
| `tf=pm` | 本月 | `https://search.brave.com/search?q=tech&tf=pm` | - Network accessline 225
| `tf=py` | 本年 | `https://search.brave.com/search?q=AI&tf=py` | - Network accessline 226
| `safesearch=strict` | 严格安全 | `https://search.brave.com/search?q=test&safesearch=strict` | - Network accessline 227
| `source=web` | 网页搜索 | 默认 | | `source=news` | 新闻搜索 | `https://search.brave.com/search?q=tech&source=news` | | `source=images` | 图片搜索 | `https://search.brave.com/search?q=cat&source=images` | - Network accessline 228
| `source=news` | 新闻搜索 | `https://search.brave.com/search?q=tech&source=news` | - Network accessline 229
| `source=images` | 图片搜索 | `https://search.brave.com/search?q=cat&source=images` | - Network accessline 230
| `source=videos` | 视频搜索 | `https://search.brave.com/search?q=music&source=videos` | - Network accessline 246
// 1. 本周科技新闻 web_fetch({"url": "https://search.brave.com/search?q=technology&tf=pw&source=news"}) - Network accessline 247
web_fetch({"url": "https://search.brave.com/search?q=technology&tf=pw&source=news"}) - Network accessline 249
// 2. 本月AI发展 web_fetch({"url": "https://search.brave.com/search?q=artificial+intelligence&tf=pm"}) - Network accessline 250
web_fetch({"url": "https://search.brave.com/search?q=artificial+intelligence&tf=pm"}) - Network accessline 252
// 3. 图片搜索 web_fetch({"url": "https://search.brave.com/search?q=machine+learning&source=images"}) - Network accessline 253
web_fetch({"url": "https://search.brave.com/search?q=machine+learning&source=images"}) - Network accessline 255
// 4. 视频教程 web_fetch({"url": "https://search.brave.com/search?q=python+tutorial&source=videos"}) - Network accessline 256
web_fetch({"url": "https://search.brave.com/search?q=python+tutorial&source=videos"}) - Network accessline 258
// 5. 使用独立索引搜索 web_fetch({"url": "https://search.brave.com/search?q=privacy+tools"}) - Network accessline 259
web_fetch({"url": "https://search.brave.com/search?q=privacy+tools"}) - Network accessline 268
| 类型 | 查询示例 | URL | |------|---------|-----| | **数学计算** | `integrate x^2 dx` | `https://www.wolframalpha.com/input?i=integrate+x%5E2+dx` | - Network accessline 269
|------|---------|-----| | **数学计算** | `integrate x^2 dx` | `https://www.wolframalpha.com/input?i=integrate+x%5E2+dx` | | **单位换算** | `100 miles to km` | `https://www.wolframalpha.com/input?i=100+miles+to+km` | - Network accessline 270
| **数学计算** | `integrate x^2 dx` | `https://www.wolframalpha.com/input?i=integrate+x%5E2+dx` | - Network accessline 271
| **单位换算** | `100 miles to km` | `https://www.wolframalpha.com/input?i=100+miles+to+km` | - Network accessline 272
| **货币转换** | `100 USD to CNY` | `https://www.wolframalpha.com/input?i=100+USD+to+CNY` | - Network accessline 273
| **股票数据** | `AAPL stock` | `https://www.wolframalpha.com/input?i=AAPL+stock` | - Network accessline 274
| **天气查询** | `weather in Beijing` | `https://www.wolframalpha.com/input?i=weather+in+Beijing` | - Network accessline 275
| **人口数据** | `population of China` | `https://www.wolframalpha.com/input?i=population+of+China` | - Network accessline 276
| **化学元素** | `properties of gold` | `https://www.wolframalpha.com/input?i=properties+of+gold` | - Network accessline 277
| **营养成分** | `nutrition of apple` | `https://www.wolframalpha.com/input?i=nutrition+of+apple` | - Network accessline 287
// 1. 计算积分 web_fetch({"url": "https://www.wolframalpha.com/input?i=integrate+sin%28x%29+from+0+to+pi"}) - Network accessline 288
web_fetch({"url": "https://www.wolframalpha.com/input?i=integrate+sin%28x%29+from+0+to+pi"}) - Network accessline 290
// 2. 解方程 web_fetch({"url": "https://www.wolframalpha.com/input?i=solve+x%5E2-5x%2B6%3D0"}) - Network accessline 291
web_fetch({"url": "https://www.wolframalpha.com/input?i=solve+x%5E2-5x%2B6%3D0"}) - Network accessline 293
// 3. 货币实时汇率 web_fetch({"url": "https://www.wolframalpha.com/input?i=100+USD+to+CNY"}) - Network accessline 294
web_fetch({"url": "https://www.wolframalpha.com/input?i=100+USD+to+CNY"}) - Network accessline 296
// 4. 股票实时数据 web_fetch({"url": "https://www.wolframalpha.com/input?i=Apple+stock+price"}) - Network accessline 297
web_fetch({"url": "https://www.wolframalpha.com/input?i=Apple+stock+price"}) - Network accessline 299
// 5. 城市天气 web_fetch({"url": "https://www.wolframalpha.com/input?i=weather+in+Shanghai+tomorrow"}) - Network accessline 300
web_fetch({"url": "https://www.wolframalpha.com/input?i=weather+in+Shanghai+tomorrow"}) - Network accessline 302
// 6. 国家统计信息 web_fetch({"url": "https://www.wolframalpha.com/input?i=GDP+of+China+vs+USA"}) - Network accessline 303
web_fetch({"url": "https://www.wolframalpha.com/input?i=GDP+of+China+vs+USA"}) - Network accessline 305
// 7. 化学计算 web_fetch({"url": "https://www.wolframalpha.com/input?i=molar+mass+of+H2SO4"}) - Network accessline 306
web_fetch({"url": "https://www.wolframalpha.com/input?i=molar+mass+of+H2SO4"}) - Network accessline 308
// 8. 物理常数 web_fetch({"url": "https://www.wolframalpha.com/input?i=speed+of+light"}) - Network accessline 309
web_fetch({"url": "https://www.wolframalpha.com/input?i=speed+of+light"}) - Network accessline 311
// 9. 营养信息 web_fetch({"url": "https://www.wolframalpha.com/input?i=calories+in+banana"}) - Network accessline 312
web_fetch({"url": "https://www.wolframalpha.com/input?i=calories+in+banana"}) - Network accessline 314
// 10. 历史日期 web_fetch({"url": "https://www.wolframalpha.com/input?i=events+on+July+20+1969"}) - Network accessline 315
web_fetch({"url": "https://www.wolframalpha.com/input?i=events+on+July+20+1969"}) - Network accessline 349
// 1. 隐私搜索 web_fetch({"url": "https://www.startpage.com/sp/search?query=privacy+tools"}) - Network accessline 350
web_fetch({"url": "https://www.startpage.com/sp/search?query=privacy+tools"}) - Network accessline 352
// 2. 图片隐私搜索 web_fetch({"url": "https://www.startpage.com/sp/search?query=nature&cat=images"}) - Network accessline 353
web_fetch({"url": "https://www.startpage.com/sp/search?query=nature&cat=images"}) - Network accessline 355
// 3. 本周新闻（隐私模式） web_fetch({"url": "https://www.startpage.com/sp/search?query=tech+news&time=week&cat=news"}) - Network accessline 356
web_fetch({"url": "https://www.startpage.com/sp/search?query=tech+news&time=week&cat=news"}) - Network accessline 358
// 4. 英文结果搜索 web_fetch({"url": "https://www.startpage.com/sp/search?query=machine+learning&language=english"}) - Network accessline 359
web_fetch({"url": "https://www.startpage.com/sp/search?query=machine+learning&language=english"}) - Network accessline 386
// 获取不同视角 const searches = [ { engine: "Google", url: `https://www.google.com/search?q=${keyword}&tbs=qdr:m` }, - Network accessline 387
const searches = [ { engine: "Google", url: `https://www.google.com/search?q=${keyword}&tbs=qdr:m` }, { engine: "Brave", url: `https://search.brave.com/search?q=${keyword}&tf=pm` }, - Network accessline 388
{ engine: "Google", url: `https://www.google.com/search?q=${keyword}&tbs=qdr:m` }, - Network accessline 389
{ engine: "Brave", url: `https://search.brave.com/search?q=${keyword}&tf=pm` }, - Network accessline 390
{ engine: "DuckDuckGo", url: `https://duckduckgo.com/html/?q=${keyword}` }, - Network accessline 391
{ engine: "Ecosia", url: `https://www.ecosia.org/search?q=${keyword}` } - Network accessline 412
// GitHub 项目搜索 web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+tensorflow+stars:%3E1000"}) - Network accessline 413
web_fetch({"url": "https://duckduckgo.com/html/?q=!gh+tensorflow+stars:%3E1000"}) - Network accessline 415
// Stack Overflow 问题 web_fetch({"url": "https://duckduckgo.com/html/?q=!so+python+memory+leak"}) - Network accessline 416
web_fetch({"url": "https://duckduckgo.com/html/?q=!so+python+memory+leak"}) - Network accessline 418
// MDN 文档 web_fetch({"url": "https://duckduckgo.com/html/?q=!mdn+javascript+async+await"}) - Network accessline 419
web_fetch({"url": "https://duckduckgo.com/html/?q=!mdn+javascript+async+await"}) - Network accessline 421
// PyPI 包 web_fetch({"url": "https://duckduckgo.com/html/?q=!pypi+requests"}) - Network accessline 422
web_fetch({"url": "https://duckduckgo.com/html/?q=!pypi+requests"}) - Network accessline 424
// npm 包 web_fetch({"url": "https://duckduckgo.com/html/?q=!npm+express"}) - Network accessline 425
web_fetch({"url": "https://duckduckgo.com/html/?q=!npm+express"}) - Network accessline 431
// Google Scholar 论文 web_fetch({"url": "https://scholar.google.com/scholar?q=deep+learning+2024"}) - Network accessline 432
web_fetch({"url": "https://scholar.google.com/scholar?q=deep+learning+2024"}) - Network accessline 434
// 搜索PDF论文 web_fetch({"url": "https://www.google.com/search?q=machine+learning+filetype:pdf+2024"}) - Network accessline 435
web_fetch({"url": "https://www.google.com/search?q=machine+learning+filetype:pdf+2024"}) - Network accessline 437
// arXiv 论文 web_fetch({"url": "https://duckduckgo.com/html/?q=site:arxiv.org+quantum+computing"}) - Network accessline 438
web_fetch({"url": "https://duckduckgo.com/html/?q=site:arxiv.org+quantum+computing"}) - Network accessline 444
// 股票实时数据 web_fetch({"url": "https://www.wolframalpha.com/input?i=AAPL+stock"}) - Network accessline 445
web_fetch({"url": "https://www.wolframalpha.com/input?i=AAPL+stock"}) - Network accessline 447
// 汇率转换 web_fetch({"url": "https://www.wolframalpha.com/input?i=EUR+to+USD"}) - Network accessline 448
web_fetch({"url": "https://www.wolframalpha.com/input?i=EUR+to+USD"}) - Network accessline 450
// 搜索财报PDF web_fetch({"url": "https://www.google.com/search?q=Apple+Q4+2024+earnings+filetype:pdf"}) - Network accessline 451
web_fetch({"url": "https://www.google.com/search?q=Apple+Q4+2024+earnings+filetype:pdf"}) - Network accessline 457
// Google新闻 web_fetch({"url": "https://www.google.com/search?q=breaking+news&tbm=nws&tbs=qdr:h"}) - Network accessline 458
web_fetch({"url": "https://www.google.com/search?q=breaking+news&tbm=nws&tbs=qdr:h"}) - Network accessline 460
// Brave新闻 web_fetch({"url": "https://search.brave.com/search?q=world+news&source=news"}) - Network accessline 461
web_fetch({"url": "https://search.brave.com/search?q=world+news&source=news"}) - Network accessline 463
// DuckDuckGo新闻 web_fetch({"url": "https://duckduckgo.com/html/?q=tech+news&ia=news"}) - Network accessline 464
web_fetch({"url": "https://duckduckgo.com/html/?q=tech+news&ia=news"}) - Network accessline 489
const encoded = encodeURIComponent(keyword); return { google: `https://www.google.com/search?q=${encoded}`, - Network accessline 490
return { google: `https://www.google.com/search?q=${encoded}`, google_hk: `https://www.google.com.hk/search?q=${encoded}`, - Network accessline 491
google: `https://www.google.com/search?q=${encoded}`, - Network accessline 492
google_hk: `https://www.google.com.hk/search?q=${encoded}`, - Network accessline 493
duckduckgo: `https://duckduckgo.com/html/?q=${encoded}`, - Network accessline 494
brave: `https://search.brave.com/search?q=${encoded}`, - Network accessline 495
startpage: `https://www.startpage.com/sp/search?query=${encoded}`, - Network accessline 496
bing_intl: `https://cn.bing.com/search?q=${encoded}&ensearch=1`, - Network accessline 497
yahoo: `https://search.yahoo.com/search?p=${encoded}`, - Network accessline 498
ecosia: `https://www.ecosia.org/search?q=${encoded}`, - Network accessline 499
qwant: `https://www.qwant.com/?q=${encoded}` - Network accessline 517
year: 'qdr:y' }; return `https://www.google.com/search?q=${encodeURIComponent(keyword)}&tbs=${periods[period]}`; - Network accessline 518
}; return `https://www.google.com/search?q=${encodeURIComponent(keyword)}&tbs=${periods[period]}`; } - Network accessline 519
return `https://www.google.com/search?q=${encodeURIComponent(keyword)}&tbs=${periods[period]}`; - Network accessline 533
// 1. 搜索GitHub上高Star的Python项目 web_fetch({"url": "https://www.google.com/search?q=site:github.com+python+stars:%3E1000"}) - Network accessline 534
web_fetch({"url": "https://www.google.com/search?q=site:github.com+python+stars:%3E1000"}) - Network accessline 536
// 2. Stack Overflow最佳答案 web_fetch({"url": "https://duckduckgo.com/html/?q=!so+best+way+to+learn+python"}) - Network accessline 537
web_fetch({"url": "https://duckduckgo.com/html/?q=!so+best+way+to+learn+python"}) - Network accessline 539
// 3. MDN文档查询 web_fetch({"url": "https://duckduckgo.com/html/?q=!mdn+promises"}) - Network accessline 540
web_fetch({"url": "https://duckduckgo.com/html/?q=!mdn+promises"}) - Network accessline 542
// 4. 搜索npm包 web_fetch({"url": "https://duckduckgo.com/html/?q=!npm+axios"}) - Network accessline 543
web_fetch({"url": "https://duckduckgo.com/html/?q=!npm+axios"}) - Network accessline 547
// 5. Google Scholar论文 web_fetch({"url": "https://scholar.google.com/scholar?q=transformer+architecture"}) - Network accessline 548
web_fetch({"url": "https://scholar.google.com/scholar?q=transformer+architecture"}) - Network accessline 550
// 6. 搜索PDF论文 web_fetch({"url": "https://www.google.com/search?q=attention+is+all+you+need+filetype:pdf"}) - Network accessline 551
web_fetch({"url": "https://www.google.com/search?q=attention+is+all+you+need+filetype:pdf"}) - Network accessline 553
// 7. arXiv最新论文 web_fetch({"url": "https://duckduckgo.com/html/?q=site:arxiv.org+abs+quantum"}) - Network accessline 554
web_fetch({"url": "https://duckduckgo.com/html/?q=site:arxiv.org+abs+quantum"}) - Network accessline 558
// 8. Google最新新闻（过去1小时） web_fetch({"url": "https://www.google.com/search?q=breaking+news&tbs=qdr:h&tbm=nws"}) - Network accessline 559
web_fetch({"url": "https://www.google.com/search?q=breaking+news&tbs=qdr:h&tbm=nws"}) - Network accessline 561
// 9. Brave本周科技新闻 web_fetch({"url": "https://search.brave.com/search?q=technology&tf=pw&source=news"}) - Network accessline 562
web_fetch({"url": "https://search.brave.com/search?q=technology&tf=pw&source=news"}) - Network accessline 564
// 10. DuckDuckGo新闻 web_fetch({"url": "https://duckduckgo.com/html/?q=world+news&ia=news"}) - Network accessline 565
web_fetch({"url": "https://duckduckgo.com/html/?q=world+news&ia=news"}) - Network accessline 569
// 11. 股票实时数据 web_fetch({"url": "https://www.wolframalpha.com/input?i=Tesla+stock"}) - Network accessline 570
web_fetch({"url": "https://www.wolframalpha.com/input?i=Tesla+stock"}) - Network accessline 572
// 12. 货币汇率 web_fetch({"url": "https://www.wolframalpha.com/input?i=1+BTC+to+USD"}) - Network accessline 573
web_fetch({"url": "https://www.wolframalpha.com/input?i=1+BTC+to+USD"}) - Network accessline 575
// 13. 公司财报PDF web_fetch({"url": "https://www.google.com/search?q=Microsoft+annual+report+2024+filetype:pdf"}) - Network accessline 576
web_fetch({"url": "https://www.google.com/search?q=Microsoft+annual+report+2024+filetype:pdf"}) - Network accessline 580
// 14. 数学计算 web_fetch({"url": "https://www.wolframalpha.com/input?i=derivative+of+x%5E3+sin%28x%29"}) - Network accessline 581
web_fetch({"url": "https://www.wolframalpha.com/input?i=derivative+of+x%5E3+sin%28x%29"}) - Network accessline 583
// 15. 单位换算 web_fetch({"url": "https://www.wolframalpha.com/input?i=convert+100+miles+to+kilometers"}) - Network accessline 584
web_fetch({"url": "https://www.wolframalpha.com/input?i=convert+100+miles+to+kilometers"}) - Network accessline 586
// 16. 营养信息 web_fetch({"url": "https://www.wolframalpha.com/input?i=protein+in+chicken+breast"}) - Network accessline 587
web_fetch({"url": "https://www.wolframalpha.com/input?i=protein+in+chicken+breast"}) - Network accessline 591
// 17. DuckDuckGo隐私搜索 web_fetch({"url": "https://duckduckgo.com/html/?q=privacy+tools"}) - Network accessline 592
web_fetch({"url": "https://duckduckgo.com/html/?q=privacy+tools"}) - Network accessline 594
// 18. Startpage匿名搜索 web_fetch({"url": "https://www.startpage.com/sp/search?query=secure+messaging"}) - Network accessline 595
web_fetch({"url": "https://www.startpage.com/sp/search?query=secure+messaging"}) - Network accessline 597
// 19. Brave无追踪搜索 web_fetch({"url": "https://search.brave.com/search?q=encryption+software"}) - Network accessline 598
web_fetch({"url": "https://search.brave.com/search?q=encryption+software"}) - Network accessline 602
// 20. Google多条件精确搜索 web_fetch({"url": "https://www.google.com/search?q=%22machine+learning%22+site:github.com+filetype:pdf+2024"}) - Network accessline 603
web_fetch({"url": "https://www.google.com/search?q=%22machine+learning%22+site:github.com+filetype:pdf+2024"}) - Network accessline 605
// 21. 排除特定站点的搜索 web_fetch({"url": "https://www.google.com/search?q=python+tutorial+-wikipedia+-w3schools"}) - Network accessline 606
web_fetch({"url": "https://www.google.com/search?q=python+tutorial+-wikipedia+-w3schools"}) - Network accessline 608
// 22. 价格范围搜索 web_fetch({"url": "https://www.google.com/search?q=laptop+%24800..%241200+best+review"}) - Network accessline 609
web_fetch({"url": "https://www.google.com/search?q=laptop+%24800..%241200+best+review"}) - Network accessline 611
// 23. 使用Bangs快速跳转 web_fetch({"url": "https://duckduckgo.com/html/?q=!g+site:medium.com+python"}) - Network accessline 612
web_fetch({"url": "https://duckduckgo.com/html/?q=!g+site:medium.com+python"}) - Network accessline 614
// 24. 图片搜索（Google） web_fetch({"url": "https://www.google.com/search?q=beautiful+landscape&tbm=isch"}) - Network accessline 615
web_fetch({"url": "https://www.google.com/search?q=beautiful+landscape&tbm=isch"}) - Network accessline 617
// 25. 学术引用搜索 web_fetch({"url": "https://scholar.google.com/scholar?q=author:%22Geoffrey+Hinton%22"}) - Network accessline 618
web_fetch({"url": "https://scholar.google.com/scholar?q=author:%22Geoffrey+Hinton%22"}) - Network accessline 648
- [Google搜索操作符完整列表](https://support.google.com/websearch/answer/...) - Network accessline 649
- [DuckDuckGo Bangs完整列表](https://duckduckgo.com/bang) - Network accessline 650
- [Brave Search文档](https://search.brave.com/help/...) - Network accessline 651
- [WolframAlpha示例](https://www.wolframalpha.com/examples/)
skills/multimodal-medical-imaging/multimodal_agent.py
- Executable scriptline 1
Executable file
skills/networkx/SKILL.md
- Network accessline 431
- **Official Documentation**: https://networkx.org/documentation/latest/ - Network accessline 432
- **Tutorial**: https://networkx.org/documentation/latest/tutorial.html - Network accessline 433
- **Gallery**: https://networkx.org/documentation/latest/auto_examples/index.html - Network accessline 434
- **GitHub**: https://github.com/networkx/networkx
skills/neurokit2/SKILL.md
- Network accessline 276
uv pip install https://github.com/neuropsychology/NeuroKit/zipball/dev - Network accessline 348
- Official Documentation: https://neuropsychology.github.io/NeuroKit/ - Network accessline 349
- GitHub Repository: https://github.com/neuropsychology/NeuroKit - Network accessline 350
- Publication: Makowski et al. (2021). NeuroKit2: A Python toolbox for neurophysiological signal processing. Behavior Research Methods. https://doi.org/10.3758/s13428-020-01516-y
skills/neuropixels-analysis/AI_CURATION.md
- Access to secretsline 299
[Credential-related source omitted] - Access to secretsline 308
[Credential-related source omitted] - Network accessline 343
- [SpikeAgent](https://github.com/SpikeAgent/SpikeAgent) - AI-powered spike sorting assistant - Network accessline 344
- [Anthropic Vision API](https://docs.anthropic.com/en/docs/vision) - Network accessline 345
- [GPT-4 Vision](https://platform.openai.com/docs/guides/vision)
skills/neuropixels-analysis/AUTOMATED_CURATION.md
- Network accessline 39
# Or development version git clone https://github.com/Julie-Fabre/bombcell.git - Network accessline 40
git clone https://github.com/Julie-Fabre/bombcell.git - Network accessline 192
pip install unitmatch # Or from source git clone https://github.com/EnnyvanBeest/UnitMatch.git - Network accessline 194
git clone https://github.com/EnnyvanBeest/UnitMatch.git - Network accessline 354
- [Bombcell GitHub](https://github.com/Julie-Fabre/bombcell) - Network accessline 355
- [UnitMatch GitHub](https://github.com/EnnyvanBeest/UnitMatch) - Network accessline 356
- [SpikeInterface Curation](https://spikeinterface.readthedocs.io/en/stable/modules/curation.html)
skills/neuropixels-analysis/MOTION_CORRECTION.md
- Network accessline 320
- [SpikeInterface Motion Correction Docs](https://spikeinterface.readthedocs.io/en/stable/modules/motion_correction.html) - Network accessline 321
- [Handle Drift Tutorial](https://spikeinterface.readthedocs.io/en/stable/how_to/handle_drift.html) - Network accessline 322
- [DREDge GitHub](https://github.com/evarol/DREDge)
skills/neuropixels-analysis/QUALITY_METRICS.md
skills/neuropixels-analysis/SKILL.md
- Network accessline 338
- **SpikeInterface Docs**: https://spikeinterface.readthedocs.io/ - Network accessline 339
- **Neuropixels Tutorial**: https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html - Network accessline 340
- **Kilosort4 GitHub**: https://github.com/MouseLand/Kilosort - Network accessline 341
- **IBL Neuropixel Tools**: https://github.com/int-brain-lab/ibl-neuropixel - Network accessline 342
- **Allen Institute ecephys**: https://github.com/AllenInstitute/ecephys_spike_sorting - Network accessline 343
- **Bombcell (Automated QC)**: https://github.com/Julie-Fabre/bombcell - Network accessline 344
- **SpikeAgent (AI Curation)**: https://github.com/SpikeAgent/SpikeAgent
skills/neuropixels-analysis/assets/analysis_template.py
- Executable scriptline 1
#!/usr/bin/env python
skills/neuropixels-analysis/scripts/compute_metrics.py
- Executable scriptline 1
#!/usr/bin/env python
skills/neuropixels-analysis/scripts/explore_recording.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/neuropixels-analysis/scripts/export_to_phy.py
- Executable scriptline 1
#!/usr/bin/env python
skills/neuropixels-analysis/scripts/neuropixels_pipeline.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 10
References: - https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html - Network accessline 11
- https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html - Network accessline 12
- https://github.com/AllenInstitute/ecephys_spike_sorting
skills/neuropixels-analysis/scripts/preprocess_recording.py
- Executable scriptline 1
#!/usr/bin/env python
skills/neuropixels-analysis/scripts/run_sorting.py
- Executable scriptline 1
#!/usr/bin/env python
skills/nextflow-development/LICENSE.txt
skills/nextflow-development/SKILL.md
- Network accessline 65
| Problem | Fix | |---------|-----| | Not installed | Install from https://docs.docker.com/get-docker/ | - Network accessline 66
|---------|-----| | Not installed | Install from https://docs.docker.com/get-docker/ | | Permission denied | `sudo usermod -aG docker $USER` then re-login | - Network accessline 67
| Not installed | Install from https://docs.docker.com/get-docker/ | - Dangerous shell operationline 68
| Permission denied | `sudo usermod -aG docker $USER` then re-login | - Dangerous shell operationline 69
| Daemon not running | `sudo systemctl start docker` | - Network accessline 73
| Problem | Fix | |---------|-----| | Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | - Network accessline 74
|---------|-----| | Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | | Version < 23.04 | `nextflow self-update` | - Dangerous shell operationline 75
| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | - Network accessline 75
| Not installed | `curl -s https://get.nextflow.io \| bash && mv nextflow ~/bin/` | - Dangerous shell operationline 82
| Not installed / < 11 | `sudo apt install openjdk-11-jdk` | - Network accessline 284
When publishing results, cite the appropriate pipeline. Citations are available in each nf-core repository's CITATIONS.md file (e.g., https://github.com/nf-core/rnaseq/blob/3.22.2/CITATIONS.md). - Network accessline 288
- **nf-core pipelines:** MIT License (https://nf-co.re/about) - Network accessline 289
- **Nextflow:** Apache License, Version 2.0 (https://www.nextflow.io/about-us.html) - Network accessline 290
- **NCBI SRA Toolkit:** Public Domain (https://github.com/ncbi/sra-tools/blob/master/LICENSE)
skills/nextflow-development/references/installation.md
- Network accessline 14
# Nextflow curl -s https://get.nextflow.io | bash - Dangerous shell operationline 15
curl -s https://get.nextflow.io | bash - Network accessline 15
curl -s https://get.nextflow.io | bash - Dangerous shell operationline 28
sudo apt-get update && sudo apt-get install docker.io - Dangerous shell operationline 29
sudo systemctl enable --now docker - Dangerous shell operationline 30
sudo usermod -aG docker $USER - Network accessline 34
### macOS Download Docker Desktop: https://docker.com/products/docker-desktop - Network accessline 35
Download Docker Desktop: https://docker.com/products/docker-desktop - Dangerous shell operationline 46
sudo apt-get install singularity-container - Dangerous shell operationline 88
sudo usermod -aG docker $USER
skills/nextflow-development/references/pipelines/atacseq.md
- Network accessline 5
**Official Documentation:** https://nf-co.re/atacseq/2.1.2/ - Network accessline 6
**GitHub:** https://github.com/nf-core/atacseq - Network accessline 8
> **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/atacseq/releases) for breaking changes and update the version in commands below. - Network accessline 136
- **Full parameter list:** https://nf-co.re/atacseq/2.1.2/parameters/ - Network accessline 137
- **Output documentation:** https://nf-co.re/atacseq/2.1.2/docs/output/ - Network accessline 138
- **Usage documentation:** https://nf-co.re/atacseq/2.1.2/docs/usage/
skills/nextflow-development/references/pipelines/rnaseq.md
- Network accessline 5
**Official Documentation:** https://nf-co.re/rnaseq/3.22.2/ - Network accessline 6
**GitHub:** https://github.com/nf-core/rnaseq - Network accessline 8
> **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/rnaseq/releases) for breaking changes and update the version in commands below. - Network accessline 116
- **Full parameter list:** https://nf-co.re/rnaseq/3.22.2/parameters/ - Network accessline 117
- **Output documentation:** https://nf-co.re/rnaseq/3.22.2/docs/output/ - Network accessline 118
- **Usage documentation:** https://nf-co.re/rnaseq/3.22.2/docs/usage/
skills/nextflow-development/references/pipelines/sarek.md
- Network accessline 5
**Official Documentation:** https://nf-co.re/sarek/3.7.1/ - Network accessline 6
**GitHub:** https://github.com/nf-core/sarek - Network accessline 8
> **Note:** When updating to a new version, check the [releases page](https://github.com/nf-core/sarek/releases) for breaking changes and update the version in commands below. - Network accessline 143
- **Full parameter list:** https://nf-co.re/sarek/3.7.1/parameters/ - Network accessline 144
- **Output documentation:** https://nf-co.re/sarek/3.7.1/docs/output/ - Network accessline 145
- **Usage documentation:** https://nf-co.re/sarek/3.7.1/docs/usage/
skills/nextflow-development/references/troubleshooting.md
- Network accessline 17
Common exit codes indicating resource issues (per [nf-core docs](https://nf-co.re/docs/usage/troubleshooting/crash_halfway)): - Dangerous shell operationline 61
rm -rf work/ .nextflow* - Network accessline 135
1. Check `.nextflow.log` for error details 2. Search nf-core Slack: https://nf-co.re/join - Network accessline 136
2. Search nf-core Slack: https://nf-co.re/join - Network accessline 137
3. Open issue on GitHub: https://github.com/nf-core/<pipeline>/issues
skills/nextflow-development/scripts/check_environment.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 52
passed=False, message="Docker not found in PATH", fix="Install Docker: https://docs.docker.com/get-docker/" - Network accessline 53
message="Docker not found in PATH", fix="Install Docker: https://docs.docker.com/get-docker/" ) - Network accessline 54
fix="Install Docker: https://docs.docker.com/get-docker/" - Dangerous shell operationline 73
fix="sudo usermod -aG docker $USER && newgrp docker" - Dangerous shell operationline 81
fix="sudo systemctl start docker" - Dangerous shell operationline 103
fix="Check Docker daemon status: sudo systemctl status docker" - Network accessline 118
passed=False, message="Nextflow not found in PATH", fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH" - Network accessline 119
message="Nextflow not found in PATH", fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH" ) - Dangerous shell operationline 120
fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH" - Network accessline 120
fix="curl -s https://get.nextflow.io | bash && mv nextflow ~/bin/ && export PATH=$HOME/bin:$PATH" - Dangerous shell operationline 187
fix="Install Java 11+: sudo apt install openjdk-11-jdk" - Dangerous shell operationline 220
fix="Install Java 11+: sudo apt install openjdk-11-jdk" - Network accessline 318
try: req = urllib.request.Request("https://hub.docker.com", headers=headers) - Network accessline 319
req = urllib.request.Request("https://hub.docker.com", headers=headers) - Network accessline 320
urllib.request.urlopen(req, timeout=10) - Network accessline 326
try: req = urllib.request.Request("https://nf-co.re", headers=headers) - Network accessline 327
req = urllib.request.Request("https://nf-co.re", headers=headers) - Network accessline 328
urllib.request.urlopen(req, timeout=10)
skills/nextflow-development/scripts/config/pipelines/atacseq.yaml
- Network accessline 5
# Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/atacseq/{version}/" - Network accessline 6
urls: documentation: "https://nf-co.re/atacseq/{version}/" parameters: "https://nf-co.re/atacseq/{version}/parameters/" - Network accessline 7
documentation: "https://nf-co.re/atacseq/{version}/" - Network accessline 8
parameters: "https://nf-co.re/atacseq/{version}/parameters/" - Network accessline 9
output_docs: "https://nf-co.re/atacseq/{version}/docs/output/" - Network accessline 10
github: "https://github.com/nf-core/atacseq" - Network accessline 11
releases: "https://github.com/nf-core/atacseq/releases"
skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml
- Network accessline 5
# Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/rnaseq/{version}/" - Network accessline 6
urls: documentation: "https://nf-co.re/rnaseq/{version}/" parameters: "https://nf-co.re/rnaseq/{version}/parameters/" - Network accessline 7
documentation: "https://nf-co.re/rnaseq/{version}/" - Network accessline 8
parameters: "https://nf-co.re/rnaseq/{version}/parameters/" - Network accessline 9
output_docs: "https://nf-co.re/rnaseq/{version}/docs/output/" - Network accessline 10
github: "https://github.com/nf-core/rnaseq" - Network accessline 11
releases: "https://github.com/nf-core/rnaseq/releases"
skills/nextflow-development/scripts/config/pipelines/sarek.yaml
- Network accessline 5
# Documentation and source - NOTE: Update version in URLs when upgrading pipeline urls: documentation: "https://nf-co.re/sarek/{version}/" - Network accessline 6
urls: documentation: "https://nf-co.re/sarek/{version}/" parameters: "https://nf-co.re/sarek/{version}/parameters/" - Network accessline 7
documentation: "https://nf-co.re/sarek/{version}/" - Network accessline 8
parameters: "https://nf-co.re/sarek/{version}/parameters/" - Network accessline 9
output_docs: "https://nf-co.re/sarek/{version}/docs/output/" - Network accessline 10
github: "https://github.com/nf-core/sarek" - Network accessline 11
releases: "https://github.com/nf-core/sarek/releases"
skills/nextflow-development/scripts/detect_data_type.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nextflow-development/scripts/generate_samplesheet.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nextflow-development/scripts/manage_genomes.py
skills/nextflow-development/scripts/sra_geo_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nextflow-development/scripts/utils/__init__.py
- Executable scriptline 1
Executable file
skills/nextflow-development/scripts/utils/file_discovery.py
- Executable scriptline 1
Executable file
skills/nextflow-development/scripts/utils/ncbi_utils.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 56
test_urls = [ ("NCBI Entrez", "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"), - Network accessline 57
("NCBI Entrez", "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi"), - Network accessline 58
("NCBI FTP", "https://ftp.ncbi.nlm.nih.gov/"), - Network accessline 59
("ENA API", "https://www.ebi.ac.uk/ena/portal/api/"), - Network accessline 67
response = requests.get(url, timeout=10) - Network accessline 99
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gds&term={geo_id}[Accession]&retmode=json" - Network accessline 101
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 102
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 103
response = requests.get(search_url, timeout=30) - Network accessline 115
uid = id_list[0] summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gds&id={uid}&retmode=json" - Network accessline 116
summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gds&id={uid}&retmode=json" - Network accessline 118
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) - Network accessline 119
if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) data = response.json() - Network accessline 120
response = requests.get(summary_url, timeout=30) - Network accessline 156
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={geo_id}[GEO]&retmode=json" - Network accessline 158
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 159
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 160
response = requests.get(search_url, timeout=30) - Network accessline 171
uid = id_list[0] summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&id={uid}&retmode=json" - Network accessline 172
summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&id={uid}&retmode=json" - Network accessline 174
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) - Network accessline 175
if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) data = response.json() - Network accessline 176
response = requests.get(summary_url, timeout=30) - Network accessline 212
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={geo_id}[GEO]&retmax=1000&retmode=json" - Network accessline 214
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 215
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 216
response = requests.get(search_url, timeout=30) - Network accessline 229
if bioproject: logger.info(f"Using BioProject {bioproject} for {geo_id}") search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={bioproject}&retmax=1000&retmode=json" - Network accessline 231
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={bioproject}&retmax=1000&retmode=json" - Network accessline 233
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 234
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 235
response = requests.get(search_url, timeout=30) - Network accessline 248
ids_str = ','.join(id_list) summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&id={ids_str}&retmode=json" - Network accessline 249
summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=sra&id={ids_str}&retmode=json" - Network accessline 251
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(summary_url, timeout=60) - Network accessline 252
if HAS_REQUESTS: response = requests.get(summary_url, timeout=60) data = response.json() - Network accessline 253
response = requests.get(summary_url, timeout=60) - Network accessline 314
ena_url = f"https://www.ebi.ac.uk/ena/portal/api/filereport?accession={study_accession}&result=read_run&fields=run_accession,sample_alias,fastq_ftp&format=tsv" - Network accessline 316
if HAS_REQUESTS: response = requests.get(ena_url, timeout=60) - Network accessline 317
response = requests.get(ena_url, timeout=60) - Network accessline 343
urls = [f"http://{url}" for url in ftp_urls.split(';') if url] - Network accessline 369
if HAS_REQUESTS: response = requests.get(url, stream=True, timeout=timeout) - Network accessline 370
response = requests.get(url, stream=True, timeout=timeout) - Network accessline 410
url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id={pmid}&retmode=json" - Network accessline 414
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(url, timeout=30) - Network accessline 415
if HAS_REQUESTS: response = requests.get(url, timeout=30) data = response.json() - Network accessline 416
response = requests.get(url, timeout=30) - Network accessline 514
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gds&term={geo_id}[Accession]&retmode=json" - Network accessline 516
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 517
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 518
response = requests.get(search_url, timeout=30) - Network accessline 529
elink_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gds&db=bioproject&id={gds_ids[0]}&retmode=json" - Network accessline 531
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(elink_url, timeout=30) - Network accessline 532
if HAS_REQUESTS: response = requests.get(elink_url, timeout=30) data = response.json() - Network accessline 533
response = requests.get(elink_url, timeout=30) - Network accessline 546
summary_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=bioproject&id={bp_ids[0]}&retmode=json" - Network accessline 547
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) - Network accessline 548
if HAS_REQUESTS: response = requests.get(summary_url, timeout=30) data = response.json() - Network accessline 549
response = requests.get(summary_url, timeout=30) - Network accessline 582
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={geo_id}[GEO]&retmax=1000&retmode=json" - Network accessline 584
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 585
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 586
response = requests.get(search_url, timeout=30) - Network accessline 601
if bioproject: logger.info(f"Found BioProject: {bioproject}") search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={bioproject}&retmax=1000&retmode=json" - Network accessline 603
search_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=sra&term={bioproject}&retmax=1000&retmode=json" - Network accessline 605
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(search_url, timeout=30) - Network accessline 606
if HAS_REQUESTS: response = requests.get(search_url, timeout=30) data = response.json() - Network accessline 607
response = requests.get(search_url, timeout=30) - Network accessline 620
ids_str = ','.join(id_list) efetch_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id={ids_str}&rettype=runinfo&retmode=csv" - Network accessline 621
efetch_url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id={ids_str}&rettype=runinfo&retmode=csv" - Network accessline 623
_rate_limit_ncbi() if HAS_REQUESTS: response = requests.get(efetch_url, timeout=60) - Network accessline 624
if HAS_REQUESTS: response = requests.get(efetch_url, timeout=60) content = response.text - Network accessline 625
response = requests.get(efetch_url, timeout=60)
skills/nextflow-development/scripts/utils/sample_inference.py
- Executable scriptline 1
Executable file
skills/nextflow-development/scripts/utils/validators.py
- Executable scriptline 1
Executable file
skills/ngs-analysis/SKILL.md
- Executable scriptline 1
Executable file
skills/nonlinear-solvers/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/nonlinear-solvers/scripts/convergence_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nonlinear-solvers/scripts/globalization_advisor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nonlinear-solvers/scripts/jacobian_diagnostics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nonlinear-solvers/scripts/residual_monitor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nonlinear-solvers/scripts/solver_selector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nonlinear-solvers/scripts/step_quality.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-integration/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/numerical-integration/scripts/adaptive_step_controller.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-integration/scripts/error_norm.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-integration/scripts/imex_split_planner.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-integration/scripts/integrator_selector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-integration/scripts/splitting_error_estimator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-stability/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/numerical-stability/scripts/cfl_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-stability/scripts/matrix_condition.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-stability/scripts/stiffness_detector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/numerical-stability/scripts/von_neumann_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/nutrition-analyzer/SKILL.md
- Network accessline 765
- 中国居民膳食营养素参考摄入量 (DRIs)：http://www.cnsoc.org/ - Network accessline 766
- 美国膳食指南：https://www.dietaryguidelines.gov/ - Network accessline 767
- USDA FoodData Central：https://fooddatacentral.usda.gov/ - Network accessline 768
- WHO营养建议：https://www.who.int/nutrition/ - Network accessline 769
- 补充剂相互作用数据库：https://naturalmedicines.therapeuticresearch.com/
skills/omero-integration/SKILL.md
- Network accessline 233
- **Official Documentation**: https://omero.readthedocs.io/en/stable/developers/Python.html - Network accessline 234
- **BlitzGateway API**: https://omero.readthedocs.io/en/stable/developers/Python.html#omero-blitzgateway - Network accessline 235
- **OMERO Model**: https://omero.readthedocs.io/en/stable/developers/Model.html - Network accessline 236
- **Community Forum**: https://forum.image.sc/tag/omero
skills/omero-integration/references/connection.md
skills/ontology-explorer/SKILL.md
- Broad permissionsline 1
Read, Bash - Network accessline 29
| Property name | A specific property to look up | `hasMaterial`, `hasSpaceGroupNumber` | | Search term | Keyword to search across labels | `crystal`, `lattice` | | OWL source | Path or URL to an OWL/XML file (for parsing/summarizing) | `ht - Network accessline 31
| OWL source | Path or URL to an OWL/XML file (for parsing/summarizing) | `https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl` | - Network accessline 119
# Parse a remote OWL file python3 skills/ontology/ontology-explorer/scripts/owl_parser.py \ --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl --json - Network accessline 120
python3 skills/ontology/ontology-explorer/scripts/owl_parser.py --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl --json - Network accessline 121
--source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl --json - Network accessline 123
# Generate a summary JSON from an OWL file python3 skills/ontology/ontology-explorer/scripts/ontology_summarizer.py \ --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl \ - Network accessline 124
python3 skills/ontology/ontology-explorer/scripts/ontology_summarizer.py --source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl - Network accessline 125
--source https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl \ - Network accessline 159
- [Ontology Registry](references/ontology_registry.json) — registered ontologies and their metadata - [CMSO Summary](references/cmso_summary.json) — pre-processed CMSO structure - [CMSO Documentation](https://ocdo.github.io/cmso/) — officia - Network accessline 160
- [CMSO Summary](references/cmso_summary.json) — pre-processed CMSO structure - [CMSO Documentation](https://ocdo.github.io/cmso/) — official CMSO docs - [CMSO Repository](https://github.com/OCDO/cmso) — source OWL file and development - Network accessline 161
- [CMSO Documentation](https://ocdo.github.io/cmso/) — official CMSO docs - Network accessline 162
- [CMSO Repository](https://github.com/OCDO/cmso) — source OWL file and development
skills/ontology-explorer/references/asmo_guide.md
- Network accessline 7
- **IRI**: `http://purls.helmholtz-metadaten.de/asmo/`
skills/ontology-explorer/references/asmo_summary.json
- Network accessline 1
{ "metadata": { "iri": "http://purls.helmholtz-metadaten.de/asmo/", - Network accessline 2
"metadata": { "iri": "http://purls.helmholtz-metadaten.de/asmo/", "title": null, - Network accessline 3
"iri": "http://purls.helmholtz-metadaten.de/asmo/", - Network accessline 5
"version": "1.0.0", "description": null, "source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", - Network accessline 6
"description": null, "source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", "generated_at": "2026-02-25T15:15:21.349259+00:00" - Network accessline 7
"source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", - Network accessline 10
"classes": { "ANNNI Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ANNNImodel", - Network accessline 11
"ANNNI Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ANNNImodel", "parent": "Simulation Algorithm", - Network accessline 12
"iri": "http://purls.helmholtz-metadaten.de/asmo/ANNNImodel", - Network accessline 16
}, "Ab Initio Molecular Dynamics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/AbInitioMolecularDynamics", - Network accessline 17
"Ab Initio Molecular Dynamics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/AbInitioMolecularDynamics", "parent": "Computational Method", - Network accessline 18
"iri": "http://purls.helmholtz-metadaten.de/asmo/AbInitioMolecularDynamics", - Network accessline 22
}, "Addition": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Addition", - Network accessline 23
"Addition": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Addition", "parent": "Mathematical Operation", - Network accessline 24
"iri": "http://purls.helmholtz-metadaten.de/asmo/Addition", - Network accessline 28
}, "Barostat": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Barostat", - Network accessline 29
"Barostat": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Barostat", "parent": "Simulation Algorithm", - Network accessline 30
"iri": "http://purls.helmholtz-metadaten.de/asmo/Barostat", - Network accessline 34
}, "Bulk Modulus": { "iri": "http://purls.helmholtz-metadaten.de/asmo/BulkModulus", - Network accessline 35
"Bulk Modulus": { "iri": "http://purls.helmholtz-metadaten.de/asmo/BulkModulus", "parent": "Calculated Property", - Network accessline 36
"iri": "http://purls.helmholtz-metadaten.de/asmo/BulkModulus", - Network accessline 40
}, "Calculated Property": { "iri": "http://purls.helmholtz-metadaten.de/asmo/CalculatedProperty", - Network accessline 41
"Calculated Property": { "iri": "http://purls.helmholtz-metadaten.de/asmo/CalculatedProperty", "parent": null, - Network accessline 42
"iri": "http://purls.helmholtz-metadaten.de/asmo/CalculatedProperty", - Network accessline 67
}, "Compression Test": { "iri": "http://purls.helmholtz-metadaten.de/asmo/CompressionTest", - Network accessline 68
"Compression Test": { "iri": "http://purls.helmholtz-metadaten.de/asmo/CompressionTest", "parent": "Simulation Algorithm", - Network accessline 69
"iri": "http://purls.helmholtz-metadaten.de/asmo/CompressionTest", - Network accessline 73
}, "Computational Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ComputationalMethod", - Network accessline 74
"Computational Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ComputationalMethod", "parent": null, - Network accessline 75
"iri": "http://purls.helmholtz-metadaten.de/asmo/ComputationalMethod", - Network accessline 85
}, "Density Functional Theory": { "iri": "http://purls.helmholtz-metadaten.de/asmo/DensityFunctionalTheory", - Network accessline 86
"Density Functional Theory": { "iri": "http://purls.helmholtz-metadaten.de/asmo/DensityFunctionalTheory", "parent": "Computational Method", - Network accessline 87
"iri": "http://purls.helmholtz-metadaten.de/asmo/DensityFunctionalTheory", - Network accessline 91
}, "Division": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Division", - Network accessline 92
"Division": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Division", "parent": "Mathematical Operation", - Network accessline 93
"iri": "http://purls.helmholtz-metadaten.de/asmo/Division", - Network accessline 97
}, "Elastic Constant": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticConstant", - Network accessline 98
"Elastic Constant": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticConstant", "parent": "Calculated Property", - Network accessline 99
"iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticConstant", - Network accessline 103
}, "Elastic Tensor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticTensor", - Network accessline 104
"Elastic Tensor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticTensor", "parent": "Calculated Property", - Network accessline 105
"iri": "http://purls.helmholtz-metadaten.de/asmo/ElasticTensor", - Network accessline 109
}, "Embedded Atom Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EmbeddedAtomModel", - Network accessline 110
"Embedded Atom Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EmbeddedAtomModel", "parent": "Interatomic Potential", - Network accessline 111
"iri": "http://purls.helmholtz-metadaten.de/asmo/EmbeddedAtomModel", - Network accessline 115
}, "Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Energy", - Network accessline 116
"Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Energy", "parent": "Physical Quantity", - Network accessline 117
"iri": "http://purls.helmholtz-metadaten.de/asmo/Energy", - Network accessline 123
}, "Energy Calculation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCalculation", - Network accessline 124
"Energy Calculation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCalculation", "parent": "Simulation", - Network accessline 125
"iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCalculation", - Network accessline 129
}, "Energy Cutoff": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCutoff", - Network accessline 130
"Energy Cutoff": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCutoff", "parent": "Input Parameter", - Network accessline 131
"iri": "http://purls.helmholtz-metadaten.de/asmo/EnergyCutoff", - Network accessline 135
}, "Equation of State Fit": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EquationOfStateFit", - Network accessline 136
"Equation of State Fit": { "iri": "http://purls.helmholtz-metadaten.de/asmo/EquationOfStateFit", "parent": "Simulation Algorithm", - Network accessline 137
"iri": "http://purls.helmholtz-metadaten.de/asmo/EquationOfStateFit", - Network accessline 141
}, "Exponentiation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Exponentiation", - Network accessline 142
"Exponentiation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Exponentiation", "parent": "Mathematical Operation", - Network accessline 143
"iri": "http://purls.helmholtz-metadaten.de/asmo/Exponentiation", - Network accessline 147
}, "Flow Stress": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FlowStress", - Network accessline 148
"Flow Stress": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FlowStress", "parent": "Calculated Property", - Network accessline 149
"iri": "http://purls.helmholtz-metadaten.de/asmo/FlowStress", - Network accessline 153
}, "Force": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Force", - Network accessline 154
"Force": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Force", "parent": "Physical Quantity", - Network accessline 155
"iri": "http://purls.helmholtz-metadaten.de/asmo/Force", - Network accessline 159
}, "Formation Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FormationEnergy", - Network accessline 160
"Formation Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FormationEnergy", "parent": "Calculated Property", - Network accessline 161
"iri": "http://purls.helmholtz-metadaten.de/asmo/FormationEnergy", - Network accessline 165
}, "Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergy", - Network accessline 166
"Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergy", "parent": "Energy", - Network accessline 167
"iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergy", - Network accessline 171
}, "Free Energy Calculation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergyCalculation", - Network accessline 172
"Free Energy Calculation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergyCalculation", "parent": "Simulation", - Network accessline 173
"iri": "http://purls.helmholtz-metadaten.de/asmo/FreeEnergyCalculation", - Network accessline 177
}, "Gibbs Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/GibbsFreeEnergy", - Network accessline 178
"Gibbs Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/GibbsFreeEnergy", "parent": "Thermodynamic Free Energy", - Network accessline 179
"iri": "http://purls.helmholtz-metadaten.de/asmo/GibbsFreeEnergy", - Network accessline 183
}, "Helmholtz Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/HelmholtzFreeEnergy", - Network accessline 184
"Helmholtz Free Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/HelmholtzFreeEnergy", "parent": "Thermodynamic Free Energy", - Network accessline 185
"iri": "http://purls.helmholtz-metadaten.de/asmo/HelmholtzFreeEnergy", - Network accessline 189
}, "Input Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/InputParameter", - Network accessline 190
"Input Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/InputParameter", "parent": "Simulation Parameter", - Network accessline 191
"iri": "http://purls.helmholtz-metadaten.de/asmo/InputParameter", - Network accessline 203
}, "Interatomic Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/InteratomicPotential", - Network accessline 204
"Interatomic Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/InteratomicPotential", "parent": null, - Network accessline 205
"iri": "http://purls.helmholtz-metadaten.de/asmo/InteratomicPotential", - Network accessline 216
}, "KPoint Mesh": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KPointMesh", - Network accessline 217
"KPoint Mesh": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KPointMesh", "parent": "Input Parameter", - Network accessline 218
"iri": "http://purls.helmholtz-metadaten.de/asmo/KPointMesh", - Network accessline 222
}, "Kinetic Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KineticEnergy", - Network accessline 223
"Kinetic Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KineticEnergy", "parent": "Calculated Property", - Network accessline 224
"iri": "http://purls.helmholtz-metadaten.de/asmo/KineticEnergy", - Network accessline 228
}, "Kinetic Monte Carlo Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KineticMonteCarloMethod", - Network accessline 229
"Kinetic Monte Carlo Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/KineticMonteCarloMethod", "parent": "Monte Carlo Method", - Network accessline 230
"iri": "http://purls.helmholtz-metadaten.de/asmo/KineticMonteCarloMethod", - Network accessline 234
}, "Length": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Length", - Network accessline 235
"Length": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Length", "parent": "Physical Quantity", - Network accessline 236
"iri": "http://purls.helmholtz-metadaten.de/asmo/Length", - Network accessline 240
}, "Lennard-Jones Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Lennard-JonesPotential", - Network accessline 241
"Lennard-Jones Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Lennard-JonesPotential", "parent": "Interatomic Potential", - Network accessline 242
"iri": "http://purls.helmholtz-metadaten.de/asmo/Lennard-JonesPotential", - Network accessline 246
}, "Machine Learning Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MachineLearningPotential", - Network accessline 247
"Machine Learning Potential": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MachineLearningPotential", "parent": "Interatomic Potential", - Network accessline 248
"iri": "http://purls.helmholtz-metadaten.de/asmo/MachineLearningPotential", - Network accessline 252
}, "Mass": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Mass", - Network accessline 253
"Mass": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Mass", "parent": "Physical Quantity", - Network accessline 254
"iri": "http://purls.helmholtz-metadaten.de/asmo/Mass", - Network accessline 258
}, "Mathematical Operation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MathematicalOperation", - Network accessline 259
"Mathematical Operation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MathematicalOperation", "parent": "Activity", - Network accessline 260
"iri": "http://purls.helmholtz-metadaten.de/asmo/MathematicalOperation", - Network accessline 270
}, "Modified Embedded Atom Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ModifiedEmbeddedAtomModel", - Network accessline 271
"Modified Embedded Atom Model": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ModifiedEmbeddedAtomModel", "parent": "Interatomic Potential", - Network accessline 272
"iri": "http://purls.helmholtz-metadaten.de/asmo/ModifiedEmbeddedAtomModel", - Network accessline 276
}, "Molecular Dynamics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularDynamics", - Network accessline 277
"Molecular Dynamics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularDynamics", "parent": "Computational Method", - Network accessline 278
"iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularDynamics", - Network accessline 282
}, "Force Field": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularForceField", - Network accessline 283
"Force Field": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularForceField", "parent": "Interatomic Potential", - Network accessline 284
"iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularForceField", - Network accessline 288
}, "Molecular Statics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularStatics", - Network accessline 289
"Molecular Statics": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularStatics", "parent": "Computational Method", - Network accessline 290
"iri": "http://purls.helmholtz-metadaten.de/asmo/MolecularStatics", - Network accessline 294
}, "Monte Carlo Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MonteCarloMethod", - Network accessline 295
"Monte Carlo Method": { "iri": "http://purls.helmholtz-metadaten.de/asmo/MonteCarloMethod", "parent": "Computational Method", - Network accessline 296
"iri": "http://purls.helmholtz-metadaten.de/asmo/MonteCarloMethod", - Network accessline 302
}, "Multiplication": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Multiplication", - Network accessline 303
"Multiplication": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Multiplication", "parent": "Mathematical Operation", - Network accessline 304
"iri": "http://purls.helmholtz-metadaten.de/asmo/Multiplication", - Network accessline 308
}, "Nanoindentation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Nanoindentation", - Network accessline 309
"Nanoindentation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Nanoindentation", "parent": "Simulation Algorithm", - Network accessline 310
"iri": "http://purls.helmholtz-metadaten.de/asmo/Nanoindentation", - Network accessline 314
}, "Number Of Ionic Steps": { "iri": "http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps", - Network accessline 315
"Number Of Ionic Steps": { "iri": "http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps", "parent": "Input Parameter", - Network accessline 316
"iri": "http://purls.helmholtz-metadaten.de/asmo/NumberOfIonicSteps", - Network accessline 320
}, "Output Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/OutputParameter", - Network accessline 321
"Output Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/OutputParameter", "parent": "Simulation Parameter", - Network accessline 322
"iri": "http://purls.helmholtz-metadaten.de/asmo/OutputParameter", - Network accessline 326
}, "Periodic Boundary Condition": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PeriodicBoundaryCondition", - Network accessline 327
"Periodic Boundary Condition": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PeriodicBoundaryCondition", "parent": "Input Parameter", - Network accessline 328
"iri": "http://purls.helmholtz-metadaten.de/asmo/PeriodicBoundaryCondition", - Network accessline 332
}, "Physical Quantity": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PhysicalQuantity", - Network accessline 333
"Physical Quantity": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PhysicalQuantity", "parent": null, - Network accessline 334
"iri": "http://purls.helmholtz-metadaten.de/asmo/PhysicalQuantity", - Network accessline 348
}, "Point Defect Creation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PointDefectCreation", - Network accessline 349
"Point Defect Creation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PointDefectCreation", "parent": "Structure Manipulation", - Network accessline 350
"iri": "http://purls.helmholtz-metadaten.de/asmo/PointDefectCreation", - Network accessline 354
}, "Poisson's Ratio": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PoissonsRatio", - Network accessline 355
"Poisson's Ratio": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PoissonsRatio", "parent": "Calculated Property", - Network accessline 356
"iri": "http://purls.helmholtz-metadaten.de/asmo/PoissonsRatio", - Network accessline 360
}, "Potential Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PotentialEnergy", - Network accessline 361
"Potential Energy": { "iri": "http://purls.helmholtz-metadaten.de/asmo/PotentialEnergy", "parent": "Calculated Property", - Network accessline 362
"iri": "http://purls.helmholtz-metadaten.de/asmo/PotentialEnergy", - Network accessline 366
}, "Pressure": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Pressure", - Network accessline 367
"Pressure": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Pressure", "parent": "Physical Quantity", - Network accessline 368
"iri": "http://purls.helmholtz-metadaten.de/asmo/Pressure", - Network accessline 372
}, "Quasi-Harmonic Approximation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/QuasiHarmonicApproximation", - Network accessline 373
"Quasi-Harmonic Approximation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/QuasiHarmonicApproximation", "parent": "Simulation Algorithm", - Network accessline 374
"iri": "http://purls.helmholtz-metadaten.de/asmo/QuasiHarmonicApproximation", - Network accessline 378
}, "Relaxation Degrees of Freedom": { "iri": "http://purls.helmholtz-metadaten.de/asmo/RelaxationDOF", - Network accessline 379
"Relaxation Degrees of Freedom": { "iri": "http://purls.helmholtz-metadaten.de/asmo/RelaxationDOF", "parent": null, - Network accessline 380
"iri": "http://purls.helmholtz-metadaten.de/asmo/RelaxationDOF", - Network accessline 384
}, "Rotation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Rotation", - Network accessline 385
"Rotation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Rotation", "parent": "Spatial Transformation", - Network accessline 386
"iri": "http://purls.helmholtz-metadaten.de/asmo/Rotation", - Network accessline 390
}, "Shear": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Shear", - Network accessline 391
"Shear": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Shear", "parent": "Spatial Transformation", - Network accessline 392
"iri": "http://purls.helmholtz-metadaten.de/asmo/Shear", - Network accessline 396
}, "Shear Modulus": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ShearModulus", - Network accessline 397
"Shear Modulus": { "iri": "http://purls.helmholtz-metadaten.de/asmo/ShearModulus", "parent": "Calculated Property", - Network accessline 398
"iri": "http://purls.helmholtz-metadaten.de/asmo/ShearModulus", - Network accessline 402
}, "Simulation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Simulation", - Network accessline 403
"Simulation": { "iri": "http://purls.helmholtz-metadaten.de/asmo/Simulation", "parent": "Activity", - Network accessline 404
"iri": "http://purls.helmholtz-metadaten.de/asmo/Simulation", - Network accessline 411
}, "Simulation Algorithm": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationAlgorithm", - Network accessline 412
"Simulation Algorithm": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationAlgorithm", "parent": null, - Network accessline 413
"iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationAlgorithm", - Network accessline 427
}, "Simulation Cell Length": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellLength", - Network accessline 428
"Simulation Cell Length": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellLength", "parent": "Calculated Property", - Network accessline 429
"iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellLength", - Network accessline 433
}, "Simulation Cell Volume": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellVolume", - Network accessline 434
"Simulation Cell Volume": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellVolume", "parent": "Calculated Property", - Network accessline 435
"iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationCellVolume", - Network accessline 439
}, "Simulation Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationParameter", - Network accessline 440
"Simulation Parameter": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationParameter", "parent": null, - Network accessline 441
"iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationParameter", - Network accessline 448
}, "Simulation Run Time": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationRunTime", - Network accessline 449
"Simulation Run Time": { "iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationRunTime", "parent": "Time", - Network accessline 450
"iri": "http://purls.helmholtz-metadaten.de/asmo/SimulationRunTime", - Network accessline 454
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"iri": "https://w3id.org/mdo/calculation/hasXCFunctional", - Network accessline 1027
"data_properties": { "has addend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasAddend", - Network accessline 1028
"has addend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasAddend", "domain": "Addition", - Network accessline 1029
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasAddend", - Network accessline 1033
}, "has base": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasBase", - Network accessline 1034
"has base": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasBase", "domain": "Exponentiation", - Network accessline 1035
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasBase", - Network accessline 1039
}, "has difference": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDifference", - Network accessline 1040
"has difference": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDifference", "domain": "Subtraction", - Network accessline 1041
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasDifference", - Network accessline 1045
}, "has dividend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDividend", - Network accessline 1046
"has dividend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDividend", "domain": "Division", - Network accessline 1047
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasDividend", - Network accessline 1051
}, "has divisor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDivisor", - Network accessline 1052
"has divisor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasDivisor", "domain": "Division", - Network accessline 1053
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasDivisor", - Network accessline 1057
}, "has exponent": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasExponent", - Network accessline 1058
"has exponent": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasExponent", "domain": "Exponentiation", - Network accessline 1059
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasExponent", - Network accessline 1063
}, "has factor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasFactor", - Network accessline 1064
"has factor": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasFactor", "domain": "Multiplication", - Network accessline 1065
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasFactor", - Network accessline 1069
}, "has minuend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasMinuend", - Network accessline 1070
"has minuend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasMinuend", "domain": "Subtraction", - Network accessline 1071
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasMinuend", - Network accessline 1075
}, "has product": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasProduct", - Network accessline 1076
"has product": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasProduct", "domain": "Multiplication", - Network accessline 1077
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasProduct", - Network accessline 1081
}, "has quotient": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasQuotient", - Network accessline 1082
"has quotient": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasQuotient", "domain": "Division", - Network accessline 1083
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasQuotient", - Network accessline 1087
}, "has reference": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasReference", - Network accessline 1088
"has reference": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasReference", "domain": "Thing", - Network accessline 1089
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasReference", - Network accessline 1093
}, "has subtrahend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasSubtrahend", - Network accessline 1094
"has subtrahend": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasSubtrahend", "domain": "Subtraction", - Network accessline 1095
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasSubtrahend", - Network accessline 1099
}, "has sum": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasSum", - Network accessline 1100
"has sum": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasSum", "domain": "Addition", - Network accessline 1101
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasSum", - Network accessline 1105
}, "has value": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasValue", - Network accessline 1106
"has value": { "iri": "http://purls.helmholtz-metadaten.de/asmo/hasValue", "domain": "Thing", - Network accessline 1107
"iri": "http://purls.helmholtz-metadaten.de/asmo/hasValue", - Network accessline 1111
}, "endedAtTime": { "iri": "http://www.w3.org/ns/prov#endedAtTime", - Network accessline 1112
"endedAtTime": { "iri": "http://www.w3.org/ns/prov#endedAtTime", "domain": "Activity", - Network accessline 1113
"iri": "http://www.w3.org/ns/prov#endedAtTime", - Network accessline 1117
}, "startedAtTime": { "iri": "http://www.w3.org/ns/prov#startedAtTime", - Network accessline 1118
"startedAtTime": { "iri": "http://www.w3.org/ns/prov#startedAtTime", "domain": "Activity", - Network accessline 1119
"iri": "http://www.w3.org/ns/prov#startedAtTime",
skills/ontology-explorer/references/cmso_guide.md
- Network accessline 7
- **IRI**: `http://purls.helmholtz-metadaten.de/cmso/` - Network accessline 7
- **IRI**: `http://purls.helmholtz-metadaten.de/cmso/` - Network accessline 7
- **IRI**: `http://purls.helmholtz-metadaten.de/cmso/` - Network accessline 8
- **Version**: 0.0.1 - **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - Network accessline 8
- **Version**: 0.0.1 - **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - Network accessline 8
- **Version**: 0.0.1 - **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - Network accessline 9
- **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - **Documentation**: https://ocdo.github.io/cmso/ - Network accessline 9
- **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - **Documentation**: https://ocdo.github.io/cmso/ - Network accessline 9
- **License**: CC-BY-4.0 - **Repository**: https://github.com/OCDO/cmso - **Documentation**: https://ocdo.github.io/cmso/ - Network accessline 10
- **Repository**: https://github.com/OCDO/cmso - Network accessline 10
- **Repository**: https://github.com/OCDO/cmso - Network accessline 10
- **Repository**: https://github.com/OCDO/cmso - Network accessline 11
- **Documentation**: https://ocdo.github.io/cmso/ - Network accessline 11
- **Documentation**: https://ocdo.github.io/cmso/ - Network accessline 11
- **Documentation**: https://ocdo.github.io/cmso/
skills/ontology-explorer/references/cmso_summary.json
- Network accessline 1
{ "metadata": { "iri": "http://purls.helmholtz-metadaten.de/cmso/", - Network accessline 2
"metadata": { "iri": "http://purls.helmholtz-metadaten.de/cmso/", "title": null, - Network accessline 3
"iri": "http://purls.helmholtz-metadaten.de/cmso/", - Network accessline 5
"version": "0.0.1", "description": null, "source_url": "https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl", - Network accessline 6
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"source_url": "https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl", - Network accessline 10
"classes": { "Crystalline Material": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial", - Network accessline 11
"Crystalline Material": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial", "parent": "Material", - Network accessline 12
"iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallineMaterial", - Network accessline 19
}, "Crystallographic Defect": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect", - Network accessline 20
"Crystallographic Defect": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect", "parent": null, - Network accessline 21
"iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/CrystallographicDefect", - Network accessline 25
}, "Material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Material", - Network accessline 26
"Material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Material", "parent": null, - Network accessline 27
"iri": "http://purls.helmholtz-metadaten.de/cmso/Material", - Network accessline 34
}, "Amorphous Material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AmorphousMaterial", - Network accessline 35
"Amorphous Material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AmorphousMaterial", "parent": "Material", - Network accessline 36
"iri": "http://purls.helmholtz-metadaten.de/cmso/AmorphousMaterial", - Network accessline 40
}, "Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Angle", - Network accessline 41
"Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Angle", "parent": null, - Network accessline 42
"iri": "http://purls.helmholtz-metadaten.de/cmso/Angle", - Network accessline 49
}, "Atom": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Atom", - Network accessline 50
"Atom": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Atom", "parent": "Chemical Species", - Network accessline 51
"iri": "http://purls.helmholtz-metadaten.de/cmso/Atom", - Network accessline 55
}, "Atom Attribute": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomAttribute", - Network accessline 56
"Atom Attribute": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomAttribute", "parent": null, - Network accessline 57
"iri": "http://purls.helmholtz-metadaten.de/cmso/AtomAttribute", - Network accessline 67
}, "Atomic Force": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicForce", - Network accessline 68
"Atomic Force": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicForce", "parent": "Atom Attribute", - Network accessline 69
"iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicForce", - Network accessline 73
}, "Atomic Position": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicPosition", - Network accessline 74
"Atomic Position": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicPosition", "parent": "Atom Attribute", - Network accessline 75
"iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicPosition", - Network accessline 79
}, "Atomic Scale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample", - Network accessline 80
"Atomic Scale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample", "parent": "Computational Sample", - Network accessline 81
"iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicScaleSample", - Network accessline 85
}, "Atomic Velocity": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicVelocity", - Network accessline 86
"Atomic Velocity": { "iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicVelocity", "parent": "Atom Attribute", - Network accessline 87
"iri": "http://purls.helmholtz-metadaten.de/cmso/AtomicVelocity", - Network accessline 91
}, "Basis": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Basis", - Network accessline 92
"Basis": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Basis", "parent": null, - Network accessline 93
"iri": "http://purls.helmholtz-metadaten.de/cmso/Basis", - Network accessline 97
}, "Bicrystal": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Bicrystal", - Network accessline 98
"Bicrystal": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Bicrystal", "parent": "Crystalline Material", - Network accessline 99
"iri": "http://purls.helmholtz-metadaten.de/cmso/Bicrystal", - Network accessline 103
}, "Chemical Composition": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalComposition", - Network accessline 104
"Chemical Composition": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalComposition", "parent": null, - Network accessline 105
"iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalComposition", - Network accessline 109
}, "Chemical Element": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalElement", - Network accessline 110
"Chemical Element": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalElement", "parent": null, - Network accessline 111
"iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalElement", - Network accessline 115
}, "Chemical Species": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalSpecies", - Network accessline 116
"Chemical Species": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalSpecies", "parent": null, - Network accessline 117
"iri": "http://purls.helmholtz-metadaten.de/cmso/ChemicalSpecies", - Network accessline 124
}, "Computational Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ComputationalSample", - Network accessline 125
"Computational Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/ComputationalSample", "parent": null, - Network accessline 126
"iri": "http://purls.helmholtz-metadaten.de/cmso/ComputationalSample", - Network accessline 136
}, "Coordination Number": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CoordinationNumber", - Network accessline 137
"Coordination Number": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CoordinationNumber", "parent": "Atom Attribute", - Network accessline 138
"iri": "http://purls.helmholtz-metadaten.de/cmso/CoordinationNumber", - Network accessline 142
}, "Crystal Defect": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalDefect", - Network accessline 143
"Crystal Defect": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalDefect", "parent": null, - Network accessline 144
"iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalDefect", - Network accessline 148
}, "Crystal Structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalStructure", - Network accessline 149
"Crystal Structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalStructure", "parent": "Structure", - Network accessline 150
"iri": "http://purls.helmholtz-metadaten.de/cmso/CrystalStructure", - Network accessline 154
}, "Lattice Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeAngle", - Network accessline 155
"Lattice Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeAngle", "parent": "Angle", - Network accessline 156
"iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeAngle", - Network accessline 160
}, "Lattice Parameter": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeParameter", - Network accessline 161
"Lattice Parameter": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeParameter", "parent": null, - Network accessline 162
"iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeParameter", - Network accessline 166
}, "Lattice Plane": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticePlane", - Network accessline 167
"Lattice Plane": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticePlane", "parent": "Plane", - Network accessline 168
"iri": "http://purls.helmholtz-metadaten.de/cmso/LatticePlane", - Network accessline 172
}, "Lattice Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeVector", - Network accessline 173
"Lattice Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeVector", "parent": "Vector", - Network accessline 174
"iri": "http://purls.helmholtz-metadaten.de/cmso/LatticeVector", - Network accessline 178
}, "Macroscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MacroscaleSample", - Network accessline 179
"Macroscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MacroscaleSample", "parent": "Computational Sample", - Network accessline 180
"iri": "http://purls.helmholtz-metadaten.de/cmso/MacroscaleSample", - Network accessline 184
}, "Mesoscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MesoscaleSample", - Network accessline 185
"Mesoscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MesoscaleSample", "parent": "Computational Sample", - Network accessline 186
"iri": "http://purls.helmholtz-metadaten.de/cmso/MesoscaleSample", - Network accessline 190
}, "Microscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MicroscaleSample", - Network accessline 191
"Microscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/MicroscaleSample", "parent": "Computational Sample", - Network accessline 192
"iri": "http://purls.helmholtz-metadaten.de/cmso/MicroscaleSample", - Network accessline 196
}, "Microstructure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Microstructure", - Network accessline 197
"Microstructure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Microstructure", "parent": "Structure", - Network accessline 198
"iri": "http://purls.helmholtz-metadaten.de/cmso/Microstructure", - Network accessline 202
}, "Molecule": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Molecule", - Network accessline 203
"Molecule": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Molecule", "parent": "Chemical Species", - Network accessline 204
"iri": "http://purls.helmholtz-metadaten.de/cmso/Molecule", - Network accessline 208
}, "Nanoscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/NanoscaleSample", - Network accessline 209
"Nanoscale Sample": { "iri": "http://purls.helmholtz-metadaten.de/cmso/NanoscaleSample", "parent": "Computational Sample", - Network accessline 210
"iri": "http://purls.helmholtz-metadaten.de/cmso/NanoscaleSample", - Network accessline 214
}, "Normal Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/NormalVector", - Network accessline 215
"Normal Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/NormalVector", "parent": "Vector", - Network accessline 216
"iri": "http://purls.helmholtz-metadaten.de/cmso/NormalVector", - Network accessline 220
}, "Occupancy": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Occupancy", - Network accessline 221
"Occupancy": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Occupancy", "parent": "Atom Attribute", - Network accessline 222
"iri": "http://purls.helmholtz-metadaten.de/cmso/Occupancy", - Network accessline 226
}, "Plane": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Plane", - Network accessline 227
"Plane": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Plane", "parent": null, - Network accessline 228
"iri": "http://purls.helmholtz-metadaten.de/cmso/Plane", - Network accessline 234
}, "Polycrystal": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Polycrystal", - Network accessline 235
"Polycrystal": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Polycrystal", "parent": "Crystalline Material", - Network accessline 236
"iri": "http://purls.helmholtz-metadaten.de/cmso/Polycrystal", - Network accessline 240
}, "Simulation Cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCell", - Network accessline 241
"Simulation Cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCell", "parent": null, - Network accessline 242
"iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCell", - Network accessline 246
}, "Simulation Cell Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellAngle", - Network accessline 247
"Simulation Cell Angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellAngle", "parent": "Angle", - Network accessline 248
"iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellAngle", - Network accessline 252
}, "Simulation Cell Length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellLength", - Network accessline 253
"Simulation Cell Length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellLength", "parent": null, - Network accessline 254
"iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellLength", - Network accessline 258
}, "Simulation Cell Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVector", - Network accessline 259
"Simulation Cell Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVector", "parent": "Vector", - Network accessline 260
"iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVector", - Network accessline 264
}, "Simulation Cell Volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVolume", - Network accessline 265
"Simulation Cell Volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVolume", "parent": null, - Network accessline 266
"iri": "http://purls.helmholtz-metadaten.de/cmso/SimulationCellVolume", - Network accessline 270
}, "Space Group": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SpaceGroup", - Network accessline 271
"Space Group": { "iri": "http://purls.helmholtz-metadaten.de/cmso/SpaceGroup", "parent": null, - Network accessline 272
"iri": "http://purls.helmholtz-metadaten.de/cmso/SpaceGroup", - Network accessline 276
}, "Structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Structure", - Network accessline 277
"Structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Structure", "parent": null, - Network accessline 278
"iri": "http://purls.helmholtz-metadaten.de/cmso/Structure", - Network accessline 285
}, "Unit Cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/UnitCell", - Network accessline 286
"Unit Cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/UnitCell", "parent": null, - Network accessline 287
"iri": "http://purls.helmholtz-metadaten.de/cmso/UnitCell", - Network accessline 291
}, "Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Vector", - Network accessline 292
"Vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/Vector", "parent": null, - Network accessline 293
"iri": "http://purls.helmholtz-metadaten.de/cmso/Vector", - Network accessline 301
}, "Unit": { "iri": "http://qudt.org/schema/qudt/Unit", - Network accessline 302
"Unit": { "iri": "http://qudt.org/schema/qudt/Unit", "parent": null, - Network accessline 303
"iri": "http://qudt.org/schema/qudt/Unit", - Network accessline 364
"object_properties": { "has crystallographic defect": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/hasCrystallographicDefect", - Network accessline 365
"has crystallographic defect": { "iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/hasCrystallographicDefect", "domain": "Crystalline Material", - Network accessline 366
"iri": "http://purls.helmholtz-metadaten.de/cdos/cdco/hasCrystallographicDefect", - Network accessline 370
}, "has angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle", - Network accessline 371
"has angle": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle", "domain": null, - Network accessline 372
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle", - Network accessline 376
}, "has attribute": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAttribute", - Network accessline 377
"has attribute": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAttribute", "domain": "Atomic Scale Sample", - Network accessline 378
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAttribute", - Network accessline 382
}, "has basis": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasBasis", - Network accessline 383
"has basis": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasBasis", "domain": "Unit Cell", - Network accessline 384
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasBasis", - Network accessline 388
}, "has element": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasElement", - Network accessline 389
"has element": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasElement", "domain": "Chemical Species", - Network accessline 390
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasElement", - Network accessline 394
}, "has lattice parameter": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLatticeParameter", - Network accessline 395
"has lattice parameter": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLatticeParameter", "domain": "Unit Cell", - Network accessline 396
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasLatticeParameter", - Network accessline 400
}, "has simulation cell length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength", - Network accessline 401
"has simulation cell length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength", "domain": "Simulation Cell", - Network accessline 402
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength", - Network accessline 406
}, "has material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasMaterial", - Network accessline 407
"has material": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasMaterial", "domain": "Computational Sample", - Network accessline 408
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasMaterial", - Network accessline 412
}, "has normal vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNormalVector", - Network accessline 413
"has normal vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNormalVector", "domain": "Plane", - Network accessline 414
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasNormalVector", - Network accessline 418
}, "has simulation cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCell", - Network accessline 419
"has simulation cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCell", "domain": "Atomic Scale Sample", - Network accessline 420
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCell", - Network accessline 424
}, "has simulation cell volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCellVolume", - Network accessline 425
"has simulation cell volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCellVolume", "domain": "Simulation Cell", - Network accessline 426
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSimulationCellVolume", - Network accessline 430
}, "has space group": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroup", - Network accessline 431
"has space group": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroup", "domain": "Crystal Structure", - Network accessline 432
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroup", - Network accessline 436
}, "has species": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpecies", - Network accessline 437
"has species": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpecies", "domain": "Computational Sample", - Network accessline 438
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpecies", - Network accessline 442
}, "has structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasStructure", - Network accessline 443
"has structure": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasStructure", "domain": "Material", - Network accessline 444
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasStructure", - Network accessline 448
}, "has unit": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnit", - Network accessline 449
"has unit": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnit", "domain": "Thing", - Network accessline 450
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnit", - Network accessline 454
}, "has unit cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnitCell", - Network accessline 455
"has unit cell": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnitCell", "domain": "Crystal Structure", - Network accessline 456
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasUnitCell", - Network accessline 460
}, "has vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVector", - Network accessline 461
"has vector": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVector", "domain": null, - Network accessline 462
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasVector", - Network accessline 466
}, "is calculated property of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isCalculatedPropertyOf", - Network accessline 467
"is calculated property of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isCalculatedPropertyOf", "domain": null, - Network accessline 468
"iri": "http://purls.helmholtz-metadaten.de/cmso/isCalculatedPropertyOf", - Network accessline 472
}, "is defect of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isDefectOf", - Network accessline 473
"is defect of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isDefectOf", "domain": null, - Network accessline 474
"iri": "http://purls.helmholtz-metadaten.de/cmso/isDefectOf", - Network accessline 478
}, "is material of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isMaterialOf", - Network accessline 479
"is material of": { "iri": "http://purls.helmholtz-metadaten.de/cmso/isMaterialOf", "domain": null, - Network accessline 480
"iri": "http://purls.helmholtz-metadaten.de/cmso/isMaterialOf", - Network accessline 486
"data_properties": { "has alternative name": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAltName", - Network accessline 487
"has alternative name": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAltName", "domain": "Thing", - Network accessline 488
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAltName", - Network accessline 492
}, "has angle alpha": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_alpha", - Network accessline 493
"has angle alpha": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_alpha", "domain": "Angle", - Network accessline 494
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_alpha", - Network accessline 498
}, "has angle beta": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_beta", - Network accessline 499
"has angle beta": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_beta", "domain": "Angle", - Network accessline 500
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_beta", - Network accessline 504
}, "has angle gamma": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_gamma", - Network accessline 505
"has angle gamma": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_gamma", "domain": "Angle", - Network accessline 506
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAngle_gamma", - Network accessline 510
}, "has atomic percent": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAtomicPercent", - Network accessline 511
"has atomic percent": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasAtomicPercent", "domain": "Chemical Element", - Network accessline 512
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasAtomicPercent", - Network accessline 516
}, "has Bravais lattice": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasBravaisLattice", - Network accessline 517
"has Bravais lattice": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasBravaisLattice", "domain": "Unit Cell", - Network accessline 518
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasBravaisLattice", - Network accessline 522
}, "has chemical symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasChemicalSymbol", - Network accessline 523
"has chemical symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasChemicalSymbol", "domain": "Chemical Element", - Network accessline 524
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasChemicalSymbol", - Network accessline 528
}, "has component x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_x", - Network accessline 529
"has component x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_x", "domain": "Vector", - Network accessline 530
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_x", - Network accessline 534
}, "has component y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_y", - Network accessline 535
"has component y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_y", "domain": "Vector", - Network accessline 536
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_y", - Network accessline 540
}, "has component z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_z", - Network accessline 541
"has component z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_z", "domain": "Vector", - Network accessline 542
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasComponent_z", - Network accessline 546
}, "has distance from origin": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasDistanceFromOrigin", - Network accessline 547
"has distance from origin": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasDistanceFromOrigin", "domain": "Plane", - Network accessline 548
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasDistanceFromOrigin", - Network accessline 552
}, "has element ratio": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasElementRatio", - Network accessline 553
"has element ratio": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasElementRatio", "domain": "Chemical Element", - Network accessline 554
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasElementRatio", - Network accessline 558
}, "has grain size": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasGrainSize", - Network accessline 559
"has grain size": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasGrainSize", "domain": "Simulation Cell", - Network accessline 560
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasGrainSize", - Network accessline 564
}, "has identifier": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasIdentifier", - Network accessline 565
"has identifier": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasIdentifier", "domain": "Thing", - Network accessline 566
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasIdentifier", - Network accessline 570
}, "has length x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_x", - Network accessline 571
"has length x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_x", "domain": "Simulation Cell Length", - Network accessline 572
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_x", - Network accessline 576
}, "has length y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_y", - Network accessline 577
"has length y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_y", "domain": "Simulation Cell Length", - Network accessline 578
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_y", - Network accessline 582
}, "has length z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_z", - Network accessline 583
"has length z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_z", "domain": "Simulation Cell Length", - Network accessline 584
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasLength_z", - Network accessline 588
}, "has name": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasName", - Network accessline 589
"has name": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasName", "domain": "Thing", - Network accessline 590
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasName", - Network accessline 594
}, "has number of atoms": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfAtoms", - Network accessline 595
"has number of atoms": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfAtoms", "domain": "Atomic Scale Sample", - Network accessline 596
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfAtoms", - Network accessline 600
}, "has number of grains": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfGrains", - Network accessline 601
"has number of grains": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfGrains", "domain": "Simulation Cell", - Network accessline 602
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasNumberOfGrains", - Network accessline 606
}, "has path": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasPath", - Network accessline 607
"has path": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasPath", "domain": "Atom Attribute", - Network accessline 608
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasPath", - Network accessline 612
}, "has reference": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasReference", - Network accessline 613
"has reference": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasReference", "domain": "Thing", - Network accessline 614
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasReference", - Network accessline 618
}, "has repetition x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_x", - Network accessline 619
"has repetition x": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_x", "domain": "Simulation Cell", - Network accessline 620
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_x", - Network accessline 624
}, "has repetition y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_y", - Network accessline 625
"has repetition y": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_y", "domain": "Simulation Cell", - Network accessline 626
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_y", - Network accessline 630
}, "has repetition z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_z", - Network accessline 631
"has repetition z": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_z", "domain": "Simulation Cell", - Network accessline 632
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasRepetition_z", - Network accessline 636
}, "has space group number": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupNumber", - Network accessline 637
"has space group number": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupNumber", "domain": "Crystal Structure", - Network accessline 638
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupNumber", - Network accessline 642
}, "has space group symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupSymbol", - Network accessline 643
"has space group symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupSymbol", "domain": "Crystal Structure", - Network accessline 644
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSpaceGroupSymbol", - Network accessline 648
}, "has symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSymbol", - Network accessline 649
"has symbol": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasSymbol", "domain": "Thing", - Network accessline 650
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasSymbol", - Network accessline 654
}, "has vacuum direction": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumDirection", - Network accessline 655
"has vacuum direction": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumDirection", "domain": "Simulation Cell", - Network accessline 656
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumDirection", - Network accessline 660
}, "has vacuum length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumLength", - Network accessline 661
"has vacuum length": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumLength", "domain": "Simulation Cell", - Network accessline 662
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasVacuumLength", - Network accessline 666
}, "has value": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasValue", - Network accessline 667
"has value": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasValue", "domain": "Thing", - Network accessline 668
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasValue", - Network accessline 672
}, "has volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVolume", - Network accessline 673
"has volume": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasVolume", "domain": "Simulation Cell", - Network accessline 674
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasVolume", - Network accessline 678
}, "has weight percent": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasWeightPercent", - Network accessline 679
"has weight percent": { "iri": "http://purls.helmholtz-metadaten.de/cmso/hasWeightPercent", "domain": "Chemical Element", - Network accessline 680
"iri": "http://purls.helmholtz-metadaten.de/cmso/hasWeightPercent",
skills/ontology-explorer/references/ontology_registry.json
- Network accessline 4
"acronym": "CMSO", "version": "0.0.1", "source_url": "https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl", - Network accessline 5
"version": "0.0.1", "source_url": "https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl", "documentation_url": "https://ocdo.github.io/cmso/", - Network accessline 6
"source_url": "https://raw.githubusercontent.com/OCDO/cmso/main/cmso.owl", - Network accessline 7
"documentation_url": "https://ocdo.github.io/cmso/", - Network accessline 16
"acronym": "ASMO", "version": "1.0.0", "source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", - Network accessline 17
"version": "1.0.0", "source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", "documentation_url": "https://ocdo.github.io/asmo/", - Network accessline 18
"source_url": "https://raw.githubusercontent.com/OCDO/asmo/main/asmo.owl", - Network accessline 19
"documentation_url": "https://ocdo.github.io/asmo/",
skills/ontology-explorer/references/owl_primer.md
- Network accessline 56
Every class, property, and individual has a unique **IRI** (like a URL). Example: - `http://purls.helmholtz-metadaten.de/cmso/UnitCell` identifies the UnitCell class in CMSO - Network accessline 57
- `http://purls.helmholtz-metadaten.de/cmso/UnitCell` identifies the UnitCell class in CMSO - Network accessline 71
| Prefix | URI | Used For | |--------|-----|----------| | `owl` | `http://www.w3.org/2002/07/owl#` | OWL language constructs | - Network accessline 72
|--------|-----|----------| | `owl` | `http://www.w3.org/2002/07/owl#` | OWL language constructs | | `rdfs` | `http://www.w3.org/2000/01/rdf-schema#` | Labels, comments, subClassOf | - Network accessline 73
| `owl` | `http://www.w3.org/2002/07/owl#` | OWL language constructs | - Network accessline 74
| `rdfs` | `http://www.w3.org/2000/01/rdf-schema#` | Labels, comments, subClassOf | - Network accessline 75
| `rdf` | `http://www.w3.org/1999/02/22-rdf-syntax-ns#` | RDF type, about, resource | - Network accessline 76
| `xsd` | `http://www.w3.org/2001/XMLSchema#` | Data types (string, float, integer) | - Network accessline 77
| `skos` | `http://www.w3.org/2004/02/skos/core#` | Preferred labels, definitions | - Network accessline 78
| `dc` | `http://purl.org/dc/elements/1.1/` | Dublin Core metadata |
skills/ontology-explorer/scripts/class_browser.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-explorer/scripts/ontology_summarizer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-explorer/scripts/owl_parser.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 13
NS = { "owl": "http://www.w3.org/2002/07/owl#", - Network accessline 14
"owl": "http://www.w3.org/2002/07/owl#", - Network accessline 15
"rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", - Network accessline 16
"rdfs": "http://www.w3.org/2000/01/rdf-schema#", - Network accessline 17
"xml": "http://www.w3.org/XML/1998/namespace", - Network accessline 18
"xsd": "http://www.w3.org/2001/XMLSchema#", - Network accessline 19
"dc": "http://purl.org/dc/elements/1.1/", - Network accessline 20
"terms": "http://purl.org/dc/terms/", - Network accessline 21
"skos": "http://www.w3.org/2004/02/skos/core#", - Network accessline 22
"obo": "http://purl.obolibrary.org/obo/", - Network accessline 26
IAO_DEFINITION = "http://purl.obolibrary.org/obo/IAO_0000115"
skills/ontology-explorer/scripts/property_lookup.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-mapper/SKILL.md
- Broad permissionsline 1
Read, Bash
skills/ontology-mapper/scripts/concept_mapper.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-mapper/scripts/crystal_mapper.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-mapper/scripts/sample_annotator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-validator/SKILL.md
- Broad permissionsline 1
Read, Bash
skills/ontology-validator/scripts/completeness_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-validator/scripts/relationship_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/ontology-validator/scripts/schema_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/open-notebook/SKILL.md
- Network accessline 24
**Repository:** https://github.com/lfnovo/open-notebook - Network accessline 38
# Download the docker-compose file curl -o docker-compose.yml https://raw.githubusercontent.com/lfnovo/open-notebook/main/docker-compose.yml - Network accessline 39
curl -o docker-compose.yml https://raw.githubusercontent.com/lfnovo/open-notebook/main/docker-compose.yml - Access to secretsline 42
[Credential-related source omitted] - Network accessline 48
Access the application: - **Frontend UI:** http://localhost:8502 - Network accessline 49
- **Frontend UI:** http://localhost:8502 - Network accessline 50
- **REST API:** http://localhost:5055 - Network accessline 51
- **API Documentation:** http://localhost:5055/docs - Network accessline 67
BASE_URL = "http://localhost:5055/api" - Network accessline 69
# Add a credential for an AI provider response = requests.post(f"{BASE_URL}/credentials", json={ - Network accessline 70
response = requests.post(f"{BASE_URL}/credentials", json={ - Access to secretsline 73
[Credential-related source omitted] - Network accessline 77
# Discover available models response = requests.post( - Network accessline 78
response = requests.post( - Network accessline 83
# Register discovered models requests.post( - Network accessline 84
requests.post( - Network accessline 98
BASE_URL = "http://localhost:5055/api" - Network accessline 100
# Create a notebook response = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 101
response = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 113
# Add a web URL source response = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 114
response = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 115
"url": "https://arxiv.org/abs/2301.00001", - Network accessline 121
# Upload a PDF file with open("paper.pdf", "rb") as f: response = requests.post( - Network accessline 122
with open("paper.pdf", "rb") as f: response = requests.post( f"{BASE_URL}/sources", - Network accessline 123
response = requests.post( - Network accessline 134
# Create a human note response = requests.post(f"{BASE_URL}/notes", json={ - Network accessline 135
response = requests.post(f"{BASE_URL}/notes", json={ - Network accessline 147
# Create a chat session session = requests.post(f"{BASE_URL}/chat/sessions", json={ - Network accessline 148
session = requests.post(f"{BASE_URL}/chat/sessions", json={ - Network accessline 153
# Send a message with context from sources response = requests.post(f"{BASE_URL}/chat/execute", json={ - Network accessline 154
response = requests.post(f"{BASE_URL}/chat/execute", json={ - Network accessline 165
# Vector search across the knowledge base results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 166
results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 172
# Ask a question with AI-powered answer answer = requests.post(f"{BASE_URL}/search/ask/simple", json={ - Network accessline 173
answer = requests.post(f"{BASE_URL}/search/ask/simple", json={ - Network accessline 182
# Generate a podcast episode job = requests.post(f"{BASE_URL}/podcasts/generate", json={ - Network accessline 183
job = requests.post(f"{BASE_URL}/podcasts/generate", json={ - Network accessline 189
# Check generation status status = requests.get(f"{BASE_URL}/podcasts/jobs/{job['job_id']}").json() - Network accessline 190
status = requests.get(f"{BASE_URL}/podcasts/jobs/{job['job_id']}").json() - Network accessline 192
# Download audio when ready audio = requests.get( - Network accessline 193
audio = requests.get( - Network accessline 202
# Create a custom transformation transform = requests.post(f"{BASE_URL}/transformations", json={ - Network accessline 203
transform = requests.post(f"{BASE_URL}/transformations", json={ - Network accessline 211
# Execute transformation on text result = requests.post(f"{BASE_URL}/transformations/execute", json={ - Network accessline 212
result = requests.post(f"{BASE_URL}/transformations/execute", json={ - Network accessline 254
The REST API is available at `http://localhost:5055/api` with interactive documentation at `/docs`.
skills/open-notebook/references/api_reference.md
skills/open-notebook/references/configuration.md
- Access to secretsline 26
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 93
[Credential-related source omitted] - Access to secretsline 94
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Access to secretsline 96
[Credential-related source omitted] - Network accessline 114
BASE_URL = "http://localhost:5055/api" - Network accessline 116
# 1. Create credential cred = requests.post(f"{BASE_URL}/credentials", json={ - Network accessline 117
cred = requests.post(f"{BASE_URL}/credentials", json={ - Access to secretsline 120
[Credential-related source omitted] - Network accessline 123
# 2. Test connection test = requests.post(f"{BASE_URL}/credentials/{cred['id']}/test").json() - Network accessline 124
test = requests.post(f"{BASE_URL}/credentials/{cred['id']}/test").json() - Network accessline 127
# 3. Discover and register models discovered = requests.post( - Network accessline 128
discovered = requests.post( - Network accessline 132
requests.post( - Network accessline 137
# 4. Auto-assign defaults requests.post(f"{BASE_URL}/models/auto-assign") - Network accessline 138
requests.post(f"{BASE_URL}/models/auto-assign") - Network accessline 156
Then configure Ollama as a provider with base URL `http://ollama:11434`. - Network accessline 178
location / { proxy_pass http://localhost:8502; - Network accessline 179
proxy_pass http://localhost:8502; - Network accessline 186
location /api/ { proxy_pass http://localhost:5055/api/; - Network accessline 187
proxy_pass http://localhost:5055/api/;
skills/open-notebook/references/examples.md
- Network accessline 11
BASE_URL = "http://localhost:5055/api" - Network accessline 17
# 1. Create a research notebook notebook = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 18
notebook = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 25
# 2. Add sources from URLs urls = [ "https://www.nature.com/articles/s41568-020-0281-y", - Network accessline 26
urls = [ "https://www.nature.com/articles/s41568-020-0281-y", "https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30211-8", - Network accessline 27
"https://www.nature.com/articles/s41568-020-0281-y", - Network accessline 28
"https://www.cell.com/cancer-cell/fulltext/S1535-6108(20)30211-8", - Network accessline 31
source_ids = [] for url in urls: source = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 32
for url in urls: source = requests.post(f"{BASE_URL}/sources", data={ "url": url, - Network accessline 33
source = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 42
for source_id in source_ids: while True: status = requests.get( - Network accessline 43
while True: status = requests.get( f"{BASE_URL}/sources/{source_id}/status" - Network accessline 44
status = requests.get( - Network accessline 52
# 4. Create a chat session and ask questions session = requests.post(f"{BASE_URL}/chat/sessions", json={ - Network accessline 53
session = requests.post(f"{BASE_URL}/chat/sessions", json={ - Network accessline 58
answer = requests.post(f"{BASE_URL}/chat/execute", json={ - Network accessline 65
# 5. Search across materials results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 66
results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 73
# 6. Create a human note summarizing findings note = requests.post(f"{BASE_URL}/notes", json={ - Network accessline 74
note = requests.post(f"{BASE_URL}/notes", json={ - Network accessline 92
BASE_URL = "http://localhost:5055/api" - Network accessline 97
for path in file_paths: with open(path, "rb") as f: response = requests.post( - Network accessline 98
with open(path, "rb") as f: response = requests.post( f"{BASE_URL}/sources", - Network accessline 99
response = requests.post( - Network accessline 127
BASE_URL = "http://localhost:5055/api" - Network accessline 136
# Submit podcast generation job job = requests.post(f"{BASE_URL}/podcasts/generate", json={ - Network accessline 137
job = requests.post(f"{BASE_URL}/podcasts/generate", json={ - Network accessline 148
# Poll for completion while True: status = requests.get(f"{BASE_URL}/podcasts/jobs/{job_id}").json() - Network accessline 149
while True: status = requests.get(f"{BASE_URL}/podcasts/jobs/{job_id}").json() print(f"Status: {status.get('status', 'processing')}") - Network accessline 150
status = requests.get(f"{BASE_URL}/podcasts/jobs/{job_id}").json() - Network accessline 157
# Download the audio episode_id = status["episode_id"] audio = requests.get( - Network accessline 158
episode_id = status["episode_id"] audio = requests.get( f"{BASE_URL}/podcasts/episodes/{episode_id}/audio" - Network accessline 159
audio = requests.get( - Network accessline 176
BASE_URL = "http://localhost:5055/api" - Network accessline 182
# Create a methodology extraction transformation transform = requests.post(f"{BASE_URL}/transformations", json={ - Network accessline 183
transform = requests.post(f"{BASE_URL}/transformations", json={ - Network accessline 195
# Get models to find a suitable one models = requests.get(f"{BASE_URL}/models", params={ - Network accessline 196
models = requests.get(f"{BASE_URL}/models", params={ - Network accessline 201
# Execute the transformation result = requests.post(f"{BASE_URL}/transformations/execute", json={ - Network accessline 202
result = requests.post(f"{BASE_URL}/transformations/execute", json={ - Network accessline 219
BASE_URL = "http://localhost:5055/api" - Network accessline 225
# Get sources from a specific notebook sources = requests.get(f"{BASE_URL}/sources", params={ - Network accessline 226
sources = requests.get(f"{BASE_URL}/sources", params={ - Network accessline 231
# Vector search restricted to notebook sources results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 232
results = requests.post(f"{BASE_URL}/search", json={ - Network accessline 245
# Get an AI-powered answer answer = requests.post(f"{BASE_URL}/search/ask/simple", json={ - Network accessline 246
answer = requests.post(f"{BASE_URL}/search/ask/simple", json={ - Network accessline 261
BASE_URL = "http://localhost:5055/api" - Network accessline 267
# Check available providers providers = requests.get(f"{BASE_URL}/models/providers").json() - Network accessline 268
providers = requests.get(f"{BASE_URL}/models/providers").json() - Network accessline 271
# Discover models from a provider discovered = requests.get( - Network accessline 272
discovered = requests.get( - Network accessline 277
# Sync models to make them available requests.post(f"{BASE_URL}/models/sync/openai") - Network accessline 278
requests.post(f"{BASE_URL}/models/sync/openai") - Network accessline 280
# Auto-assign default models requests.post(f"{BASE_URL}/models/auto-assign") - Network accessline 281
requests.post(f"{BASE_URL}/models/auto-assign") - Network accessline 283
# Check current defaults defaults = requests.get(f"{BASE_URL}/models/defaults").json() - Network accessline 284
defaults = requests.get(f"{BASE_URL}/models/defaults").json()
skills/open-notebook/scripts/chat_interaction.py
- Executable scriptline 1
Executable file - Network accessline 10
Usage: export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 11
export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 18
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api" - Network accessline 27
if model_override: payload["model_override"] = model_override response = requests.post(f"{BASE_URL}/chat/sessions", json=payload) - Network accessline 28
payload["model_override"] = model_override response = requests.post(f"{BASE_URL}/chat/sessions", json=payload) response.raise_for_status() - Network accessline 29
response = requests.post(f"{BASE_URL}/chat/sessions", json=payload) - Network accessline 38
response = requests.get( - Network accessline 62
if model_override: payload["model_override"] = model_override response = requests.post(f"{BASE_URL}/chat/execute", json=payload) - Network accessline 63
payload["model_override"] = model_override response = requests.post(f"{BASE_URL}/chat/execute", json=payload) response.raise_for_status() - Network accessline 64
response = requests.post(f"{BASE_URL}/chat/execute", json=payload) - Network accessline 74
response = requests.get(f"{BASE_URL}/chat/sessions/{session_id}") - Network accessline 91
if note_ids: payload["note_ids"] = note_ids response = requests.post(f"{BASE_URL}/chat/context", json=payload) - Network accessline 92
payload["note_ids"] = note_ids response = requests.post(f"{BASE_URL}/chat/context", json=payload) response.raise_for_status() - Network accessline 93
response = requests.post(f"{BASE_URL}/chat/context", json=payload) - Network accessline 103
response = requests.post(f"{BASE_URL}/search", json={ - Network accessline 120
response = requests.post(f"{BASE_URL}/search/ask/simple", json={ - Network accessline 132
response = requests.delete(f"{BASE_URL}/chat/sessions/{session_id}") - Network accessline 141
notebook = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 148
requests.post(f"{BASE_URL}/sources", data={ - Network accessline 187
print() delete_chat_session(session["id"]) requests.delete(f"{BASE_URL}/notebooks/{notebook_id}") - Network accessline 188
delete_chat_session(session["id"]) requests.delete(f"{BASE_URL}/notebooks/{notebook_id}") print("Cleanup complete") - Network accessline 189
requests.delete(f"{BASE_URL}/notebooks/{notebook_id}")
skills/open-notebook/scripts/notebook_management.py
- Executable scriptline 1
Executable file - Network accessline 10
Usage: export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 11
export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 18
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api" - Network accessline 23
response = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 35
response = requests.get(f"{BASE_URL}/notebooks", params={ - Network accessline 50
response = requests.get(f"{BASE_URL}/notebooks/{notebook_id}") - Network accessline 62
if archived is not None: payload["archived"] = archived response = requests.put( - Network accessline 63
payload["archived"] = archived response = requests.put( f"{BASE_URL}/notebooks/{notebook_id}", json=payload - Network accessline 64
response = requests.put( - Network accessline 76
preview = requests.get( - Network accessline 82
response = requests.delete( - Network accessline 92
response = requests.post( - Network accessline 101
response = requests.delete(
skills/open-notebook/scripts/source_ingestion.py
- Executable scriptline 1
Executable file - Network accessline 10
Usage: export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 11
export OPEN_NOTEBOOK_URL="http://localhost:5055" - Network accessline 19
BASE_URL = os.getenv("OPEN_NOTEBOOK_URL", "http://localhost:5055") + "/api" - Network accessline 24
response = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 37
response = requests.post(f"{BASE_URL}/sources", data={ - Network accessline 50
filename = os.path.basename(file_path) with open(file_path, "rb") as f: response = requests.post( - Network accessline 51
with open(file_path, "rb") as f: response = requests.post( f"{BASE_URL}/sources", - Network accessline 52
response = requests.post( - Network accessline 68
elapsed = 0 while elapsed < timeout: response = requests.get(f"{BASE_URL}/sources/{source_id}/status") - Network accessline 69
while elapsed < timeout: response = requests.get(f"{BASE_URL}/sources/{source_id}/status") response.raise_for_status() - Network accessline 70
response = requests.get(f"{BASE_URL}/sources/{source_id}/status") - Network accessline 88
if notebook_id: params["notebook_id"] = notebook_id response = requests.get(f"{BASE_URL}/sources", params=params) - Network accessline 89
params["notebook_id"] = notebook_id response = requests.get(f"{BASE_URL}/sources", params=params) response.raise_for_status() - Network accessline 90
response = requests.get(f"{BASE_URL}/sources", params=params) - Network accessline 101
response = requests.get(f"{BASE_URL}/sources/{source_id}/insights") - Network accessline 108
response = requests.post(f"{BASE_URL}/sources/{source_id}/retry") - Network accessline 116
response = requests.delete(f"{BASE_URL}/sources/{source_id}") - Network accessline 125
notebook = requests.post(f"{BASE_URL}/notebooks", json={ - Network accessline 133
url_source = add_url_source( notebook_id, "https://en.wikipedia.org/wiki/CRISPR_gene_editing", - Network accessline 134
notebook_id, "https://en.wikipedia.org/wiki/CRISPR_gene_editing", ) - Network accessline 135
"https://en.wikipedia.org/wiki/CRISPR_gene_editing", - Network accessline 157
delete_source(url_source["id"]) delete_source(text_source["id"]) requests.delete(f"{BASE_URL}/notebooks/{notebook_id}") - Network accessline 158
delete_source(text_source["id"]) requests.delete(f"{BASE_URL}/notebooks/{notebook_id}") print("Cleanup complete") - Network accessline 159
requests.delete(f"{BASE_URL}/notebooks/{notebook_id}")
skills/open-notebook/scripts/test_open_notebook_skill.py
- Executable scriptline 1
Executable file
skills/open-targets-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search Open Targets, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search Open Targets, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Target-Disease Association", "url": "https://platform.opentargets.org/...", - Network accessline 79
"title": "Target-Disease Association", "url": "https://platform.opentargets.org/...", "content": "Association data, evidence, scores...", - Network accessline 80
"url": "https://platform.opentargets.org/...", - Network accessline 82
"source": "open-targets", "relevance_score": 0.95, "images": ["https://example.com/pathway.png"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/pathway.png"] } - Network accessline 84
"images": ["https://example.com/pathway.png"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/open-targets-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/open-targets-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/openalex-database/SKILL.md
- Network accessline 175
dois = [ "https://doi.org/10.1038/s41586-021-03819-2", - Network accessline 176
"https://doi.org/10.1038/s41586-021-03819-2", - Network accessline 177
"https://doi.org/10.1126/science.abc1234", - Network accessline 213
# Get the work work = client.get_entity('works', 'https://doi.org/10.1038/s41586-021-03819-2') - Network accessline 214
work = client.get_entity('works', 'https://doi.org/10.1038/s41586-021-03819-2') - Network accessline 216
# Get citing papers using cited_by_api_url import requests citing_response = requests.get( - Network accessline 217
import requests citing_response = requests.get( work['cited_by_api_url'], - Network accessline 218
citing_response = requests.get( - Network accessline 400
# DOI for works work = client.get_entity('works', 'https://doi.org/10.7717/peerj.4375') - Network accessline 401
work = client.get_entity('works', 'https://doi.org/10.7717/peerj.4375') - Network accessline 403
# ORCID for authors author = client.get_entity('authors', 'https://orcid.org/0000-0003-1613-5981') - Network accessline 404
author = client.get_entity('authors', 'https://orcid.org/0000-0003-1613-5981') - Network accessline 406
# ROR for institutions institution = client.get_entity('institutions', 'https://ror.org/02y3ad647') - Network accessline 407
institution = client.get_entity('institutions', 'https://ror.org/02y3ad647')
skills/openalex-database/references/api_guide.md
- Network accessline 5
**Base URL:** `https://api.openalex.org` - Network accessline 15
https://api.openalex.org/works?sample=20&seed=123 - Network accessline 51
for attempt in range(max_retries): try: response = requests.get(url) - Network accessline 52
try: response = requests.get(url) if response.status_code == 200: - Network accessline 53
response = requests.get(url) - Network accessline 127
# Small sample https://api.openalex.org/works?sample=20&seed=42 - Network accessline 128
https://api.openalex.org/works?sample=20&seed=42 - Network accessline 130
# Large sample (10k+) - make multiple requests https://api.openalex.org/works?sample=1000&seed=1 - Network accessline 131
https://api.openalex.org/works?sample=1000&seed=1 - Network accessline 132
https://api.openalex.org/works?sample=1000&seed=2 - Network accessline 138
# Simple search https://api.openalex.org/works?search=machine+learning - Network accessline 139
https://api.openalex.org/works?search=machine+learning - Network accessline 141
# Search specific field https://api.openalex.org/works?filter=title.search:CRISPR - Network accessline 142
https://api.openalex.org/works?filter=title.search:CRISPR - Network accessline 144
# Search + filter https://api.openalex.org/works?search=climate&filter=publication_year:2023 - Network accessline 145
https://api.openalex.org/works?search=climate&filter=publication_year:2023 - Network accessline 150
# Step 1: Get author ID https://api.openalex.org/authors?search=Heather+Piwowar - Network accessline 151
https://api.openalex.org/authors?search=Heather+Piwowar - Network accessline 152
# Returns: "id": "https://openalex.org/A5023888391" - Network accessline 154
# Step 2: Get their works https://api.openalex.org/works?filter=authorships.author.id:A5023888391 - Network accessline 155
https://api.openalex.org/works?filter=authorships.author.id:A5023888391 - Network accessline 160
# Step 1: Get institution ID https://api.openalex.org/institutions?search=MIT - Network accessline 161
https://api.openalex.org/institutions?search=MIT - Network accessline 162
# Returns: "id": "https://openalex.org/I136199984" - Network accessline 164
# Step 2: Get their works https://api.openalex.org/works?filter=authorships.institutions.id:I136199984 - Network accessline 165
https://api.openalex.org/works?filter=authorships.institutions.id:I136199984 - Network accessline 170
https://api.openalex.org/works?filter=publication_year:>2020&sort=cited_by_count:desc&per-page=200 - Network accessline 175
# All OA https://api.openalex.org/works?filter=is_oa:true - Network accessline 176
https://api.openalex.org/works?filter=is_oa:true - Network accessline 178
# Gold OA only https://api.openalex.org/works?filter=open_access.oa_status:gold - Network accessline 179
https://api.openalex.org/works?filter=open_access.oa_status:gold - Network accessline 184
# Recent OA works about COVID from top institutions https://api.openalex.org/works?filter=publication_year:2022,is_oa:true,title.search:covid,authorships.institutions.id:I136199984|I27837315 - Network accessline 185
https://api.openalex.org/works?filter=publication_year:2022,is_oa:true,title.search:covid,authorships.institutions.id:I136199984|I27837315 - Network accessline 190
# Get specific works by DOI (up to 50 per request) https://api.openalex.org/works?filter=doi:https://doi.org/10.1371/journal.pone.0266781|https://doi.org/10.1371/journal.pone.0267149&per-page=50 - Network accessline 191
https://api.openalex.org/works?filter=doi:https://doi.org/10.1371/journal.pone.0266781|https://doi.org/10.1371/journal.pone.0267149&per-page=50 - Network accessline 196
# Top topics https://api.openalex.org/works?group_by=topics.id - Network accessline 197
https://api.openalex.org/works?group_by=topics.id - Network accessline 199
# Papers per year https://api.openalex.org/works?group_by=publication_year - Network accessline 200
https://api.openalex.org/works?group_by=publication_year - Network accessline 202
# Most prolific institutions https://api.openalex.org/works?group_by=authorships.institutions.id - Network accessline 203
https://api.openalex.org/works?group_by=authorships.institutions.id - Network accessline 208
# First page https://api.openalex.org/works?filter=publication_year:2023&per-page=200 - Network accessline 209
https://api.openalex.org/works?filter=publication_year:2023&per-page=200 - Network accessline 211
# Next pages https://api.openalex.org/works?filter=publication_year:2023&per-page=200&page=2 - Network accessline 212
https://api.openalex.org/works?filter=publication_year:2023&per-page=200&page=2 - Network accessline 234
https://api.openalex.org/works/W2741809807 - Network accessline 242
"group_by": [ { "key": "https://openalex.org/T10001", - Network accessline 243
{ "key": "https://openalex.org/T10001", "key_display_name": "Artificial Intelligence", - Network accessline 244
"key": "https://openalex.org/T10001", - Network accessline 280
DOI: /works/https://doi.org/10.7717/peerj.4375 - Network accessline 286
ORCID: /authors/https://orcid.org/0000-0003-1613-5981 - Network accessline 291
ROR: /institutions/https://ror.org/02y3ad647 - Network accessline 319
for attempt in range(max_retries): try: response = requests.get(url, timeout=30) - Network accessline 320
try: response = requests.get(url, timeout=30) if response.status_code == 200: - Network accessline 321
response = requests.get(url, timeout=30) - Network accessline 367
- Full documentation: https://docs.openalex.org - Network accessline 368
- API Overview: https://docs.openalex.org/how-to-use-the-api/api-overview - Network accessline 369
- Entity schemas: https://docs.openalex.org/api-entities - Network accessline 370
- Help: https://openalex.org/help - Network accessline 371
- User group: https://groups.google.com/g/openalex-users
skills/openalex-database/references/common_queries.md
- Network accessline 149
dois = [ "https://doi.org/10.1371/journal.pone.0266781", - Network accessline 150
"https://doi.org/10.1371/journal.pone.0266781", - Network accessline 151
"https://doi.org/10.1371/journal.pone.0267149", - Network accessline 152
"https://doi.org/10.1038/s41586-021-03819-2", - Network accessline 286
# Get the work doi = "https://doi.org/10.1038/s41586-021-03819-2" - Network accessline 287
doi = "https://doi.org/10.1038/s41586-021-03819-2" - Network accessline 293
# Extract just the query part and use it import requests response = requests.get(cited_by_url, params={'mailto': client.email}) - Network accessline 294
import requests response = requests.get(cited_by_url, params={'mailto': client.email}) citing_works = response.json() - Network accessline 295
response = requests.get(cited_by_url, params={'mailto': client.email})
skills/openalex-database/scripts/openalex_client.py
skills/openalex-database/scripts/query_helpers.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/opentargets-database/SKILL.md
- Network accessline 224
Key information: - **Endpoint:** `https://api.platform.opentargets.org/api/v4/graphql` - Network accessline 225
- **Endpoint:** `https://api.platform.opentargets.org/api/v4/graphql` - Network accessline 226
- **Interactive browser:** `https://api.platform.opentargets.org/api/v4/graphql/browser` - Network accessline 355
**Release information:** Check https://platform-docs.opentargets.org/release-notes for the latest updates.
skills/opentargets-database/references/api_reference.md
- Network accessline 6
https://api.platform.opentargets.org/api/v4/graphql - Network accessline 11
https://api.platform.opentargets.org/api/v4/graphql/browser - Network accessline 18
1. **GraphQL API** - Best for single entity queries and flexible data retrieval 2. **Web Interface** - Interactive platform at https://platform.opentargets.org - Network accessline 19
2. **Web Interface** - Interactive platform at https://platform.opentargets.org - Network accessline 20
3. **Data Downloads** - FTP at https://ftp.ebi.ac.uk/pub/databases/opentargets/platform/ - Network accessline 64
# Make the request base_url = "https://api.platform.opentargets.org/api/v4/graphql" response = requests.post(base_url, json={"query": query_string, "variables": variables}) - Network accessline 65
base_url = "https://api.platform.opentargets.org/api/v4/graphql" response = requests.post(base_url, json={"query": query_string, "variables": variables}) data = json.loads(response.text) - Network accessline 66
response = requests.post(base_url, json={"query": query_string, "variables": variables})
skills/opentargets-database/scripts/query_opentargets.py
skills/opentrons-integration/scripts/basic_protocol_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/opentrons-integration/scripts/pcr_setup_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/opentrons-integration/scripts/serial_dilution_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/opentrons-protocol-agent/opentrons_generator.py
- Executable scriptline 1
Executable file
skills/opentrons-protocol-agent/opentrons_protocol_template.py
- Executable scriptline 1
Executable file
skills/paper-2-web/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Network accessline 135
git clone https://github.com/YuhangChen1/Paper2All.git - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 145
[Credential-related source omitted] - Network accessline 467
**External Resources**: - GitHub Repository: https://github.com/YuhangChen1/Paper2All - Network accessline 468
- GitHub Repository: https://github.com/YuhangChen1/Paper2All
skills/paper-2-web/references/installation.md
- Network accessline 20
git clone https://github.com/YuhangChen1/Paper2All.git - Dangerous shell operationline 39
sudo apt-get install libreoffice poppler-utils - Network accessline 47
**Windows:** - Download and install LibreOffice from https://www.libreoffice.org/ - Network accessline 48
- Download and install LibreOffice from https://www.libreoffice.org/ - Network accessline 49
- Download and install Poppler from https://github.com/oschwartz10612/poppler-windows - Access to secretsline 59
[Credential-related source omitted] - Access to secretsline 64
[Credential-related source omitted] - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted]
skills/parameter-optimization/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/parameter-optimization/scripts/doe_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/parameter-optimization/scripts/optimizer_selector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/parameter-optimization/scripts/sensitivity_summary.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/parameter-optimization/scripts/surrogate_builder.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/patents-search/SKILL.md
- Network accessline 29
1. Node.js 18+ (uses built-in fetch) 2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 30
2. Valyu API key from https://platform.valyu.ai ($10 free credits) - Network accessline 51
1. **Ask the user for their API key:** "To search patents, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 52
"To search patents, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai" - Network accessline 78
{ "title": "Patent Title", "url": "https://patents.google.com/...", - Network accessline 79
"title": "Patent Title", "url": "https://patents.google.com/...", "content": "Patent claims, description, technical details...", - Network accessline 80
"url": "https://patents.google.com/...", - Network accessline 82
"source": "patents", "relevance_score": 0.95, "images": ["https://example.com/diagram.png"] - Network accessline 83
"relevance_score": 0.95, "images": ["https://example.com/diagram.png"] } - Network accessline 84
"images": ["https://example.com/diagram.png"] - Network accessline 154
- Base URL: `https://api.valyu.ai/v1` - Network accessline 166
Direct API calls using Node.js built-in `fetch()`, zero external dependencies. - Access to secretsline 177
[Credential-related source omitted] - Network accessline 211
See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.
skills/patents-search/scripts/search
- Executable scriptline 1
#!/bin/bash
skills/patents-search/scripts/search.mjs
- Executable scriptline 1
#!/usr/bin/env node - Network accessline 12
const VALYU_API_BASE = 'https://api.valyu.ai/v1'; - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Network accessline 67
success: false, setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 68
setup_required: true, message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" }; - Network accessline 69
message: "Valyu API key not configured. Get your free API key ($10 credits) at https://platform.valyu.ai" - Network accessline 83
try { const response = await fetch(`${VALYU_API_BASE}/search`, { - Network accessline 84
const response = await fetch(`${VALYU_API_BASE}/search`, {
skills/pathml/references/data_management.md
- Network accessline 738
- **HDF5 Documentation:** https://www.hdfgroup.org/solutions/hdf5/ - Network accessline 739
- **h5py:** https://docs.h5py.org/ - Network accessline 740
- **DVC (Data Version Control):** https://dvc.org/ - Network accessline 741
- **Dask:** https://docs.dask.org/ - Network accessline 742
- **PathML Data Management API:** https://pathml.readthedocs.io/en/latest/api_data_reference.html
skills/pathml/references/graphs.md
skills/pathml/references/image_loading.md
- Network accessline 445
- **PathML Documentation:** https://pathml.readthedocs.io/ - Network accessline 446
- **OpenSlide:** https://openslide.org/ (underlying library for WSI formats) - Network accessline 447
- **Bio-Formats:** https://www.openmicroscopy.org/bio-formats/ (alternative backend) - Network accessline 448
- **DICOM Standard:** https://www.dicomstandard.org/
skills/pathml/references/machine_learning.md
- Network accessline 721
- **PathML ML API:** https://pathml.readthedocs.io/en/latest/api_ml_reference.html - Network accessline 722
- **HoVer-Net Paper:** Graham et al., "HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images," Medical Image Analysis, 2019 - **PanNuke Dataset:** https://warwick.ac.uk/fac/cross_fac/tia/data/pan - Network accessline 723
- **PanNuke Dataset:** https://warwick.ac.uk/fac/cross_fac/tia/data/pannuke - Network accessline 724
- **PyTorch Lightning:** https://www.pytorchlightning.ai/ - Network accessline 725
- **ONNX Runtime:** https://onnxruntime.ai/
skills/pathml/references/multiparametric.md
- Network accessline 173
cytoplasm_channel='CD45', model='mesmer', api_url='https://deepcell.org/api/predict', - Network accessline 174
model='mesmer', api_url='https://deepcell.org/api/predict', timeout=300 # Timeout in seconds - Network accessline 175
api_url='https://deepcell.org/api/predict', - Network accessline 681
- **PathML Multiparametric API:** https://pathml.readthedocs.io/en/latest/api_multiparametric_reference.html - Network accessline 682
- **CODEX:** https://www.akoyabio.com/codex/ - Network accessline 683
- **Vectra:** https://www.akoyabio.com/vectra/ - Network accessline 684
- **DeepCell Mesmer:** https://www.deepcell.org/ - Network accessline 685
- **Scanpy:** https://scanpy.readthedocs.io/ (single-cell analysis) - Network accessline 686
- **Squidpy:** https://squidpy.readthedocs.io/ (spatial omics analysis)
skills/pathml/references/preprocessing.md
- Network accessline 353
cytoplasm_channel='CD45', model='mesmer', api_url='https://deepcell.org/api' - Network accessline 354
model='mesmer', api_url='https://deepcell.org/api' ) - Network accessline 355
api_url='https://deepcell.org/api' - Network accessline 718
- **PathML Preprocessing API:** https://pathml.readthedocs.io/en/latest/api_preprocessing_reference.html - Network accessline 720
- Macenko et al. 2009: "A method for normalizing histology slides for quantitative analysis" - Vahadane et al. 2016: "Structure-Preserving Color Normalization and Sparse Stain Separation" - **DeepCell Mesmer:** https://www.deepcell.org/ ( - Network accessline 722
- **DeepCell Mesmer:** https://www.deepcell.org/ (cell segmentation model)
skills/patiently-ai/SKILL.md
- Broad permissionsline 1
Unsupported or unresolved allowed-tools declaration - Network accessline 7
{ "emoji": "🩺", "homepage": "https://pharmatools.ai", - Network accessline 8
"emoji": "🩺", "homepage": "https://pharmatools.ai", }, - Network accessline 9
"homepage": "https://pharmatools.ai", - Network accessline 103
Built by [PharmaTools.AI](https://pharmatools.ai) — applied AI for pharma and healthcare.
skills/pdb-database/SKILL.md
- Possible obfuscationline 54
value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM", - Network accessline 100
# Get entry-level data entry_data = fetch("4HHB", schema=Schema.ENTRY) - Network accessline 101
entry_data = fetch("4HHB", schema=Schema.ENTRY) - Network accessline 108
# Get protein/nucleic acid information entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY) - Network accessline 109
entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY) - Network accessline 132
} """ data = fetch(query_type="graphql", query=query) - Network accessline 134
data = fetch(query_type="graphql", query=query) - Network accessline 141
**Download Methods:** - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb` - Network accessline 142
- **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb` - Network accessline 143
- **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif` - Network accessline 145
- **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1) - Network accessline 153
# Download PDB format pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" - Network accessline 154
pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" - Network accessline 155
response = requests.get(pdb_url) - Network accessline 159
# Download mmCIF format cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif" - Network accessline 160
cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif" - Network accessline 161
response = requests.get(cif_url) - Network accessline 190
# Get experimental details data = fetch("4HHB", schema=Schema.ENTRY) - Network accessline 191
data = fetch("4HHB", schema=Schema.ENTRY) - Network accessline 212
for pdb_id in pdb_ids: try: data = fetch(pdb_id, schema=Schema.ENTRY) - Network accessline 213
try: data = fetch(pdb_id, schema=Schema.ENTRY) results[pdb_id] = { - Network accessline 214
data = fetch(pdb_id, schema=Schema.ENTRY) - Network accessline 298
- **RCSB PDB Website:** https://www.rcsb.org - Network accessline 299
- **PDB-101 Educational Portal:** https://pdb101.rcsb.org - Network accessline 300
- **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview - Network accessline 301
- **Python Package Docs:** https://rcsbapi.readthedocs.io/ - Network accessline 302
- **Data API Documentation:** https://data.rcsb.org/ - Network accessline 303
- **GitHub Repository:** https://github.com/rcsb/py-rcsb-api
skills/pdb-database/references/api_reference.md
- Network accessline 32
Base URL: `https://data.rcsb.org/rest/v1/` - Network accessline 36
GET https://data.rcsb.org/rest/v1/core/entry/{entry_id} - Network accessline 41
GET https://data.rcsb.org/rest/v1/core/polymer_entity/{entry_id}_{entity_id} - Network accessline 46
GET https://data.rcsb.org/rest/v1/core/assembly/{entry_id}/{assembly_id} - Network accessline 51
# Get entry data for hemoglobin curl https://data.rcsb.org/rest/v1/core/entry/4HHB - Network accessline 52
curl https://data.rcsb.org/rest/v1/core/entry/4HHB - Network accessline 54
# Get first polymer entity curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1 - Network accessline 55
curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1 - Network accessline 57
# Get biological assembly 1 curl https://data.rcsb.org/rest/v1/core/assembly/4HHB/1 - Network accessline 58
curl https://data.rcsb.org/rest/v1/core/assembly/4HHB/1 - Network accessline 63
Endpoint: `https://data.rcsb.org/graphql` - Network accessline 113
response = requests.post( - Network accessline 114
"https://data.rcsb.org/graphql", - Possible obfuscationline 239
value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM", - Network accessline 363
https://files.rcsb.org/download/{PDB_ID}.pdb - Network accessline 368
https://files.rcsb.org/download/{PDB_ID}.cif - Network accessline 373
https://files.rcsb.org/download/{PDB_ID}-sf.cif - Network accessline 378
https://files.rcsb.org/download/{PDB_ID}.pdb1 # Assembly 1 - Network accessline 379
https://files.rcsb.org/download/{PDB_ID}.pdb2 # Assembly 2 - Network accessline 384
https://www.rcsb.org/fasta/entry/{PDB_ID} - Network accessline 399
output_dir: Directory to save file """ base_url = "https://files.rcsb.org/download" - Network accessline 400
""" base_url = "https://files.rcsb.org/download" url = f"{base_url}/{pdb_id}.{format}" - Network accessline 401
base_url = "https://files.rcsb.org/download" - Network accessline 404
response = requests.get(url) - Network accessline 446
for attempt in range(max_retries): response = requests.get(url) - Network accessline 447
response = requests.get(url) - Network accessline 488
for i, pdb_id in enumerate(pdb_ids): try: data = fetch(pdb_id, schema=Schema.ENTRY) - Network accessline 489
try: data = fetch(pdb_id, schema=Schema.ENTRY) results[pdb_id] = data - Network accessline 490
data = fetch(pdb_id, schema=Schema.ENTRY) - Network accessline 600
# Test with curl import subprocess - Network accessline 601
import subprocess result = subprocess.run( ["curl", "https://data.rcsb.org/rest/v1/core/entry/4HHB"], - Network accessline 602
result = subprocess.run( ["curl", "https://data.rcsb.org/rest/v1/core/entry/4HHB"], capture_output=True, - Network accessline 603
["curl", "https://data.rcsb.org/rest/v1/core/entry/4HHB"], - Network accessline 612
- **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview - Network accessline 613
- **Data API Redoc:** https://data.rcsb.org/redoc/index.html - Network accessline 614
- **GraphQL Schema:** https://data.rcsb.org/graphql - Network accessline 615
- **Python Package Docs:** https://rcsbapi.readthedocs.io/ - Network accessline 616
- **GitHub Issues:** https://github.com/rcsb/py-rcsb-api/issues - Network accessline 617
- **Community Forum:** https://www.rcsb.org/help
skills/pdb/SKILL.md
- Network accessline 26
# Download PDB file curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb" - Network accessline 27
curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb" - Network accessline 29
# Download mmCIF curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif" - Network accessline 30
curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif" - Network accessline 45
def fetch_pdb(pdb_id: str, format: str = "pdb") -> str: """Fetch structure from RCSB PDB.""" url = f"https://files.rcsb.org/download/{pdb_id}.{format}" - Network accessline 46
"""Fetch structure from RCSB PDB.""" url = f"https://files.rcsb.org/download/{pdb_id}.{format}" response = requests.get(url) - Network accessline 47
url = f"https://files.rcsb.org/download/{pdb_id}.{format}" - Network accessline 48
response = requests.get(url) - Network accessline 52
def fetch_fasta(pdb_id: str) -> str: """Fetch sequence in FASTA format.""" url = f"https://www.rcsb.org/fasta/entry/{pdb_id}" - Network accessline 53
"""Fetch sequence in FASTA format.""" url = f"https://www.rcsb.org/fasta/entry/{pdb_id}" return requests.get(url).text - Network accessline 54
url = f"https://www.rcsb.org/fasta/entry/{pdb_id}" - Network accessline 55
return requests.get(url).text - Network accessline 129
response = requests.post( - Network accessline 130
"https://search.rcsb.org/rcsbsearch/v2/query", - Network accessline 201
### Target Preparation Checklist 1. Download structure: `curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"` - Network accessline 202
1. Download structure: `curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb"`
skills/pdf-anthropic/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/pdf-anthropic/scripts/check_bounding_boxes.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/check_bounding_boxes_test.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/check_fillable_fields.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/convert_pdf_to_images.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/create_validation_image.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/extract_form_field_info.py
- Executable scriptline 1
Executable file - Network accessline 31
# "/Off" seems to always be the unchecked value, as suggested by # https://opensource.adobe.com/dc-acrobat-sdk-docs/standards/pdfstandards/pdf/PDF32000_2008.pdf#page=448 - Network accessline 32
# https://opensource.adobe.com/dc-acrobat-sdk-docs/standards/pdfstandards/pdf/PDF32000_2008.pdf#page=448 - Network accessline 79
# Radio button options have a separate annotation for each choice; # all choices have the same field name. # See https://westhealth.github.io/exploring-fillable-forms-with-pdfrw.html - Network accessline 81
# See https://westhealth.github.io/exploring-fillable-forms-with-pdfrw.html
skills/pdf-anthropic/scripts/fill_fillable_fields.py
- Executable scriptline 1
Executable file
skills/pdf-anthropic/scripts/fill_pdf_form_with_annotations.py
skills/pdf-processing-pro/OCR.md
- Dangerous shell operationline 32
sudo apt-get install tesseract-ocr - Network accessline 35
**Windows:** Download from: https://github.com/UB-Mannheim/tesseract/wiki - Network accessline 36
Download from: https://github.com/UB-Mannheim/tesseract/wiki - Dangerous shell operationline 63
sudo apt-get install tesseract-ocr-spa tesseract-ocr-fra
skills/pdf-processing-pro/scripts/analyze_form.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pdf/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/pdf/scripts/check_bounding_boxes.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/check_fillable_fields.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/convert_pdf_to_images.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/create_validation_image.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/extract_form_field_info.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/extract_form_structure.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/fill_fillable_fields.py
- Executable scriptline 1
Executable file
skills/pdf/scripts/fill_pdf_form_with_annotations.py
- Executable scriptline 1
Executable file
skills/peer-review/SKILL.md
- Broad permissionsline 1
Bash
skills/peer-review/references/reporting_standards.md
- Network accessline 20
**Reference:** http://www.consort-statement.org/ - Network accessline 36
**Reference:** https://www.strobe-statement.org/ - Network accessline 53
**Reference:** http://www.prisma-statement.org/ - Network accessline 64
**Reference:** https://www.spirit-statement.org/ - Network accessline 78
**Reference:** https://www.care-statement.org/ - Network accessline 100
**Reference:** https://arriveguidelines.org/ - Network accessline 116
**Reference:** http://fged.org/projects/miame/ - Network accessline 140
**Reference:** https://gensc.org/ - Network accessline 156
**Reference:** https://www.wwpdb.org/ - Network accessline 172
**Reference:** http://www.psidev.info/ - Network accessline 187
**Reference:** https://www.humanbrainmapping.org/cobidas - Network accessline 203
**Reference:** http://flowcyt.org/ - Network accessline 217
**Reference:** https://www.miappe.org/
skills/performance-profiling/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/performance-profiling/scripts/bottleneck_detector.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/performance-profiling/scripts/memory_profiler.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/performance-profiling/scripts/scaling_analyzer.py
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#!/usr/bin/env python3
skills/performance-profiling/scripts/timing_analyzer.py
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#!/usr/bin/env python3
skills/perplexity-search/SKILL.md
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1. **Get OpenRouter API key**: - Visit https://openrouter.ai/keys - Network accessline 36
- Visit https://openrouter.ai/keys - Access to secretsline 43
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3. Reserve `sonar-pro-search` for complex analysis 4. Set `--max-tokens` to limit response length 5. Monitor usage at https://openrouter.ai/activity - Network accessline 253
4. Set `--max-tokens` to limit response length 5. Monitor usage at https://openrouter.ai/activity 6. Set spending limits in OpenRouter dashboard - Network accessline 254
5. Monitor usage at https://openrouter.ai/activity - Access to secretsline 265
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**Solutions**: - Wait a few seconds before retrying - Increase rate limit at https://openrouter.ai/keys - Network accessline 284
- Wait a few seconds before retrying - Increase rate limit at https://openrouter.ai/keys - Add delays between requests in batch processing - Network accessline 285
- Increase rate limit at https://openrouter.ai/keys - Network accessline 292
**Solution**: - Add credits at https://openrouter.ai/account - Network accessline 293
- Add credits at https://openrouter.ai/account - Network accessline 385
**OpenRouter:** - Dashboard: https://openrouter.ai/account - Network accessline 386
- Dashboard: https://openrouter.ai/account - Network accessline 387
- API Keys: https://openrouter.ai/keys - Network accessline 388
- Perplexity Models: https://openrouter.ai/perplexity - Network accessline 389
- Usage Monitoring: https://openrouter.ai/activity - Network accessline 390
- Documentation: https://openrouter.ai/docs - Network accessline 392
**LiteLLM:** - Documentation: https://docs.litellm.ai/ - Network accessline 393
- Documentation: https://docs.litellm.ai/ - Network accessline 394
- OpenRouter Provider: https://docs.litellm.ai/docs/providers/openrouter - Network accessline 395
- GitHub: https://github.com/BerriAI/litellm - Network accessline 397
**Perplexity:** - Official Docs: https://docs.perplexity.ai/ - Network accessline 398
- Official Docs: https://docs.perplexity.ai/ - Access to secretsline 412
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skills/perplexity-search/assets/.env.example
skills/perplexity-search/references/model_comparison.md
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skills/perplexity-search/references/openrouter_setup.md
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1. Visit https://openrouter.ai/ - Network accessline 30
1. Navigate to https://openrouter.ai/account - Network accessline 36
**Pricing notes:** - Models have different per-token costs - See https://openrouter.ai/perplexity for Perplexity pricing - Network accessline 37
- Models have different per-token costs - See https://openrouter.ai/perplexity for Perplexity pricing - Monitor usage at https://openrouter.ai/activity - Network accessline 38
- See https://openrouter.ai/perplexity for Perplexity pricing - Network accessline 39
- Monitor usage at https://openrouter.ai/activity - Network accessline 43
1. Go to https://openrouter.ai/keys - Access to secretsline 65
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1. Visit https://openrouter.ai/activity 2. View requests, tokens, and costs - Network accessline 198
1. Go to https://openrouter.ai/keys 2. Click on your key 3. Set "Rate limit" (requests per minute) - Access to secretsline 227
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**Solutions**: 1. Verify key at https://openrouter.ai/keys - Network accessline 245
1. Verify key at https://openrouter.ai/keys - Network accessline 254
**Solution**: 1. Go to https://openrouter.ai/account - Network accessline 255
1. Go to https://openrouter.ai/account - Network accessline 264
**Solutions**: 1. Wait a few seconds before retrying 2. Increase rate limit at https://openrouter.ai/keys - Network accessline 265
1. Wait a few seconds before retrying 2. Increase rate limit at https://openrouter.ai/keys 3. Implement exponential backoff in code - Network accessline 266
2. Increase rate limit at https://openrouter.ai/keys 3. Implement exponential backoff in code 4. Batch requests or reduce frequency - Network accessline 274
**Solution**: 1. Check available models at https://openrouter.ai/models - Network accessline 275
1. Check available models at https://openrouter.ai/models - Access to secretsline 306
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model="openrouter/perplexity/sonar-pro", messages=[{"role": "user", "content": "query"}], api_base="https://custom-endpoint.com/v1" # Custom URL - Network accessline 323
messages=[{"role": "user", "content": "query"}], api_base="https://custom-endpoint.com/v1" # Custom URL ) - Network accessline 324
api_base="https://custom-endpoint.com/v1" # Custom URL - Network accessline 337
messages=[{"role": "user", "content": "query"}], extra_headers={ "HTTP-Referer": "https://your-app.com", - Network accessline 338
extra_headers={ "HTTP-Referer": "https://your-app.com", "X-Title": "Your App Name" - Network accessline 339
"HTTP-Referer": "https://your-app.com", - Access to secretsline 374
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1. Go to https://openrouter.ai/keys immediately - Network accessline 402
A: Pricing varies by model. Sonar is cheapest (~$0.001-0.002 per query), Sonar Pro is moderate (~$0.002-0.005), and Sonar Pro Search is most expensive (~$0.02-0.05+ per query). See https://openrouter.ai/perplexity for exact pricing. - Network accessline 426
**Official Documentation:** - OpenRouter: https://openrouter.ai/docs - Network accessline 427
- OpenRouter: https://openrouter.ai/docs - Network accessline 428
- Perplexity Models: https://openrouter.ai/perplexity - Network accessline 429
- LiteLLM: https://docs.litellm.ai/ - Network accessline 431
**Account Management:** - Dashboard: https://openrouter.ai/account - Network accessline 432
- Dashboard: https://openrouter.ai/account - Network accessline 433
- API Keys: https://openrouter.ai/keys - Network accessline 434
- Usage: https://openrouter.ai/activity - Network accessline 435
- Billing: https://openrouter.ai/credits - Network accessline 437
**Community:** - OpenRouter Discord: https://discord.gg/openrouter - Network accessline 438
- OpenRouter Discord: https://discord.gg/openrouter - Network accessline 439
- GitHub Issues: https://github.com/OpenRouter - Network accessline 440
- LiteLLM GitHub: https://github.com/BerriAI/litellm - Network accessline 446
1. Create account at https://openrouter.ai - Network accessline 447
2. Add payment method and credits 3. Generate API key at https://openrouter.ai/keys 4. Set `OPENROUTER_API_KEY` environment variable - Network accessline 448
3. Generate API key at https://openrouter.ai/keys - Access to secretsline 449
[Credential-related source omitted]
skills/perplexity-search/scripts/perplexity_search.py
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#!/usr/bin/env python3 - Access to secretsline 12
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print("\nTo set up your API key:", file=sys.stderr) print("1. Get an API key from https://openrouter.ai/keys", file=sys.stderr) print("2. Set the environment variable:", file=sys.stderr) - Network accessline 43
print("1. Get an API key from https://openrouter.ai/keys", file=sys.stderr) - Access to secretsline 45
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skills/perplexity-search/scripts/setup_env.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 20
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[Credential-related source omitted] - Network accessline 75
print() print("To set up your API key:") print("1. Get an API key from https://openrouter.ai/keys") - Network accessline 76
print("To set up your API key:") print("1. Get an API key from https://openrouter.ai/keys") print("2. Run this script with --api-key flag:") - Network accessline 77
print("1. Get an API key from https://openrouter.ai/keys") - Access to secretsline 84
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[Credential-related source omitted] - Network accessline 120
Get your OpenRouter API key from: https://openrouter.ai/keys - Network accessline 121
https://openrouter.ai/keys - Access to secretsline 132
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skills/pharmgx-reporter/SKILL.md
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always: false emoji: "💊" homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: "💊" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 133
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 134
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels
skills/pharmgx-reporter/api.py
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Executable file
skills/pharmgx-reporter/demo_patient.txt
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# Real pharmacogenomic data from Manuel Corpas's publicly available 23andMe # genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 2
# genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 # - Network accessline 3
# Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682
skills/pharmgx-reporter/demo_report/report.md
skills/pharmgx-reporter/examples/demo_report.html
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<div class="disclaimer"><strong>Disclaimer:</strong> ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.</div - Network accessline 296
<div class="report-header"><svg class="header-logo" viewBox="0 0 200 200" xmlns="http://www.w3.org/2000/svg"><g fill="white" fill-rule="evenodd"><path d="M60 30 C55 80, 40 130, 50 170 C55 175, 65 175, 68 168 C78 130, 70 80, 75 35 Z"/><path - Network accessline 297
<div class="exec-summary"><h3>Summary</h3><div class="exec-summary-grid"><div class="exec-stat stat-avoid"><span class="stat-icon">⛔</span><div class="stat-text"><strong>1 drug(s) to avoid</strong><span>Warfarin (Coumadin)</span></div></div - Network accessline 298
<h2>Drug Recommendations</h2> <div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td> - Network accessline 299
<div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td><td><span class="badge badge-a - Network accessline 300
<tr class="row-caution"><td><strong>Amitriptyline</strong> (Elavil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 301
<tr class="row-caution"><td><strong>Celecoxib</strong> (Celebrex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 302
<tr class="row-caution"><td><strong>Clomipramine</strong> (Anafranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 303
<tr class="row-caution"><td><strong>Clopidogrel</strong> (Plavix)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 304
<tr class="row-caution"><td><strong>Codeine</strong> (Tylenol w/ Codeine)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation C - Network accessline 305
<tr class="row-caution"><td><strong>Desipramine</strong> (Norpramin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 306
<tr class="row-caution"><td><strong>Doxepin</strong> (Sinequan)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium" - Network accessline 307
<tr class="row-caution"><td><strong>Efavirenz</strong> (Sustiva)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 308
<tr class="row-caution"><td><strong>Flurbiprofen</strong> (Ansaid)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 309
<tr class="row-caution"><td><strong>Haloperidol</strong> (Haldol)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div></ - Network accessline 310
<tr class="row-caution"><td><strong>Hydrocodone</strong> (Vicodin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 311
<tr class="row-caution"><td><strong>Imipramine</strong> (Tofranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 312
<tr class="row-caution"><td><strong>Meloxicam</strong> (Mobic)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 313
<tr class="row-caution"><td><strong>Nortriptyline</strong> (Pamelor)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 314
<tr class="row-caution"><td><strong>Phenytoin</strong> (Dilantin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 315
<tr class="row-caution"><td><strong>Piroxicam</strong> (Feldene)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 316
<tr class="row-caution"><td><strong>Risperidone</strong> (Risperdal)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div - Network accessline 317
<tr class="row-caution"><td><strong>Tamoxifen</strong> (Nolvadex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 318
<tr class="row-caution"><td><strong>Tramadol</strong> (Ultram)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 319
<tr class="row-caution"><td><strong>Trimipramine</strong> (Surmontil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 320
<details><summary>Standard Drugs (30 medications — click to expand)</summary><div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-stand - Network accessline 321
<tr class="row-standard"><td><strong>Atazanavir</strong> (Reyataz)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 322
<tr class="row-standard"><td><strong>Atomoxetine</strong> (Strattera)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 323
<tr class="row-standard"><td><strong>Atorvastatin</strong> (Lipitor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 324
<tr class="row-standard"><td><strong>Azathioprine</strong> (Imuran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 325
<tr class="row-standard"><td><strong>Capecitabine</strong> (Xeloda)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 326
<tr class="row-standard"><td><strong>Citalopram</strong> (Celexa)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 327
<tr class="row-standard"><td><strong>Clozapine</strong> (Clozaril)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 328
<tr class="row-standard"><td><strong>Dexlansoprazole</strong> (Dexilant)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation - Network accessline 329
<tr class="row-standard"><td><strong>Escitalopram</strong> (Lexapro)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 330
<tr class="row-standard"><td><strong>Esomeprazole</strong> (Nexium)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 331
<tr class="row-standard"><td><strong>Fluorouracil</strong> (5-FU)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 332
<tr class="row-standard"><td><strong>Fluoxetine</strong> (Prozac)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 333
<tr class="row-standard"><td><strong>Irinotecan</strong> (Camptosar)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div> - Network accessline 334
<tr class="row-standard"><td><strong>Lansoprazole</strong> (Prevacid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 335
<tr class="row-standard"><td><strong>Mercaptopurine</strong> (Purinethol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span>< - Network accessline 336
<tr class="row-standard"><td><strong>Metoprolol</strong> (Lopressor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 337
<tr class="row-standard"><td><strong>Omeprazole</strong> (Prilosec)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 338
<tr class="row-standard"><td><strong>Ondansetron</strong> (Zofran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 339
<tr class="row-standard"><td><strong>Oxycodone</strong> (OxyContin)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 340
<tr class="row-standard"><td><strong>Pantoprazole</strong> (Protonix)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 341
<tr class="row-standard"><td><strong>Paroxetine</strong> (Paxil)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 342
<tr class="row-standard"><td><strong>Pravastatin</strong> (Pravachol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 343
<tr class="row-standard"><td><strong>Rosuvastatin</strong> (Crestor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 344
<tr class="row-standard"><td><strong>Sertraline</strong> (Zoloft)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 345
<tr class="row-standard"><td><strong>Simvastatin</strong> (Zocor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 346
<tr class="row-standard"><td><strong>Tacrolimus</strong> (Prograf)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 347
<tr class="row-standard"><td><strong>Thioguanine</strong> (Tabloid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 348
<tr class="row-standard"><td><strong>Venlafaxine</strong> (Effexor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 349
<tr class="row-standard"><td><strong>Voriconazole</strong> (Vfend)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor
skills/pharmgx-reporter/pharmgx_reporter.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 1476
lines.append("## References") lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1476
lines.append("## References") lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1477
lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1477
lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1478
lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1478
lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1479
lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1479
lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1480
lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.pharmgkb.org/") lines.append("") - Network accessline 1480
lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.pharmgkb.org/") lines.append("") - Network accessline 1481
lines.append("- PharmGKB. https://www.pharmgkb.org/") - Network accessline 1481
lines.append("- PharmGKB. https://www.pharmgkb.org/") - Network accessline 1506
for rsid, _allele in rsids: lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1506
for rsid, _allele in rsids: lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1507
lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' f'target="_blank" rel="noopener">' - Network accessline 1507
lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' f'target="_blank" rel="noopener">' - Network accessline 1508
f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1508
f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1512
if not rsids: lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1512
if not rsids: lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1513
lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' f'target="_blank" rel="noopener">{_html.escape(gene)}</a>' - Network accessline 1513
lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' f'target="_blank" rel="noopener">{_html.escape(gene)}</a>' - Network accessline 1514
f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1514
f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" '
skills/pharmgx-reporter/tests/test_pharmgx.py
- Executable scriptline 1
Executable file
skills/phylogenetics/SKILL.md
- Network accessline 397
- **MAFFT**: https://mafft.cbrc.jp/alignment/software/ - Network accessline 398
- **IQ-TREE 2**: http://www.iqtree.org/ | Tutorial: https://www.iqtree.org/workshop/molevol2022 - Network accessline 399
- **FastTree**: http://www.microbesonline.org/fasttree/ - Network accessline 400
- **ETE3**: http://etetoolkit.org/ - Network accessline 401
- **FigTree** (GUI visualization): https://tree.bio.ed.ac.uk/software/figtree/ - Network accessline 402
- **iTOL** (web visualization): https://itol.embl.de/ - Network accessline 403
- **MUSCLE** (alternative aligner): https://www.drive5.com/muscle/ - Network accessline 404
- **TrimAl** (alignment trimming): https://vicfero.github.io/trimal/
skills/phylogenetics/scripts/phylogenetic_analysis.py
- Executable scriptline 1
Executable file
skills/plotly/SKILL.md
skills/polars/SKILL.md
- Network accessline 2
name: polars description: Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pi - Network accessline 3
description: Fast in-memory DataFrame library for datasets that fit in RAM. Use when pandas is too slow but data still fits in memory. Lazy evaluation, parallel execution, Apache Arrow backend. Best for 1-100GB datasets, ETL pipelines, fast - Network accessline 4
license: https://github.com/pola-rs/polars/blob/main/LICENSE
skills/polars/references/io_guide.md
- Access to secretsline 270
[Credential-related source omitted] - Access to secretsline 271
[Credential-related source omitted] - Access to secretsline 272
[Credential-related source omitted] - Access to secretsline 287
[Credential-related source omitted] - Access to secretsline 288
[Credential-related source omitted] - Access to secretsline 301
[Credential-related source omitted]
skills/post-processing/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/post-processing/scripts/comparison_tool.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/derived_quantities.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/field_extractor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/profile_extractor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/report_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/statistical_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/post-processing/scripts/time_series_analyzer.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-official/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/pptx-official/SKILL.md
skills/pptx-official/html2pptx.md
skills/pptx-official/ooxml.md
- Network accessline 235
</p:xfrm> <a:graphic> <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/table"> - Network accessline 236
<a:graphic> <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/table"> <a:tbl> - Network accessline 237
<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/table"> - Network accessline 321
<Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/slide1.xml"/> - Network accessline 322
<Relationship Id="rId2" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slideMaster" Target="slideMasters/slideMaster1.xml"/> - Network accessline 327
<Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slideLayout" Target="../slideLayouts/slideLayout1.xml"/> - Network accessline 328
<Relationship Id="rId2" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/image" Target="../media/image1.png"/>
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 6
xmlns:cdr="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 9
elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" schemaLocation="dml-chartDrawing.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 15
schemaLocation="dml-chartDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 8
elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 12
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 11
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" schemaLocation="dml-diagram.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 13
schemaLocation="dml-diagram.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" schemaLocation="dml-chart.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 15
schemaLocation="dml-chart.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" schemaLocation="dml-picture.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 17
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" schemaLocation="dml-lockedCanvas.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" elementFormDefault="qualified" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 6
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 9
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> - Network accessline 10
<xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> <xsd:element name="from" type="CT_Marker"/> - Network accessline 11
namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/>
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 5
xmlns:dpct="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 9
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 11
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 12
<xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 13
namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 15
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 4
xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 5
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/characteristics" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/characteristics"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 6
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 7
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 9
schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 6
elementFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 6
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/ - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 10
schemaLocation="wml.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/> <xsd:simpleType name="ST_Integer255"> - Network accessline 13
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" blockDefault="#all"> - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 8
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" schemaLocation="dml-spreadsheetDrawing.xsd"/> - Network accessline 14
namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 3
xmlns:pvml="urn:schemas-microsoft-com:office:powerpoint" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 4
xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:w10="urn:schemas-microsoft-com:office:word" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:x="urn:schemas-microsoft-com:office:excel" - Network accessline 7
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:vml" elementFormDefault="qualified" - Network accessline 9
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
<xsd:import namespace="urn:schemas-microsoft-com:office:office" schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 13
schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="wml.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 16
<xsd:import namespace="urn:schemas-microsoft-com:office:word" schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 17
schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 22
<xsd:import namespace="urn:schemas-microsoft-com:office:powerpoint" schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 23
schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 24
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedT - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
attributeFormDefault="unqualified"> <xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
<xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:sl="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 6
xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 8
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 9
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 10
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/markup-compatib - Network accessline 11
targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/markup-compatibility/2006" schemaLocation="../mce/mc.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 14
schemaLocation="dml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" schemaLocation="shared-math.xsd"/> - Network accessline 15
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 16
schemaLocation="shared-math.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 17
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 18
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 19
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 20
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" schemaLocation="shared-customXmlSchemaProperties.xsd"/> - Network accessline 21
<xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 22
schemaLocation="shared-customXmlSchemaProperties.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace"/> <xsd:complexType name="CT_Empty"/> - Network accessline 23
<xsd:import namespace="http://www.w3.org/XML/1998/namespace"/>
skills/pptx-official/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd
- Network accessline 1
<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 2
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 4
<xs:annotation> <xs:documentation> See http://www.w3.org/XML/1998/namespace.html and - Network accessline 5
<xs:documentation> See http://www.w3.org/XML/1998/namespace.html and http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 6
See http://www.w3.org/XML/1998/namespace.html and - Network accessline 7
http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 55
<schema . . .> . . . <import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 56
. . . <import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 57
<import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 58
schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 72
<xs:documentation>In keeping with the XML Schema WG's standard versioning policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. - Network accessline 73
policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. At the date of issue it can also be found at - Network accessline 74
http://www.w3.org/2001/03/xml.xsd. - Network accessline 75
At the date of issue it can also be found at http://www.w3.org/2001/xml.xsd. The schema document at that URI may however change in the future, - Network accessline 76
http://www.w3.org/2001/xml.xsd. - Network accessline 79
itself. In other words, if the XML Schema namespace changes, the version of this document at http://www.w3.org/2001/xml.xsd will change - Network accessline 80
of this document at http://www.w3.org/2001/xml.xsd will change accordingly; the version at - Network accessline 81
http://www.w3.org/2001/xml.xsd will change - Network accessline 82
accordingly; the version at http://www.w3.org/2001/03/xml.xsd will not change. </xs:documentation> - Network accessline 83
http://www.w3.org/2001/03/xml.xsd will not change. - Network accessline 103
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for - Network accessline 104
<xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for information about this attribute.</xs:documentation> - Network accessline 105
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
skills/pptx-official/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 2
<xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 3
xmlns:xs="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/content-types"
skills/pptx-official/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 2
<xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 4
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/" - Network accessline 5
xmlns:dcterms="http://purl.org/dc/terms/" elementFormDefault="qualified" blockDefault="#all"> - Network accessline 7
<xs:import namespace="http://purl.org/dc/elements/1.1/" - Network accessline 8
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd"/> - Network accessline 9
<xs:import namespace="http://purl.org/dc/terms/" - Network accessline 10
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms.xsd"/> - Network accessline 11
<xs:import id="xml" namespace="http://www.w3.org/XML/1998/namespace"/>
skills/pptx-official/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd
- Network accessline 1
<?xml version="1.0" encoding="UTF-8"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/digital-signature"
skills/pptx-official/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/relationships"
skills/pptx-official/ooxml/schemas/mce/mc.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 2
<xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 3
attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 5
xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 7
<!-- This XSD is a modified version of the one found at: https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 9
https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 15
<w:document xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 16
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 17
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/pptx-official/ooxml/schemas/microsoft/wml-2010.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns:r="http://schemas.op - Network accessline 2
<!-- <xsd:import id="rel" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="orel.xsd"/> --> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<!-- <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartbasetypes.xsd"/> - Network accessline 5
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartsplineproperties.xsd"/> -->
skills/pptx-official/ooxml/schemas/microsoft/wml-2012.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" elementFormDefault="qualified" att - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 3
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/pptx-official/ooxml/schemas/microsoft/wml-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx-official/ooxml/schemas/microsoft/wml-cex-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" xmlns:w16="http://schemas.microsoft. - Network accessline 2
<xsd:import id="w16" namespace="http://schemas.microsoft.com/office/word/2018/wordml" schemaLocation="wml-2018.xsd"/> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<xsd:import id="s" namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/pptx-official/ooxml/schemas/microsoft/wml-cid-2016.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx-official/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx-official/ooxml/schemas/microsoft/wml-symex-2015.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx-official/ooxml/scripts/pack.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-official/ooxml/scripts/unpack.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-official/ooxml/scripts/validate.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-official/ooxml/scripts/validation/__init__.py
- Executable scriptline 1
Executable file
skills/pptx-official/ooxml/scripts/validation/base.py
- Executable scriptline 1
Executable file - Network accessline 70
MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 71
XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace" - Network accessline 74
PACKAGE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 75
"http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 76
) OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 77
OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" ) - Network accessline 78
"http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 79
) CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 80
CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" ) - Network accessline 81
"http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 88
OOXML_NAMESPACES = { "http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 89
"http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 90
"http://schemas.openxmlformats.org/officeDocument/2006/relationships", - Network accessline 91
"http://schemas.openxmlformats.org/schemaLibrary/2006/main", - Network accessline 92
"http://schemas.openxmlformats.org/drawingml/2006/main", - Network accessline 93
"http://schemas.openxmlformats.org/drawingml/2006/chart", - Network accessline 94
"http://schemas.openxmlformats.org/drawingml/2006/chartDrawing", - Network accessline 95
"http://schemas.openxmlformats.org/drawingml/2006/diagram", - Network accessline 96
"http://schemas.openxmlformats.org/drawingml/2006/picture", - Network accessline 97
"http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing", - Network accessline 98
"http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", - Network accessline 99
"http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 100
"http://schemas.openxmlformats.org/presentationml/2006/main", - Network accessline 101
"http://schemas.openxmlformats.org/spreadsheetml/2006/main", - Network accessline 102
"http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes", - Network accessline 103
"http://www.w3.org/XML/1998/namespace",
skills/pptx-official/ooxml/scripts/validation/docx.py
skills/pptx-official/ooxml/scripts/validation/pptx.py
skills/pptx-official/ooxml/scripts/validation/redlining.py
- Executable scriptline 1
Executable file - Network accessline 17
self.verbose = verbose self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 18
self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" } - Network accessline 19
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/pptx-official/scripts/html2pptx.js
- Executable scriptline 1
Executable file
skills/pptx-official/scripts/inventory.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 166
): pPr = paragraph._p.pPr ns = "{http://schemas.openxmlformats.org/drawingml/2006/main}" - Network accessline 167
pPr = paragraph._p.pPr ns = "{http://schemas.openxmlformats.org/drawingml/2006/main}" if ( - Network accessline 168
ns = "{http://schemas.openxmlformats.org/drawingml/2006/main}"
skills/pptx-official/scripts/rearrange.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 103
for blip in blips: old_rId = blip.get( "{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed" - Network accessline 104
old_rId = blip.get( "{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed" ) - Network accessline 105
"{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed" - Network accessline 115
blip.set( "{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed", - Network accessline 116
"{http://schemas.openxmlformats.org/officeDocument/2006/relationships}embed",
skills/pptx-official/scripts/replace.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-official/scripts/thumbnail.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pptx-posters/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash
skills/pptx-posters/assets/poster_quality_checklist.md
- Network accessline 202
### Color Contrast Test at: https://webaim.org/resources/contrastchecker/ - Network accessline 203
Test at: https://webaim.org/resources/contrastchecker/ - Network accessline 209
### Color Blindness Test with simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 210
Test with simulator: https://www.color-blindness.com/coblis-color-blindness-simulator/
skills/pptx-posters/references/poster_design_principles.md
skills/pptx-posters/references/poster_layout_design.md
- Network accessline 508
\begin{column}{0.25\linewidth} \centering \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ - Network accessline 509
\centering \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\ \tiny Scan for full paper - Network accessline 510
\qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
skills/pptx/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/pptx/pptxgenjs.md
- Network accessline 145
// From URL slide.addImage({ path: "https://example.com/image.jpg", x: 1, y: 1, w: 5, h: 3 }); - Network accessline 146
slide.addImage({ path: "https://example.com/image.jpg", x: 1, y: 1, w: 5, h: 3 }); - Network accessline 162
flipV: false, // Vertical flip altText: "Description", // Accessibility hyperlink: { url: "https://example.com" } - Network accessline 163
altText: "Description", // Accessibility hyperlink: { url: "https://example.com" } }); - Network accessline 164
hyperlink: { url: "https://example.com" } - Network accessline 257
// Image from URL slide.background = { path: "https://example.com/bg.jpg" }; - Network accessline 258
slide.background = { path: "https://example.com/bg.jpg" };
skills/pptx/scripts/__init__.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/add_slide.py
- Executable scriptline 1
Executable file - Network accessline 48
slide_xml = '''<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <p:sld xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:p="http://sche - Network accessline 49
<p:sld xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 73
rels_dir.mkdir(exist_ok=True) rels_xml = f'''<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"> - Network accessline 74
rels_xml = f'''<?xml version="1.0" encoding="UTF-8" standalone="yes"?> <Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"> <Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/200 - Network accessline 75
<Relationships xmlns="http://schemas.openxmlformats.org/package/2006/relationships"> - Network accessline 76
<Relationship Id="rId1" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slideLayout" Target="../slideLayouts/{layout_file}"/> - Network accessline 149
new_rel = f'<Relationship Id="{rid}" Type="http://schemas.openxmlformats.org/officeDocument/2006/relationships/slide" Target="slides/{dest}"/>'
skills/pptx/scripts/clean.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/helpers/__init__.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/helpers/merge_runs.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/helpers/simplify_redlines.py
skills/pptx/scripts/office/pack.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 6
xmlns:cdr="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 9
elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" schemaLocation="dml-chartDrawing.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 15
schemaLocation="dml-chartDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 8
elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 12
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 11
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" schemaLocation="dml-diagram.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 13
schemaLocation="dml-diagram.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" schemaLocation="dml-chart.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 15
schemaLocation="dml-chart.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" schemaLocation="dml-picture.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 17
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" schemaLocation="dml-lockedCanvas.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" elementFormDefault="qualified" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 6
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 9
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> - Network accessline 10
<xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> <xsd:element name="from" type="CT_Marker"/> - Network accessline 11
namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/>
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 5
xmlns:dpct="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 9
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 11
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 12
<xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 13
namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 15
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 4
xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 5
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/characteristics" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/characteristics"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 6
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 7
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 9
schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 6
elementFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 6
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/ - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 10
schemaLocation="wml.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/> <xsd:simpleType name="ST_Integer255"> - Network accessline 13
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" blockDefault="#all"> - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 8
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" schemaLocation="dml-spreadsheetDrawing.xsd"/> - Network accessline 14
namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 3
xmlns:pvml="urn:schemas-microsoft-com:office:powerpoint" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 4
xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:w10="urn:schemas-microsoft-com:office:word" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:x="urn:schemas-microsoft-com:office:excel" - Network accessline 7
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:vml" elementFormDefault="qualified" - Network accessline 9
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
<xsd:import namespace="urn:schemas-microsoft-com:office:office" schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 13
schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="wml.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 16
<xsd:import namespace="urn:schemas-microsoft-com:office:word" schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 17
schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 22
<xsd:import namespace="urn:schemas-microsoft-com:office:powerpoint" schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 23
schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 24
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedT - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
attributeFormDefault="unqualified"> <xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
<xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:sl="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 6
xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 8
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 9
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 10
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/markup-compatib - Network accessline 11
targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/markup-compatibility/2006" schemaLocation="../mce/mc.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 14
schemaLocation="dml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" schemaLocation="shared-math.xsd"/> - Network accessline 15
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 16
schemaLocation="shared-math.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 17
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 18
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 19
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 20
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" schemaLocation="shared-customXmlSchemaProperties.xsd"/> - Network accessline 21
<xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 22
schemaLocation="shared-customXmlSchemaProperties.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace"/> <xsd:complexType name="CT_Empty"/> - Network accessline 23
<xsd:import namespace="http://www.w3.org/XML/1998/namespace"/>
skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd
- Network accessline 1
<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 2
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 4
<xs:annotation> <xs:documentation> See http://www.w3.org/XML/1998/namespace.html and - Network accessline 5
<xs:documentation> See http://www.w3.org/XML/1998/namespace.html and http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 6
See http://www.w3.org/XML/1998/namespace.html and - Network accessline 7
http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 55
<schema . . .> . . . <import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 56
. . . <import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 57
<import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 58
schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 72
<xs:documentation>In keeping with the XML Schema WG's standard versioning policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. - Network accessline 73
policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. At the date of issue it can also be found at - Network accessline 74
http://www.w3.org/2001/03/xml.xsd. - Network accessline 75
At the date of issue it can also be found at http://www.w3.org/2001/xml.xsd. The schema document at that URI may however change in the future, - Network accessline 76
http://www.w3.org/2001/xml.xsd. - Network accessline 79
itself. In other words, if the XML Schema namespace changes, the version of this document at http://www.w3.org/2001/xml.xsd will change - Network accessline 80
of this document at http://www.w3.org/2001/xml.xsd will change accordingly; the version at - Network accessline 81
http://www.w3.org/2001/xml.xsd will change - Network accessline 82
accordingly; the version at http://www.w3.org/2001/03/xml.xsd will not change. </xs:documentation> - Network accessline 83
http://www.w3.org/2001/03/xml.xsd will not change. - Network accessline 103
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for - Network accessline 104
<xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for information about this attribute.</xs:documentation> - Network accessline 105
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 2
<xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 3
xmlns:xs="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/content-types"
skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 2
<xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 4
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/" - Network accessline 5
xmlns:dcterms="http://purl.org/dc/terms/" elementFormDefault="qualified" blockDefault="#all"> - Network accessline 7
<xs:import namespace="http://purl.org/dc/elements/1.1/" - Network accessline 8
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd"/> - Network accessline 9
<xs:import namespace="http://purl.org/dc/terms/" - Network accessline 10
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms.xsd"/> - Network accessline 11
<xs:import id="xml" namespace="http://www.w3.org/XML/1998/namespace"/>
skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd
- Network accessline 1
<?xml version="1.0" encoding="UTF-8"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/digital-signature"
skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/relationships"
skills/pptx/scripts/office/schemas/mce/mc.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 2
<xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 3
attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 5
xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 7
<!-- This XSD is a modified version of the one found at: https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 9
https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 15
<w:document xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 16
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 17
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns:r="http://schemas.op - Network accessline 2
<!-- <xsd:import id="rel" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="orel.xsd"/> --> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<!-- <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartbasetypes.xsd"/> - Network accessline 5
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartsplineproperties.xsd"/> -->
skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" elementFormDefault="qualified" att - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 3
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" xmlns:w16="http://schemas.microsoft. - Network accessline 2
<xsd:import id="w16" namespace="http://schemas.microsoft.com/office/word/2018/wordml" schemaLocation="wml-2018.xsd"/> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<xsd:import id="s" namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/pptx/scripts/office/soffice.py
- Executable scriptline 1
Executable file - Access to secretsline 25
[Credential-related source omitted] - Network accessline 44
def _needs_shim() -> bool: try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) - Network accessline 45
try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) s.close() - Network accessline 46
s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
skills/pptx/scripts/office/unpack.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/validate.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/validators/__init__.py
- Executable scriptline 1
Executable file
skills/pptx/scripts/office/validators/base.py
- Executable scriptline 1
Executable file - Network accessline 61
MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 62
XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace" - Network accessline 64
PACKAGE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 65
"http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 66
) OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 67
OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" ) - Network accessline 68
"http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 69
) CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 70
CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" ) - Network accessline 71
"http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 76
OOXML_NAMESPACES = { "http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 77
"http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 78
"http://schemas.openxmlformats.org/officeDocument/2006/relationships", - Network accessline 79
"http://schemas.openxmlformats.org/schemaLibrary/2006/main", - Network accessline 80
"http://schemas.openxmlformats.org/drawingml/2006/main", - Network accessline 81
"http://schemas.openxmlformats.org/drawingml/2006/chart", - Network accessline 82
"http://schemas.openxmlformats.org/drawingml/2006/chartDrawing", - Network accessline 83
"http://schemas.openxmlformats.org/drawingml/2006/diagram", - Network accessline 84
"http://schemas.openxmlformats.org/drawingml/2006/picture", - Network accessline 85
"http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing", - Network accessline 86
"http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", - Network accessline 87
"http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 88
"http://schemas.openxmlformats.org/presentationml/2006/main", - Network accessline 89
"http://schemas.openxmlformats.org/spreadsheetml/2006/main", - Network accessline 90
"http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes", - Network accessline 91
"http://www.w3.org/XML/1998/namespace",
skills/pptx/scripts/office/validators/docx.py
- Executable scriptline 1
Executable file - Network accessline 18
WORD_2006_NAMESPACE = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 19
W14_NAMESPACE = "http://schemas.microsoft.com/office/word/2010/wordml" - Network accessline 20
W16CID_NAMESPACE = "http://schemas.microsoft.com/office/word/2016/wordml/cid"
skills/pptx/scripts/office/validators/pptx.py
skills/pptx/scripts/office/validators/redlining.py
- Executable scriptline 1
Executable file - Network accessline 17
self.author = author self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 18
self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" } - Network accessline 19
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/pptx/scripts/thumbnail.py
- Executable scriptline 1
Executable file
skills/prior-auth-coworker/agent.py
- Executable scriptline 1
Executable file
skills/prior-auth-coworker/anthropic_coworker.py
- Executable scriptline 1
Executable file
skills/prior-auth-coworker/appeals_agent.py
- Executable scriptline 1
Executable file
skills/prior-auth-review-skill/references/01-intake-assessment.md
- Network accessline 32
**Allowed Resources:** - **Primary:** Physician Fee Schedule - https://www.cms.gov/medicare/physician-fee-schedule/search - Network accessline 33
- **Primary:** Physician Fee Schedule - https://www.cms.gov/medicare/physician-fee-schedule/search - Network accessline 34
- **Secondary:** NCCI Edits - https://www.cms.gov/medicare/coding-billing/national-correct-coding-initiative-ncci-edits - Network accessline 35
- **Reference:** Provider Taxonomy - https://taxonomy.nucc.org/ - Network accessline 194
for code in cpt_hcpcs_codes: result = WebFetch( url=f"https://www.cms.gov/medicare/physician-fee-schedule/search?Y=0&T=4&P=0&L={code}", - Network accessline 195
result = WebFetch( url=f"https://www.cms.gov/medicare/physician-fee-schedule/search?Y=0&T=4&P=0&L={code}", prompt="Extract the following information: 1) Is this CPT/HCPCS code valid and currently active? 2) Short description - Network accessline 196
url=f"https://www.cms.gov/medicare/physician-fee-schedule/search?Y=0&T=4&P=0&L={code}",
skills/profile-report/SKILL.md
skills/profile-report/profile_report.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/profile-report/tests/__init__.py
- Executable scriptline 1
Executable file
skills/profile-report/tests/test_profile_report.py
- Executable scriptline 1
Executable file
skills/protein-design-workflow/SKILL.md
skills/protein-design-workflow/references/standard-pipeline.md
- Network accessline 15
# From PDB curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" - Network accessline 16
curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" - Network accessline 18
# Or use AlphaFold DB for modeled structures curl -o target.pdb "https://alphafold.ebi.ac.uk/files/AF-PXXXXX-F1-model_v4.pdb" - Network accessline 19
curl -o target.pdb "https://alphafold.ebi.ac.uk/files/AF-PXXXXX-F1-model_v4.pdb"
skills/protein-structure-prediction/README.md
- Network accessline 110
base_url = "https://alphafold.ebi.ac.uk/api" - Network accessline 112
# Get structure metadata response = requests.get(f"{base_url}/prediction/{uniprot_id}") - Network accessline 113
response = requests.get(f"{base_url}/prediction/{uniprot_id}") - Network accessline 120
# Download PDB file pdb_url = metadata['pdbUrl'] pdb_content = requests.get(pdb_url).text - Network accessline 122
pdb_content = requests.get(pdb_url).text - Network accessline 124
# Download confidence data confidence_url = metadata['cifUrl'].replace('.cif', '_local_plddt.json') plddt_data = requests.get(confidence_url).json() - Network accessline 126
plddt_data = requests.get(confidence_url).json() - Possible obfuscationline 185
"MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL" # Protein B - Network accessline 262
# Get AlphaFold structure base_url = "https://alphafold.ebi.ac.uk/api" response = requests.get(f"{base_url}/prediction/{uniprot_id}") - Network accessline 263
base_url = "https://alphafold.ebi.ac.uk/api" - Network accessline 264
response = requests.get(f"{base_url}/prediction/{uniprot_id}") - Network accessline 280
if include_analysis: # Download and analyze structure pdb_content = requests.get(metadata['pdbUrl']).text - Network accessline 282
pdb_content = requests.get(metadata['pdbUrl']).text - Network accessline 390
# Get functional annotations uniprot_data = requests.get( - Network accessline 391
uniprot_data = requests.get( - Network accessline 392
f"https://rest.uniprot.org/uniprotkb/{uniprot_id}.json" - Network accessline 470
> **Jumper, J. et al.** *Highly accurate protein structure prediction with AlphaFold.* Nature (2021). https://github.com/google-deepmind/alphafold - Network accessline 494
# AlphaFold 2 git clone https://github.com/google-deepmind/alphafold.git - Network accessline 495
git clone https://github.com/google-deepmind/alphafold.git - Network accessline 497
# AlphaFold 3 git clone https://github.com/google-deepmind/alphafold3.git - Network accessline 498
git clone https://github.com/google-deepmind/alphafold3.git - Network accessline 500
# OpenFold 3 git clone https://github.com/aqlaboratory/openfold-3.git - Network accessline 501
git clone https://github.com/aqlaboratory/openfold-3.git - Network accessline 529
- [AlphaFold Database](https://alphafold.ebi.ac.uk/) - Network accessline 530
- [AlphaFold GitHub](https://github.com/google-deepmind/alphafold) - Network accessline 531
- [AlphaFold 3 GitHub](https://github.com/google-deepmind/alphafold3) - Network accessline 532
- [OpenFold 3](https://github.com/aqlaboratory/openfold-3) - Network accessline 533
- [AlphaFold MCP Server](https://github.com/Augmented-Nature/AlphaFold-MCP-Server)
skills/protein-structure-prediction/esmfold_client.py
- Executable scriptline 1
Executable file
skills/proteinmpnn/SKILL.md
- Network accessline 37
git clone https://github.com/dauparas/ProteinMPNN.git
skills/protocolsio-integration/SKILL.md
- Access to secretsline 121
[Credential-related source omitted] - Network accessline 149
https://protocols.io/api/v3 - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 251
[Credential-related source omitted] - Network accessline 254
# Search for CRISPR protocols response = requests.get( - Network accessline 255
response = requests.get( - Network accessline 256
"https://protocols.io/api/v3/protocols", - Access to secretsline 276
[Credential-related source omitted] - Network accessline 289
response = requests.post( - Network accessline 290
"https://protocols.io/api/v3/protocols", - Access to secretsline 304
[Credential-related source omitted] - Network accessline 316
response = requests.post( - Network accessline 317
"https://protocols.io/api/v3/workspaces/12345/files/upload", - Network accessline 336
for attempt in range(max_retries): try: response = requests.get(url, headers=headers) - Network accessline 338
response = requests.get(url, headers=headers) - Network accessline 388
- **Official API Documentation**: https://apidoc.protocols.io/ - Network accessline 389
- **Protocols.io Platform**: https://www.protocols.io/
skills/protocolsio-integration/references/additional_features.md
- Network accessline 9
All endpoints use the base URL: `https://protocols.io/api/v3` - Network accessline 31
[Credential-related source omitted] - Network accessline 32
"https://protocols.io/api/v3/profile" - Network accessline 54
curl -X PATCH \ - Network accessline 60
"orcid": "0000-0001-2345-6789" }' \ "https://protocols.io/api/v3/profile" - Network accessline 61
}' "https://protocols.io/api/v3/profile" - Network accessline 62
"https://protocols.io/api/v3/profile" - Network accessline 103
[Credential-related source omitted] - Network accessline 104
"https://protocols.io/api/v3/publications?category=molecular-biology&date_from=2025-01-01&order_field=published_on&order_dir=desc" - Network accessline 142
curl -X POST \ - Network accessline 151
"results": "Flow cytometry confirmed 87% GFP+ cells after 72h. Western blot showed complete knockout in positive population." }' \ "https://protocols.io/api/v3/protocols/12345/runs" - Network accessline 152
}' "https://protocols.io/api/v3/protocols/12345/runs" - Network accessline 153
"https://protocols.io/api/v3/protocols/12345/runs" - Network accessline 217
[Credential-related source omitted] - Network accessline 218
"https://protocols.io/api/v3/notifications?read=false&type=comment" - Network accessline 266
[Credential-related source omitted] - Network accessline 267
"https://protocols.io/api/v3/organizations/12345/export?format=json&include_files=true&include_comments=true" - Network accessline 277
# Search for relevant protocols response = requests.get( - Network accessline 278
response = requests.get( - Network accessline 279
'https://protocols.io/api/v3/publications', - Network accessline 285
for protocol in response.json()['items']: # Get full details details = requests.get( - Network accessline 286
# Get full details details = requests.get( f'https://protocols.io/api/v3/protocols/{protocol["id"]}', - Network accessline 287
details = requests.get( - Network accessline 288
f'https://protocols.io/api/v3/protocols/{protocol["id"]}',
skills/protocolsio-integration/references/authentication.md
- Access to secretsline 9
[Credential-related source omitted] - Access to secretsline 15
[Credential-related source omitted] - Access to secretsline 26
[Credential-related source omitted] - Network accessline 36
GET https://protocols.io/api/v3/oauth/authorize - Network accessline 47
https://protocols.io/api/v3/oauth/authorize?client_id=YOUR_CLIENT_ID&redirect_uri=YOUR_REDIRECT_URI&response_type=code&state=RANDOM_STRING - Network accessline 55
POST https://protocols.io/api/v3/oauth/token - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted] - Network accessline 76
POST https://protocols.io/api/v3/oauth/token - Access to secretsline 83
[Credential-related source omitted]
skills/protocolsio-integration/references/discussions.md
- Network accessline 9
All discussion endpoints use the base URL: `https://protocols.io/api/v3` - Network accessline 44
curl -X POST \ - Network accessline 49
}' \ "https://protocols.io/api/v3/protocols/12345/comments" - Network accessline 50
"https://protocols.io/api/v3/protocols/12345/comments" - Network accessline 58
curl -X POST \ - Network accessline 63
"parent_comment_id": 67890 }' \ "https://protocols.io/api/v3/protocols/12345/comments" - Network accessline 64
}' "https://protocols.io/api/v3/protocols/12345/comments" - Network accessline 65
"https://protocols.io/api/v3/protocols/12345/comments" - Network accessline 117
curl -X POST \ - Network accessline 122
}' \ "https://protocols.io/api/v3/protocols/12345/steps/67890/comments" - Network accessline 123
"https://protocols.io/api/v3/protocols/12345/steps/67890/comments" - Network accessline 187
{ "body": "## Important Note\n\nWe achieved better results with:\n\n- Increasing temperature to 37°C\n- Extending incubation to 2 hours\n- Using freshly prepared reagents\n\nSee our publication: [doi:10.xxxx/xxxxx](https://doi.org/...)" - Network accessline 188
"body": "## Important Note\n\nWe achieved better results with:\n\n- Increasing temperature to 37°C\n- Extending incubation to 2 hours\n- Using freshly prepared reagents\n\nSee our publication: [doi:10.xxxx/xxxxx](https://doi.org/...)"
skills/protocolsio-integration/references/file_manager.md
- Network accessline 9
All file manager endpoints use the base URL: `https://protocols.io/api/v3` - Network accessline 41
[Credential-related source omitted] - Network accessline 42
"https://protocols.io/api/v3/workspaces/12345/files/search?query=microscopy&type=file" - Network accessline 63
[Credential-related source omitted] - Network accessline 64
"https://protocols.io/api/v3/workspaces/12345/folders/root?order_by=modified&order_dir=desc" - Network accessline 86
curl -X POST \ - Network accessline 90
-F "description=Experimental results from trial #3" \ -F "tags=experiment,data,2025" \ "https://protocols.io/api/v3/workspaces/12345/files/upload" - Network accessline 92
"https://protocols.io/api/v3/workspaces/12345/files/upload" - Network accessline 122
[Credential-related source omitted] - Network accessline 124
"https://protocols.io/api/v3/workspaces/12345/files/67890/download" - Network accessline 155
curl -X PATCH \ - Network accessline 160
"tags": "experiment,data,2025,revised" }' \ "https://protocols.io/api/v3/workspaces/12345/files/67890" - Network accessline 161
}' "https://protocols.io/api/v3/workspaces/12345/files/67890" - Network accessline 162
"https://protocols.io/api/v3/workspaces/12345/files/67890" - Network accessline 194
curl -X POST \ - Network accessline 200
"description": "All experimental data from 2025" }' \ "https://protocols.io/api/v3/workspaces/12345/folders" - Network accessline 201
}' "https://protocols.io/api/v3/workspaces/12345/folders" - Network accessline 202
"https://protocols.io/api/v3/workspaces/12345/folders" - Network accessline 237
# Upload the data file curl -X POST \ - Network accessline 238
curl -X POST \ - Network accessline 240
-F "file=@results.csv" \ -F "description=Results from protocol execution" \ "https://protocols.io/api/v3/workspaces/12345/files/upload" - Network accessline 242
"https://protocols.io/api/v3/workspaces/12345/files/upload"
skills/protocolsio-integration/references/protocols_api.md
- Network accessline 9
All protocol endpoints use the base URL: `https://protocols.io/api/v3` - Network accessline 45
[Credential-related source omitted] - Network accessline 46
"https://protocols.io/api/v3/protocols?filter=public&key=CRISPR&page_size=20&content_format=html" - Network accessline 97
curl -X POST \ - Network accessline 103
"tags": ["CRISPR", "gene editing", "molecular biology"] }' \ "https://protocols.io/api/v3/protocols" - Network accessline 104
}' "https://protocols.io/api/v3/protocols" - Network accessline 105
"https://protocols.io/api/v3/protocols" - Network accessline 135
curl -X POST \ - Network accessline 142
"temperature": 25 }' \ "https://protocols.io/api/v3/protocols/12345/steps" - Network accessline 143
}' "https://protocols.io/api/v3/protocols/12345/steps" - Network accessline 144
"https://protocols.io/api/v3/protocols/12345/steps" - Network accessline 200
curl -X POST \ - Network accessline 205
"publish_type": "new" }' \ "https://protocols.io/api/v3/protocols/12345/publish" - Network accessline 206
}' "https://protocols.io/api/v3/protocols/12345/publish" - Network accessline 207
"https://protocols.io/api/v3/protocols/12345/publish" - Network accessline 243
https://protocols.io/api/v3/view/crispr-protocol-abc123.pdf?compact=1
skills/protocolsio-integration/references/workspaces.md
- Network accessline 9
All workspace endpoints use the base URL: `https://protocols.io/api/v3` - Network accessline 32
[Credential-related source omitted] - Network accessline 33
"https://protocols.io/api/v3/workspaces" - Network accessline 80
curl -X POST \ - Network accessline 85
}' \ "https://protocols.io/api/v3/workspaces/12345/join-request" - Network accessline 86
"https://protocols.io/api/v3/workspaces/12345/join-request" - Network accessline 119
[Credential-related source omitted] - Network accessline 120
"https://protocols.io/api/v3/workspaces/12345/protocols?filter=all&order_field=modified_on&order_dir=desc"
skills/psychologist-analyst/SKILL.md
- Network accessline 137
- [Cognitive Psychology - Wikipedia](https://en.wikipedia.org/wiki/Cognitive_psychology) - Network accessline 253
- [Social Psychology - Wikipedia](https://en.wikipedia.org/wiki/Social_psychology) - Network accessline 341
- [Developmental Psychology - Wikipedia](https://en.wikipedia.org/wiki/Developmental_psychology) - Network accessline 443
- [DSM-5 - APA](https://www.psychiatry.org/psychiatrists/practice/dsm) - Network accessline 444
- [Clinical Psychology - Wikipedia](https://en.wikipedia.org/wiki/Clinical_psychology) - Network accessline 531
- [Neuroscience - Wikipedia](https://en.wikipedia.org/wiki/Neuroscience) - Network accessline 532
- [Biological Psychology - Wikipedia](https://en.wikipedia.org/wiki/Behavioral_neuroscience) - Network accessline 728
- Henri Tajfel, John Turner - [Social Identity Theory - Wikipedia](https://en.wikipedia.org/wiki/Social_identity_theory) - Network accessline 729
- [Social Identity Theory - Wikipedia](https://en.wikipedia.org/wiki/Social_identity_theory) - Network accessline 1681
- Professional organization for psychologists - Website: https://www.apa.org/ - Network accessline 1682
- Website: https://www.apa.org/ - Network accessline 1683
- APA Style (citation format) - [APA Journals - 120+ peer-reviewed journals](https://www.apa.org/pubs/journals/) - [APA PsycArticles Database - EBSCO](https://about.ebsco.com/products/research-databases/apa-psycarticles) - Full-text journal - Network accessline 1684
- [APA Journals - 120+ peer-reviewed journals](https://www.apa.org/pubs/journals/) - Network accessline 1685
- [APA PsycArticles Database - EBSCO](https://about.ebsco.com/products/research-databases/apa-psycarticles) - Full-text journal collection - Network accessline 1689
- [Psychological Science Journal - APS](https://journals.sagepub.com/home/pss) - Flagship empirical psychology journal, highest ranked in the field - Network accessline 1690
- [APS Publications](https://www.psychologicalscience.org/publications) - Leading empirical research journals - Network accessline 1697
- [APA Journals - East Carolina Guide](https://libguides.ecu.edu/APA_journals) - Guide to APA journal collection - Network accessline 1698
- [Journal Articles - Psychology - George Mason](https://infoguides.gmu.edu/psychology/journals) - Comprehensive psychology journal guide - Network accessline 1699
- [APA Journals on JSTOR](https://www.jstor.org/publisher/apapubs) - Historical archives of APA journals - Network accessline 1700
- [Category: APA Journals - Wikipedia](https://en.wikipedia.org/wiki/Category:American_Psychological_Association_academic_journals) - Complete list of APA journals
skills/pubchem-database/SKILL.md
- Network accessline 196
cid = 2244 # Aspirin url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?image_size=large" response = requests.get(url) - Network accessline 197
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?image_size=large" - Network accessline 198
response = requests.get(url) - Network accessline 230
# Get bioassay summary for a compound cid = 2244 # Aspirin url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON" - Network accessline 232
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON" - Network accessline 234
response = requests.get(url) - Network accessline 256
cid = 2244 url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON" - Network accessline 257
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON" - Network accessline 259
response = requests.get(url) - Network accessline 274
# Get only drug information url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?heading=Drug and Medication Information" - Network accessline 275
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?heading=Drug and Medication Information" - Network accessline 564
- PubChem Home: https://pubchem.ncbi.nlm.nih.gov/ - Network accessline 565
- PUG-REST Documentation: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest - Network accessline 566
- PUG-REST Tutorial: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest-tutorial - Network accessline 567
- PubChemPy Documentation: https://pubchempy.readthedocs.io/ - Network accessline 568
- PubChemPy GitHub: https://github.com/mcs07/PubChemPy
skills/pubchem-database/references/api_reference.md
- Network accessline 20
https://pubchem.ncbi.nlm.nih.gov/rest/pug/<input>/<operation>/<output> - Network accessline 154
# Step 1: Submit similarity search response = requests.post( - Network accessline 155
response = requests.post( - Network accessline 156
"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/similarity/smiles/{smiles}/cids/JSON", - Network accessline 161
# Step 2: Check status status_url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/listkey/{listkey}/cids/JSON" - Network accessline 162
status_url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/listkey/{listkey}/cids/JSON" - Network accessline 411
cid = 2244 # Aspirin url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON" - Network accessline 412
url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON" - Network accessline 414
response = requests.get(url) - Network accessline 429
8. **Use asynchronous pattern**: For large similarity/substructure searches 9. **Specify output format**: Choose JSON for programmatic access, SDF for cheminformatics tools 10. **Read documentation**: Full PUG-REST documentation available a - Network accessline 431
10. **Read documentation**: Full PUG-REST documentation available at https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest - Network accessline 435
- PubChem Home: https://pubchem.ncbi.nlm.nih.gov/ - Network accessline 436
- PUG-REST Documentation: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest - Network accessline 437
- PUG-REST Tutorial: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest-tutorial - Network accessline 438
- PubChemPy Documentation: https://pubchempy.readthedocs.io/ - Network accessline 439
- PubChemPy GitHub: https://github.com/mcs07/PubChemPy - Network accessline 440
- IUPAC Tutorial: https://iupac.github.io/WFChemCookbook/datasources/pubchem_pugrest.html
skills/pubchem-database/scripts/bioactivity_query.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 21
BASE_URL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug" - Network accessline 22
PUG_VIEW_URL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug_view" - Network accessline 42
try: if method.upper() == 'GET': response = requests.get(url, **kwargs) - Network accessline 43
if method.upper() == 'GET': response = requests.get(url, **kwargs) else: - Network accessline 44
response = requests.get(url, **kwargs) - Network accessline 46
response = requests.post(url, **kwargs)
skills/pubchem-database/scripts/compound_search.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pubmed-database/SKILL.md
- Network accessline 124
# Step 1: Search for articles base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 125
base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/" - Network accessline 132
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Network accessline 133
} response = requests.get(search_url, params=params) pmids = response.json()["esearchresult"]["idlist"] - Network accessline 134
response = requests.get(search_url, params=params) - Network accessline 144
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Network accessline 145
} response = requests.get(fetch_url, params=params) abstracts = response.text - Network accessline 146
response = requests.get(fetch_url, params=params) - Network accessline 450
- **PubMed Help**: https://pubmed.ncbi.nlm.nih.gov/help/ - Network accessline 451
- **E-utilities Documentation**: https://www.ncbi.nlm.nih.gov/books/NBK25501/
skills/pubmed-database/references/api_reference.md
- Network accessline 8
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ - Access to secretsline 15
[Credential-related source omitted] - Access to secretsline 17
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Access to secretsline 80
[Credential-related source omitted] - Access to secretsline 105
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 175
[Credential-related source omitted] - Access to secretsline 195
[Credential-related source omitted] - Access to secretsline 210
[Credential-related source omitted] - Access to secretsline 242
[Credential-related source omitted] - Access to secretsline 247
[Credential-related source omitted] - Access to secretsline 248
[Credential-related source omitted] - Access to secretsline 257
[Credential-related source omitted] - Access to secretsline 260
[Credential-related source omitted] - Network accessline 295
- **API Documentation**: https://www.ncbi.nlm.nih.gov/books/NBK25501/
skills/pubmed-search/SKILL.md
- Network accessline 67
print(f"Journal: {journal} ({year})") print(f"Abstract: {abstract}...") print(f"Link: https://pubmed.ncbi.nlm.nih.gov/{pmid}/") - Network accessline 68
print(f"Abstract: {abstract}...") print(f"Link: https://pubmed.ncbi.nlm.nih.gov/{pmid}/") print() - Network accessline 69
print(f"Link: https://pubmed.ncbi.nlm.nih.gov/{pmid}/")
skills/pydeseq2/SKILL.md
skills/pydeseq2/scripts/run_deseq2_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pydicom/SKILL.md
- Network accessline 424
Official pydicom documentation: https://pydicom.github.io/pydicom/dev/ - Network accessline 425
- User Guide: https://pydicom.github.io/pydicom/dev/guides/user/index.html - Network accessline 426
- Tutorials: https://pydicom.github.io/pydicom/dev/tutorials/index.html - Network accessline 427
- API Reference: https://pydicom.github.io/pydicom/dev/reference/index.html - Network accessline 428
- Examples: https://pydicom.github.io/pydicom/dev/auto_examples/index.html
skills/pydicom/references/common_tags.md
skills/pydicom/references/transfer_syntaxes.md
- Network accessline 350
- DICOM Standard Part 5 (Data Structures and Encoding): https://dicom.nema.org/medical/dicom/current/output/chtml/part05/PS3.5.html - Network accessline 351
- Pydicom Transfer Syntax Documentation: https://pydicom.github.io/pydicom/stable/guides/user/transfer_syntaxes.html - Network accessline 352
- Pydicom Compression Guide: https://pydicom.github.io/pydicom/stable/old/image_data_compression.html
skills/pydicom/scripts/anonymize_dicom.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pydicom/scripts/dicom_to_image.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pydicom/scripts/extract_metadata.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pyhealth/SKILL.md
skills/pylabrobot/SKILL.md
- Network accessline 126
6. **Temperature Control**: Set temperatures early as heating/cooling takes time 7. **Modular Protocols**: Break complex workflows into reusable functions 8. **Documentation**: Reference official docs at https://docs.pylabrobot.org for late - Network accessline 128
8. **Documentation**: Reference official docs at https://docs.pylabrobot.org for latest features - Network accessline 174
- **Official Documentation**: https://docs.pylabrobot.org - Network accessline 175
- **GitHub Repository**: https://github.com/PyLabRobot/pylabrobot - Network accessline 176
- **Community Forum**: https://discuss.pylabrobot.org - Network accessline 177
- **PyPI Package**: https://pypi.org/project/PyLabRobot/
skills/pylabrobot/references/analytical-equipment.md
- Network accessline 461
- Plate Reading Documentation: https://docs.pylabrobot.org/user_guide/02_analytical/ - Network accessline 462
- BMG CLARIOstar Guide: https://docs.pylabrobot.org/user_guide/02_analytical/plate-reading/bmg-clariostar.html - Network accessline 463
- API Reference: https://docs.pylabrobot.org/api/pylabrobot.plate_reading.html - Network accessline 464
- Supported Equipment: https://docs.pylabrobot.org/user_guide/machines.html
skills/pylabrobot/references/hardware-backends.md
- Network accessline 477
- Backend Documentation: https://docs.pylabrobot.org/user_guide/backends.html - Network accessline 478
- Supported Machines: https://docs.pylabrobot.org/user_guide/machines.html - Network accessline 479
- API Reference: https://docs.pylabrobot.org/api/pylabrobot.liquid_handling.backends.html - Network accessline 480
- GitHub Examples: https://github.com/PyLabRobot/pylabrobot/tree/main/examples
skills/pylabrobot/references/liquid-handling.md
- Network accessline 401
- Official Liquid Handling Guide: https://docs.pylabrobot.org/user_guide/basic.html - Network accessline 402
- API Reference: https://docs.pylabrobot.org/api/pylabrobot.liquid_handling.html - Network accessline 403
- Example Protocols: https://github.com/PyLabRobot/pylabrobot/tree/main/examples
skills/pylabrobot/references/material-handling.md
- Network accessline 617
- Material Handling Documentation: https://docs.pylabrobot.org/user_guide/01_material-handling/ - Network accessline 618
- Heater Shakers: https://docs.pylabrobot.org/user_guide/01_material-handling/heating_shaking/ - Network accessline 619
- API Reference: https://docs.pylabrobot.org/api/ - Network accessline 620
- Supported Equipment: https://docs.pylabrobot.org/user_guide/machines.html
skills/pylabrobot/references/resources.md
- Network accessline 486
- Resource Documentation: https://docs.pylabrobot.org/resources/introduction.html - Network accessline 487
- Custom Resources Guide: https://docs.pylabrobot.org/resources/custom-resources.html - Network accessline 488
- API Reference: https://docs.pylabrobot.org/api/pylabrobot.resources.html - Network accessline 489
- Deck Layouts: https://github.com/PyLabRobot/pylabrobot/tree/main/pylabrobot/resources/deck
skills/pylabrobot/references/visualization.md
- Network accessline 35
**Default Settings:** - Port: 1234 (http://localhost:1234) - Network accessline 36
- Port: 1234 (http://localhost:1234) - Network accessline 529
- Visualizer Documentation: https://docs.pylabrobot.org/user_guide/using-the-visualizer.html (if available) - Network accessline 530
- Simulation Guide: https://docs.pylabrobot.org/user_guide/simulation.html (if available) - Network accessline 531
- API Reference: https://docs.pylabrobot.org/api/pylabrobot.visualizer.html - Network accessline 532
- GitHub Examples: https://github.com/PyLabRobot/pylabrobot/tree/main/examples
skills/pymc/assets/hierarchical_model_template.py
- Executable scriptline 1
Executable file
skills/pymc/assets/linear_regression_template.py
- Executable scriptline 1
Executable file
skills/pymc/scripts/model_comparison.py
- Executable scriptline 1
Executable file
skills/pymc/scripts/model_diagnostics.py
- Executable scriptline 1
Executable file
skills/pymoo/SKILL.md
- Network accessline 556
**Documentation:** https://pymoo.org/
skills/pymoo/scripts/custom_problem_example.py
- Executable scriptline 1
Executable file
skills/pymoo/scripts/decision_making_example.py
- Executable scriptline 1
Executable file
skills/pymoo/scripts/many_objective_example.py
- Executable scriptline 1
Executable file
skills/pymoo/scripts/multi_objective_example.py
- Executable scriptline 1
Executable file
skills/pymoo/scripts/single_objective_example.py
- Executable scriptline 1
Executable file
skills/pyopenms/SKILL.md
skills/pyopenms/references/identification.md
- Possible obfuscationline 231
protein_seq = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPS
skills/pysam/SKILL.md
- Network accessline 37
# Open BAM file and fetch reads in region samfile = pysam.AlignmentFile("example.bam", "rb") for read in samfile.fetch("chr1", 1000, 2000): - Network accessline 38
samfile = pysam.AlignmentFile("example.bam", "rb") for read in samfile.fetch("chr1", 1000, 2000): print(f"{read.query_name}: {read.reference_start}") - Network accessline 39
for read in samfile.fetch("chr1", 1000, 2000): - Network accessline 55
# Open FASTA and extract sequence fasta = pysam.FastaFile("reference.fasta") sequence = fasta.fetch("chr1", 1000, 2000) - Network accessline 56
fasta = pysam.FastaFile("reference.fasta") sequence = fasta.fetch("chr1", 1000, 2000) print(sequence) - Network accessline 57
sequence = fasta.fetch("chr1", 1000, 2000) - Network accessline 78
- Opening and reading alignment files - AlignedSegment attributes and methods - Region-based fetching with `fetch()` - Network accessline 79
- AlignedSegment attributes and methods - Region-based fetching with `fetch()` - Pileup analysis for coverage - Network accessline 80
- Region-based fetching with `fetch()` - Network accessline 161
**Exception:** Region strings in `fetch()` follow samtools convention (1-based): - Network accessline 163
samfile.fetch("chr1", 999, 2000) # 0-based: positions 999-1999 - Network accessline 164
samfile.fetch("chr1:1000-2000") # 1-based string: positions 1000-2000 - Network accessline 178
Without an index, use `fetch(until_eof=True)` for sequential reading. - Network accessline 202
1. **Coordinate confusion:** Remember 0-based vs 1-based systems in different contexts 2. **Missing indices:** Many operations require index files—create them first 3. **Partial overlaps:** `fetch()` returns reads overlapping region boundar - Network accessline 203
2. **Missing indices:** Many operations require index files—create them first 3. **Partial overlaps:** `fetch()` returns reads overlapping region boundaries, not just those fully contained 4. **Iterator scope:** Keep pileup iterator referen - Network accessline 204
3. **Partial overlaps:** `fetch()` returns reads overlapping region boundaries, not just those fully contained - Network accessline 259
Official documentation: https://pysam.readthedocs.io/
skills/pysam/references/alignment_files.md
- Network accessline 56
### fetch() - Region-Based Retrieval - Network accessline 61
# Fetch specific region for read in samfile.fetch("chr1", 1000, 2000): - Network accessline 62
for read in samfile.fetch("chr1", 1000, 2000): - Network accessline 65
# Fetch entire contig for read in samfile.fetch("chr1"): - Network accessline 66
for read in samfile.fetch("chr1"): - Network accessline 69
# Fetch without index (sequential read) for read in samfile.fetch(until_eof=True): - Network accessline 70
for read in samfile.fetch(until_eof=True): - Network accessline 77
- Use `until_eof=True` for non-indexed files or sequential reading - By default, only returns mapped reads - For unmapped reads, use `fetch("*")` or `until_eof=True` - Network accessline 79
- For unmapped reads, use `fetch("*")` or `until_eof=True` - Network accessline 86
samfile = pysam.AlignmentFile("example.bam", "rb", multiple_iterators=True) iter1 = samfile.fetch("chr1", 1000, 2000) - Network accessline 87
iter1 = samfile.fetch("chr1", 1000, 2000) - Network accessline 88
iter2 = samfile.fetch("chr2", 5000, 6000) - Network accessline 91
Without `multiple_iterators=True`, a new fetch() call repositions the file pointer and breaks existing iterators. - Network accessline 163
for read in samfile.fetch("chr1", 1000, 2000): - Network accessline 247
**Exception:** Region strings in `fetch()` and `pileup()` follow samtools conventions (1-based): - Network accessline 249
# These are equivalent: samfile.fetch("chr1", 999, 2000) # Python style: 0-based - Network accessline 250
samfile.fetch("chr1", 999, 2000) # Python style: 0-based - Network accessline 251
samfile.fetch("chr1:1000-2000") # samtools style: 1-based - Network accessline 268
1. **Use indexed access** when querying specific regions repeatedly 2. **Use `pileup()` for column-wise analysis** instead of repeated fetch operations 3. **Use `fetch(until_eof=True)` for sequential reading** of non-indexed files - Network accessline 269
2. **Use `pileup()` for column-wise analysis** instead of repeated fetch operations 3. **Use `fetch(until_eof=True)` for sequential reading** of non-indexed files 4. **Avoid multiple iterators** unless necessary (performance cost) - Network accessline 270
3. **Use `fetch(until_eof=True)` for sequential reading** of non-indexed files - Network accessline 276
1. **Partial overlaps:** `fetch()` returns reads that overlap region boundaries—implement explicit filtering if exact boundaries are needed - Network accessline 277
2. **Quality score editing:** Cannot edit `query_qualities` in place after modifying `query_sequence`. Create a copy first: `quals = read.query_qualities` 3. **Missing index:** `fetch()` without `until_eof=True` requires an index file 4. ** - Network accessline 278
3. **Missing index:** `fetch()` without `until_eof=True` requires an index file
skills/pysam/references/common_workflows.md
- Network accessline 29
for read in samfile.fetch(until_eof=True): - Network accessline 68
for read in samfile.fetch(): - Network accessline 72
# Get reference sequence for aligned region ref_seq = fasta.fetch( - Network accessline 73
ref_seq = fasta.fetch( - Network accessline 204
for gene in bed.fetch(parser=pysam.asBed()): - Network accessline 208
# Find variants in gene region for variant in vcf.fetch(gene.contig, gene.start, gene.end): - Network accessline 209
for variant in vcf.fetch(gene.contig, gene.start, gene.end): - Network accessline 317
context = fasta.fetch(variant.chrom, start, end) - Network accessline 340
with open(output_fasta, 'w') as out: for gene in bed.fetch(parser=pysam.asBed()): - Network accessline 341
for gene in bed.fetch(parser=pysam.asBed()): - Network accessline 342
sequence = fasta.fetch(gene.contig, gene.start, gene.end) - Network accessline 370
for read in infile.fetch(chrom, start, end): - Network accessline 397
for read in samfile.fetch(variant.chrom, start, end): - Network accessline 404
for read in samfile.fetch(until_eof=True):
skills/pysam/references/sequence_files.md
- Network accessline 56
# Fetch specific region sequence = fasta.fetch("chr1", 1000, 2000) - Network accessline 57
sequence = fasta.fetch("chr1", 1000, 2000) - Network accessline 60
# Fetch entire chromosome chr1_seq = fasta.fetch("chr1") - Network accessline 61
chr1_seq = fasta.fetch("chr1") - Network accessline 63
# Fetch using region string (1-based) sequence = fasta.fetch(region="chr1:1001-2000") - Network accessline 64
sequence = fasta.fetch(region="chr1:1001-2000") - Network accessline 75
start = max(0, pos - window - 1) # Convert to 0-based end = pos + window return fasta.fetch(chrom, start, end) - Network accessline 77
return fasta.fetch(chrom, start, end) - Network accessline 80
def get_gene_sequence(fasta, chrom, start, end, strand): """Get gene sequence with strand awareness.""" seq = fasta.fetch(chrom, start, end) - Network accessline 82
seq = fasta.fetch(chrom, start, end) - Network accessline 92
def check_ref_allele(fasta, chrom, pos, expected_ref): """Verify reference allele at position (1-based pos).""" actual = fasta.fetch(chrom, pos-1, pos) # Convert to 0-based - Network accessline 93
"""Verify reference allele at position (1-based pos).""" actual = fasta.fetch(chrom, pos-1, pos) # Convert to 0-based return actual.upper() == expected_ref.upper() - Network accessline 94
actual = fasta.fetch(chrom, pos-1, pos) # Convert to 0-based - Network accessline 109
for chrom, start, end in regions: seq_id = f"{chrom}:{start}-{end}" sequences[seq_id] = fasta.fetch(chrom, start, end) - Network accessline 111
sequences[seq_id] = fasta.fetch(chrom, start, end) - Network accessline 137
def has_quality_sequence(fasta, chrom, start, end, max_n_frac=0.1): """Check if region has acceptable N content.""" seq = fasta.fetch(chrom, start, end) - Network accessline 138
"""Check if region has acceptable N content.""" seq = fasta.fetch(chrom, start, end) n_count = seq.upper().count('N') - Network accessline 139
seq = fasta.fetch(chrom, start, end) - Network accessline 342
# Fetch region for row in tabix.fetch("chr1", 1000000, 2000000): - Network accessline 343
for row in tabix.fetch("chr1", 1000000, 2000000): - Network accessline 346
# Parse with specific parser for row in tabix.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()): - Network accessline 347
for row in tabix.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()): - Network accessline 358
# Access BED fields by name for interval in bed.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()): - Network accessline 359
for interval in bed.fetch("chr1", 1000000, 2000000, parser=pysam.asBed()): - Network accessline 371
# Access GTF fields for feature in gtf.fetch("chr1", 1000000, 2000000, parser=pysam.asGTF()): - Network accessline 372
for feature in gtf.fetch("chr1", 1000000, 2000000, parser=pysam.asGTF()): - Network accessline 401
1. **FASTA coordinate system:** fetch() uses 0-based coordinates, region strings use 1-based
skills/pysam/references/variant_files.md
- Network accessline 64
# Fetch variants in region (1-based coordinates for region string) for variant in vcf.fetch("chr1", 1000000, 2000000): - Network accessline 65
for variant in vcf.fetch("chr1", 1000000, 2000000): - Network accessline 68
# Using region string (1-based) for variant in vcf.fetch("chr1:1000000-2000000"): - Network accessline 69
for variant in vcf.fetch("chr1:1000000-2000000"): - Network accessline 73
**Note:** Uses **1-based coordinates** in `fetch()` calls to match VCF specification. - Network accessline 362
3. **Genotype tuples:** Genotypes are tuples, not lists—handle None values for missing data 4. **Allele indexing:** In genotype (0, 1), 0=REF, 1=first ALT, 2=second ALT, etc. 5. **Index requirement:** Region-based `fetch()` requires tabix i - Network accessline 363
4. **Allele indexing:** In genotype (0, 1), 0=REF, 1=first ALT, 2=second ALT, etc. 5. **Index requirement:** Region-based `fetch()` requires tabix index for VCF.gz 6. **Header modification:** When subsetting samples, properly update header - Network accessline 364
5. **Index requirement:** Region-based `fetch()` requires tabix index for VCF.gz
skills/pytdc/SKILL.md
skills/pytdc/references/datasets.md
- Network accessline 244
- New datasets are regularly added to TDC - Some datasets may require additional dependencies - Check the official TDC website for the most up-to-date dataset list: https://tdcommons.ai/overview/ - Network accessline 246
- Check the official TDC website for the most up-to-date dataset list: https://tdcommons.ai/overview/
skills/pytdc/references/oracles.md
- Network accessline 372
- Different oracles may have different score ranges and interpretations - Some oracles require additional dependencies or API access - Check oracle documentation for specific details: https://tdcommons.ai/functions/oracles/ - Network accessline 374
- Check oracle documentation for specific details: https://tdcommons.ai/functions/oracles/ - Network accessline 398
- TDC Oracles Documentation: https://tdcommons.ai/functions/oracles/
skills/pytdc/references/utilities.md
- Network accessline 681
- TDC Documentation: https://tdc.readthedocs.io - Network accessline 682
- Data Functions: https://tdcommons.ai/fct_overview/ - Network accessline 683
- Evaluation Metrics: https://tdcommons.ai/functions/model_eval/ - Network accessline 684
- Data Splits: https://tdcommons.ai/functions/data_split/
skills/pytdc/scripts/benchmark_evaluation.py
skills/pytdc/scripts/load_and_split_data.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pytdc/scripts/molecular_generation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/pytorch-lightning/references/data_module.md
skills/pytorch-lightning/references/distributed_training.md
- Access to secretsline 522
[Credential-related source omitted]
skills/pytorch-lightning/references/logging.md
- Network accessline 80
mlflow_logger = pl_loggers.MLFlowLogger( experiment_name="my_experiment", tracking_uri="http://localhost:5000", - Network accessline 81
experiment_name="my_experiment", tracking_uri="http://localhost:5000", run_name="run_1" - Network accessline 82
tracking_uri="http://localhost:5000", - Access to secretsline 103
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted]
skills/pytorch-lightning/scripts/quick_trainer_setup.py
- Executable scriptline 1
Executable file
skills/pytorch-lightning/scripts/template_datamodule.py
- Executable scriptline 1
Executable file
skills/pytorch-lightning/scripts/template_lightning_module.py
- Executable scriptline 1
Executable file
skills/pyzotero/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Network accessline 12
Pyzotero is a Python wrapper for the [Zotero API v3](https://www.zotero.org/support/dev/web_api/v3/start). Use it to programmatically manage Zotero libraries: read items and collections, create and update references, upload attachments, man - Network accessline 16
**Required credentials** — get from https://www.zotero.org/settings/keys: - Network accessline 17
- **User ID**: shown as "Your userID for use in API calls" - **API Key**: create at https://www.zotero.org/settings/keys/new - **Library ID**: for group libraries, the integer after `/groups/` in the group URL - Network accessline 18
- **API Key**: create at https://www.zotero.org/settings/keys/new - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted]
skills/pyzotero/references/authentication.md
- Network accessline 5
Obtain from https://www.zotero.org/settings/keys: - Network accessline 9
| **User ID** | "Your userID for use in API calls" section | | **API Key** | Create new key at /settings/keys/new | | **Group Library ID** | Integer after `/groups/` in group URL (e.g. `https://www.zotero.org/groups/169947`) | - Network accessline 11
| **Group Library ID** | Integer after `/groups/` in group URL (e.g. `https://www.zotero.org/groups/169947`) | - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 31
[Credential-related source omitted] - Access to secretsline 32
[Credential-related source omitted] - Access to secretsline 33
[Credential-related source omitted] - Access to secretsline 64
[Credential-related source omitted] - Network accessline 86
When creating an API key at https://www.zotero.org/settings/keys/new, choose appropriate permissions:
skills/pyzotero/references/exports.md
- Network accessline 45
Pass any valid CSL style name from the [Zotero style repository](https://www.zotero.org/styles):
skills/rdkit/scripts/molecular_properties.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/rdkit/scripts/similarity_search.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/rdkit/scripts/substructure_filter.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/reactome-database/SKILL.md
- Network accessline 38
**API Base URL:** `https://reactome.org/ContentService` - Network accessline 49
**API Base URL:** `https://reactome.org/AnalysisService` - Network accessline 72
response = requests.get("https://reactome.org/ContentService/data/database/version") - Network accessline 81
entity_id = "R-HSA-69278" # Example pathway ID response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}") - Network accessline 82
response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}") - Network accessline 90
event_id = "R-HSA-69278" response = requests.get( - Network accessline 91
response = requests.get( - Network accessline 92
f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities" - Network accessline 126
# Submit analysis response = requests.post( - Network accessline 127
response = requests.post( - Network accessline 128
"https://reactome.org/AnalysisService/identifiers/", - Network accessline 143
# Token is valid for 7 days response = requests.get(f"https://reactome.org/AnalysisService/token/{token}") - Network accessline 144
response = requests.get(f"https://reactome.org/AnalysisService/token/{token}") - Network accessline 168
response = requests.post( - Network accessline 169
"https://reactome.org/AnalysisService/identifiers/", - Network accessline 182
response = requests.post( - Network accessline 183
"https://reactome.org/AnalysisService/identifiers/projection/", - Network accessline 194
[Credential-related source omitted] - Network accessline 195
pathway_id = "R-HSA-69278" url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}" print(f"View results: {url}") - Network accessline 196
url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}" - Network accessline 257
- **API Documentation**: https://reactome.org/dev - Network accessline 258
- **User Guide**: https://reactome.org/userguide - **Documentation Portal**: https://reactome.org/documentation - **Data Downloads**: https://reactome.org/download-data - Network accessline 259
- **Documentation Portal**: https://reactome.org/documentation - **Data Downloads**: https://reactome.org/download-data - **reactome2py Docs**: https://reactome.github.io/reactome2py/ - Network accessline 260
- **Data Downloads**: https://reactome.org/download-data - Network accessline 261
- **reactome2py Docs**: https://reactome.github.io/reactome2py/
skills/reactome-database/references/api_reference.md
- Network accessline 7
- **Content Service**: `https://reactome.org/ContentService` - Network accessline 8
- **Analysis Service**: `https://reactome.org/AnalysisService` - Network accessline 25
import requests response = requests.get("https://reactome.org/ContentService/data/database/version") - Network accessline 26
response = requests.get("https://reactome.org/ContentService/data/database/version") - Network accessline 56
import requests response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278") - Network accessline 57
response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278") - Network accessline 76
response = requests.get("https://reactome.org/ContentService/data/query/R-HSA-69278/displayName") - Network accessline 94
response = requests.get( - Network accessline 95
"https://reactome.org/ContentService/data/event/R-HSA-69278/participatingPhysicalEntities" - Network accessline 126
response = requests.get( - Network accessline 127
"https://reactome.org/ContentService/data/query", - Network accessline 207
response = requests.post( - Network accessline 208
"https://reactome.org/AnalysisService/identifiers/", - Network accessline 257
[Credential-related source omitted] - Network accessline 258
response = requests.get(f"https://reactome.org/AnalysisService/token/{token}") - Network accessline 371
# Retrieve results later result = requests.get(f"https://reactome.org/AnalysisService/token/{token}") - Network accessline 372
result = requests.get(f"https://reactome.org/AnalysisService/token/{token}") - Network accessline 390
# For mouse genes, project to human pathways response = requests.post( - Network accessline 391
response = requests.post( - Network accessline 392
"https://reactome.org/AnalysisService/identifiers/projection/", - Network accessline 418
# Submit analysis data = "\n".join(genes) response = requests.post( - Network accessline 419
data = "\n".join(genes) response = requests.post( "https://reactome.org/AnalysisService/identifiers/", - Network accessline 420
response = requests.post( - Network accessline 421
"https://reactome.org/AnalysisService/identifiers/", - Network accessline 448
if significant: top_pathway = significant[0] url = f"https://reactome.org/PathwayBrowser/#{top_pathway['stId']}&DTAB=AN&ANALYSIS={token}" - Network accessline 449
top_pathway = significant[0] url = f"https://reactome.org/PathwayBrowser/#{top_pathway['stId']}&DTAB=AN&ANALYSIS={token}" print(f"View top result: {url}") - Network accessline 450
url = f"https://reactome.org/PathwayBrowser/#{top_pathway['stId']}&DTAB=AN&ANALYSIS={token}" - Network accessline 462
- **Interactive API Documentation**: https://reactome.org/dev/content-service - Network accessline 463
- **Analysis Service Docs**: https://reactome.org/dev/analysis - **User Guide**: https://reactome.org/userguide - **Data Downloads**: https://reactome.org/download-data - Network accessline 464
- **User Guide**: https://reactome.org/userguide - Network accessline 465
- **Data Downloads**: https://reactome.org/download-data
skills/reactome-database/scripts/reactome_query.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 31
CONTENT_BASE = "https://reactome.org/ContentService" - Network accessline 32
ANALYSIS_BASE = "https://reactome.org/AnalysisService" - Network accessline 36
response = requests.get(f"{self.CONTENT_BASE}/data/database/version") - Network accessline 42
response = requests.get(f"{self.CONTENT_BASE}/data/query/{pathway_id}") - Network accessline 48
response = requests.get( - Network accessline 56
response = requests.get( - Network accessline 65
data = "\n".join(gene_list) response = requests.post( - Network accessline 66
response = requests.post( - Network accessline 76
response = requests.get(f"{self.ANALYSIS_BASE}/token/{token}") - Network accessline 219
[Credential-related source omitted] - Network accessline 220
top_pathway = pathways[0]['stId'] url = f"https://reactome.org/PathwayBrowser/#{top_pathway}&DTAB=AN&ANALYSIS={token}" print(f"\nView top result in browser:") - Network accessline 221
url = f"https://reactome.org/PathwayBrowser/#{top_pathway}&DTAB=AN&ANALYSIS={token}"
skills/recovery-community-moderator/SKILL.md
- Network accessline 173
- [SAMHSA Trauma-Informed Care](https://www.samhsa.gov/mental-health/trauma-violence/trauma-informed-approaches-programs) - Network accessline 174
- [Harm Reduction Principles](https://harmreduction.org/about-us/principles-of-harm-reduction/) - Network accessline 175
- [Policy-as-Prompt AI Moderation](https://arxiv.org/html/2502.18695v1)
skills/recovery-community-moderator/docs/COMMUNITY_STANDARDS.md
- Network accessline 118
*These standards are informed by the [National Harm Reduction Coalition's Principles](https://harmreduction.org/about-us/principles-of-harm-reduction/) and [SAMHSA's Trauma-Informed Care Guidelines](https://www.samhsa.gov/mental-health/trau
skills/recovery-community-moderator/scripts/moderate_content.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/regulatory-drafter/anthropic_regulatory_coworker.py
- Executable scriptline 1
Executable file
skills/regulatory-drafter/compliance_checker.py
- Executable scriptline 1
Executable file
skills/regulatory-drafter/submission_drafter.py
- Executable scriptline 1
Executable file
skills/regulatory-drafting/coworker.py
- Executable scriptline 1
Executable file
skills/repro-enforcer/SKILL.md
skills/research-grants/README.md
- Network accessline 247
### Official Resources - NSF: https://www.nsf.gov/funding/ - Network accessline 248
- NSF: https://www.nsf.gov/funding/ - Network accessline 249
- NIH: https://grants.nih.gov/ - Network accessline 250
- DOE: https://science.osti.gov/grants/ - Network accessline 251
- DARPA: https://www.darpa.mil/work-with-us/opportunities
skills/research-grants/SKILL.md
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Bash
skills/research-grants/references/broader_impacts.md
- Network accessline 372
### NSF Resources - **NSF Broader Impacts Website**: https://www.nsf.gov/od/oia/special/broaderimpacts/ - Network accessline 373
- **NSF Broader Impacts Website**: https://www.nsf.gov/od/oia/special/broaderimpacts/ - Network accessline 374
- **BI Examples Repository**: https://www.cmu.edu/uro/resources for undergraduate research/best practices/broader-impacts.html
skills/research-grants/references/darpa_guidelines.md
- Network accessline 11
**Website**: https://www.darpa.mil - Network accessline 620
- **DARPA Website**: https://www.darpa.mil - Network accessline 621
- **DARPA Opportunities**: https://www.darpa.mil/work-with-us/opportunities - Network accessline 622
- **BAA Listings**: https://beta.sam.gov (search "DARPA") - Network accessline 623
- **DARPA Social Media**: Twitter @DARPA (PMs often announce programs) - **SBIR/STTR**: https://www.darpa.mil/work-with-us/for-small-businesses - **Heilmeier Catechism**: https://www.darpa.mil/about-us/timeline/heilmeier-catechism - Network accessline 624
- **SBIR/STTR**: https://www.darpa.mil/work-with-us/for-small-businesses - Network accessline 625
- **Heilmeier Catechism**: https://www.darpa.mil/about-us/timeline/heilmeier-catechism
skills/research-grants/references/doe_guidelines.md
- Network accessline 9
**Website**: https://www.energy.gov - Network accessline 435
**Sources**: - **EERE Exchange**: https://eere-exchange.energy.gov - Network accessline 436
- **EERE Exchange**: https://eere-exchange.energy.gov - Network accessline 437
- **ARPA-E OPEN**: https://arpa-e.energy.gov - Network accessline 438
- **Office of Science FOAs**: https://science.osti.gov/grants/Funding-Opportunities - Network accessline 575
- **DOE Office of Science**: https://science.osti.gov - Network accessline 576
- **ARPA-E**: https://arpa-e.energy.gov - Network accessline 577
- **EERE**: https://www.energy.gov/eere - Network accessline 578
- **DOE National Laboratories**: https://www.energy.gov/national-laboratories - Network accessline 579
- **EERE Exchange**: https://eere-exchange.energy.gov - Network accessline 580
- **Grants.gov**: https://www.grants.gov - Network accessline 581
- **SAM.gov**: https://sam.gov
skills/research-grants/references/nih_guidelines.md
- Network accessline 9
**Website**: https://www.nih.gov - Network accessline 839
- **NIH Homepage**: https://www.nih.gov - Network accessline 840
- **NIH RePORTER (funded grants)**: https://reporter.nih.gov - Network accessline 841
- **Grants & Funding**: https://grants.nih.gov - Network accessline 842
- **eRA Commons**: https://commons.era.nih.gov - Network accessline 843
- **ASSIST**: https://public.era.nih.gov/assist - Network accessline 844
- **Application Forms and Instructions**: https://grants.nih.gov/grants/how-to-apply-application-guide.html - Network accessline 845
- **NIH Data Sharing Policy**: https://sharing.nih.gov - Network accessline 846
- **Rigor and Reproducibility**: https://grants.nih.gov/reproducibility/index.htm
skills/research-grants/references/nsf_guidelines.md
- Network accessline 9
**Website**: https://www.nsf.gov - Network accessline 559
- **NSF Homepage**: https://www.nsf.gov - Network accessline 560
- **Award Search**: https://www.nsf.gov/awardsearch/ - Network accessline 561
- **Proposal & Award Policies & Procedures Guide (PAPPG)**: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg - Network accessline 562
- **FastLane**: https://www.fastlane.nsf.gov/ - Network accessline 563
- **Research.gov**: https://www.research.gov/ - Network accessline 564
- **Broader Impacts Resources**: https://www.nsf.gov/od/oia/special/broaderimpacts/ - Network accessline 565
- **NSF Funding Statistics**: https://www.nsf.gov/statistics/
skills/research-literature/coworker.py
skills/research-lookup/README.md
skills/research-lookup/SKILL.md
skills/research-lookup/examples.py
skills/research-lookup/lookup.py
skills/research-lookup/research_lookup.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Network accessline 48
self.base_url = "https://openrouter.ai/api/v1" - Network accessline 51
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Network accessline 52
"Content-Type": "application/json", "HTTP-Referer": "https://scientific-writer.local", "X-Title": "Scientific Writer Research Tool" - Network accessline 53
"HTTP-Referer": "https://scientific-writer.local", - Network accessline 101
try: response = requests.post( - Network accessline 102
response = requests.post( - Network accessline 253
# Look for DOI patterns first (most reliable) # Matches: doi:10.xxx, DOI: 10.xxx, https://doi.org/10.xxx - Network accessline 254
# Matches: doi:10.xxx, DOI: 10.xxx, https://doi.org/10.xxx - Network accessline 265
"type": "doi", "doi": doi_clean, "url": f"https://doi.org/{doi_clean}" - Network accessline 266
"doi": doi_clean, "url": f"https://doi.org/{doi_clean}" }) - Network accessline 267
"url": f"https://doi.org/{doi_clean}" - Network accessline 304
try: response = requests.get( - Network accessline 305
response = requests.get( - Access to secretsline 330
[Credential-related source omitted] - Access to secretsline 331
[Credential-related source omitted] - Access to secretsline 332
[Credential-related source omitted] - Access to secretsline 333
[Credential-related source omitted]
skills/research-lookup/scripts/research_lookup.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Network accessline 48
self.base_url = "https://openrouter.ai/api/v1" - Network accessline 51
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Network accessline 52
"Content-Type": "application/json", "HTTP-Referer": "https://scientific-writer.local", "X-Title": "Scientific Writer Research Tool" - Network accessline 53
"HTTP-Referer": "https://scientific-writer.local", - Network accessline 101
try: response = requests.post( - Network accessline 102
response = requests.post( - Network accessline 253
# Look for DOI patterns first (most reliable) # Matches: doi:10.xxx, DOI: 10.xxx, https://doi.org/10.xxx - Network accessline 254
# Matches: doi:10.xxx, DOI: 10.xxx, https://doi.org/10.xxx - Network accessline 265
"type": "doi", "doi": doi_clean, "url": f"https://doi.org/{doi_clean}" - Network accessline 266
"doi": doi_clean, "url": f"https://doi.org/{doi_clean}" }) - Network accessline 267
"url": f"https://doi.org/{doi_clean}" - Network accessline 304
try: response = requests.get( - Network accessline 305
response = requests.get( - Access to secretsline 330
[Credential-related source omitted] - Access to secretsline 331
[Credential-related source omitted] - Access to secretsline 332
[Credential-related source omitted] - Access to secretsline 333
[Credential-related source omitted]
skills/rfdiffusion/SKILL.md
- Network accessline 17
tags: [structure-design, diffusion, backbone, binder] proteinbase_slug: rfdiffusion proteinbase_url: https://proteinbase.com/design-methods/rfdiffusion - Network accessline 18
proteinbase_slug: rfdiffusion proteinbase_url: https://proteinbase.com/design-methods/rfdiffusion biomodals_script: modal_rfdiffusion.py - Network accessline 19
proteinbase_url: https://proteinbase.com/design-methods/rfdiffusion - Network accessline 40
# Clone biomodals git clone https://github.com/hgbrian/biomodals && cd biomodals - Network accessline 41
git clone https://github.com/hgbrian/biomodals && cd biomodals - Network accessline 61
# Clone and install git clone https://github.com/RosettaCommons/RFdiffusion.git - Network accessline 62
git clone https://github.com/RosettaCommons/RFdiffusion.git - Network accessline 65
# Download weights wget http://files.ipd.uw.edu/pub/RFdiffusion/models/Complex_base_ckpt.pt - Network accessline 66
wget http://files.ipd.uw.edu/pub/RFdiffusion/models/Complex_base_ckpt.pt
skills/rfdiffusion/examples/binder-walkthrough.md
skills/scanpy/SKILL.md
skills/scanpy/assets/analysis_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scanpy/scripts/qc_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-critical-thinking/SKILL.md
- Broad permissionsline 1
Bash
skills/scientific-manuscript/SKILL.md
- Executable scriptline 1
Executable file
skills/scientific-problem-selection/LICENSE.txt
skills/scientific-schematics/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Access to secretsline 76
[Credential-related source omitted] - Network accessline 79
Get an API key at: https://openrouter.ai/keys - Access to secretsline 261
[Credential-related source omitted] - Network accessline 525
**Python Libraries** - Schemdraw Documentation: https://schemdraw.readthedocs.io/ - Network accessline 526
- Schemdraw Documentation: https://schemdraw.readthedocs.io/ - Network accessline 527
- NetworkX Documentation: https://networkx.org/documentation/ - Network accessline 528
- Matplotlib Documentation: https://matplotlib.org/ - Network accessline 530
**Publication Standards** - Nature Figure Guidelines: https://www.nature.com/nature/for-authors/final-submission - Network accessline 531
- Nature Figure Guidelines: https://www.nature.com/nature/for-authors/final-submission - Network accessline 532
- Science Figure Guidelines: https://www.science.org/content/page/instructions-preparing-initial-manuscript - Network accessline 533
- CONSORT Diagram: http://www.consort-statement.org/consort-statement/flow-diagram - Access to secretsline 603
[Credential-related source omitted] - Network accessline 605
# Get key at: https://openrouter.ai/keys
skills/scientific-schematics/references/QUICK_REFERENCE.md
- Network accessline 8
# Get API key from https://openrouter.ai/keys - Access to secretsline 9
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 118
[Credential-related source omitted] - Access to secretsline 136
[Credential-related source omitted] - Access to secretsline 139
[Credential-related source omitted] - Access to secretsline 193
[Credential-related source omitted] - Network accessline 204
- Implementation details: `IMPLEMENTATION_SUMMARY.md` - Example script: `example_usage.sh` - Get API key: https://openrouter.ai/keys - Network accessline 206
- Get API key: https://openrouter.ai/keys
skills/scientific-schematics/references/README.md
- Access to secretsline 13
[Credential-related source omitted] - Network accessline 58
# Get OpenRouter API key # Visit: https://openrouter.ai/keys - Network accessline 59
# Visit: https://openrouter.ai/keys - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 64
[Credential-related source omitted] - Access to secretsline 65
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Access to secretsline 244
[Credential-related source omitted] - Access to secretsline 247
[Credential-related source omitted] - Access to secretsline 250
[Credential-related source omitted] - Network accessline 269
# Check API status curl https://openrouter.ai/api/v1/models - Network accessline 270
curl https://openrouter.ai/api/v1/models
skills/scientific-schematics/references/best_practices.md
- Network accessline 534
**Contrast Checking** - WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/ - Network accessline 535
- WebAIM Contrast Checker: https://webaim.org/resources/contrastchecker/ - Network accessline 536
- Colorable: https://colorable.jxnblk.com/ - Network accessline 553
- **Nature Figure Preparation**: https://www.nature.com/nature/for-authors/final-submission - Network accessline 554
- **Science Figure Guidelines**: https://www.science.org/content/page/instructions-preparing-initial-manuscript - Network accessline 555
- **WCAG Accessibility Standards**: https://www.w3.org/WAI/WCAG21/quickref/ - Network accessline 556
- **Color Universal Design (CUD)**: https://jfly.uni-koeln.de/color/ - Network accessline 557
- **ColorBrewer**: https://colorbrewer2.org/
skills/scientific-schematics/scripts/example_usage.sh
- Executable scriptline 1
#!/bin/bash - Access to secretsline 5
[Credential-related source omitted] - Access to secretsline 18
[Credential-related source omitted] - Network accessline 19
[Credential-related source omitted] - Access to secretsline 19
[Credential-related source omitted] - Network accessline 20
[Credential-related source omitted] - Network accessline 21
echo "Get an API key at: https://openrouter.ai/keys" - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 26
[Credential-related source omitted]
skills/scientific-schematics/scripts/generate_schematic.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 71
[Credential-related source omitted] - Access to secretsline 86
[Credential-related source omitted] - Access to secretsline 93
[Credential-related source omitted] - Access to secretsline 94
[Credential-related source omitted] - Network accessline 95
[Credential-related source omitted] - Access to secretsline 95
[Credential-related source omitted] - Network accessline 96
print("\nFor AI generation, you need an OpenRouter API key.") print("Get one at: https://openrouter.ai/keys") print("\nSet it with:") - Network accessline 97
print("Get one at: https://openrouter.ai/keys") - Access to secretsline 99
[Credential-related source omitted] - Access to secretsline 122
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted]
skills/scientific-schematics/scripts/generate_schematic_ai.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 40
[Credential-related source omitted] - Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 57
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[Credential-related source omitted] - Access to secretsline 146
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[Credential-related source omitted] - Access to secretsline 160
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[Credential-related source omitted] - Access to secretsline 164
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[Credential-related source omitted] - Access to secretsline 167
[Credential-related source omitted] - Network accessline 168
"Get your API key from: https://openrouter.ai/keys" - Network accessline 171
self.verbose = verbose self._last_error = None # Track last error for better reporting self.base_url = "https://openrouter.ai/api/v1" - Network accessline 173
self.base_url = "https://openrouter.ai/api/v1" - Network accessline 174
# Nano Banana 2 - Google's advanced image generation model # https://openrouter.ai/google/gemini-3-pro-image-preview - Network accessline 175
# https://openrouter.ai/google/gemini-3-pro-image-preview - Network accessline 199
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Network accessline 200
"Content-Type": "application/json", "HTTP-Referer": "https://github.com/scientific-writer", "X-Title": "Scientific Schematic Generator" - Network accessline 201
"HTTP-Referer": "https://github.com/scientific-writer", - Network accessline 215
try: response = requests.post( - Network accessline 216
response = requests.post( - Possible obfuscationline 283
return base64.b64decode(base64_str) - Possible obfuscationline 298
return base64.b64decode(base64_str) - Possible obfuscationline 310
return base64.b64decode(base64_str) - Access to secretsline 787
[Credential-related source omitted] - Access to secretsline 800
[Credential-related source omitted] - Access to secretsline 807
[Credential-related source omitted] - Access to secretsline 808
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[Credential-related source omitted] - Access to secretsline 811
[Credential-related source omitted] - Access to secretsline 821
[Credential-related source omitted]
skills/scientific-slides/SKILL.md
skills/scientific-slides/assets/beamer_template_conference.tex
skills/scientific-slides/assets/beamer_template_seminar.tex
skills/scientific-slides/references/beamer_guide.md
- Network accessline 749
% External links \begin{frame}{Resources} Visit \url{https://example.com} for more information. - Network accessline 751
Visit \url{https://example.com} for more information. - Network accessline 753
\href{https://github.com/user/repo}{GitHub Repository} - Network accessline 762
\begin{frame}{Scan for Paper} \begin{center} \qrcode[height=3cm]{https://doi.org/10.1234/paper} - Network accessline 764
\qrcode[height=3cm]{https://doi.org/10.1234/paper} - Network accessline 996
- Beamer User Guide: `texdoc beamer` - Theme Gallery: https://deic.uab.cat/~iblanes/beamer_gallery/ - Network accessline 997
- Theme Gallery: https://deic.uab.cat/~iblanes/beamer_gallery/ - Network accessline 998
- TikZ Examples: https://texample.net/tikz/
skills/scientific-slides/references/visual_review_workflow.md
skills/scientific-slides/scripts/generate_slide_image.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 72
[Credential-related source omitted] - Access to secretsline 84
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[Credential-related source omitted] - Access to secretsline 91
[Credential-related source omitted] - Network accessline 92
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Network accessline 93
print("\nFor AI generation, you need an OpenRouter API key.") print("Get one at: https://openrouter.ai/keys") print("\nSet it with:") - Network accessline 94
print("Get one at: https://openrouter.ai/keys") - Access to secretsline 96
[Credential-related source omitted] - Access to secretsline 124
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted]
skills/scientific-slides/scripts/generate_slide_image_ai.py
- Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 57
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[Credential-related source omitted] - Access to secretsline 188
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[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Network accessline 190
"Get your API key from: https://openrouter.ai/keys" - Network accessline 193
self.verbose = verbose self._last_error = None self.base_url = "https://openrouter.ai/api/v1" - Network accessline 195
self.base_url = "https://openrouter.ai/api/v1" - Network accessline 210
[Credential-related source omitted] - Access to secretsline 210
[Credential-related source omitted] - Network accessline 211
"Content-Type": "application/json", "HTTP-Referer": "https://github.com/scientific-writer", "X-Title": "Scientific Slide Generator" - Network accessline 212
"HTTP-Referer": "https://github.com/scientific-writer", - Network accessline 226
try: response = requests.post( - Network accessline 227
response = requests.post( - Possible obfuscationline 277
return base64.b64decode(base64_str) - Possible obfuscationline 288
return base64.b64decode(base64_str) - Possible obfuscationline 299
return base64.b64decode(base64_str) - Access to secretsline 706
[Credential-related source omitted] - Access to secretsline 718
[Credential-related source omitted] - Access to secretsline 723
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[Credential-related source omitted] - Access to secretsline 727
[Credential-related source omitted] - Access to secretsline 742
[Credential-related source omitted]
skills/scientific-slides/scripts/pdf_to_images.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-slides/scripts/slides_to_pdf.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-slides/scripts/validate_presentation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-visualization/assets/color_palettes.py
skills/scientific-visualization/references/color_palettes.md
- Network accessline 233
### Online Simulators - **Coblis**: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 234
- **Coblis**: https://www.color-blindness.com/coblis-color-blindness-simulator/ - Network accessline 344
- **ColorBrewer**: http://colorbrewer2.org/ - Choose palettes by colorblind-safe option - Network accessline 345
- **Paul Tol's palettes**: https://personal.sron.nl/~pault/ - Network accessline 346
- **Okabe-Ito palette origin**: "Color Universal Design" (Okabe & Ito, 2008) - **Matplotlib colormaps**: https://matplotlib.org/stable/tutorials/colors/colormaps.html - **Seaborn palettes**: https://seaborn.pydata.org/tutorial/color_palette - Network accessline 347
- **Matplotlib colormaps**: https://matplotlib.org/stable/tutorials/colors/colormaps.html - Network accessline 348
- **Seaborn palettes**: https://seaborn.pydata.org/tutorial/color_palettes.html
skills/scientific-visualization/references/matplotlib_examples.md
skills/scientific-visualization/scripts/figure_export.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-visualization/scripts/style_presets.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scientific-writing/SKILL.md
- Broad permissionsline 1
Bash
skills/scientific-writing/references/citation_styles.md
- Network accessline 204
Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. Journal Name, Volume(Issue), page range. https://doi.org/xx.xxxx - Network accessline 209
Smith, J. D., Johnson, A. B., & Williams, C. D. (2023). Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry, 80(5), 456-464. https://doi.org/10.1001/jamapsychiatry.2023.0123 - Network accessline 214
Author, A. A. (Year). Book title: Subtitle (Edition). Publisher. https://doi.org/xx.xxxx - Network accessline 453
doi:10.1001/jamapsychiatry.2023.0123 or https://doi.org/10.1001/jamapsychiatry.2023.0123 - Network accessline 455
https://doi.org/10.1001/jamapsychiatry.2023.0123 - Network accessline 459
- Required by most journals for recent publications - Preferred over URLs because DOIs don't change - Look up DOIs at https://www.crossref.org/ if not provided - Network accessline 461
- Look up DOIs at https://www.crossref.org/ if not provided - Network accessline 463
### Style-specific formatting: - **AMA**: `doi:10.xxxx/xxxxx` - **APA**: `https://doi.org/10.xxxx/xxxxx` - Network accessline 464
- **AMA**: `doi:10.xxxx/xxxxx` - **APA**: `https://doi.org/10.xxxx/xxxxx` - **Vancouver**: Often omitted or added at journal's discretion - Network accessline 465
- **APA**: `https://doi.org/10.xxxx/xxxxx` - Network accessline 467
- **Chicago**: `https://doi.org/10.xxxx/xxxxx` - Network accessline 473
| **AMA** | Author AA, Author BB. Title of article. *Journal*. Year;Vol(Iss):pp. doi:xx | | **Vancouver** | Author AA, Author BB. Title of article. Journal. Year;Vol(Iss):pp. | | **APA** | Author, A. A., & Author, B. B. (Year). Title of art - Network accessline 474
| **Vancouver** | Author AA, Author BB. Title of article. Journal. Year;Vol(Iss):pp. | | **APA** | Author, A. A., & Author, B. B. (Year). Title of article. *Journal*, Vol(Iss), pp. https://doi.org/xx | | **Chicago A-D** | Author, A. A., and - Network accessline 475
| **APA** | Author, A. A., & Author, B. B. (Year). Title of article. *Journal*, Vol(Iss), pp. https://doi.org/xx | - Network accessline 499
APA: Author, A. A. (Year). Title [Preprint]. Repository Name. https://doi.org/xx.xxxx - Network accessline 519
APA: Author, A. A. (Year). Title of dataset (Version X) [Data set]. Repository. https://doi.org/xx.xxxx - Network accessline 694
### Official Manuals - AMA: https://www.amamanualofstyle.com/ - Network accessline 695
- AMA: https://www.amamanualofstyle.com/ - Network accessline 696
- Vancouver/ICMJE: http://www.icmje.org/ - Network accessline 697
- APA: https://apastyle.apa.org/ - Network accessline 698
- Chicago: https://www.chicagomanualofstyle.org/ - Network accessline 699
- IEEE: https://ieeeauthorcenter.ieee.org/ - Network accessline 701
### Journal-Specific Style Guides - Nature: https://www.nature.com/nature/for-authors/formatting-guide - Network accessline 702
- Nature: https://www.nature.com/nature/for-authors/formatting-guide - Network accessline 703
- Science: https://www.science.org/content/page/instructions-authors - Network accessline 704
- Cell: https://www.cell.com/cell/authors - Network accessline 705
- JAMA: https://jamanetwork.com/journals/jama/pages/instructions-for-authors - Network accessline 707
### Quick Reference Guides - Purdue OWL: https://owl.purdue.edu/ - Network accessline 708
- Purdue OWL: https://owl.purdue.edu/ - Network accessline 709
- Citation Machine: https://www.citationmachine.net/ - Network accessline 710
- EasyBib: https://www.easybib.com/ - Network accessline 712
### Reference Management - Zotero: https://www.zotero.org/ - Network accessline 713
- Zotero: https://www.zotero.org/ - Network accessline 714
- Mendeley: https://www.mendeley.com/ - Network accessline 715
- EndNote: https://endnote.com/ - Network accessline 718
- Journal Citation Reports (Clarivate): Lists journal citation styles - EndNote style repository: >7000 journal-specific styles - Zotero Style Repository: https://www.zotero.org/styles - Network accessline 720
- Zotero Style Repository: https://www.zotero.org/styles
skills/scientific-writing/references/reporting_guidelines.md
- Network accessline 86
**Where to access:** http://www.consort-statement.org/ - Network accessline 130
**Where to access:** https://www.strobe-statement.org/ - Network accessline 181
**Where to access:** http://www.prisma-statement.org/ - Network accessline 218
**Where to access:** https://www.spirit-statement.org/ - Network accessline 247
**Where to access:** https://www.equator-network.org/reporting-guidelines/stard/ - Network accessline 281
**Where to access:** https://www.tripod-statement.org/ - Network accessline 314
**Where to access:** https://arriveguidelines.org/ - Network accessline 338
**Where to access:** https://www.care-statement.org/ - Network accessline 356
**Where to access:** http://www.squire-statement.org/ - Network accessline 384
**Where to access:** https://www.equator-network.org/reporting-guidelines/cheers/ - Network accessline 403
**Where to access:** https://www.equator-network.org/reporting-guidelines/srqr/ - Network accessline 440
**Website:** https://www.equator-network.org/ - Network accessline 619
- **EQUATOR Network**: https://www.equator-network.org/ - Network accessline 620
- **CONSORT**: http://www.consort-statement.org/ - Network accessline 621
- **STROBE**: https://www.strobe-statement.org/ - Network accessline 622
- **PRISMA**: http://www.prisma-statement.org/ - Network accessline 623
- **SPIRIT**: https://www.spirit-statement.org/ - Network accessline 624
- **ARRIVE**: https://arriveguidelines.org/ - Network accessline 625
- **CARE**: https://www.care-statement.org/ - Network accessline 635
- **Some reference managers** can insert reporting guideline citations - **Covidence, RevMan** for systematic review reporting - **PRISMA flow diagram generator**: http://prisma.thetacollaborative.ca/ - Network accessline 637
- **PRISMA flow diagram generator**: http://prisma.thetacollaborative.ca/
skills/scikit-bio/SKILL.md
skills/scikit-learn/SKILL.md
- Network accessline 512
- Official Documentation: https://scikit-learn.org/stable/ - Network accessline 513
- User Guide: https://scikit-learn.org/stable/user_guide.html - Network accessline 514
- API Reference: https://scikit-learn.org/stable/api/index.html - Network accessline 515
- Examples Gallery: https://scikit-learn.org/stable/auto_examples/index.html
skills/scikit-learn/references/quick_reference.md
- Network accessline 429
- Official Documentation: https://scikit-learn.org/stable/ - Network accessline 430
- User Guide: https://scikit-learn.org/stable/user_guide.html - Network accessline 431
- API Reference: https://scikit-learn.org/stable/api/index.html - Network accessline 432
- Examples: https://scikit-learn.org/stable/auto_examples/index.html - Network accessline 433
- Tutorials: https://scikit-learn.org/stable/tutorial/index.html
skills/scikit-learn/scripts/classification_pipeline.py
- Executable scriptline 1
Executable file
skills/scikit-learn/scripts/clustering_analysis.py
- Executable scriptline 1
Executable file
skills/scikit-survival/SKILL.md
- Network accessline 354
- **Official Documentation**: https://scikit-survival.readthedocs.io/ - Network accessline 355
- **GitHub Repository**: https://github.com/sebp/scikit-survival - Network accessline 357
- **API Reference**: Complete list of classes and functions at https://scikit-survival.readthedocs.io/en/stable/api/index.html
skills/scrna-orchestrator/SKILL.md
- Network accessline 15
always: false emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio os: [macos, linux] - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 202
- [Scanpy documentation](https://scanpy.readthedocs.io/) — analysis API and methods. - Network accessline 203
- [AnnData documentation](https://anndata.readthedocs.io/) — data model. - Network accessline 204
- [Leiden algorithm paper](https://www.nature.com/articles/s41598-019-41695-z) — community detection.
skills/scrna-orchestrator/scrna_orchestrator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/scrna-orchestrator/tests/test_scrna_orchestrator.py
skills/scrna-qc/qc_analysis.py
- Executable scriptline 1
Executable file - Network accessline 13
Quality Control Analysis for Single-Cell RNA-seq Data Following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html - Network accessline 15
https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html
skills/scrna-qc/qc_core.py
- Executable scriptline 1
Executable file - Network accessline 15
This module provides building blocks for metrics calculation and filtering while following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html - Network accessline 16
while following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html """ - Network accessline 17
https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html
skills/scrna-qc/qc_plotting.py
- Executable scriptline 1
Executable file
skills/scvelo/SKILL.md
- Network accessline 17
**Key resources:** - Documentation: https://scvelo.readthedocs.io/ - Network accessline 18
- Documentation: https://scvelo.readthedocs.io/ - Network accessline 19
- GitHub: https://github.com/theislab/scvelo - Network accessline 315
- **scVelo documentation**: https://scvelo.readthedocs.io/ - Network accessline 316
- **Tutorial notebooks**: https://scvelo.readthedocs.io/tutorials/ - Network accessline 317
- **GitHub**: https://github.com/theislab/scvelo - Network accessline 318
- **Paper**: Bergen V et al. (2020) Nature Biotechnology. PMID: 32747759 - **velocyto** (preprocessing): http://velocyto.org/ - **CellRank** (fate prediction, extends scVelo): https://cellrank.readthedocs.io/ - Network accessline 319
- **velocyto** (preprocessing): http://velocyto.org/ - Network accessline 320
- **CellRank** (fate prediction, extends scVelo): https://cellrank.readthedocs.io/ - Network accessline 321
- **dynamo** (metabolic labeling alternative): https://dynamo-release.readthedocs.io/
skills/scvelo/scripts/rna_velocity_workflow.py
- Executable scriptline 1
Executable file
skills/scvi-tools/SKILL.md
- Network accessline 162
- **Workflows**: `references/workflows.md` contains common workflows, best practices, hyperparameter tuning, and GPU optimization - **Model References**: Detailed documentation for each model category in the `references/` directory - **Offi - Network accessline 163
- **Model References**: Detailed documentation for each model category in the `references/` directory - **Official Documentation**: https://docs.scvi-tools.org/en/stable/ - **Tutorials**: https://docs.scvi-tools.org/en/stable/tutorials/inde - Network accessline 164
- **Official Documentation**: https://docs.scvi-tools.org/en/stable/ - Network accessline 165
- **Tutorials**: https://docs.scvi-tools.org/en/stable/tutorials/index.html - Network accessline 166
- **API Reference**: https://docs.scvi-tools.org/en/stable/api/index.html
skills/seq-wrangler/SKILL.md
skills/shap/SKILL.md
skills/simpy/scripts/basic_simulation_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simpy/scripts/resource_monitor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-orchestrator/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/simulation-orchestrator/scripts/campaign_manager.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-orchestrator/scripts/job_tracker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-orchestrator/scripts/result_aggregator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-orchestrator/scripts/sweep_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-validator/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/simulation-validator/scripts/failure_diagnoser.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-validator/scripts/preflight_checker.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-validator/scripts/result_validator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/simulation-validator/scripts/runtime_monitor.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/single-annotation/SKILL.md
- Network accessline 18
2. **MetaTiME tumour microenvironment states** - *Data requirements*: Batched TME AnnData with an scVI latent embedding. The tutorial uses `TiME_adata_scvi.h5ad` from Figshare (`https://figshare.com/ndownloader/files/41440050`). If start - Network accessline 19
- *Data requirements*: Batched TME AnnData with an scVI latent embedding. The tutorial uses `TiME_adata_scvi.h5ad` from Figshare (`https://figshare.com/ndownloader/files/41440050`). If starting from counts, run scVI (`scvi.model.SCVI`) firs - Access to secretsline 34
[Credential-related source omitted]
skills/single-annotation/reference.md
- Network accessline 34
data_path = 'TiME_adata_scvi.h5ad' # download from https://figshare.com/ndownloader/files/41440050 - Network accessline 63
mkdir -p new_ontology wget http://purl.obolibrary.org/obo/cl/cl.json -O new_ontology/cl.json - Network accessline 64
wget http://purl.obolibrary.org/obo/cl/cl.json -O new_ontology/cl.json - Network accessline 65
wget https://download.cncb.ac.cn/celltaxonomy/Cell_Taxonomy_resource.txt -O new_ontology/Cell_Taxonomy_resource.txt - Access to secretsline 98
[Credential-related source omitted]
skills/single-cell-rna-qc/LICENSE.txt
skills/single-cell-rna-qc/references/scverse_qc_guidelines.md
- Network accessline 183
- scverse Best Practices: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html
skills/single-cell-rna-qc/scripts/qc_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 3
Quality Control Analysis for Single-Cell RNA-seq Data Following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html - Network accessline 5
https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html
skills/single-cell-rna-qc/scripts/qc_core.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 5
This module provides building blocks for metrics calculation and filtering while following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html - Network accessline 6
while following scverse best practices from: https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html """ - Network accessline 7
https://www.sc-best-practices.org/preprocessing_visualization/quality_control.html
skills/single-cell-rna-qc/scripts/qc_plotting.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/single-downstream-analysis/SKILL.md
- Network accessline 69
- Gene annotations via `ov.utils.get_gene_annotation` (requires GTF from GENCODE or T2T-CHM13). - `ov.utils.download_GDSC_data()` and `ov.utils.download_CaDRReS_model()` for drug-response models. - Clone CaDRReS-Sc repo (`git clone - Network accessline 70
- `ov.utils.download_GDSC_data()` and `ov.utils.download_CaDRReS_model()` for drug-response models. - Clone CaDRReS-Sc repo (`git clone https://github.com/CSB5/CaDRReS-Sc`). - **Core calls** - Network accessline 71
- Clone CaDRReS-Sc repo (`git clone https://github.com/CSB5/CaDRReS-Sc`).
skills/single-preprocessing/reference.md
- Network accessline 17
conda activate rapids pip install rapids-singlecell curl -sSL https://raw.githubusercontent.com/Starlitnightly/omicverse/refs/heads/master/install.sh | bash -s - Dangerous shell operationline 19
curl -sSL https://raw.githubusercontent.com/Starlitnightly/omicverse/refs/heads/master/install.sh | bash -s - Network accessline 19
curl -sSL https://raw.githubusercontent.com/Starlitnightly/omicverse/refs/heads/master/install.sh | bash -s - Network accessline 24
mkdir -p data write wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz - Network accessline 25
wget http://cf.10xgenomics.com/samples/cell-exp/1.1.0/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz -O data/pbmc3k_filtered_gene_bc_matrices.tar.gz
skills/sleep-analyzer/SKILL.md
skills/slurm-job-script-generator/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/slurm-job-script-generator/scripts/slurm_script_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/solublempnn/SKILL.md
- Network accessline 49
git clone https://github.com/dauparas/ProteinMPNN.git
skills/spatial-transcriptomics-agent/SKILL.md
skills/spatial-transcriptomics-agent/repo/README.md
- Network accessline 16
[](https://github.com/LiuLab-Bioelectronics-Harvard/STAgent/stargazers) - Network accessline 17
[](https://opensource.org/licenses/MIT) - Network accessline 19
https://doi.org/10.1101/2025.04.01.646731 - Network accessline 35
STAgent is part of a broader AI agent ecosystem we developed for specialized biological data analysis. A complementary tool in this ecosystem is [SpikeAgent](https://github.com/LiuLab-Bioelectronics-Harvard/SpikeAgent.git), which focuses on - Network accessline 37
SpikeAgent is described in our recent preprint: [https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1](https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1) - Network accessline 41
Check out our [demo video](https://www.youtube.com/watch?v=aEUop05RINY&t=2s) to see STAgent in action. - Network accessline 76
git clone https://github.com/LiuLab-Bioelectronics-Harvard/STAgent.git - Network accessline 96
# OpenAI models (https://platform.openai.com/api-keys) - Access to secretsline 97
[Credential-related source omitted] - Access to secretsline 98
[Credential-related source omitted] - Access to secretsline 99
[Credential-related source omitted] - Network accessline 101
# Claude models (https://www.anthropic.com/api) - Access to secretsline 102
[Credential-related source omitted] - Network accessline 104
# Google Scholar search via SerpAPI (https://serpapi.com/) - Access to secretsline 105
[Credential-related source omitted] - Network accessline 115
Download the .h5ad data files from [Google Drive](https://drive.google.com/drive/folders/1RqWGBhCia06-vQnqHUnid63MybQIKwFJ) and place them in the `./data` directory. - Network accessline 148
If you use STAgent in your research, please cite: > *Lin, Z., *Wang, W., et al. Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo. (2025). _bioRxiv_. > https://doi.org/10.1101/2025.04.01.646731 - Network accessline 150
> https://doi.org/10.1101/2025.04.01.646731
skills/spatial-transcriptomics-agent/repo/src/.env
skills/spatial-transcriptomics-agent/repo/src/graph.py
- Executable scriptline 1
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skills/spatial-transcriptomics-agent/repo/src/graph_anthropic.py
- Executable scriptline 1
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skills/spatial-transcriptomics-agent/repo/src/prompt.py
- Executable scriptline 1
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skills/spatial-transcriptomics-agent/repo/src/speech_to_text.py
skills/spatial-transcriptomics-agent/repo/src/squidpy_rag.py
- Executable scriptline 1
Executable file - Network accessline 54
if not os.path.exists(REPO_PATH): print(f"Cloning Squidpy repository to {REPO_PATH}...") Repo.clone_from("https://github.com/scverse/squidpy", to_path=REPO_PATH) - Network accessline 56
Repo.clone_from("https://github.com/scverse/squidpy", to_path=REPO_PATH)
skills/spatial-transcriptomics-agent/repo/src/tools.py
- Executable scriptline 1
Executable file - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 39
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Dangerous shell operationline 520
exec(cleaned_command, globals, locals)
skills/spatial-transcriptomics-agent/repo/src/unified_app.py
- Executable scriptline 1
Executable file - Access to secretsline 276
[Credential-related source omitted] - Access to secretsline 282
[Credential-related source omitted] - Access to secretsline 283
[Credential-related source omitted] - Access to secretsline 284
[Credential-related source omitted] - Access to secretsline 287
[Credential-related source omitted] - Access to secretsline 289
[Credential-related source omitted] - Access to secretsline 290
[Credential-related source omitted] - Access to secretsline 291
[Credential-related source omitted]
skills/spatial-transcriptomics-agent/repo/src/util.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-agent/repo/src/util_anthropic.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-agent/st_agent_wrapper.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/STAgent/SKILL.md
skills/spatial-transcriptomics-analysis/STAgent/repo/README.md
- Network accessline 16
[](https://github.com/LiuLab-Bioelectronics-Harvard/STAgent/stargazers) - Network accessline 17
[](https://opensource.org/licenses/MIT) - Network accessline 19
https://doi.org/10.1101/2025.04.01.646731 - Network accessline 35
STAgent is part of a broader AI agent ecosystem we developed for specialized biological data analysis. A complementary tool in this ecosystem is [SpikeAgent](https://github.com/LiuLab-Bioelectronics-Harvard/SpikeAgent.git), which focuses on - Network accessline 37
SpikeAgent is described in our recent preprint: [https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1](https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1) - Network accessline 41
Check out our [demo video](https://www.youtube.com/watch?v=aEUop05RINY&t=2s) to see STAgent in action. - Network accessline 76
git clone https://github.com/LiuLab-Bioelectronics-Harvard/STAgent.git - Network accessline 96
# OpenAI models (https://platform.openai.com/api-keys) - Access to secretsline 97
[Credential-related source omitted] - Access to secretsline 98
[Credential-related source omitted] - Access to secretsline 99
[Credential-related source omitted] - Network accessline 101
# Claude models (https://www.anthropic.com/api) - Access to secretsline 102
[Credential-related source omitted] - Network accessline 104
# Google Scholar search via SerpAPI (https://serpapi.com/) - Access to secretsline 105
[Credential-related source omitted] - Network accessline 115
Download the .h5ad data files from [Google Drive](https://drive.google.com/drive/folders/1RqWGBhCia06-vQnqHUnid63MybQIKwFJ) and place them in the `./data` directory. - Network accessline 148
If you use STAgent in your research, please cite: > *Lin, Z., *Wang, W., et al. Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo. (2025). _bioRxiv_. > https://doi.org/10.1101/2025.04.01.646731 - Network accessline 150
> https://doi.org/10.1101/2025.04.01.646731
skills/spatial-transcriptomics-analysis/STAgent/repo/src/.env
skills/spatial-transcriptomics-analysis/STAgent/repo/src/graph.py
- Executable scriptline 1
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skills/spatial-transcriptomics-analysis/STAgent/repo/src/graph_anthropic.py
- Executable scriptline 1
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skills/spatial-transcriptomics-analysis/STAgent/repo/src/prompt.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/STAgent/repo/src/speech_to_text.py
skills/spatial-transcriptomics-analysis/STAgent/repo/src/squidpy_rag.py
- Executable scriptline 1
Executable file - Network accessline 54
if not os.path.exists(REPO_PATH): print(f"Cloning Squidpy repository to {REPO_PATH}...") Repo.clone_from("https://github.com/scverse/squidpy", to_path=REPO_PATH) - Network accessline 56
Repo.clone_from("https://github.com/scverse/squidpy", to_path=REPO_PATH)
skills/spatial-transcriptomics-analysis/STAgent/repo/src/tools.py
- Executable scriptline 1
Executable file - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 39
[Credential-related source omitted] - Access to secretsline 45
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Dangerous shell operationline 520
exec(cleaned_command, globals, locals)
skills/spatial-transcriptomics-analysis/STAgent/repo/src/unified_app.py
- Executable scriptline 1
Executable file - Access to secretsline 276
[Credential-related source omitted] - Access to secretsline 282
[Credential-related source omitted] - Access to secretsline 283
[Credential-related source omitted] - Access to secretsline 284
[Credential-related source omitted] - Access to secretsline 287
[Credential-related source omitted] - Access to secretsline 289
[Credential-related source omitted] - Access to secretsline 290
[Credential-related source omitted] - Access to secretsline 291
[Credential-related source omitted]
skills/spatial-transcriptomics-analysis/STAgent/repo/src/util.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/STAgent/repo/src/util_anthropic.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/STAgent/st_agent_wrapper.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/image-analysis/examples/extract_features.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-communication/examples/ligrec_analysis.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-data-io/examples/load_visium.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-deconvolution/examples/deconvolve_spatial.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-domains/examples/detect_domains.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-multiomics/examples/spatialdata_workflow.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-multiomics/examples/squidpy_highres.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-neighbors/examples/build_spatial_graph.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-preprocessing/examples/preprocess_spatial.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-proteomics/examples/spatial_proteomics_analysis.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-statistics/examples/spatial_autocorr.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/bioSkills/spatial-visualization/examples/spatial_plot.py
- Executable scriptline 1
Executable file
skills/spatial-transcriptomics-analysis/spatial_analyzer.py
- Executable scriptline 1
Executable file
skills/speech-pathology-ai/SKILL.md
- Broad permissionsline 1
Read,Write,Edit,Bash(python:*,pip:*),mcp__firecrawl__firecrawl_search,WebFetch,mcp__ElevenLabs__text_to_speech,mcp__ElevenLabs__speech_to_text
skills/statistical-analysis/SKILL.md
skills/statistical-analysis/references/reporting_standards.md
skills/statistical-analysis/scripts/assumption_checks.py
- Executable scriptline 1
Executable file
skills/statsmodels/SKILL.md
- Network accessline 604
For detailed documentation and examples: - Official docs: https://www.statsmodels.org/stable/ - Network accessline 605
- Official docs: https://www.statsmodels.org/stable/ - Network accessline 606
- User guide: https://www.statsmodels.org/stable/user-guide.html - Network accessline 607
- Examples: https://www.statsmodels.org/stable/examples/index.html - Network accessline 608
- API reference: https://www.statsmodels.org/stable/api.html
skills/string-database/SKILL.md
- Network accessline 410
Full list available at: https://string-db.org/cgi/input?input_page_active_form=organisms - Network accessline 510
For proteome-scale analysis or complete species network upload: - Visit https://string-db.org - Network accessline 511
- Visit https://string-db.org - Network accessline 515
For bulk downloads of complete datasets: - Download page: https://string-db.org/cgi/download - Network accessline 516
- Download page: https://string-db.org/cgi/download - Network accessline 528
When using STRING in publications, cite the most recent publication from: https://string-db.org/cgi/about
skills/string-database/references/string_reference.md
- Network accessline 17
- **Current version**: https://string-db.org/api - Network accessline 18
- **Version-specific**: https://version-12-0.string-db.org/api (for reproducibility) - Network accessline 19
- **API documentation**: https://string-db.org/help/api/ - Network accessline 265
Full list: https://string-db.org/cgi/input?input_page_active_form=organisms - Network accessline 337
For complete proteome analysis: 1. Navigate to https://string-db.org/ - Network accessline 338
1. Navigate to https://string-db.org/ - Access to secretsline 349
[Credential-related source omitted] - Network accessline 386
import requests url = "https://string-db.org/api/tsv/network" - Network accessline 387
url = "https://string-db.org/api/tsv/network" params = {"identifiers": "TP53", "species": 9606} response = requests.get(url, params=params) - Network accessline 389
response = requests.get(url, params=params) - Network accessline 394
import urllib.request url = "https://string-db.org/api/tsv/network?identifiers=TP53&species=9606" - Network accessline 395
url = "https://string-db.org/api/tsv/network?identifiers=TP53&species=9606" - Network accessline 396
response = urllib.request.urlopen(url) - Network accessline 426
- **Rate limiting**: No strict limit, but avoid rapid-fire requests - **Recommendation**: Wait 1 second between calls - **Large datasets**: Use bulk download from https://string-db.org/cgi/download - Network accessline 427
- **Recommendation**: Wait 1 second between calls - **Large datasets**: Use bulk download from https://string-db.org/cgi/download - **Proteome-scale**: Use web upload feature instead of API - Network accessline 428
- **Large datasets**: Use bulk download from https://string-db.org/cgi/download - Network accessline 433
- **STRING website**: https://string-db.org - **Download page**: https://string-db.org/cgi/download - Network accessline 434
- **Download page**: https://string-db.org/cgi/download - Network accessline 435
- **Help center**: https://string-db.org/help/ - Network accessline 436
- **API documentation**: https://string-db.org/help/api/ - Network accessline 437
- **Publications**: https://string-db.org/cgi/about
skills/string-database/scripts/string_api.py
- Executable scriptline 1
Executable file - Network accessline 7
API Base URL: https://string-db.org/api - Network accessline 8
Documentation: https://string-db.org/help/api/ - Network accessline 21
STRING_BASE_URL = "https://string-db.org/api" - Network accessline 65
try: with urllib.request.urlopen(url, data=data) as response: - Network accessline 66
with urllib.request.urlopen(url, data=data) as response: - Network accessline 118
try: with urllib.request.urlopen(url) as response: - Network accessline 119
with urllib.request.urlopen(url) as response: - Network accessline 167
try: with urllib.request.urlopen(url) as response: - Network accessline 168
with urllib.request.urlopen(url) as response: - Network accessline 211
try: with urllib.request.urlopen(url) as response: - Network accessline 212
with urllib.request.urlopen(url) as response: - Network accessline 250
try: with urllib.request.urlopen(url) as response: - Network accessline 251
with urllib.request.urlopen(url) as response: - Network accessline 292
try: with urllib.request.urlopen(url) as response: - Network accessline 293
with urllib.request.urlopen(url) as response: - Network accessline 330
try: with urllib.request.urlopen(url) as response: - Network accessline 331
with urllib.request.urlopen(url) as response: - Network accessline 349
try: with urllib.request.urlopen(url) as response: - Network accessline 350
with urllib.request.urlopen(url) as response:
skills/struct-predictor/SKILL.md
skills/systematic-debugging/SKILL.md
skills/systematic-debugging/condition-based-waiting-example.ts
- Executable scriptline 1
Executable file
skills/systematic-debugging/find-polluter.sh
- Executable scriptline 1
#!/usr/bin/env bash
skills/tiledbvcf/SKILL.md
- Network accessline 310
**Open Source Documentation:** - TileDB Academy: https://cloud.tiledb.com/academy/ - Network accessline 311
- TileDB Academy: https://cloud.tiledb.com/academy/ - Network accessline 312
- Population Genomics Guide: https://cloud.tiledb.com/academy/structure/life-sciences/population-genomics/ - Network accessline 313
- TileDB-VCF GitHub: https://github.com/TileDB-Inc/TileDB-VCF - Network accessline 317
**For Large-Scale/Production Genomics:** - TileDB-Cloud Platform: https://cloud.tiledb.com - Network accessline 318
- TileDB-Cloud Platform: https://cloud.tiledb.com - Network accessline 319
- TileDB Academy (All Documentation): https://cloud.tiledb.com/academy/ - Network accessline 321
**Getting Started:** - Free account signup: https://cloud.tiledb.com - Network accessline 322
- Free account signup: https://cloud.tiledb.com - Network accessline 335
# Sign up at https://cloud.tiledb.com - Access to secretsline 351
[Credential-related source omitted] - Network accessline 452
**Next Steps:** - Visit https://cloud.tiledb.com to create account - Network accessline 453
- Visit https://cloud.tiledb.com to create account - Network accessline 454
- Review documentation at https://cloud.tiledb.com/academy/
skills/time-stepping/SKILL.md
- Broad permissionsline 1
Read, Bash, Write, Grep, Glob
skills/time-stepping/scripts/checkpoint_planner.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/time-stepping/scripts/output_schedule.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/time-stepping/scripts/timestep_planner.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/SKILL.md
- Broad permissionsline 1
Read Write Edit Bash - Network accessline 135
# CUDA 12.1 (NVIDIA GPU) pip install torch>=2.0.0 --index-url https://download.pytorch.org/whl/cu121 - Network accessline 136
pip install torch>=2.0.0 --index-url https://download.pytorch.org/whl/cu121 - Network accessline 138
# CPU only pip install torch>=2.0.0 --index-url https://download.pytorch.org/whl/cpu - Network accessline 139
pip install torch>=2.0.0 --index-url https://download.pytorch.org/whl/cpu - Network accessline 681
- **Paper**: [A Decoder-Only Foundation Model for Time-Series Forecasting](https://arxiv.org/abs/2310.10688) (ICML 2024) - Network accessline 682
- **Repository**: https://github.com/google-research/timesfm - Network accessline 683
- **Hugging Face**: https://huggingface.co/collections/google/timesfm-release-66e4be5fdb56e960c1e482a6 - Network accessline 684
- **Google Blog**: https://research.google/blog/a-decoder-only-foundation-model-for-time-series-forecasting/ - Network accessline 685
- **BigQuery Integration**: https://cloud.google.com/bigquery/docs/timesfm-model
skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 20
import tempfile, urllib.request tmp = tempfile.mkdtemp(prefix="timesfm_retail_") # urllib.request.urlretrieve("https://...store_sales.csv", f"{tmp}/store_sales.csv") - Network accessline 21
tmp = tempfile.mkdtemp(prefix="timesfm_retail_") # urllib.request.urlretrieve("https://...store_sales.csv", f"{tmp}/store_sales.csv") # df = pd.read_csv(f"{tmp}/store_sales.csv") - Network accessline 22
# urllib.request.urlretrieve("https://...store_sales.csv", f"{tmp}/store_sales.csv")
skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/examples/global-temperature/generate_gif.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/examples/global-temperature/generate_html.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 23
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>TimesFM Interactive Forecast Animation</title> <script src="https://cdn.jsdelivr.net/npm/chart.js"></script> - Network accessline 24
<title>TimesFM Interactive Forecast Animation</title> <script src="https://cdn.jsdelivr.net/npm/chart.js"></script> <style> - Network accessline 25
<script src="https://cdn.jsdelivr.net/npm/chart.js"></script> - Network accessline 218
<footer> <p>TimesFM 1.0 (200M) PyTorch • <a href="https://github.com/google-research/timesfm">Google Research</a></p> - Network accessline 219
<p>TimesFM 1.0 (200M) PyTorch • <a href="https://github.com/google-research/timesfm">Google Research</a></p>
skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png
- Network accessline 1
version https://git-lfs.github.com/spec/v1
skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html
- Network accessline 5
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>TimesFM Interactive Forecast Animation</title> <script src="https://cdn.jsdelivr.net/npm/chart.js"></script> - Network accessline 6
<title>TimesFM Interactive Forecast Animation</title> <script src="https://cdn.jsdelivr.net/npm/chart.js"></script> <style> - Network accessline 7
<script src="https://cdn.jsdelivr.net/npm/chart.js"></script> - Network accessline 200
<footer> <p>TimesFM 1.0 (200M) PyTorch • <a href="https://github.com/google-research/timesfm">Google Research</a></p> - Network accessline 201
<p>TimesFM 1.0 (200M) PyTorch • <a href="https://github.com/google-research/timesfm">Google Research</a></p>
skills/timesfm-forecasting/examples/global-temperature/run_example.sh
- Executable scriptline 1
#!/bin/bash
skills/timesfm-forecasting/examples/global-temperature/run_forecast.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/timesfm-forecasting/scripts/check_system.py
skills/timesfm-forecasting/scripts/forecast_csv.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-adverse-event-detection/test_adverse_event_detection.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-antibody-engineering/.env.template
- Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 4
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
[Credential-related source omitted] - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-antibody-engineering/README.md
- Network accessline 347
### Key Databases - **IMGT**: http://www.imgt.org/ (germline genes, numbering) - Network accessline 348
- **IMGT**: http://www.imgt.org/ (germline genes, numbering) - Network accessline 349
- **SAbDab**: http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ (antibody structures) - Network accessline 350
- **TheraSAbDab**: http://opig.stats.ox.ac.uk/webapps/newsabdab/ (therapeutic antibodies) - Network accessline 351
- **IEDB**: http://www.iedb.org/ (epitope database)
skills/tooluniverse-antibody-engineering/antibody_pipeline.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-antibody-engineering/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-binder-discovery/CHECKLIST.md
- Access to secretsline 23
[Credential-related source omitted]
skills/tooluniverse-binder-discovery/EXAMPLES.md
skills/tooluniverse-binder-discovery/SKILL.md
- Access to secretsline 370
[Credential-related source omitted] - Access to secretsline 747
[Credential-related source omitted] - Access to secretsline 867
[Credential-related source omitted] - Access to secretsline 1414
[Credential-related source omitted] - Access to secretsline 1417
[Credential-related source omitted]
skills/tooluniverse-binder-discovery/TOOLS_REFERENCE.md
- Access to secretsline 212
[Credential-related source omitted] - Access to secretsline 462
[Credential-related source omitted] - Access to secretsline 568
[Credential-related source omitted] - Access to secretsline 690
[Credential-related source omitted] - Access to secretsline 961
[Credential-related source omitted] - Access to secretsline 962
[Credential-related source omitted]
skills/tooluniverse-cancer-variant-interpretation/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-chemical-safety/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-clinical-guidelines/SKILL.md
- Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Network accessline 172
`NCCN_get_patient_guideline(url)` — Get full text of a patient guideline. - Parameter: `url` (string) — the full URL from NCCN_list_patient_guidelines - Example: `NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient - Network accessline 173
- Parameter: `url` (string) — the full URL from NCCN_list_patient_guidelines - Example: `NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient-resources/guidelines-for-patients/guidelines-for-patients-details?patient - Network accessline 174
- Example: `NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient-resources/guidelines-for-patients/guidelines-for-patients-details?patientGuidelineId=61')` - Access to secretsline 337
[Credential-related source omitted] - Network accessline 342
| NCI_search_cancer_resources | `q='...'`, `size=N` (NOT `limit`) | ❌ `query=...` or `limit=N` | | NCCN_list_patient_guidelines | field `cancer_type` (not `title`) | ❌ `.get('title')` | | NCCN_get_patient_guideline | `url='https://...'` (fu - Network accessline 343
| NCCN_list_patient_guidelines | field `cancer_type` (not `title`) | ❌ `.get('title')` | | NCCN_get_patient_guideline | `url='https://...'` (full URL string) | ❌ integer patientGuidelineId | | MAGICapp_list_guidelines | `r.get('data', [])` - Network accessline 344
| NCCN_get_patient_guideline | `url='https://...'` (full URL string) | ❌ integer patientGuidelineId |
skills/tooluniverse-clinical-guidelines/TOOLS_REFERENCE.md
- Access to secretsline 56
[Credential-related source omitted] - Network accessline 200
- **Returns**: dict with patient guideline text - **⚠<U+FE0F> CRITICAL**: Pass full URL, NOT integer ID - **Example**: `NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient-resources/guidelines-for-patients/guidelines-for- - Network accessline 202
- **Example**: `NCCN_get_patient_guideline(url='https://www.nccn.org/patientresources/patient-resources/guidelines-for-patients/guidelines-for-patients-details?patientGuidelineId=61')`
skills/tooluniverse-clinical-trial-design/.env.template
- Access to secretsline 2
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[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
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[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-clinical-trial-design/README.md
- Access to secretsline 295
[Credential-related source omitted] - Access to secretsline 296
[Credential-related source omitted] - Network accessline 406
- **ToolUniverse Docs**: https://zitniklab.hms.harvard.edu/ToolUniverse/ - Network accessline 407
- **Slack Community**: https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ - Network accessline 408
- **GitHub**: https://github.com/mims-harvard/ToolUniverse - Network accessline 409
- **Issues**: https://github.com/mims-harvard/ToolUniverse/issues
skills/tooluniverse-clinical-trial-design/SKILL.md
- Network accessline 1192
- **ToolUniverse Docs**: https://zitniklab.hms.harvard.edu/ToolUniverse/ - Network accessline 1193
- **FDA Guidance Documents**: https://www.fda.gov/regulatory-information/search-fda-guidance-documents - Network accessline 1194
- **ClinicalTrials.gov**: https://clinicaltrials.gov/ - Network accessline 1195
- **Slack Community**: https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ
skills/tooluniverse-clinical-trial-design/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-clinical-trial-design/trial_pipeline.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-clinical-trial-matching/QUICK_START.md
- Network accessline 136
- Trial availability changes frequently; always verify current status at [ClinicalTrials.gov](https://clinicaltrials.gov)
skills/tooluniverse-clinical-trial-matching/SKILL.md
- Network accessline 1141
This report is for informational and research purposes only. Clinical trial eligibility is ultimately determined by the trial investigators based on complete medical records. Patients should discuss all options with their healthcare team. T
skills/tooluniverse-clinical-trial-matching/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-crispr-screen-analysis/README.md
skills/tooluniverse-disease-research/TOOLS_REFERENCE.md
- Access to secretsline 49
[Credential-related source omitted]
skills/tooluniverse-drug-drug-interaction/.env.template
- Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 4
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
[Credential-related source omitted] - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-drug-drug-interaction/ddi_pipeline.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-drug-drug-interaction/ddi_working_example.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-drug-drug-interaction/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-drug-repurposing/README.md
- Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 193
[Credential-related source omitted] - Network accessline 288
- ToolUniverse: https://github.com/mims-harvard/ToolUniverse - Network accessline 294
- **ToolUniverse Docs**: https://zitniklab.hms.harvard.edu/ToolUniverse/ - Network accessline 295
- **Slack Community**: https://join.slack.com/t/tooluniversehq/shared_invite/zt-3dic3eoio-5xxoJch7TLNibNQn5_AREQ - Network accessline 296
- **GitHub Issues**: https://github.com/mims-harvard/ToolUniverse/issues
skills/tooluniverse-drug-repurposing/REFERENCE.md
- Network accessline 651
- **ToolUniverse Documentation**: https://zitniklab.hms.harvard.edu/ToolUniverse/ - Network accessline 652
- **Tool Catalog**: https://zitniklab.hms.harvard.edu/ToolUniverse/tools/ - Network accessline 653
- **DrugBank**: https://go.drugbank.com/ - Network accessline 654
- **OpenTargets**: https://platform.opentargets.org/ - Network accessline 655
- **ChEMBL**: https://www.ebi.ac.uk/chembl/ - Network accessline 656
- **OpenFDA**: https://open.fda.gov/ - Network accessline 657
- **PubMed**: https://pubmed.ncbi.nlm.nih.gov/
skills/tooluniverse-drug-research/EXAMPLES.md
- Network accessline 38
| Identifier | Value | Link | |------------|-------|------| | **PubChem CID** | 4091 | [Link](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | - Network accessline 39
|------------|-------|------| | **PubChem CID** | 4091 | [Link](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | | **ChEMBL ID** | CHEMBL1431 | [Link](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1431/) | - Network accessline 40
| **PubChem CID** | 4091 | [Link](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | - Network accessline 41
| **ChEMBL ID** | CHEMBL1431 | [Link](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1431/) | - Network accessline 42
| **RxNorm CUI** | 6809 | RxNorm | | **PharmGKB ID** | PA450657 | [Link](https://www.pharmgkb.org/chemical/PA450657) | | **DailyMed** | Multiple | FDA approved | - Network accessline 43
| **PharmGKB ID** | PA450657 | [Link](https://www.pharmgkb.org/chemical/PA450657) |
skills/tooluniverse-drug-research/SKILL.md
- Network accessline 457
skills/tooluniverse-drug-research/TOOL_AUDIT.md
- Network accessline 600
| Database | Identifier | Link | |----------|-----------|------| | **PubChem** | CID: 4091 | [View](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | - Network accessline 601
|----------|-----------|------| | **PubChem** | CID: 4091 | [View](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | | **ChEMBL** | CHEMBL1431 | [View](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1431/) | - Network accessline 602
| **PubChem** | CID: 4091 | [View](https://pubchem.ncbi.nlm.nih.gov/compound/4091) | - Network accessline 603
| **ChEMBL** | CHEMBL1431 | [View](https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL1431/) | - Network accessline 604
| **RxNorm** | RXCUI: 6809 | - | | **DailyMed** | Set ID: 030d9bca-... | [View Label](https://dailymed.nlm.nih.gov/dailymed/...) | | **PharmGKB** | PA450440 | [View](https://www.pharmgkb.org/chemical/PA450440) | - Network accessline 605
| **DailyMed** | Set ID: 030d9bca-... | [View Label](https://dailymed.nlm.nih.gov/dailymed/...) | - Network accessline 606
| **PharmGKB** | PA450440 | [View](https://www.pharmgkb.org/chemical/PA450440) | - Network accessline 657
**Pathway Involvement**: - [AMPK signaling pathway (Reactome:R-HSA-9648002)](https://reactome.org/PathwayBrowser/#/R-HSA-9648002) - Network accessline 658
- [AMPK signaling pathway (Reactome:R-HSA-9648002)](https://reactome.org/PathwayBrowser/#/R-HSA-9648002) - Network accessline 659
- [Insulin signaling (KEGG:hsa04910)](https://www.genome.jp/kegg-bin/show_pathway?hsa04910)
skills/tooluniverse-drug-target-validation/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-epigenomics/.env.template
- Access to secretsline 2
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[Credential-related source omitted]
skills/tooluniverse-epigenomics/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-expression-data-retrieval/SKILL.md
skills/tooluniverse-gene-enrichment/.env.template
- Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 4
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
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[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-gene-enrichment/SKILL.md
- Network accessline 399
gseapy documentation: https://gseapy.readthedocs.io/ - Network accessline 400
PANTHER API: http://pantherdb.org/services/oai/pantherdb/ - Network accessline 401
STRING API: https://string-db.org/cgi/help?sessionId=&subpage=api - Network accessline 402
Reactome Analysis: https://reactome.org/AnalysisService/
skills/tooluniverse-gene-enrichment/SKILL_OLD.md
- Network accessline 1197
gseapy documentation: https://gseapy.readthedocs.io/ - Network accessline 1198
PANTHER API: http://pantherdb.org/services/oai/pantherdb/ - Network accessline 1199
STRING API: https://string-db.org/cgi/help?sessionId=&subpage=api - Network accessline 1200
Reactome Analysis: https://reactome.org/AnalysisService/
skills/tooluniverse-gene-enrichment/references/troubleshooting.md
- Network accessline 603
1. **Check gseapy documentation**: https://gseapy.readthedocs.io/
skills/tooluniverse-gene-enrichment/scripts/format_enrichment_output.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-gene-enrichment/test_gene_enrichment.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-gwas-drug-discovery/QUICK_START.md
- Network accessline 30
# Or from source git clone https://github.com/example/tooluniverse.git - Network accessline 31
git clone https://github.com/example/tooluniverse.git - Network accessline 121
// Initialize MCP client const client = new MCPClient({ serverUrl: "http://localhost:3000/tooluniverse" - Network accessline 122
const client = new MCPClient({ serverUrl: "http://localhost:3000/tooluniverse" }); - Network accessline 123
serverUrl: "http://localhost:3000/tooluniverse" - Network accessline 1021
- [GWAS Catalog Documentation](https://www.ebi.ac.uk/gwas/docs) - Network accessline 1022
- [Open Targets Platform](https://platform.opentargets.org/) - Network accessline 1023
- [ChEMBL Database](https://www.ebi.ac.uk/chembl/) - Network accessline 1024
- [ToolUniverse Documentation](https://docs.tooluniverse.org)
skills/tooluniverse-gwas-drug-discovery/README.md
- Network accessline 53
# Clone repository git clone https://github.com/example/tooluniverse.git - Network accessline 54
git clone https://github.com/example/tooluniverse.git - Network accessline 237
year = {2026}, version = {1.0.0}, url = {https://github.com/example/tooluniverse/skills/tooluniverse-gwas-drug-discovery} - Network accessline 238
version = {1.0.0}, url = {https://github.com/example/tooluniverse/skills/tooluniverse-gwas-drug-discovery} } - Network accessline 239
url = {https://github.com/example/tooluniverse/skills/tooluniverse-gwas-drug-discovery} - Network accessline 290
- ToolUniverse Team - Contributors: [GitHub Contributors](https://github.com/example/tooluniverse/contributors) - Network accessline 291
- Contributors: [GitHub Contributors](https://github.com/example/tooluniverse/contributors)
skills/tooluniverse-gwas-drug-discovery/SKILL.md
- Network accessline 490
**GWAS**: - [GWAS Catalog](https://www.ebi.ac.uk/gwas/) - Curated GWAS results - Network accessline 491
- [GWAS Catalog](https://www.ebi.ac.uk/gwas/) - Curated GWAS results - Network accessline 492
- [Open Targets Genetics](https://genetics.opentargets.org/) - Fine-mapping, L2G - Network accessline 493
- [PhenoScanner](http://www.phenoscanner.medschl.cam.ac.uk/) - Cross-trait lookups - Network accessline 495
**Drugs**: - [ChEMBL](https://www.ebi.ac.uk/chembl/) - Bioactivity database - Network accessline 496
- [ChEMBL](https://www.ebi.ac.uk/chembl/) - Bioactivity database - Network accessline 497
- [DrugBank](https://go.drugbank.com/) - Comprehensive drug information - Network accessline 498
- [DGIdb](https://www.dgidb.org/) - Drug-gene interactions - Network accessline 500
**Targets**: - [Open Targets Platform](https://platform.opentargets.org/) - Target-disease associations - Network accessline 501
- [Open Targets Platform](https://platform.opentargets.org/) - Target-disease associations - Network accessline 502
- [PHAROS](https://pharos.nih.gov/) - Target development level (Tdark to Tclin) - Network accessline 504
**Clinical**: - [ClinicalTrials.gov](https://clinicaltrials.gov/) - Clinical trial registry - Network accessline 505
- [ClinicalTrials.gov](https://clinicaltrials.gov/) - Clinical trial registry - Network accessline 506
- [FDA Labels](https://labels.fda.gov/) - Drug labeling information
skills/tooluniverse-gwas-drug-discovery/python_implementation.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-drug-discovery/test_gwas_drug_tools.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-drug-discovery/test_gwas_drug_tools_v2.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-finemapping/.env.template
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[Credential-related source omitted]
skills/tooluniverse-gwas-finemapping/QUICK_START.md
- Network accessline 265
Use disease ontology browsers: - **EFO**: [EMBL-EBI Ontology Lookup](https://www.ebi.ac.uk/ols/ontologies/efo) - Network accessline 266
- **EFO**: [EMBL-EBI Ontology Lookup](https://www.ebi.ac.uk/ols/ontologies/efo) - Network accessline 267
- **MONDO**: [Monarch Disease Ontology](https://monarchinitiative.org/disease) - Network accessline 315
- Read the full [SKILL.md](./SKILL.md) for detailed concepts - Review [test_skill_comprehensive.py](./test_skill_comprehensive.py) for more examples - Explore the [GWAS Catalog documentation](https://www.ebi.ac.uk/gwas/docs) - Network accessline 316
- Review [test_skill_comprehensive.py](./test_skill_comprehensive.py) for more examples - Explore the [GWAS Catalog documentation](https://www.ebi.ac.uk/gwas/docs) - Check [Open Targets Genetics](https://genetics.opentargets.org/) for web i - Network accessline 317
- Explore the [GWAS Catalog documentation](https://www.ebi.ac.uk/gwas/docs) - Network accessline 318
- Check [Open Targets Genetics](https://genetics.opentargets.org/) for web interface - Network accessline 322
- **Open Targets Genetics**: https://genetics.opentargets.org/ - Network accessline 323
- **GWAS Catalog**: https://www.ebi.ac.uk/gwas/ - Network accessline 324
- **SuSiE paper**: https://doi.org/10.1111/rssb.12388 - Network accessline 325
- **L2G paper**: https://doi.org/10.1038/s41588-021-00945-5
skills/tooluniverse-gwas-finemapping/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-gwas-finemapping/test_skill_comprehensive.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-gwas-snp-interpretation/.env.template
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[Credential-related source omitted]
skills/tooluniverse-gwas-snp-interpretation/README.md
- Network accessline 5
[]() - Network accessline 6
[]() - Network accessline 7
[]() - Network accessline 8
[]()
skills/tooluniverse-gwas-snp-interpretation/SKILL.md
skills/tooluniverse-gwas-snp-interpretation/python_implementation.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-snp-interpretation/test_gwas_snp_tools.py
- Executable scriptline 1
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skills/tooluniverse-gwas-snp-interpretation/test_gwas_snp_tools_simple.py
- Executable scriptline 1
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skills/tooluniverse-gwas-snp-interpretation/test_skill_comprehensive.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-study-explorer/.env.template
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[Credential-related source omitted]
skills/tooluniverse-gwas-study-explorer/python_implementation.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-study-explorer/test_skill_comprehensive.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-trait-to-gene/.env.template
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skills/tooluniverse-gwas-trait-to-gene/QUICK_START.md
- Network accessline 504
1. **Explore SKILL.md** for complete workflow documentation 2. **Check test_gwas_tools.py** for more code examples 3. **Read GWAS Catalog docs**: https://www.ebi.ac.uk/gwas/docs - Network accessline 505
2. **Check test_gwas_tools.py** for more code examples 3. **Read GWAS Catalog docs**: https://www.ebi.ac.uk/gwas/docs 4. **Read Open Targets docs**: https://genetics-docs.opentargets.org/ - Network accessline 506
3. **Read GWAS Catalog docs**: https://www.ebi.ac.uk/gwas/docs - Network accessline 507
4. **Read Open Targets docs**: https://genetics-docs.opentargets.org/ - Network accessline 528
Find more IDs at: https://www.ebi.ac.uk/ols/ontologies/mondo
skills/tooluniverse-gwas-trait-to-gene/README.md
- Network accessline 5
[]() - Network accessline 6
[]() - Network accessline 7
[]() - Network accessline 186
- **GWAS Catalog** - EBI/NHGRI curated GWAS catalog - URL: https://www.ebi.ac.uk/gwas/ - Network accessline 187
- URL: https://www.ebi.ac.uk/gwas/ - Network accessline 190
- **Open Targets Genetics** - Fine-mapped GWAS with L2G predictions - URL: https://genetics.opentargets.org/ - Network accessline 191
- URL: https://genetics.opentargets.org/ - Network accessline 231
Find more at: https://www.ebi.ac.uk/ols/ontologies/mondo - Network accessline 235
- **Documentation**: Start with [QUICK_START.md](QUICK_START.md) - **Issues**: Check [SKILL_TESTING_REPORT.md](SKILL_TESTING_REPORT.md) - **GWAS data**: https://www.ebi.ac.uk/gwas/docs - Network accessline 236
- **Issues**: Check [SKILL_TESTING_REPORT.md](SKILL_TESTING_REPORT.md) - **GWAS data**: https://www.ebi.ac.uk/gwas/docs - **Open Targets**: https://genetics-docs.opentargets.org/ - Network accessline 237
- **GWAS data**: https://www.ebi.ac.uk/gwas/docs - Network accessline 238
- **Open Targets**: https://genetics-docs.opentargets.org/
skills/tooluniverse-gwas-trait-to-gene/SKILL.md
- Network accessline 206
**GWAS Catalog** - Curator: EBI and NHGRI - URL: https://www.ebi.ac.uk/gwas/ - Network accessline 207
- Curator: EBI and NHGRI - URL: https://www.ebi.ac.uk/gwas/ - Coverage: 100,000+ publications, 500,000+ associations - Network accessline 208
- URL: https://www.ebi.ac.uk/gwas/ - Network accessline 212
**Open Targets Genetics** - Curator: Open Targets consortium - URL: https://genetics.opentargets.org/ - Network accessline 213
- Curator: Open Targets consortium - URL: https://genetics.opentargets.org/ - Coverage: Fine-mapped GWAS, L2G predictions, QTL colocalization - Network accessline 214
- URL: https://genetics.opentargets.org/
skills/tooluniverse-gwas-trait-to-gene/python_implementation.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-trait-to-gene/test_gwas_tools.py
- Executable scriptline 1
Executable file
skills/tooluniverse-gwas-trait-to-gene/test_skill_comprehensive.py
- Executable scriptline 1
Executable file
skills/tooluniverse-image-analysis/scripts/batch_process.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-image-analysis/scripts/measure_fluorescence.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-image-analysis/scripts/segment_cells.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-image-analysis/test_image_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 30
DATA_DIR = "/tmp/bixbench_image_data" BASE_URL = "https://huggingface.co/datasets/futurehouse/BixBench/resolve/main/" - Network accessline 31
BASE_URL = "https://huggingface.co/datasets/futurehouse/BixBench/resolve/main/" - Network accessline 48
zip_name = f"CapsuleFolder-{uuid}.zip" url = BASE_URL + zip_name r = requests.get(url) - Network accessline 49
url = BASE_URL + zip_name r = requests.get(url) r.raise_for_status() - Network accessline 50
r = requests.get(url)
skills/tooluniverse-immune-repertoire-analysis/SKILL.md
skills/tooluniverse-immunotherapy-response-prediction/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-infectious-disease/CHECKLIST.md
- Access to secretsline 33
[Credential-related source omitted]
skills/tooluniverse-infectious-disease/TOOLS_REFERENCE.md
skills/tooluniverse-literature-deep-research/EXAMPLES.md
- Network accessline 439
"citation_count": 612, "oa_status": "gold", "oa_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704954/" - Network accessline 440
"oa_status": "gold", "oa_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704954/" } - Network accessline 441
"oa_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5704954/"
skills/tooluniverse-literature-deep-research/SKILL.md
- Network accessline 449
# For paywalled PDFs accessible via institution webpage_text = get_webpage_text_from_url( url="https://doi.org/10.1016/...", - Network accessline 450
webpage_text = get_webpage_text_from_url( url="https://doi.org/10.1016/...", # Requires institutional proxy or VPN - Network accessline 451
url="https://doi.org/10.1016/...", - Network accessline 903
"themes": ["lysosomal_acidification", "autophagy"], "oa_status": "gold", "oa_url": "https://...", - Network accessline 904
"oa_status": "gold", "oa_url": "https://...", "citation_count": 45, - Network accessline 905
"oa_url": "https://...",
skills/tooluniverse-metabolomics-analysis/SKILL.md
- Network accessline 756
**Methods**: - MetaboAnalyst: https://doi.org/10.1093/nar/gkab382 - Network accessline 757
- MetaboAnalyst: https://doi.org/10.1093/nar/gkab382 - Network accessline 758
- XCMS: https://doi.org/10.1021/ac051437y - Network accessline 759
- MSEA: https://doi.org/10.1186/1471-2105-11-395 - Network accessline 761
**Databases**: - HMDB: https://hmdb.ca - Network accessline 762
- HMDB: https://hmdb.ca - Network accessline 763
- KEGG Compound: https://www.genome.jp/kegg/compound/ - Network accessline 764
- Reactome: https://reactome.org
skills/tooluniverse-metabolomics/.env.template
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skills/tooluniverse-metabolomics/COMPARISON_ORIGINAL_VS_FIXED.md
- Network accessline 23
**Formula**: C6H12O6 **Molecular Weight**: 180.16 **HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 24
**Molecular Weight**: 180.16 **HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 25
**HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 33
**Modified Time**: 2025-09-02T13:34:14.536288 **First Public Date**: 2012-02-14T00:00:00 **HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 - Network accessline 34
**First Public Date**: 2012-02-14T00:00:00 **HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 **FTP URL**: ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 - Network accessline 35
**HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1
skills/tooluniverse-metabolomics/QUICK_START.md
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[Credential-related source omitted] - Network accessline 501
- **ToolUniverse Documentation**: https://github.com/mims-harvard/ToolUniverse - Network accessline 502
- **HMDB Database**: https://hmdb.ca - Network accessline 503
- **MetaboLights**: https://www.ebi.ac.uk/metabolights/ - Network accessline 504
- **Metabolomics Workbench**: https://www.metabolomicsworkbench.org - Network accessline 505
- **PubChem**: https://pubchem.ncbi.nlm.nih.gov
skills/tooluniverse-metabolomics/diabetes_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-metabolomics/diabetes_metabolomics_report_FIXED.md
- Network accessline 15
**Formula**: C6H12O6 **Molecular Weight**: 180.16 **HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 16
**Molecular Weight**: 180.16 **HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 17
**HMDB Search**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 23
**Formula**: C3H5O3- **Molecular Weight**: 89.07 **HMDB Search**: https://hmdb.ca/unearth/q?query=lactate&searcher=metabolites - Network accessline 24
**Molecular Weight**: 89.07 **HMDB Search**: https://hmdb.ca/unearth/q?query=lactate&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 25
**HMDB Search**: https://hmdb.ca/unearth/q?query=lactate&searcher=metabolites - Network accessline 31
**Formula**: C3H3O3- **Molecular Weight**: 87.05 **HMDB Search**: https://hmdb.ca/unearth/q?query=pyruvate&searcher=metabolites - Network accessline 32
**Molecular Weight**: 87.05 **HMDB Search**: https://hmdb.ca/unearth/q?query=pyruvate&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 33
**HMDB Search**: https://hmdb.ca/unearth/q?query=pyruvate&searcher=metabolites - Network accessline 39
**Formula**: C6H5O7-3 **Molecular Weight**: 189.10 **HMDB Search**: https://hmdb.ca/unearth/q?query=citrate&searcher=metabolites - Network accessline 40
**Molecular Weight**: 189.10 **HMDB Search**: https://hmdb.ca/unearth/q?query=citrate&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 41
**HMDB Search**: https://hmdb.ca/unearth/q?query=citrate&searcher=metabolites - Network accessline 47
**Formula**: C4H4O4-2 **Molecular Weight**: 116.07 **HMDB Search**: https://hmdb.ca/unearth/q?query=succinate&searcher=metabolites - Network accessline 48
**Molecular Weight**: 116.07 **HMDB Search**: https://hmdb.ca/unearth/q?query=succinate&searcher=metabolites *Note: Data retrieved from PubChem proxy* - Network accessline 49
**HMDB Search**: https://hmdb.ca/unearth/q?query=succinate&searcher=metabolites - Network accessline 57
**Modified Time**: 2025-09-02T13:34:14.536288 **First Public Date**: 2012-02-14T00:00:00 **HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 - Network accessline 58
**First Public Date**: 2012-02-14T00:00:00 **HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 **FTP URL**: ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 - Network accessline 59
**HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1
skills/tooluniverse-metabolomics/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-metabolomics/python_implementation_fixed.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-metabolomics/test1_metabolites.md
- Network accessline 13
**Formula**: C6H12O6 **Molecular Weight**: 180.16 **HMDB Search URL**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 15
**HMDB Search URL**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 20
**Formula**: C3H5O3- **Molecular Weight**: 89.07 **HMDB Search URL**: https://hmdb.ca/unearth/q?query=lactate&searcher=metabolites - Network accessline 22
**HMDB Search URL**: https://hmdb.ca/unearth/q?query=lactate&searcher=metabolites
skills/tooluniverse-metabolomics/test2_study.md
skills/tooluniverse-metabolomics/test4_comprehensive.md
- Network accessline 15
**Formula**: C6H12O6 **Molecular Weight**: 180.16 **HMDB Search URL**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 17
**HMDB Search URL**: https://hmdb.ca/unearth/q?query=glucose&searcher=metabolites - Network accessline 22
**Formula**: C3H3O3- **Molecular Weight**: 87.05 **HMDB Search URL**: https://hmdb.ca/unearth/q?query=pyruvate&searcher=metabolites - Network accessline 24
**HMDB Search URL**: https://hmdb.ca/unearth/q?query=pyruvate&searcher=metabolites - Network accessline 30
**Release Date**: N/A **Modified Time**: 2025-09-02T13:34:14.536288 **HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1 - Network accessline 32
**HTTP URL**: http://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS1
skills/tooluniverse-metabolomics/test_detailed.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-metabolomics/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-metabolomics/test_tools_debug.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-multi-omics-integration/SKILL.md
- Network accessline 697
**Methods**: - MOFA+: https://doi.org/10.1186/s13059-020-02015-1 - Network accessline 698
- MOFA+: https://doi.org/10.1186/s13059-020-02015-1 - Network accessline 699
- Similarity Network Fusion: https://doi.org/10.1038/nmeth.2810 - Network accessline 700
- Multi-omics review: https://doi.org/10.1038/s41576-019-0093-7
skills/tooluniverse-multiomic-disease-characterization/.env.template
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skills/tooluniverse-multiomic-disease-characterization/test_multiomic_disease.py
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#!/usr/bin/env python3
skills/tooluniverse-network-pharmacology/test_network_pharmacology.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-phylogenetics/SKILL.md
- Network accessline 453
For issues with: - **PhyKIT functions**: Check PhyKIT documentation at https://jlsteenwyk.com/PhyKIT/ - Network accessline 454
- **PhyKIT functions**: Check PhyKIT documentation at https://jlsteenwyk.com/PhyKIT/ - Network accessline 455
- **Biopython tree/alignment parsing**: See https://biopython.org/wiki/Phylo - Network accessline 456
- **DendroPy operations**: See https://dendropy.org/
skills/tooluniverse-phylogenetics/references/troubleshooting.md
- Network accessline 570
- `tree_building.md` - Tree construction methods - `parsimony_analysis.md` - Statistical workflows - PhyKIT documentation: https://jlsteenwyk.com/PhyKIT/ - Network accessline 571
- `parsimony_analysis.md` - Statistical workflows - PhyKIT documentation: https://jlsteenwyk.com/PhyKIT/ - Biopython Phylo tutorial: https://biopython.org/wiki/Phylo - Network accessline 572
- PhyKIT documentation: https://jlsteenwyk.com/PhyKIT/ - Network accessline 573
- Biopython Phylo tutorial: https://biopython.org/wiki/Phylo
skills/tooluniverse-phylogenetics/scripts/format_alignment.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-phylogenetics/scripts/tree_statistics.py
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#!/usr/bin/env python3
skills/tooluniverse-phylogenetics/test_phylogenetics.py
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#!/usr/bin/env python3
skills/tooluniverse-polygenic-risk-score/.env.template
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skills/tooluniverse-polygenic-risk-score/QUICK_START.md
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1. **Read SKILL.md** for comprehensive methodology and best practices 2. **Run test_skill_comprehensive.py** to see all features in action 3. **Explore PGS Catalog** (https://www.pgscatalog.org/) for validated PRS models - Network accessline 467
2. **Run test_skill_comprehensive.py** to see all features in action 3. **Explore PGS Catalog** (https://www.pgscatalog.org/) for validated PRS models 4. **Consider LD clumping** for production PRS (use PLINK or PRSice) - Network accessline 468
3. **Explore PGS Catalog** (https://www.pgscatalog.org/) for validated PRS models
skills/tooluniverse-polygenic-risk-score/README.md
- Network accessline 274
### Recommendations - **For clinical use**: Consult genetic counselors and use validated PRS from [PGS Catalog](https://www.pgscatalog.org/) - Network accessline 275
- **For clinical use**: Consult genetic counselors and use validated PRS from [PGS Catalog](https://www.pgscatalog.org/) - Network accessline 293
- **PGS Catalog**: https://www.pgscatalog.org/ - Published PRS models - Network accessline 294
- **GWAS Catalog**: https://www.ebi.ac.uk/gwas/ - Association database - Network accessline 295
- **PRSice**: https://www.prsice.info/ - PRS calculation software - Network accessline 296
- **LD Hub**: http://ldsc.broadinstitute.org/ - Genetic correlations
skills/tooluniverse-polygenic-risk-score/SKILL.md
- Network accessline 212
1. **Lambert et al. (2021)**: "The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation" - PGS Catalog: https://www.pgscatalog.org/ - Network accessline 213
- PGS Catalog: https://www.pgscatalog.org/ - Network accessline 234
- **PGS Catalog**: https://www.pgscatalog.org/ - Published PRS models - Network accessline 235
- **LD Hub**: http://ldsc.broadinstitute.org/ - Genetic correlations - Network accessline 236
- **PRSice**: https://www.prsice.info/ - PRS calculation software - Network accessline 237
- **GWAS Catalog**: https://www.ebi.ac.uk/gwas/ - Association database
skills/tooluniverse-polygenic-risk-score/check_data.py
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Executable file
skills/tooluniverse-polygenic-risk-score/python_implementation.py
skills/tooluniverse-polygenic-risk-score/test_prs_tools.py
- Executable scriptline 1
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skills/tooluniverse-polygenic-risk-score/test_skill_comprehensive.py
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Executable file
skills/tooluniverse-precision-medicine-stratification/.env.template
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skills/tooluniverse-precision-medicine-stratification/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-protein-interactions/.env.template
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skills/tooluniverse-protein-interactions/DOMAIN_ANALYSIS.md
skills/tooluniverse-protein-interactions/PHASE2_COMPLETE.md
skills/tooluniverse-protein-interactions/PHASE2_DISCOVERIES.md
skills/tooluniverse-protein-interactions/QUICK_START.md
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skills/tooluniverse-protein-interactions/SKILL.md
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1. Register for free API key: https://webservice.thebiogrid.org/ - Network accessline 338
1. Register for free API key: https://webservice.thebiogrid.org/ - Network accessline 338
1. Register for free API key: https://webservice.thebiogrid.org/ - Access to secretsline 341
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[Credential-related source omitted] - Network accessline 413
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- Check API key is valid at https://webservice.thebiogrid.org/ - Network accessline 414
- Check API key is valid at https://webservice.thebiogrid.org/ - Network accessline 414
- Check API key is valid at https://webservice.thebiogrid.org/ - Network accessline 432
- **STRING**: https://string-db.org/ (14M+ proteins, 5,000+ organisms) - Network accessline 432
- **STRING**: https://string-db.org/ (14M+ proteins, 5,000+ organisms) - Network accessline 432
- **STRING**: https://string-db.org/ (14M+ proteins, 5,000+ organisms) - Network accessline 433
- **BioGRID**: https://thebiogrid.org/ (2.3M+ interactions, experimentally validated) - Network accessline 433
- **BioGRID**: https://thebiogrid.org/ (2.3M+ interactions, experimentally validated) - Network accessline 433
- **BioGRID**: https://thebiogrid.org/ (2.3M+ interactions, experimentally validated) - Network accessline 434
- **SASBDB**: https://www.sasbdb.org/ (2,000+ SAXS/SANS entries) - Network accessline 434
- **SASBDB**: https://www.sasbdb.org/ (2,000+ SAXS/SANS entries) - Network accessline 434
- **SASBDB**: https://www.sasbdb.org/ (2,000+ SAXS/SANS entries) - Network accessline 435
- **ToolUniverse**: https://github.com/mims-harvard/ToolUniverse - Network accessline 435
- **ToolUniverse**: https://github.com/mims-harvard/ToolUniverse - Network accessline 435
- **ToolUniverse**: https://github.com/mims-harvard/ToolUniverse
skills/tooluniverse-protein-interactions/TOOL_DESCRIPTION_OPTIMIZATION.md
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"Query protein and genetic interactions from the BioGRID database. **Prerequisites**: Requires BIOGRID_API_KEY environment variable (request at https://webservice.thebiogrid.org/). Returns experimentally - Network accessline 34
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(request at https://webservice.thebiogrid.org/). Returns experimentally - Network accessline 94
- `species`: "NCBI taxonomy ID specifying organism. Common values: 9606 (Homo sapiens/human), 10090 (Mus musculus/mouse), 10116 (Rattus norvegicus/rat), 7227 (Drosophila melanogaster). Default 9606 (human). Find taxonomy IDs at https://www. - Network accessline 228
for Interaction Datasets). Returns curated interactions from published studies with evidence methods, PubMed citations, and throughput information. **Prerequisites**: Requires BIOGRID_API_KEY environment variable (free academic API key at h - Access to secretsline 229
[Credential-related source omitted] - Network accessline 230
variable (free academic API key at https://webservice.thebiogrid.org/). - Network accessline 267
ubiquitination, acetylation, methylation, and other covalent protein modifications with site positions, modifying enzymes, and literature evidence. **Prerequisites**: Requires BIOGRID_API_KEY environment variable (request at https://webserv - Access to secretsline 268
[Credential-related source omitted] - Network accessline 269
variable (request at https://webservice.thebiogrid.org/). - Access to secretsline 296
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**Parameter Improvements**: - `pubmed_ids`: "List of PubMed IDs (PMIDs) to query. **Note: plural parameter** - pass as list. Example: ['17200106'] (single paper) or ['17200106', '12345678'] (multiple papers). Returns all protein interaction - Network accessline 337
- `pubmed_ids`: "List of PubMed IDs (PMIDs) to query. **Note: plural parameter** - pass as list. Example: ['17200106'] (single paper) or ['17200106', '12345678'] (multiple papers). Returns all protein interactions curated from these publica - Network accessline 389
**Parameter Improvements**: - `sasbdb_id`: "SASBDB entry identifier. Format: 'SASDXXX' where XXX is alphanumeric (e.g., 'SASDAB7', 'SASD1P8'). Find IDs using SASBDB_search_entries or at https://www.sasbdb.org/. Example: 'SASDAB7' (p53 core - Network accessline 390
- `sasbdb_id`: "SASBDB entry identifier. Format: 'SASDXXX' where XXX is alphanumeric (e.g., 'SASDAB7', 'SASD1P8'). Find IDs using SASBDB_search_entries or at https://www.sasbdb.org/. Example: 'SASDAB7' (p53 core domain structure)." - Access to secretsline 439
[Credential-related source omitted]
skills/tooluniverse-protein-interactions/python_implementation.py
- Executable scriptline 1
Executable file
skills/tooluniverse-protein-interactions/test_protein_tools.py
skills/tooluniverse-protein-interactions/test_skill_comprehensive.py
skills/tooluniverse-protein-structure-retrieval/SKILL.md
- Network accessline 292
### Database Links - RCSB PDB: https://www.rcsb.org/structure/[pdb_id] - Network accessline 293
- RCSB PDB: https://www.rcsb.org/structure/[pdb_id] - Network accessline 294
- PDBe: https://www.ebi.ac.uk/pdbe/entry/pdb/[pdb_id] - Network accessline 295
- AlphaFold: https://alphafold.ebi.ac.uk/entry/[uniprot_id]
skills/tooluniverse-protein-therapeutic-design/CHECKLIST.md
skills/tooluniverse-protein-therapeutic-design/TOOLS_REFERENCE.md
skills/tooluniverse-proteomics-analysis/SKILL.md
- Network accessline 835
**Methods**: - MaxQuant: https://doi.org/10.1038/nbt.1511 - Network accessline 836
- MaxQuant: https://doi.org/10.1038/nbt.1511 - Network accessline 837
- Limma for proteomics: https://doi.org/10.1093/nar/gkv007 - Network accessline 838
- DEP workflow: https://doi.org/10.1038/nprot.2018.107 - Network accessline 840
**Databases**: - STRING: https://string-db.org - Network accessline 841
- STRING: https://string-db.org - Network accessline 842
- PhosphoSitePlus: https://www.phosphosite.org - Network accessline 843
- CORUM: https://mips.helmholtz-muenchen.de/corum
skills/tooluniverse-rare-disease-diagnosis/CHECKLIST.md
- Access to secretsline 51
[Credential-related source omitted]
skills/tooluniverse-rare-disease-diagnosis/TOOLS_REFERENCE.md
skills/tooluniverse-rnaseq-deseq2/.env.template
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skills/tooluniverse-rnaseq-deseq2/scripts/convert_rds_to_csv.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 177
print(" macOS: brew install r") print(" Ubuntu: sudo apt-get install r-base") print(" Or visit: https://cran.r-project.org/") - Dangerous shell operationline 178
print(" Ubuntu: sudo apt-get install r-base") - Network accessline 178
print(" Ubuntu: sudo apt-get install r-base") print(" Or visit: https://cran.r-project.org/") sys.exit(1) - Network accessline 179
print(" Or visit: https://cran.r-project.org/")
skills/tooluniverse-rnaseq-deseq2/scripts/format_deseq2_output.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-rnaseq-deseq2/scripts/load_count_matrix.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-rnaseq-deseq2/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-single-cell/.env.template
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skills/tooluniverse-single-cell/scripts/find_markers.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-single-cell/scripts/normalize_data.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-single-cell/scripts/qc_metrics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-single-cell/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-spatial-omics-analysis/test_spatial_omics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-spatial-transcriptomics/SKILL.md
- Network accessline 780
**Methods**: - Squidpy: https://doi.org/10.1038/s41592-021-01358-2 - Network accessline 781
- Squidpy: https://doi.org/10.1038/s41592-021-01358-2 - Network accessline 782
- Cell2location: https://doi.org/10.1038/s41587-021-01139-4 - Network accessline 783
- SpatialDE: https://doi.org/10.1038/nmeth.4636 - Network accessline 785
**Platforms**: - 10x Visium: https://www.10xgenomics.com/products/spatial-gene-expression - Network accessline 786
- 10x Visium: https://www.10xgenomics.com/products/spatial-gene-expression - Network accessline 787
- MERFISH: https://doi.org/10.1126/science.aaa6090 - Network accessline 788
- Slide-seq: https://doi.org/10.1126/science.aaw1219
skills/tooluniverse-statistical-modeling/SKILL.md
skills/tooluniverse-statistical-modeling/scripts/format_statistical_output.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-statistical-modeling/scripts/model_diagnostics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-statistical-modeling/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-structural-variant-analysis/README.md
- Network accessline 310
1. **ACMG SV Guidelines**: Riggs et al., Genet Med 2020 (PMID: 31690835) - "Technical standards for the interpretation and reporting of constitutional copy-number variants" 2. **ClinGen Dosage Sensitivity**: https://www.ncbi.nlm.nih.gov/ - Network accessline 311
- "Technical standards for the interpretation and reporting of constitutional copy-number variants" 2. **ClinGen Dosage Sensitivity**: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ 3. **DECIPHER**: https://www.deciphergenomics.org/ - Network accessline 312
2. **ClinGen Dosage Sensitivity**: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ - Network accessline 313
3. **DECIPHER**: https://www.deciphergenomics.org/ - Network accessline 314
4. **gnomAD SVs**: https://gnomad.broadinstitute.org/ - Network accessline 316
### Educational Materials - **ClinGen Dosage Sensitivity Tutorial**: https://www.clinicalgenome.org/working-groups/dosage-sensitivity-curation/ - Network accessline 317
- **ClinGen Dosage Sensitivity Tutorial**: https://www.clinicalgenome.org/working-groups/dosage-sensitivity-curation/ - Network accessline 319
- **DECIPHER Training**: https://www.deciphergenomics.org/about/training - Network accessline 354
- ToolUniverse: [GitHub repository] - ACMG SV Guidelines: Riggs et al., Genet Med 2020 (PMID: 31690835) - ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ - Network accessline 355
- ACMG SV Guidelines: Riggs et al., Genet Med 2020 (PMID: 31690835) - ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ - DECIPHER: Firth et al., Am J Hum Genet 2009 (PMID: 19344873) - Network accessline 356
- ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/
skills/tooluniverse-structural-variant-analysis/SKILL.md
- Network accessline 1353
- `README.md` - Quick start guide - `tooluniverse-variant-interpretation` - For SNVs and small indels - ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ - Network accessline 1354
- `tooluniverse-variant-interpretation` - For SNVs and small indels - ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/ - ACMG SV Guidelines: Riggs et al., Genet Med 2020 (PMID: 31690835) - Network accessline 1355
- ClinGen Dosage Sensitivity Map: https://www.ncbi.nlm.nih.gov/projects/dbvar/clingen/
skills/tooluniverse-systems-biology/.env.template
- Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 4
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
[Credential-related source omitted] - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-systems-biology/QUICK_START.md
- Network accessline 440
- **Reactome**: https://reactome.org - Network accessline 441
- **KEGG**: https://www.genome.jp/kegg/ - Network accessline 442
- **WikiPathways**: https://www.wikipathways.org - Network accessline 443
- **Pathway Commons**: https://www.pathwaycommons.org - Network accessline 444
- **BioModels**: https://www.ebi.ac.uk/biomodels/ - Network accessline 445
- **Enrichr**: https://maayanlab.cloud/Enrichr/
skills/tooluniverse-systems-biology/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-systems-biology/test_skill.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-target-research/REFERENCE.md
skills/tooluniverse-target-research/SKILL.md
- Access to secretsline 668
[Credential-related source omitted]
skills/tooluniverse-variant-analysis/.env.template
- Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 4
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 16
[Credential-related source omitted] - Access to secretsline 18
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted]
skills/tooluniverse-variant-analysis/python_implementation.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-variant-analysis/scripts/annotate_variants.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-variant-analysis/scripts/filter_variants.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-variant-analysis/scripts/parse_vcf.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-variant-analysis/test_variant_analysis.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/tooluniverse-variant-interpretation/CHECKLIST.md
- Access to secretsline 257
[Credential-related source omitted]
skills/tooluniverse-variant-interpretation/TOOLS_REFERENCE.md
skills/torch-geometric/SKILL.md
- Network accessline 36
uv pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html - Network accessline 670
- **Documentation**: https://pytorch-geometric.readthedocs.io/ - Network accessline 671
- **GitHub**: https://github.com/pyg-team/pytorch_geometric - Network accessline 672
- **Tutorials**: https://pytorch-geometric.readthedocs.io/en/latest/get_started/introduction.html - Network accessline 673
- **Examples**: https://github.com/pyg-team/pytorch_geometric/tree/master/examples
skills/torch-geometric/scripts/benchmark_model.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torch-geometric/scripts/create_gnn_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torch-geometric/scripts/visualize_graph.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torch_geometric/SKILL.md
- Network accessline 33
uv pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-${TORCH}+${CUDA}.html - Network accessline 667
- **Documentation**: https://pytorch-geometric.readthedocs.io/ - Network accessline 668
- **GitHub**: https://github.com/pyg-team/pytorch_geometric - Network accessline 669
- **Tutorials**: https://pytorch-geometric.readthedocs.io/en/latest/get_started/introduction.html - Network accessline 670
- **Examples**: https://github.com/pyg-team/pytorch_geometric/tree/master/examples
skills/torch_geometric/scripts/benchmark_model.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torch_geometric/scripts/create_gnn_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torch_geometric/scripts/visualize_graph.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/torchdrug/SKILL.md
skills/transformers/SKILL.md
skills/transformers/references/pipelines.md
- Network accessline 298
pipe("https://example.com/image.jpg")
skills/travel-health-analyzer/SKILL.md
skills/treatment-plans/SKILL.md
- Broad permissionsline 1
Bash - Dangerous shell operationline 1387
sudo cp assets/medical_treatment_plan.sty /usr/local/texlive/texmf-local/tex/latex/ - Dangerous shell operationline 1388
sudo texhash - Network accessline 1410
**Download from CTAN:** - Visit: https://ctan.org/ - Network accessline 1411
- Visit: https://ctan.org/ - Search for medical document classes - Download and install per package instructions - Dangerous shell operationline 1420
sudo tlmgr update --self - Dangerous shell operationline 1421
sudo tlmgr install tcolorbox tikz pgf - Dangerous shell operationline 1436
sudo tlmgr install tcolorbox tikz pgf
skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md
- Dangerous shell operationline 171
sudo tlmgr install tcolorbox tikz pgf
skills/treatment-plans/scripts/check_completeness.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/treatment-plans/scripts/generate_template.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/treatment-plans/scripts/timeline_generator.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/treatment-plans/scripts/validate_treatment_plan.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/trialgpt-matching/README.md
- Network accessline 16
**Source:** [ncbi-nlp/TrialGPT](https://github.com/ncbi-nlp/TrialGPT)
skills/trialgpt-matching/repo/README.md
- Network accessline 19
 - Access to secretsline 27
[Credential-related source omitted] - Network accessline 38
We used the clinical trial information on https://clinicaltrials.gov/. Please download our parsed dataset by: - Network accessline 41
wget -O dataset/trial_info.json https://ftp.ncbi.nlm.nih.gov/pub/lu/TrialGPT/trial_info.json - Network accessline 44
Three publicly available datasets are used in the study (please properly cite these datasets if you use them; see details about citations in the bottom): - The SIGIR 2016 corpus, available at: https://data.csiro.au/collection/csiro:17152 - Network accessline 45
- The SIGIR 2016 corpus, available at: https://data.csiro.au/collection/csiro:17152 - Network accessline 46
- The TREC Clinical Trials 2021 corpus, available at: https://www.trec-cds.org/2021.html - Network accessline 47
- The TREC Clinical Trials 2022 corpus, available at: https://www.trec-cds.org/2022.html - Network accessline 52
wget -O dataset/trec_2021/corpus.jsonl https://ftp.ncbi.nlm.nih.gov/pub/lu/TrialGPT/trec_2021_corpus.jsonl - Network accessline 53
wget -O dataset/trec_2022/corpus.jsonl https://ftp.ncbi.nlm.nih.gov/pub/lu/TrialGPT/trec_2022_corpus.jsonl
skills/trialgpt-matching/repo/dataset/trec_2021/id2queries.json
skills/trialgpt-matching/repo/results/__init__.py
- Executable scriptline 1
Executable file
skills/trialgpt-matching/repo/trialgpt_matching/TrialGPT.py
skills/trialgpt-matching/repo/trialgpt_matching/run_matching.py
- Executable scriptline 1
Executable file
skills/trialgpt-matching/repo/trialgpt_ranking/TrialGPT.py
skills/trialgpt-matching/repo/trialgpt_ranking/rank_results.py
- Executable scriptline 1
Executable file
skills/trialgpt-matching/repo/trialgpt_ranking/run_aggregation.py
- Executable scriptline 1
Executable file
skills/trialgpt-matching/repo/trialgpt_retrieval/hybrid_fusion_retrieval.py
- Executable scriptline 1
Executable file
skills/trialgpt-matching/repo/trialgpt_retrieval/keyword_generation.py
skills/ukb-navigator/SKILL.md
skills/ukb-navigator/ukb_navigator.py
skills/uniprot-database/SKILL.md
- Network accessline 51
Use the API search endpoint: `https://rest.uniprot.org/uniprotkb/search?query={query}&format={format}` - Network accessline 63
**Retrieve endpoint:** `https://rest.uniprot.org/uniprotkb/{accession}.{format}` - Network accessline 65
Example: `https://rest.uniprot.org/uniprotkb/P12345.fasta` - Network accessline 71
**ID Mapping workflow:** 1. Submit mapping job to: `https://rest.uniprot.org/idmapping/run` - Network accessline 72
1. Submit mapping job to: `https://rest.uniprot.org/idmapping/run` - Network accessline 73
2. Check job status: `https://rest.uniprot.org/idmapping/status/{jobId}` - Network accessline 74
3. Retrieve results: `https://rest.uniprot.org/idmapping/results/{jobId}` - Network accessline 92
`https://rest.uniprot.org/uniprotkb/stream?query={query}&format={format}` - Network accessline 112
**Example:** `https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length,sequence&format=tsv` - Network accessline 185
- **API Documentation**: https://www.uniprot.org/help/api - Network accessline 186
- **Interactive API Explorer**: https://www.uniprot.org/api-documentation - Network accessline 187
- **REST Tutorial**: https://www.uniprot.org/help/uniprot_rest_tutorial - Network accessline 188
- **Query Syntax Help**: https://www.uniprot.org/help/query-fields - Network accessline 189
- **SPARQL Endpoint**: https://sparql.uniprot.org/ (for advanced graph queries)
skills/uniprot-database/references/api_examples.md
- Network accessline 11
# Search for human insulin proteins url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 12
url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 19
response = requests.get(url, params=params) - Network accessline 30
# Get human insulin sequence in FASTA format accession = "P01308" url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta" - Network accessline 32
url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta" - Network accessline 34
response = requests.get(url) - Network accessline 42
# Get specific fields only url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 43
url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 50
response = requests.get(url, params=params) - Network accessline 59
def map_uniprot_ids(ids, from_db, to_db): # Submit job submit_url = "https://rest.uniprot.org/idmapping/run" - Network accessline 60
# Submit job submit_url = "https://rest.uniprot.org/idmapping/run" data = { - Network accessline 61
submit_url = "https://rest.uniprot.org/idmapping/run" - Network accessline 68
response = requests.post(submit_url, data=data) - Network accessline 71
# Poll for completion status_url = f"https://rest.uniprot.org/idmapping/status/{job_id}" - Network accessline 72
status_url = f"https://rest.uniprot.org/idmapping/status/{job_id}" while True: response = requests.get(status_url) - Network accessline 73
while True: response = requests.get(status_url) status = response.json() - Network accessline 74
response = requests.get(status_url) - Network accessline 80
# Get results results_url = f"https://rest.uniprot.org/idmapping/results/{job_id}" response = requests.get(results_url) - Network accessline 81
results_url = f"https://rest.uniprot.org/idmapping/results/{job_id}" response = requests.get(results_url) return response.json() - Network accessline 82
response = requests.get(results_url) - Network accessline 95
# Stream all reviewed human proteins url = "https://rest.uniprot.org/uniprotkb/stream" - Network accessline 96
url = "https://rest.uniprot.org/uniprotkb/stream" - Network accessline 102
response = requests.get(url, params=params, stream=True) - Network accessline 115
def get_all_results(query, fields=None): """Get all results with pagination""" url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 116
"""Get all results with pagination""" url = "https://rest.uniprot.org/uniprotkb/search" all_results = [] - Network accessline 117
url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 129
while True: response = requests.get(url, params=params) - Network accessline 130
response = requests.get(url, params=params) - Network accessline 150
## cURL Examples - Network accessline 154
# Search for insulin proteins curl "https://rest.uniprot.org/uniprotkb/search?query=insulin&format=json&size=5" - Network accessline 155
curl "https://rest.uniprot.org/uniprotkb/search?query=insulin&format=json&size=5" - Network accessline 160
# Get human insulin in FASTA format curl "https://rest.uniprot.org/uniprotkb/P01308.fasta" - Network accessline 161
curl "https://rest.uniprot.org/uniprotkb/P01308.fasta" - Network accessline 166
# Get specific fields in TSV format curl "https://rest.uniprot.org/uniprotkb/search?query=gene:BRCA1&format=tsv&fields=accession,gene_names,length" - Network accessline 167
curl "https://rest.uniprot.org/uniprotkb/search?query=gene:BRCA1&format=tsv&fields=accession,gene_names,length" - Network accessline 172
# Submit mapping job curl -X POST "https://rest.uniprot.org/idmapping/run" \ - Network accessline 173
curl -X POST "https://rest.uniprot.org/idmapping/run" \ - Network accessline 180
# Get mapping results (replace JOB_ID) curl "https://rest.uniprot.org/idmapping/results/JOB_ID" - Network accessline 181
curl "https://rest.uniprot.org/idmapping/results/JOB_ID" - Network accessline 186
# Download all human reviewed proteins curl "https://rest.uniprot.org/uniprotkb/stream?query=organism_id:9606+AND+reviewed:true&format=fasta" \ - Network accessline 187
curl "https://rest.uniprot.org/uniprotkb/stream?query=organism_id:9606+AND+reviewed:true&format=fasta" \ - Network accessline 198
# Search for insulin proteins url <- "https://rest.uniprot.org/uniprotkb/search" - Network accessline 199
url <- "https://rest.uniprot.org/uniprotkb/search" - Network accessline 218
# Get protein sequence accession <- "P01308" url <- paste0("https://rest.uniprot.org/uniprotkb/", accession, ".fasta") - Network accessline 220
url <- paste0("https://rest.uniprot.org/uniprotkb/", accession, ".fasta") - Network accessline 232
# Get data as TSV url <- "https://rest.uniprot.org/uniprotkb/search" - Network accessline 233
url <- "https://rest.uniprot.org/uniprotkb/search" - Network accessline 249
// Search for proteins async function searchUniProt(query) { const url = `https://rest.uniprot.org/uniprotkb/search?query=${encodeURIComponent(query)}&format=json&size=10`; - Network accessline 251
const url = `https://rest.uniprot.org/uniprotkb/search?query=${encodeURIComponent(query)}&format=json&size=10`; - Network accessline 253
const response = await fetch(url); - Network accessline 266
async function getProtein(accession, format = "json") { const url = `https://rest.uniprot.org/uniprotkb/${accession}.${format}`; - Network accessline 267
const url = `https://rest.uniprot.org/uniprotkb/${accession}.${format}`; - Network accessline 269
const response = await fetch(url); - Network accessline 285
async function mapIds(ids, fromDb, toDb) { // Submit job const submitUrl = "https://rest.uniprot.org/idmapping/run"; - Network accessline 286
// Submit job const submitUrl = "https://rest.uniprot.org/idmapping/run"; const formData = new URLSearchParams({ - Network accessline 287
const submitUrl = "https://rest.uniprot.org/idmapping/run"; - Network accessline 294
const submitResponse = await fetch(submitUrl, { - Network accessline 300
// Poll for completion const statusUrl = `https://rest.uniprot.org/idmapping/status/${jobId}`; - Network accessline 301
const statusUrl = `https://rest.uniprot.org/idmapping/status/${jobId}`; while (true) { const statusResponse = await fetch(statusUrl); - Network accessline 302
while (true) { const statusResponse = await fetch(statusUrl); const status = await statusResponse.json(); - Network accessline 303
const statusResponse = await fetch(statusUrl); - Network accessline 313
// Get results const resultsUrl = `https://rest.uniprot.org/idmapping/results/${jobId}`; const resultsResponse = await fetch(resultsUrl); - Network accessline 314
const resultsUrl = `https://rest.uniprot.org/idmapping/results/${jobId}`; const resultsResponse = await fetch(resultsUrl); return await resultsResponse.json(); - Network accessline 315
const resultsResponse = await fetch(resultsUrl); - Network accessline 332
class UniProtClient: def __init__(self, rate_limit=1.0): self.base_url = "https://rest.uniprot.org" - Network accessline 333
def __init__(self, rate_limit=1.0): self.base_url = "https://rest.uniprot.org" self.rate_limit = rate_limit - Network accessline 334
self.base_url = "https://rest.uniprot.org" - Network accessline 356
response = requests.get( - Network accessline 384
def download_with_progress(query, output_file, format="fasta"): """Download results with progress bar""" url = "https://rest.uniprot.org/uniprotkb/stream" - Network accessline 385
"""Download results with progress bar""" url = "https://rest.uniprot.org/uniprotkb/stream" params = { - Network accessline 386
url = "https://rest.uniprot.org/uniprotkb/stream" - Network accessline 392
response = requests.get(url, params=params, stream=True) - Network accessline 410
- API Documentation: https://www.uniprot.org/help/api - Network accessline 411
- Interactive API Explorer: https://www.uniprot.org/api-documentation - Network accessline 412
- Python client (Unipressed): https://github.com/multimeric/Unipressed - Network accessline 413
- Bioservices package: https://bioservices.readthedocs.io/
skills/uniprot-database/references/api_fields.md
- Network accessline 9
https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length - Network accessline 217
curl https://rest.uniprot.org/configure/uniprotkb/result-fields - Network accessline 222
import requests response = requests.get("https://rest.uniprot.org/configure/uniprotkb/result-fields") - Network accessline 223
response = requests.get("https://rest.uniprot.org/configure/uniprotkb/result-fields") - Network accessline 273
- Interactive field explorer: https://www.uniprot.org/api-documentation - Network accessline 274
- API fields endpoint: https://rest.uniprot.org/configure/uniprotkb/result-fields - Network accessline 275
- Return fields documentation: https://www.uniprot.org/help/return_fields
skills/uniprot-database/references/id_mapping_databases.md
- Network accessline 8
import requests response = requests.get("https://rest.uniprot.org/configure/idmapping/fields") - Network accessline 9
response = requests.get("https://rest.uniprot.org/configure/idmapping/fields") - Network accessline 260
GET https://rest.uniprot.org/configure/idmapping/fields - Network accessline 265
POST https://rest.uniprot.org/idmapping/run - Network accessline 273
GET https://rest.uniprot.org/idmapping/status/{jobId} - Network accessline 278
GET https://rest.uniprot.org/idmapping/results/{jobId} - Network accessline 283
- ID Mapping tool: https://www.uniprot.org/id-mapping - Network accessline 284
- API documentation: https://www.uniprot.org/help/id_mapping - Network accessline 285
- Programmatic access: https://www.uniprot.org/help/api_idmapping
skills/uniprot-database/references/query_syntax.md
- Network accessline 220
Test queries using: - **Web interface**: https://www.uniprot.org/uniprotkb - Network accessline 221
- **Web interface**: https://www.uniprot.org/uniprotkb - Network accessline 222
- **API**: https://rest.uniprot.org/uniprotkb/search?query=YOUR_QUERY - Network accessline 223
- **API documentation**: https://www.uniprot.org/help/query-fields - Network accessline 254
- Full query field reference: https://www.uniprot.org/help/query-fields - Network accessline 255
- API query documentation: https://www.uniprot.org/help/api_queries - Network accessline 256
- Text search documentation: https://www.uniprot.org/help/text-search
skills/uniprot-database/scripts/uniprot_client.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 31
BASE_URL = "https://rest.uniprot.org" - Network accessline 61
response = requests.get(endpoint, params=params) - Network accessline 83
response = requests.get(endpoint) - Network accessline 134
response = requests.get(endpoint, params=params, stream=True) - Network accessline 173
response = requests.post(submit_endpoint, data=data) - Network accessline 180
while True: response = requests.get(status_endpoint) - Network accessline 181
response = requests.get(status_endpoint) - Network accessline 193
params = {"format": format} response = requests.get(results_endpoint, params=params) - Network accessline 194
response = requests.get(results_endpoint, params=params) - Network accessline 212
response = requests.get(endpoint) - Network accessline 227
response = requests.get(endpoint)
skills/universal-single-cell-annotator/cellidentifierdx-main/cellidentifierdx/__init__.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/cellidentifierdx-main/cellidentifierdx/cli.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/cellidentifierdx-main/cellidentifierdx/scoring.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/cellidentifierdx-main/cellidentifierdx/utils.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/cellidentifierdx-main/setup.py
- Executable scriptline 1
Executable file - Network accessline 20
long_description=open('README.md').read(), long_description_content_type='text/markdown', url='https://github.com/yourusername/cellidentifierdx', - Network accessline 21
long_description_content_type='text/markdown', url='https://github.com/yourusername/cellidentifierdx', classifiers=[ - Network accessline 22
url='https://github.com/yourusername/cellidentifierdx',
skills/universal-single-cell-annotator/cellidentifierdx-main/tests/__init__.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/cellidentifierdx-main/tests/test_scoring.py
- Executable scriptline 1
Executable file
skills/universal-single-cell-annotator/universal_annotator.py
skills/uspto-database/SKILL.md
- Network accessline 35
- Access to patent data through June 30, 2025 - 45 requests/minute rate limit - **Base URL**: `https://search.patentsview.org/api/v1/` - Network accessline 37
- **Base URL**: `https://search.patentsview.org/api/v1/` - Network accessline 46
- Trademark status, ownership, prosecution history - Search by serial or registration number - **Base URL**: `https://tsdrapi.uspto.gov/ts/cd/` - Network accessline 48
- **Base URL**: `https://tsdrapi.uspto.gov/ts/cd/` - Network accessline 66
All USPTO APIs require an API key. Register at: **https://account.uspto.gov/api-manager/** - Network accessline 67
**https://account.uspto.gov/api-manager/** - Access to secretsline 71
[Credential-related source omitted] - Network accessline 146
url = "https://search.patentsview.org/api/v1/patent" - Access to secretsline 148
[Credential-related source omitted] - Network accessline 165
response = requests.post(url, headers=headers, json=query) - Access to secretsline 347
[Credential-related source omitted] - Access to secretsline 349
[Credential-related source omitted] - Network accessline 397
**Base URL**: `https://assignment-api.uspto.gov/patent/v1.4/` - Network accessline 404
[Credential-related source omitted] - Access to secretsline 404
[Credential-related source omitted] - Network accessline 405
url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}" - Access to secretsline 406
[Credential-related source omitted] - Network accessline 408
response = requests.get(url, headers=headers) - Access to secretsline 412
[Credential-related source omitted] - Network accessline 427
[Credential-related source omitted] - Access to secretsline 427
[Credential-related source omitted] - Network accessline 428
url = "https://assignment-api.uspto.gov/patent/v1.4/assignment/search" - Access to secretsline 429
[Credential-related source omitted] - Network accessline 432
response = requests.post(url, headers=headers, json=data) - Access to secretsline 494
[Credential-related source omitted] - Access to secretsline 504
[Credential-related source omitted] - Network accessline 513
# 3. Get assignment history import requests assign_url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}" - Network accessline 514
[Credential-related source omitted] - Network accessline 515
[Credential-related source omitted] - Network accessline 516
[Credential-related source omitted] - Access to secretsline 516
[Credential-related source omitted] - Network accessline 578
### API Documentation - **PatentSearch API**: https://search.patentsview.org/docs/ - Network accessline 579
- **PatentSearch API**: https://search.patentsview.org/docs/ - Network accessline 580
- **USPTO Developer Portal**: https://developer.uspto.gov/ - Network accessline 581
- **USPTO Open Data Portal**: https://data.uspto.gov/ - Network accessline 582
- **API Key Registration**: https://account.uspto.gov/api-manager/ - Network accessline 584
### Python Libraries - **uspto-opendata-python**: https://pypi.org/project/uspto-opendata-python/ - Network accessline 585
- **uspto-opendata-python**: https://pypi.org/project/uspto-opendata-python/ - Network accessline 586
- **USPTO Docs**: https://docs.ip-tools.org/uspto-opendata-python/
skills/uspto-database/references/additional_apis.md
- Access to secretsline 56
[Credential-related source omitted] - Network accessline 124
**Base URL:** `https://assignment-api.uspto.gov/patent/` - Network accessline 168
[Credential-related source omitted] - Access to secretsline 168
[Credential-related source omitted] - Network accessline 169
[Credential-related source omitted] - Network accessline 170
url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}" - Access to secretsline 171
[Credential-related source omitted] - Network accessline 173
response = requests.get(url, headers=headers) - Network accessline 179
[Credential-related source omitted] - Access to secretsline 179
[Credential-related source omitted] - Network accessline 180
[Credential-related source omitted] - Network accessline 181
url = "https://assignment-api.uspto.gov/patent/v1.4/assignment/search" - Access to secretsline 182
[Credential-related source omitted] - Network accessline 185
response = requests.post(url, headers=headers, json=data) - Access to secretsline 295
[Credential-related source omitted] - Access to secretsline 300
[Credential-related source omitted] - Access to secretsline 303
[Credential-related source omitted] - Access to secretsline 312
[Credential-related source omitted] - Access to secretsline 319
[Credential-related source omitted] - Access to secretsline 322
[Credential-related source omitted] - Access to secretsline 325
[Credential-related source omitted] - Access to secretsline 328
[Credential-related source omitted] - Access to secretsline 331
[Credential-related source omitted] - Access to secretsline 334
[Credential-related source omitted] - Access to secretsline 342
[Credential-related source omitted] - Access to secretsline 347
[Credential-related source omitted] - Access to secretsline 355
[Credential-related source omitted] - Access to secretsline 356
[Credential-related source omitted] - Access to secretsline 357
[Credential-related source omitted] - Network accessline 384
All APIs require registration at: **https://account.uspto.gov/api-manager/** - Network accessline 385
**https://account.uspto.gov/api-manager/** - Network accessline 391
- **Developer Portal**: https://developer.uspto.gov/ - Network accessline 392
- **Open Data Portal**: https://data.uspto.gov/ - Network accessline 393
- **API Catalog**: https://developer.uspto.gov/api-catalog
skills/uspto-database/references/patentsearch_api.md
- Network accessline 7
**Base URL:** `https://search.patentsview.org/api/v1/` - Access to secretsline 14
[Credential-related source omitted] - Network accessline 17
Register for an API key at: https://account.uspto.gov/api-manager/ - Network accessline 176
[Credential-related source omitted] - Access to secretsline 176
[Credential-related source omitted] - Access to secretsline 177
[Credential-related source omitted] - Network accessline 197
url = "https://search.patentsview.org/api/v1/patent" - Access to secretsline 199
[Credential-related source omitted] - Network accessline 214
response = requests.post(url, headers=headers, json=data) - Network accessline 234
Refer to the full field dictionary at: https://search.patentsview.org/docs/ - Network accessline 264
- **Official Documentation**: https://search.patentsview.org/docs/ - Network accessline 265
- **API Key Registration**: https://account.uspto.gov/api-manager/
skills/uspto-database/references/peds_api.md
- Network accessline 209
- **Library Documentation**: https://docs.ip-tools.org/uspto-opendata-python/ - Network accessline 210
- **PyPI Package**: https://pypi.org/project/uspto-opendata-python/ - Network accessline 211
- **GitHub Repository**: https://github.com/ip-tools/uspto-opendata-python - Network accessline 212
- **USPTO PEDS Portal**: https://ped.uspto.gov/
skills/uspto-database/references/trademark_api.md
- Network accessline 18
**Base URL:** `https://tsdrapi.uspto.gov/ts/cd/` - Network accessline 22
Requires API key registration at: https://account.uspto.gov/api-manager/ - Access to secretsline 26
[Credential-related source omitted] - Network accessline 39
[Credential-related source omitted] - Network accessline 40
"https://tsdrapi.uspto.gov/ts/cd/casedocs/sn87654321/info.json" - Network accessline 111
[Credential-related source omitted] - Access to secretsline 111
[Credential-related source omitted] - Network accessline 112
[Credential-related source omitted] - Network accessline 113
url = f"https://tsdrapi.uspto.gov/ts/cd/casedocs/sn{serial_number}/info.json" - Access to secretsline 114
[Credential-related source omitted] - Network accessline 116
response = requests.get(url, headers=headers) - Access to secretsline 123
[Credential-related source omitted] - Network accessline 141
**Base URL:** `https://assignment-api.uspto.gov/trademark/` - Access to secretsline 147
[Credential-related source omitted] - Network accessline 228
[Credential-related source omitted] - Access to secretsline 228
[Credential-related source omitted] - Network accessline 229
[Credential-related source omitted] - Network accessline 230
url = f"https://assignment-api.uspto.gov/trademark/v1.4/assignment/application/{registration_number}" - Access to secretsline 231
[Credential-related source omitted] - Network accessline 233
response = requests.get(url, headers=headers) - Access to secretsline 240
[Credential-related source omitted] - Access to secretsline 263
[Credential-related source omitted] - Access to secretsline 265
[Credential-related source omitted] - Access to secretsline 288
[Credential-related source omitted] - Access to secretsline 290
[Credential-related source omitted] - Access to secretsline 311
[Credential-related source omitted] - Access to secretsline 321
[Credential-related source omitted] - Network accessline 354
- **TSDR API**: https://developer.uspto.gov/api-catalog/tsdr-data-api - Network accessline 355
- **Assignment API**: https://developer.uspto.gov/api-catalog/trademark-assignment-search-data-api - Network accessline 356
- **API Key Registration**: https://account.uspto.gov/api-manager/ - Network accessline 357
- **Trademark Search**: https://tmsearch.uspto.gov/ - Network accessline 358
- **Swagger Documentation**: https://developer.uspto.gov/swagger/tsdr-api-v1
skills/uspto-database/scripts/patent_search.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Requires: - requests library: pip install requests - USPTO API key from https://account.uspto.gov/api-manager/ - Network accessline 10
- USPTO API key from https://account.uspto.gov/api-manager/ - Access to secretsline 13
[Credential-related source omitted] - Network accessline 27
BASE_URL = "https://search.patentsview.org/api/v1" - Access to secretsline 29
[Credential-related source omitted] - Access to secretsline 34
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 41
[Credential-related source omitted] - Network accessline 70
response = requests.post(url, headers=self.headers, json=data)
skills/uspto-database/scripts/peds_client.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/uspto-database/scripts/trademark_client.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Requires: - requests library: pip install requests - USPTO API key from https://account.uspto.gov/api-manager/ - Network accessline 10
- USPTO API key from https://account.uspto.gov/api-manager/ - Access to secretsline 13
[Credential-related source omitted] - Network accessline 26
TSDR_BASE_URL = "https://tsdrapi.uspto.gov/ts/cd" - Network accessline 27
ASSIGNMENT_BASE_URL = "https://assignment-api.uspto.gov/trademark" - Access to secretsline 29
[Credential-related source omitted] - Access to secretsline 34
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 40
[Credential-related source omitted] - Network accessline 54
try: response = requests.get(url, headers=self.headers) - Network accessline 55
response = requests.get(url, headers=self.headers) - Network accessline 75
try: response = requests.get(url, headers=self.headers) - Network accessline 76
response = requests.get(url, headers=self.headers) - Network accessline 256
Environment: Set USPTO_API_KEY environment variable with your API key from: https://account.uspto.gov/api-manager/ - Network accessline 257
[Credential-related source omitted] - Access to secretsline 257
[Credential-related source omitted] - Network accessline 258
https://account.uspto.gov/api-manager/ - Access to secretsline 273
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted]
skills/variant-interpretation-acmg/acmg_classifier.py
- Executable scriptline 1
Executable file
skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md
- Network accessline 55
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 56
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 116
git clone https://github.com/WGLab/InterVar.git cd InterVar # Download databases per documentation
skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/examples/clinical_filter.py
- Executable scriptline 1
Executable file
skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/usage-guide.md
- Network accessline 26
# ClinVar database wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 27
wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 137
- [ACMG guidelines](https://www.acmg.net/ACMG/Medical-Genetics-Practice-Resources/) - Network accessline 138
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/)
skills/variant-interpretation-acmg/bioSkills/consensus-sequences/examples/generate_consensus.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/consensus-sequences/usage-guide.md
- Network accessline 371
- [bcftools consensus documentation](http://www.htslib.org/doc/bcftools.html#consensus)
skills/variant-interpretation-acmg/bioSkills/deepvariant/examples/run_deepvariant.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/deepvariant/usage-guide.md
skills/variant-interpretation-acmg/bioSkills/filtering-best-practices/examples/filter_variants.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling/examples/joint_calling.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling/examples/single_sample.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling/usage-guide.md
skills/variant-interpretation-acmg/bioSkills/joint-calling/examples/joint_calling_gatk.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/joint-calling/usage-guide.md
- Network accessline 176
- [GATK joint calling tutorial](https://gatk.broadinstitute.org/hc/en-us/articles/360035531152)
skills/variant-interpretation-acmg/bioSkills/structural-variant-calling/examples/call_svs.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/variant-annotation/SKILL.md
- Network accessline 255
# Download from https://annovar.openbioinformatics.org/ (registration required)
skills/variant-interpretation-acmg/bioSkills/variant-annotation/examples/annotate_vcf.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/variant-annotation/usage-guide.md
- Network accessline 271
# Download wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz - Network accessline 272
wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz - Network accessline 273
wget https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.40.gz.tbi - Network accessline 284
# Download chromosome 1 wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz - Network accessline 285
wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz - Network accessline 286
wget https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.0/vcf/genomes/gnomad.genomes.v4.0.sites.chr1.vcf.bgz.tbi - Network accessline 298
# Download wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 299
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz - Network accessline 300
wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi - Network accessline 401
- [bcftools annotate documentation](http://www.htslib.org/doc/bcftools.html#annotate) - Network accessline 402
- [bcftools csq documentation](http://www.htslib.org/doc/bcftools.html#csq)
skills/variant-interpretation-acmg/bioSkills/variant-calling/examples/call_variants.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/variant-calling/usage-guide.md
skills/variant-interpretation-acmg/bioSkills/variant-normalization/examples/normalize_vcf.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/variant-normalization/usage-guide.md
skills/variant-interpretation-acmg/bioSkills/vcf-basics/examples/view_vcf.py
- Executable scriptline 1
Executable file
skills/variant-interpretation-acmg/bioSkills/vcf-manipulation/examples/compare_vcfs.sh
- Executable scriptline 1
#!/bin/bash
skills/variant-interpretation-acmg/bioSkills/vcf-manipulation/usage-guide.md
- Network accessline 424
- [bcftools merge documentation](http://www.htslib.org/doc/bcftools.html#merge) - Network accessline 425
- [bcftools concat documentation](http://www.htslib.org/doc/bcftools.html#concat) - Network accessline 426
- [bcftools isec documentation](http://www.htslib.org/doc/bcftools.html#isec)
skills/variant-interpretation-acmg/bioSkills/vcf-statistics/examples/vcf_stats.py
- Executable scriptline 1
Executable file
skills/variant-interpretation-acmg/bioSkills/vcf-statistics/usage-guide.md
skills/vcf-annotator/SKILL.md
skills/wearable-analysis-agent/arrhythmia_detector.py
- Executable scriptline 1
Executable file
skills/wearable-analysis-agent/health_copilot.py
- Executable scriptline 1
Executable file
skills/wellally-tech/SKILL.md
- Network accessline 9
Integrate multiple digital health data sources, connect to [WellAlly.tech](https://www.wellally.tech/) knowledge base, providing data import and knowledge reference for personal health management systems. - Network accessline 20
- **Categorized Article Index**: Nutrition, fitness, sleep, mental health, chronic disease management - **Intelligent Recommendations**: Recommend relevant articles based on user health data - **URL References**: Provide direct links to [We - Network accessline 22
- **URL References**: Provide direct links to [WellAlly.tech](https://www.wellally.tech/) platform - Network accessline 63
Determine what the user wants: 1. **Import Data**: Import data from external health platforms 2. **Query Knowledge Base**: Find [WellAlly.tech](https://www.wellally.tech/) related articles - Network accessline 64
1. **Import Data**: Import data from external health platforms 2. **Query Knowledge Base**: Find [WellAlly.tech](https://www.wellally.tech/) related articles 3. **Get Recommendations**: Recommend articles based on health data - Network accessline 65
2. **Query Knowledge Base**: Find [WellAlly.tech](https://www.wellally.tech/) related articles - Network accessline 181
{ title: "Hypertension Monitoring and Management", url: "https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring", - Network accessline 182
title: "Hypertension Monitoring and Management", url: "https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring", category: "Chronic Disease Management", - Network accessline 183
url: "https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring", - Network accessline 187
{ title: "Blood Pressure Lowering Strategies", url: "https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies", - Network accessline 188
title: "Blood Pressure Lowering Strategies", url: "https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies", category: "Chronic Disease Management", - Network accessline 189
url: "https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies", - Network accessline 335
1. Hypertension Monitoring and Management Category: Chronic Disease Management Link: https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring - Network accessline 336
Category: Chronic Disease Management Link: https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring Description: Learn how to effectively monitor and manage blood pressure - Network accessline 337
Link: https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring - Network accessline 340
2. Blood Pressure Lowering Strategies Category: Chronic Disease Management Link: https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies - Network accessline 341
Category: Chronic Disease Management Link: https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies Description: Improve blood pressure levels through lifestyle modifications - Network accessline 342
Link: https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies - Network accessline 352
💡 Tips: Click links to visit [WellAlly.tech](https://www.wellally.tech/) platform for full articles - Network accessline 353
Click links to visit [WellAlly.tech](https://www.wellally.tech/) platform for full articles - Network accessline 369
Recommended Articles: 1. Hypertension Monitoring and Management https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring - Network accessline 371
https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring - Network accessline 373
2. Blood Pressure Lowering Strategies https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies - Network accessline 374
https://wellally.tech/knowledge-base/chronic-disease/bp-lowering-strategies - Network accessline 376
3. Antihypertensive Medication Adherence Guide https://wellally.tech/knowledge-base/chronic-disease/medication-adherence - Network accessline 377
https://wellally.tech/knowledge-base/chronic-disease/medication-adherence - Network accessline 385
Recommended Articles: 1. Sleep Hygiene Basics https://wellally.tech/knowledge-base/sleep/sleep-hygiene - Network accessline 387
https://wellally.tech/knowledge-base/sleep/sleep-hygiene - Network accessline 389
2. Improve Sleep Quality https://wellally.tech/knowledge-base/sleep/sleep-quality-improvement - Network accessline 390
https://wellally.tech/knowledge-base/sleep/sleep-quality-improvement - Network accessline 398
Related Reading: 1. Maintain Active Lifestyle https://wellally.tech/knowledge-base/fitness/active-lifestyle - Network accessline 400
https://wellally.tech/knowledge-base/fitness/active-lifestyle - Network accessline 404
Summary: 5 related articles recommended Visit [WellAlly.tech](https://www.wellally.tech/) Knowledge Base for full content - Network accessline 405
Visit [WellAlly.tech](https://www.wellally.tech/) Knowledge Base for full content - Access to secretsline 511
[Credential-related source omitted] - Network accessline 666
- **WellAlly.tech**: https://www.wellally.tech/ - Network accessline 667
- **WellAlly Knowledge Base**: https://wellally.tech/knowledge-base/ - Network accessline 668
- **WellAlly Blog**: https://wellally.tech/blog/ - Network accessline 669
- **Apple HealthKit**: https://developer.apple.com/documentation/healthkit - Network accessline 670
- **Fitbit API**: https://dev.fitbit.com/ - Network accessline 671
- **Oura Ring API**: https://cloud.ouraring.com/api/ - Network accessline 681
**Q: Are WellAlly.tech knowledge base articles offline?** A: No. Knowledge base articles are referenced via URLs, requiring network connection to access the [WellAlly.tech](https://www.wellally.tech/) platform. - Network accessline 682
A: No. Knowledge base articles are referenced via URLs, requiring network connection to access the [WellAlly.tech](https://www.wellally.tech/) platform.
skills/wellally-tech/data-sources.md
- Access to secretsline 106
[Credential-related source omitted] - Network accessline 114
# Get today's steps curl -X GET "https://api.fitbit.com/1/user/-/activities/steps/date/today/1d.json" \ - Network accessline 115
[Credential-related source omitted] - Access to secretsline 115
[Credential-related source omitted] - Access to secretsline 116
[Credential-related source omitted] - Network accessline 118
# Get heart rate data curl -X GET "https://api.fitbit.com/1/user/-/activities/heart/date/today/1d.json" \ - Network accessline 119
[Credential-related source omitted] - Access to secretsline 119
[Credential-related source omitted] - Access to secretsline 120
[Credential-related source omitted] - Network accessline 122
# Get sleep data curl -X GET "https://api.fitbit.com/1.2/user/-/sleep/date/today.json" \ - Network accessline 123
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted] - Access to secretsline 124
[Credential-related source omitted] - Network accessline 199
# Get sleep data curl -X GET "https://api.ouraring.com/v2/usercollection/daily_sleep?start_date=2025-01-22&end_date=2025-01-22" \ - Network accessline 200
[Credential-related source omitted] - Access to secretsline 200
[Credential-related source omitted] - Access to secretsline 201
[Credential-related source omitted] - Network accessline 203
# Get readiness score curl -X GET "https://api.ouraring.com/v2/usercollection/daily_readiness?start_date=2025-01-22&end_date=2025-01-22" \ - Network accessline 204
[Credential-related source omitted] - Access to secretsline 204
[Credential-related source omitted] - Access to secretsline 205
[Credential-related source omitted]
skills/wellally-tech/knowledge-base/chronic-disease.md
- Network accessline 35
**Hypertension** - Hypertension basics: https://wellally.tech/knowledge-base/chronic-disease/hypertension-basics - Network accessline 36
- Hypertension basics: https://wellally.tech/knowledge-base/chronic-disease/hypertension-basics - Network accessline 37
- Blood pressure monitoring guide: https://wellally.tech/knowledge-base/chronic-disease/blood-pressure-monitoring - Network accessline 38
- Home blood pressure measurement: https://wellally.tech/knowledge-base/chronic-disease/home-bp-monitoring - Network accessline 39
- Blood pressure target setting: https://wellally.tech/knowledge-base/chronic-disease/bp-targets - Network accessline 41
**Diabetes** - Diabetes basics: https://wellally.tech/knowledge-base/chronic-disease/diabetes-basics - Network accessline 42
- Diabetes basics: https://wellally.tech/knowledge-base/chronic-disease/diabetes-basics - Network accessline 43
- Blood glucose monitoring guide: https://wellally.tech/knowledge-base/chronic-disease/blood-glucose-monitoring - Network accessline 44
- HbA1c testing: https://wellally.tech/knowledge-base/chronic-disease/hba1c-testing - Network accessline 45
- Diabetes complication screening: https://wellally.tech/knowledge-base/chronic-disease/diabetes-complications - Network accessline 47
**COPD** - COPD basics: https://wellally.tech/knowledge-base/chronic-disease/copd-basics - Network accessline 48
- COPD basics: https://wellally.tech/knowledge-base/chronic-disease/copd-basics - Network accessline 49
- Lung function monitoring: https://wellally.tech/knowledge-base/chronic-disease/lung-function-monitoring - Network accessline 50
- CAT score: https://wellally.tech/knowledge-base/chronic-disease/cat-score - Network accessline 51
- COPD exacerbation prevention: https://wellally.tech/knowledge-base/chronic-disease/copd-exacerbation-prevention - Network accessline 53
**Cardiovascular Disease** - Cardiovascular risk assessment: https://wellally.tech/knowledge-base/chronic-disease/cv-risk-assessment - Network accessline 54
- Cardiovascular risk assessment: https://wellally.tech/knowledge-base/chronic-disease/cv-risk-assessment - Network accessline 55
- Coronary artery disease management: https://wellally.tech/knowledge-base/chronic-disease/cad-management - Network accessline 56
- Heart failure management: https://wellally.tech/knowledge-base/chronic-disease/heart-failure-management - Network accessline 57
- Arrhythmia: https://wellally.tech/knowledge-base/chronic-disease/arrhythmia - Network accessline 91
**Blood Pressure Monitoring** - Proper blood pressure measurement: https://wellally.tech/knowledge-base/chronic-disease/proper-bp-measurement - Network accessline 92
- Proper blood pressure measurement: https://wellally.tech/knowledge-base/chronic-disease/proper-bp-measurement - Network accessline 93
- Blood pressure monitor selection: https://wellally.tech/knowledge-base/chronic-disease/bp-monitor-selection - Network accessline 94
- Measurement frequency recommendations: https://wellally.tech/knowledge-base/chronic-disease/bp-measurement-frequency - Network accessline 95
- Blood pressure variability analysis: https://wellally.tech/knowledge-base/chronic-disease/bp-variability - Network accessline 97
**Lifestyle Intervention** - DASH diet: https://wellally.tech/knowledge-base/chronic-disease/dash-diet - Network accessline 98
- DASH diet: https://wellally.tech/knowledge-base/chronic-disease/dash-diet - Network accessline 99
- Sodium reduction strategies: https://wellally.tech/knowledge-base/chronic-disease/sodium-reduction - Network accessline 100
- Exercise for blood pressure: https://wellally.tech/knowledge-base/chronic-disease/exercise-bp - Network accessline 101
- Weight and blood pressure: https://wellally.tech/knowledge-base/chronic-disease/weight-bp - Network accessline 103
**Medication Treatment** - Antihypertensive drug classes: https://wellally.tech/knowledge-base/chronic-disease/antihypertensive-classes - Network accessline 104
- Antihypertensive drug classes: https://wellally.tech/knowledge-base/chronic-disease/antihypertensive-classes - Network accessline 105
- Medication adherence: https://wellally.tech/knowledge-base/chronic-disease/medication-adherence - Network accessline 106
- Side effect management: https://wellally.tech/knowledge-base/chronic-disease/bp-med-side-effects - Network accessline 107
- Combination therapy: https://wellally.tech/knowledge-base/chronic-disease/combo-therapy - Network accessline 109
**Complication Prevention** - Target organ damage: https://wellally.tech/knowledge-base/chronic-disease/target-organ-damage - Network accessline 110
- Target organ damage: https://wellally.tech/knowledge-base/chronic-disease/target-organ-damage - Network accessline 111
- Cardiovascular risk assessment: https://wellally.tech/knowledge-base/chronic-disease/cv-risk-hypertension - Network accessline 112
- Kidney protection: https://wellally.tech/knowledge-base/chronic-disease/kidney-protection - Network accessline 116
**Blood Glucose Monitoring** - Self-monitoring of blood glucose (SMBG): https://wellally.tech/knowledge-base/chronic-disease/smbg-guide - Network accessline 117
- Self-monitoring of blood glucose (SMBG): https://wellally.tech/knowledge-base/chronic-disease/smbg-guide - Network accessline 118
- Continuous glucose monitoring (CGM): https://wellally.tech/knowledge-base/chronic-disease/cgm-guide - Network accessline 119
- Blood glucose targets: https://wellally.tech/knowledge-base/chronic-disease/glucose-targets - Network accessline 120
- Blood glucose pattern recognition: https://wellally.tech/knowledge-base/chronic-disease/glucose-patterns - Network accessline 122
**Dietary Management** - Diabetes diet principles: https://wellally.tech/knowledge-base/chronic-disease/diabetes-diet-principles - Network accessline 123
- Diabetes diet principles: https://wellally.tech/knowledge-base/chronic-disease/diabetes-diet-principles - Network accessline 124
- Carbohydrate counting: https://wellally.tech/knowledge-base/chronic-disease/carb-counting - Network accessline 125
- Glycemic index: https://wellally.tech/knowledge-base/chronic-disease/glycemic-index - Network accessline 126
- Postprandial glucose management: https://wellally.tech/knowledge-base/chronic-disease/postprandial-glucose - Network accessline 128
**Exercise Therapy** - Exercise and blood glucose: https://wellally.tech/knowledge-base/chronic-disease/exercise-diabetes - Network accessline 129
- Exercise and blood glucose: https://wellally.tech/knowledge-base/chronic-disease/exercise-diabetes - Network accessline 130
- Exercise safety for diabetes: https://wellally.tech/knowledge-base/chronic-disease/exercise-safety-diabetes - Network accessline 131
- Exercise type selection: https://wellally.tech/knowledge-base/chronic-disease/exercise-types-diabetes - Network accessline 132
- Exercise timing: https://wellally.tech/knowledge-base/chronic-disease/timing-exercise-diabetes - Network accessline 134
**Complication Prevention** - Diabetic nephropathy: https://wellally.tech/knowledge-base/chronic-disease/diabetic-nephropathy - Network accessline 135
- Diabetic nephropathy: https://wellally.tech/knowledge-base/chronic-disease/diabetic-nephropathy - Network accessline 136
- Diabetic retinopathy: https://wellally.tech/knowledge-base/chronic-disease/diabetic-retinopathy - Network accessline 137
- Diabetic neuropathy: https://wellally.tech/knowledge-base/chronic-disease/diabetic-neuropathy - Network accessline 138
- Foot care for diabetes: https://wellally.tech/knowledge-base/chronic-disease/foot-care-diabetes - Network accessline 142
**Symptom Management** - Dyspnea management: https://wellally.tech/knowledge-base/chronic-disease/dyspnea-management - Network accessline 143
- Dyspnea management: https://wellally.tech/knowledge-base/chronic-disease/dyspnea-management - Network accessline 144
- Cough and sputum management: https://wellally.tech/knowledge-base/chronic-disease/cough-management - Network accessline 145
- Breathing techniques: https://wellally.tech/knowledge-base/chronic-disease/breathing-techniques - Network accessline 146
- Sputum clearance: https://wellally.tech/knowledge-base/chronic-disease/sputum-clearance - Network accessline 148
**Exacerbation Prevention** - Trigger identification: https://wellally.tech/knowledge-base/chronic-disease/copd-triggers - Network accessline 149
- Trigger identification: https://wellally.tech/knowledge-base/chronic-disease/copd-triggers - Network accessline 150
- Vaccinations: https://wellally.tech/knowledge-base/chronic-disease/copd-vaccinations - Network accessline 151
- Early recognition of exacerbation: https://wellally.tech/knowledge-base/chronic-disease/exacerbation-early-recognition - Network accessline 152
- COPD action plan: https://wellally.tech/knowledge-base/chronic-disease/copd-action-plan - Network accessline 154
**Rehabilitation Training** - Pulmonary rehabilitation: https://wellally.tech/knowledge-base/chronic-disease/pulmonary-rehab - Network accessline 155
- Pulmonary rehabilitation: https://wellally.tech/knowledge-base/chronic-disease/pulmonary-rehab - Network accessline 156
- Exercise training: https://wellally.tech/knowledge-base/chronic-disease/exercise-copd - Network accessline 157
- Breathing training: https://wellally.tech/knowledge-base/chronic-disease/breathing-training - Network accessline 158
- Energy conservation in daily activities: https://wellally.tech/knowledge-base/chronic-disease/energy-conservation - Network accessline 447
- [Chronic Disease Long-term Management](https://wellally.tech/blog/chronic-disease-management) - Network accessline 448
- [Medication Adherence Strategies](https://wellally.tech/blog/medication-adherence) - Network accessline 453
- Chinese Guidelines for the Prevention and Treatment of Type 2 Diabetes - Guidelines for the Diagnosis and Treatment of Chronic Obstructive Pulmonary Disease - American College of Cardiology (ACC): https://www.acc.org/ - Network accessline 454
- Guidelines for the Diagnosis and Treatment of Chronic Obstructive Pulmonary Disease - American College of Cardiology (ACC): https://www.acc.org/ - American Diabetes Association (ADA): https://www.diabetes.org/ - Network accessline 455
- American College of Cardiology (ACC): https://www.acc.org/ - Network accessline 456
- American Diabetes Association (ADA): https://www.diabetes.org/
skills/wellally-tech/knowledge-base/fitness.md
- Network accessline 30
**Basic Exercise Knowledge** - Exercise basics: https://wellally.tech/knowledge-base/fitness/exercise-basics - Network accessline 31
- Exercise basics: https://wellally.tech/knowledge-base/fitness/exercise-basics - Network accessline 32
- Exercise intensity assessment: https://wellally.tech/knowledge-base/fitness/exercise-intensity - Network accessline 33
- Types of exercise: https://wellally.tech/knowledge-base/fitness/types-of-exercise - Network accessline 35
**Exercise Tracking** - Step tracking guide: https://wellally.tech/knowledge-base/fitness/step-tracking - Network accessline 36
- Step tracking guide: https://wellally.tech/knowledge-base/fitness/step-tracking - Network accessline 37
- Heart rate monitoring: https://wellally.tech/knowledge-base/fitness/heart-rate-monitoring - Network accessline 38
- Active minutes recording: https://wellally.tech/knowledge-base/fitness/active-minutes - Network accessline 40
**Exercise and Health Management** - Exercise and weight loss: https://wellally.tech/knowledge-base/fitness/exercise-weight-loss - Network accessline 41
- Exercise and weight loss: https://wellally.tech/knowledge-base/fitness/exercise-weight-loss - Network accessline 42
- Exercise and heart health: https://wellally.tech/knowledge-base/fitness/exercise-heart-health - Network accessline 43
- Exercise and sleep: https://wellally.tech/knowledge-base/fitness/exercise-sleep - Network accessline 44
- Exercise and stress: https://wellally.tech/knowledge-base/fitness/exercise-stress - Network accessline 46
**Training Plans** - Cardio exercise plans: https://wellally.tech/knowledge-base/fitness/cardio-plans - Network accessline 47
- Cardio exercise plans: https://wellally.tech/knowledge-base/fitness/cardio-plans - Network accessline 48
- Strength training guide: https://wellally.tech/knowledge-base/fitness/strength-training - Network accessline 49
- Flexibility training: https://wellally.tech/knowledge-base/fitness/flexibility-training - Network accessline 50
- Balance training: https://wellally.tech/knowledge-base/fitness/balance-training - Network accessline 78
**Weight Loss** - Weight loss exercise guide: https://wellally.tech/knowledge-base/fitness/weight-loss-exercise - Network accessline 79
- Weight loss exercise guide: https://wellally.tech/knowledge-base/fitness/weight-loss-exercise - Network accessline 80
- Cardio exercise selection: https://wellally.tech/knowledge-base/fitness/cardio-for-weight-loss - Network accessline 81
- HIIT training introduction: https://wellally.tech/knowledge-base/fitness/hiit-guide - Network accessline 83
**Improve Fitness** - Endurance training basics: https://wellally.tech/knowledge-base/fitness/endurance-training - Network accessline 84
- Endurance training basics: https://wellally.tech/knowledge-base/fitness/endurance-training - Network accessline 85
- VO2max: https://wellally.tech/knowledge-base/fitness/vo2max - Network accessline 86
- Fitness improvement plan: https://wellally.tech/knowledge-base/fitness/fitness-improvement - Network accessline 88
**Muscle Building** - Strength training introduction: https://wellally.tech/knowledge-base/fitness/strength-training-basics - Network accessline 89
- Strength training introduction: https://wellally.tech/knowledge-base/fitness/strength-training-basics - Network accessline 90
- Muscle growth principles: https://wellally.tech/knowledge-base/fitness/muscle-growth - Network accessline 91
- Muscle building diet: https://wellally.tech/knowledge-base/fitness/muscle-building-diet - Network accessline 93
**Improve Health** - Heart healthy exercise: https://wellally.tech/knowledge-base/fitness/heart-healthy-exercise - Network accessline 94
- Heart healthy exercise: https://wellally.tech/knowledge-base/fitness/heart-healthy-exercise - Network accessline 95
- Blood pressure lowering exercise: https://wellally.tech/knowledge-base/fitness/bp-lowering-exercise - Network accessline 96
- Blood sugar control exercise: https://wellally.tech/knowledge-base/fitness/blood-sugar-exercise - Network accessline 100
**Aerobic Exercise** - Running guide: https://wellally.tech/knowledge-base/fitness/running-guide - Network accessline 101
- Running guide: https://wellally.tech/knowledge-base/fitness/running-guide - Network accessline 102
- Walking plans: https://wellally.tech/knowledge-base/fitness/walking-plans - Network accessline 103
- Swimming training: https://wellally.tech/knowledge-base/fitness/swimming-training - Network accessline 104
- Cycling training: https://wellally.tech/knowledge-base/fitness/cycling-training - Network accessline 106
**Strength Training** - Bodyweight training: https://wellally.tech/knowledge-base/fitness/bodyweight-training - Network accessline 107
- Bodyweight training: https://wellally.tech/knowledge-base/fitness/bodyweight-training - Network accessline 108
- Dumbbell training: https://wellally.tech/knowledge-base/fitness/dumbbell-training - Network accessline 109
- Barbell training: https://wellally.tech/knowledge-base/fitness/barbell-training - Network accessline 110
- Resistance band training: https://wellally.tech/knowledge-base/fitness/resistance-band-training - Network accessline 112
**Flexibility and Balance** - Stretching guide: https://wellally.tech/knowledge-base/fitness/stretching-guide - Network accessline 113
- Stretching guide: https://wellally.tech/knowledge-base/fitness/stretching-guide - Network accessline 114
- Yoga basics: https://wellally.tech/knowledge-base/fitness/yoga-basics - Network accessline 115
- Pilates introduction: https://wellally.tech/knowledge-base/fitness/pilates-intro - Network accessline 116
- Balance exercises: https://wellally.tech/knowledge-base/fitness/balance-exercises - Network accessline 302
- [Exercise Data Analysis](https://wellally.tech/blog/exercise-data-analysis) - Network accessline 303
- [Exercise and Mental Health](https://wellally.tech/blog/exercise-mental-health) - Network accessline 307
- WHO Physical Activity Guidelines: https://www.who.int/news-room/fact-sheets/detail/physical-activity - Network accessline 308
- American College of Sports Medicine (ACSM): https://www.acsm.org/ - Network accessline 309
- Chinese Sports Medicine: http://www.casm.org.cn/
skills/wellally-tech/knowledge-base/index.md
- Network accessline 17
- **Official Website**: https://www.wellally.tech/ - Network accessline 18
- **Knowledge Base**: https://wellally.tech/knowledge-base/ - Network accessline 19
- **Blog**: https://wellally.tech/blog/ - Network accessline 20
- **Features**: https://wellally.tech/features/ - Network accessline 21
- **About Us**: https://wellally.tech/about/ - Network accessline 46
**Key Links**: - Home: https://wellally.tech/knowledge-base/nutrition/ - Network accessline 47
- Home: https://wellally.tech/knowledge-base/nutrition/ - Network accessline 48
- Diet tracking guide: https://wellally.tech/knowledge-base/nutrition/diet-tracking - Network accessline 49
- Nutritional analysis: https://wellally.tech/knowledge-base/nutrition/nutritional-analysis - Network accessline 64
**Key Links**: - Home: https://wellally.tech/knowledge-base/fitness/ - Network accessline 65
- Home: https://wellally.tech/knowledge-base/fitness/ - Network accessline 66
- Exercise tracking: https://wellally.tech/knowledge-base/fitness/exercise-tracking - Network accessline 67
- Activity recommendations: https://wellally.tech/knowledge-base/fitness/activity-recommendations - Network accessline 82
**Key Links**: - Home: https://wellally.tech/knowledge-base/sleep/ - Network accessline 83
- Home: https://wellally.tech/knowledge-base/sleep/ - Network accessline 84
- Sleep analysis: https://wellally.tech/knowledge-base/sleep/sleep-analysis - Network accessline 85
- Sleep improvement: https://wellally.tech/knowledge-base/sleep/sleep-improvement - Network accessline 100
**Key Links**: - Home: https://wellally.tech/knowledge-base/mental-health/ - Network accessline 101
- Home: https://wellally.tech/knowledge-base/mental-health/ - Network accessline 102
- Stress management: https://wellally.tech/knowledge-base/mental-health/stress-management - Network accessline 103
- Emotional wellness: https://wellally.tech/knowledge-base/mental-health/emotional-wellness - Network accessline 118
**Key Links**: - Home: https://wellally.tech/knowledge-base/chronic-disease/ - Network accessline 119
- Home: https://wellally.tech/knowledge-base/chronic-disease/ - Network accessline 120
- Hypertension management: https://wellally.tech/knowledge-base/chronic-disease/hypertension - Network accessline 121
- Diabetes management: https://wellally.tech/knowledge-base/chronic-disease/diabetes - Network accessline 122
- COPD care: https://wellally.tech/knowledge-base/chronic-disease/copd - Network accessline 130
1. **[Building the Future of Care: An Architectural Deep Dive into the AI-Driven WellAlly Health Platform](https://coderlegion.com/9809/building-the-future-care-architectural-deep-dive-into-the-driven-wellally-health-platform)** - Network accessline 135
2. **[Nutrition Chatbots + Evidence-Based AI: How to Build a Reliable Health Assistant](https://dev.to/wellallytech/nutrition-chatbots-evidence-based-ai-how-to-build-a-reliable-health-assistant-21nd)** - Network accessline 140
3. **[From Monolith to Microservices: A DDD Approach for a Wellness App](https://www.wellally.tech/blog/refactor-monolith-microservices-ddd-guide)** - Network accessline 149
- [Hypertension Monitoring Basics](https://wellally.tech/knowledge-base/chronic-disease/hypertension-monitoring) - Network accessline 150
- [Home Blood Pressure Measurement Guide](https://wellally.tech/knowledge-base/chronic-disease/bp-home-monitoring) - Network accessline 151
- [Dietary Strategies for Lowering Blood Pressure](https://wellally.tech/knowledge-base/chronic-disease/bp-diet-strategies) - Network accessline 152
- [Antihypertensive Medication Adherence](https://wellally.tech/knowledge-base/chronic-disease/antihypertensive-adherence) - Network accessline 158
- [Diabetes Basics](https://wellally.tech/knowledge-base/chronic-disease/diabetes-basics) - Network accessline 159
- [Blood Glucose Monitoring Guide](https://wellally.tech/knowledge-base/chronic-disease/blood-glucose-monitoring) - Network accessline 160
- [Diabetes Diet Management](https://wellally.tech/knowledge-base/nutrition/diabetic-diet) - Network accessline 161
- [HbA1c Testing and Interpretation](https://wellally.tech/knowledge-base/chronic-disease/hba1c-testing) - Network accessline 167
- [Sleep Hygiene Basics](https://wellally.tech/knowledge-base/sleep/sleep-hygiene) - Network accessline 168
- [Cognitive Behavioral Therapy for Insomnia](https://wellally.tech/knowledge-base/sleep/cbt-insomnia) - Network accessline 169
- [Sleep Apnea](https://wellally.tech/knowledge-base/sleep/sleep-apnea) - Network accessline 170
- [Circadian Rhythm Adjustment](https://wellally.tech/knowledge-base/sleep/circadian-rhythm) - Network accessline 176
- [Healthy Weight Loss Guide](https://wellally.tech/knowledge-base/nutrition/healthy-weight-loss) - Network accessline 177
- [Basal Metabolic Rate Calculator](https://wellally.tech/knowledge-base/nutrition/bmr-calculator) - Network accessline 178
- [Diet Recording Methods](https://wellally.tech/knowledge-base/nutrition/diet-tracking) - Network accessline 179
- [Exercise and Weight Loss](https://wellally.tech/knowledge-base/fitness/exercise-weight-loss) - Network accessline 187
1. **[Beyond the Snapshot: Building Resilient Health Monitoring through Long-Term Trend Analysis](https://www.wellally.tech/blog/long-term-trend-analysis)** - Network accessline 191
2. **[Memory is Not a Database: Implementing a Deterministic Family Health Ledger](https://www.wellally.tech/blog/family-health-ledger)** - Network accessline 195
3. **[Understanding AI Design Patterns: A Deep Dive into the RAG Design Pattern](https://www.wellally.tech/blog/rag-design-pattern)**
skills/wellally-tech/knowledge-base/mental-health.md
- Network accessline 35
**Stress Management** - Stress basics: https://wellally.tech/knowledge-base/mental-health/stress-basics - Network accessline 36
- Stress basics: https://wellally.tech/knowledge-base/mental-health/stress-basics - Network accessline 37
- Stress identification: https://wellally.tech/knowledge-base/mental-health/stress-identification - Network accessline 38
- Stress coping strategies: https://wellally.tech/knowledge-base/mental-health/stress-coping - Network accessline 39
- Work stress management: https://wellally.tech/knowledge-base/mental-health/work-stress - Network accessline 41
**Emotional Health** - Emotion basics: https://wellally.tech/knowledge-base/mental-health/emotions-basics - Network accessline 42
- Emotion basics: https://wellally.tech/knowledge-base/mental-health/emotions-basics - Network accessline 43
- Emotion recognition techniques: https://wellally.tech/knowledge-base/mental-health/emotion-recognition - Network accessline 44
- Emotion regulation methods: https://wellally.tech/knowledge-base/mental-health/emotion-regulation - Network accessline 45
- Mood tracking guide: https://wellally.tech/knowledge-base/mental-health/mood-tracking - Network accessline 47
**Anxiety and Depression** - Anxiety basics: https://wellally.tech/knowledge-base/mental-health/anxiety-basics - Network accessline 48
- Anxiety basics: https://wellally.tech/knowledge-base/mental-health/anxiety-basics - Network accessline 49
- Anxiety coping strategies: https://wellally.tech/knowledge-base/mental-health/anxiety-coping - Network accessline 50
- Depression recognition: https://wellally.tech/knowledge-base/mental-health/depression-recognition - Network accessline 51
- Depression self-help: https://wellally.tech/knowledge-base/mental-health/depression-self-help - Network accessline 53
**Mindfulness and Relaxation** - Mindfulness introduction: https://wellally.tech/knowledge-base/mental-health/mindfulness-intro - Network accessline 54
- Mindfulness introduction: https://wellally.tech/knowledge-base/mental-health/mindfulness-intro - Network accessline 55
- Meditation practice: https://wellally.tech/knowledge-base/mental-health/meditation-practice - Network accessline 56
- Progressive muscle relaxation: https://wellally.tech/knowledge-base/mental-health/progressive-relaxation - Network accessline 57
- Breathing exercises: https://wellally.tech/knowledge-base/mental-health/breathing-exercises - Network accessline 85
**Work Stress** - Workplace stress coping: https://wellally.tech/knowledge-base/mental-health/workplace-stress - Network accessline 86
- Workplace stress coping: https://wellally.tech/knowledge-base/mental-health/workplace-stress - Network accessline 87
- Burnout prevention: https://wellally.tech/knowledge-base/mental-health/burnout-prevention - Network accessline 88
- Work-life balance: https://wellally.tech/knowledge-base/mental-health/work-life-balance - Network accessline 89
- Time management techniques: https://wellally.tech/knowledge-base/mental-health/time-management - Network accessline 91
**Mood Swings** - Emotional stability techniques: https://wellally.tech/knowledge-base/mental-health/emotional-stability - Network accessline 92
- Emotional stability techniques: https://wellally.tech/knowledge-base/mental-health/emotional-stability - Network accessline 93
- Emotional journaling: https://wellally.tech/knowledge-base/mental-health/emotional-journaling - Network accessline 94
- Identify emotional triggers: https://wellally.tech/knowledge-base/mental-health/identify-triggers - Network accessline 95
- Emotion regulation strategies: https://wellally.tech/knowledge-base/mental-health/regulation-strategies - Network accessline 97
**Anxiety Symptoms** - Anxiety self-management: https://wellally.tech/knowledge-base/mental-health/anxiety-self-management - Network accessline 98
- Anxiety self-management: https://wellally.tech/knowledge-base/mental-health/anxiety-self-management - Network accessline 99
- Anxiety relaxation techniques: https://wellally.tech/knowledge-base/mental-health/anxiety-relaxation - Network accessline 100
- Cognitive reframing for anxiety: https://wellally.tech/knowledge-base/mental-health/cognitive-reframing - Network accessline 101
- Exposure therapy for anxiety: https://wellally.tech/knowledge-base/mental-health/exposure-therapy - Network accessline 103
**Low Mood** - Mood boosting strategies: https://wellally.tech/knowledge-base/mental-health/mood-boosting - Network accessline 104
- Mood boosting strategies: https://wellally.tech/knowledge-base/mental-health/mood-boosting - Network accessline 105
- Positive psychology: https://wellally.tech/knowledge-base/mental-health/positive-psychology - Network accessline 106
- Gratitude practice: https://wellally.tech/knowledge-base/mental-health/gratitude-practice - Network accessline 107
- Building social support: https://wellally.tech/knowledge-base/mental-health/social-support - Network accessline 111
**Mindfulness Practice** - Mindful breathing: https://wellally.tech/knowledge-base/mental-health/mindful-breathing - Network accessline 112
- Mindful breathing: https://wellally.tech/knowledge-base/mental-health/mindful-breathing - Network accessline 113
- Body scan: https://wellally.tech/knowledge-base/mental-health/body-scan - Network accessline 114
- Mindful walking: https://wellally.tech/knowledge-base/mental-health/mindful-walking - Network accessline 115
- Mindful eating: https://wellally.tech/knowledge-base/mental-health/mindful-eating - Network accessline 117
**Relaxation Techniques** - Deep breathing exercises: https://wellally.tech/knowledge-base/mental-health/deep-breathing - Network accessline 118
- Deep breathing exercises: https://wellally.tech/knowledge-base/mental-health/deep-breathing - Network accessline 119
- Progressive muscle relaxation (PMR): https://wellally.tech/knowledge-base/mental-health/pmr-technique - Network accessline 120
- Guided imagery: https://wellally.tech/knowledge-base/mental-health/guided-imagery - Network accessline 121
- Self-hypnosis: https://wellally.tech/knowledge-base/mental-health/self-hypnosis - Network accessline 123
**Cognitive Techniques** - Cognitive reframing: https://wellally.tech/knowledge-base/mental-health/cognitive-reframing - Network accessline 124
- Cognitive reframing: https://wellally.tech/knowledge-base/mental-health/cognitive-reframing - Network accessline 125
- Thought records: https://wellally.tech/knowledge-base/mental-health/thought-records - Network accessline 126
- Positive self-talk: https://wellally.tech/knowledge-base/mental-health/positive-self-talk - Network accessline 127
- Problem-solving techniques: https://wellally.tech/knowledge-base/mental-health/problem-solving - Network accessline 333
- [Mental Health Data Analysis](https://wellally.tech/blog/mental-health-data) - Network accessline 334
- [Stress and Health](https://wellally.tech/blog/stress-health) - Network accessline 338
- Chinese Mental Health Association: http://www.camp.org.cn/ - Network accessline 339
- American Psychological Association (APA): https://www.apa.org/ - Network accessline 340
- Mental Health Screening Tools: https://screening.mentalhealthscreening.org/
skills/wellally-tech/knowledge-base/nutrition.md
- Network accessline 29
**Basic Nutrition** - Nutrition basics: https://wellally.tech/knowledge-base/nutrition/nutrition-basics - Network accessline 30
- Nutrition basics: https://wellally.tech/knowledge-base/nutrition/nutrition-basics - Network accessline 31
- Macronutrients guide: https://wellally.tech/knowledge-base/nutrition/macronutrients - Network accessline 32
- Micronutrients guide: https://wellally.tech/knowledge-base/nutrition/micronutrients - Network accessline 34
**Diet Tracking** - How to track your diet: https://wellally.tech/knowledge-base/nutrition/diet-tracking - Network accessline 35
- How to track your diet: https://wellally.tech/knowledge-base/nutrition/diet-tracking - Network accessline 36
- Using the food database: https://wellally.tech/knowledge-base/nutrition/food-database - Network accessline 37
- Reading nutrition labels: https://wellally.tech/knowledge-base/nutrition/reading-labels - Network accessline 39
**Weight Management** - Healthy weight loss strategies: https://wellally.tech/knowledge-base/nutrition/healthy-weight-loss - Network accessline 40
- Healthy weight loss strategies: https://wellally.tech/knowledge-base/nutrition/healthy-weight-loss - Network accessline 41
- BMR calculator: https://wellally.tech/knowledge-base/nutrition/bmr-calculator - Network accessline 42
- Energy balance principles: https://wellally.tech/knowledge-base/nutrition/energy-balance - Network accessline 44
**Special Diets** - Diabetic diet: https://wellally.tech/knowledge-base/nutrition/diabetic-diet - Network accessline 45
- Diabetic diet: https://wellally.tech/knowledge-base/nutrition/diabetic-diet - Network accessline 46
- Low-sodium diet: https://wellally.tech/knowledge-base/nutrition/low-sodium-diet - Network accessline 47
- Low-fat diet: https://wellally.tech/knowledge-base/nutrition/low-fat-diet - Network accessline 48
- Vegetarian nutrition: https://wellally.tech/knowledge-base/nutrition/vegetarian-nutrition - Network accessline 73
**Hypertension** - DASH diet guide: https://wellally.tech/knowledge-base/nutrition/dash-diet - Network accessline 74
- DASH diet guide: https://wellally.tech/knowledge-base/nutrition/dash-diet - Network accessline 75
- Low-sodium diet tips: https://wellally.tech/knowledge-base/nutrition/low-sodium-tips - Network accessline 76
- Blood pressure lowering foods: https://wellally.tech/knowledge-base/nutrition/bp-lowering-foods - Network accessline 78
**Diabetes** - Carbohydrate counting: https://wellally.tech/knowledge-base/nutrition/carb-counting - Network accessline 79
- Carbohydrate counting: https://wellally.tech/knowledge-base/nutrition/carb-counting - Network accessline 80
- Glycemic index (GI) explained: https://wellally.tech/knowledge-base/nutrition/glycemic-index - Network accessline 81
- Diabetes diet principles: https://wellally.tech/knowledge-base/nutrition/diabetes-diet-principles - Network accessline 83
**High Cholesterol** - Cholesterol-lowering diet guide: https://wellally.tech/knowledge-base/nutrition/cholesterol-lowering-diet - Network accessline 84
- Cholesterol-lowering diet guide: https://wellally.tech/knowledge-base/nutrition/cholesterol-lowering-diet - Network accessline 85
- Healthy fat choices: https://wellally.tech/knowledge-base/nutrition/healthy-fats - Network accessline 86
- Dietary fiber and cholesterol: https://wellally.tech/knowledge-base/nutrition/fiber-cholesterol - Network accessline 88
**Obesity/Overweight** - Weight loss diet strategies: https://wellally.tech/knowledge-base/nutrition/weight-loss-diet - Network accessline 89
- Weight loss diet strategies: https://wellally.tech/knowledge-base/nutrition/weight-loss-diet - Network accessline 90
- Hunger control: https://wellally.tech/knowledge-base/nutrition/hunger-control - Network accessline 91
- Long-term weight maintenance: https://wellally.tech/knowledge-base/nutrition/weight-maintenance - Network accessline 95
**Protein** - Protein intake guide: https://wellally.tech/knowledge-base/nutrition/protein-guide - Network accessline 96
- Protein intake guide: https://wellally.tech/knowledge-base/nutrition/protein-guide - Network accessline 97
- High-quality protein sources: https://wellally.tech/knowledge-base/nutrition/protein-sources - Network accessline 98
- Exercise and protein: https://wellally.tech/knowledge-base/nutrition/protein-exercise - Network accessline 100
**Dietary Fiber** - Importance of dietary fiber: https://wellally.tech/knowledge-base/nutrition/fiber-importance - Network accessline 101
- Importance of dietary fiber: https://wellally.tech/knowledge-base/nutrition/fiber-importance - Network accessline 102
- High-fiber foods: https://wellally.tech/knowledge-base/nutrition/high-fiber-foods - Network accessline 103
- Dietary fiber and digestion: https://wellally.tech/knowledge-base/nutrition/fiber-digestion - Network accessline 105
**Vitamins and Minerals** - Complete vitamin guide: https://wellally.tech/knowledge-base/nutrition/vitamins-guide - Network accessline 106
- Complete vitamin guide: https://wellally.tech/knowledge-base/nutrition/vitamins-guide - Network accessline 107
- Complete mineral guide: https://wellally.tech/knowledge-base/nutrition/minerals-guide - Network accessline 108
- Nutritional supplements: https://wellally.tech/knowledge-base/nutrition/supplements-guide - Network accessline 212
- [Nutrition Chatbots and AI](https://dev.to/wellallytech/nutrition-chatbots-evidence-based-ai-how-to-build-a-reliable-health-assistant-21nd) - Network accessline 213
- [Nutritional Data Analysis Methods](https://wellally.tech/blog/nutritional-data-analysis) - Network accessline 217
- Chinese Dietary Guidelines (2022): http://dg.cnsoc.org/ - Network accessline 218
- USDA MyPlate: https://www.myplate.gov/ - Network accessline 219
- WHO Healthy Diet: https://www.who.int/news-room/fact-sheets/detail/healthy-diet
skills/wellally-tech/knowledge-base/sleep.md
- Network accessline 35
**Sleep Basics** - Sleep basics: https://wellally.tech/knowledge-base/sleep/sleep-basics - Network accessline 36
- Sleep basics: https://wellally.tech/knowledge-base/sleep/sleep-basics - Network accessline 37
- Sleep stages explained: https://wellally.tech/knowledge-base/sleep/sleep-stages - Network accessline 38
- Sleep cycles: https://wellally.tech/knowledge-base/sleep/sleep-cycles - Network accessline 39
- Circadian rhythm: https://wellally.tech/knowledge-base/sleep/circadian-rhythm - Network accessline 41
**Sleep Quality Assessment** - Sleep quality metrics: https://wellally.tech/knowledge-base/sleep/sleep-quality-metrics - Network accessline 42
- Sleep quality metrics: https://wellally.tech/knowledge-base/sleep/sleep-quality-metrics - Network accessline 43
- Sleep efficiency calculation: https://wellally.tech/knowledge-base/sleep/sleep-efficiency - Network accessline 44
- Sleep score interpretation: https://wellally.tech/knowledge-base/sleep/sleep-score-interpretation - Network accessline 45
- Sleep tracking devices: https://wellally.tech/knowledge-base/sleep/sleep-tracking-devices - Network accessline 47
**Sleep Disorders** - Insomnia: https://wellally.tech/knowledge-base/sleep/insomnia - Network accessline 48
- Insomnia: https://wellally.tech/knowledge-base/sleep/insomnia - Network accessline 49
- Obstructive sleep apnea: https://wellally.tech/knowledge-base/sleep/obstructive-sleep-apnea - Network accessline 50
- Restless legs syndrome: https://wellally.tech/knowledge-base/sleep/restless-legs-syndrome - Network accessline 51
- Circadian rhythm disorders: https://wellally.tech/knowledge-base/sleep/circadian-disorders - Network accessline 53
**Sleep Improvement** - Sleep hygiene guide: https://wellally.tech/knowledge-base/sleep/sleep-hygiene - Network accessline 54
- Sleep hygiene guide: https://wellally.tech/knowledge-base/sleep/sleep-hygiene - Network accessline 55
- Improve sleep environment: https://wellally.tech/knowledge-base/sleep/sleep-environment - Network accessline 56
- Relaxation techniques: https://wellally.tech/knowledge-base/sleep/relaxation-techniques - Network accessline 57
- CBT for insomnia: https://wellally.tech/knowledge-base/sleep/cbt-insomnia - Network accessline 84
**Difficulty Falling Asleep** - Fall asleep faster techniques: https://wellally.tech/knowledge-base/sleep/fall-asleep-faster - Network accessline 85
- Fall asleep faster techniques: https://wellally.tech/knowledge-base/sleep/fall-asleep-faster - Network accessline 86
- Bedtime routine: https://wellally.tech/knowledge-base/sleep/bedtime-routine - Network accessline 87
- Relaxation breathing exercises: https://wellally.tech/knowledge-base/sleep/breathing-exercises - Network accessline 89
**Early Awakening** - Early awakening causes: https://wellally.tech/knowledge-base/sleep/early-awakening-causes - Network accessline 90
- Early awakening causes: https://wellally.tech/knowledge-base/sleep/early-awakening-causes - Network accessline 91
- Extend sleep duration: https://wellally.tech/knowledge-base/sleep/extend-sleep-duration - Network accessline 92
- Morning light management: https://wellally.tech/knowledge-base/sleep/morning-light - Network accessline 94
**Poor Sleep Quality** - Deep sleep improvement: https://wellally.tech/knowledge-base/sleep/deep-sleep-improvement - Network accessline 95
- Deep sleep improvement: https://wellally.tech/knowledge-base/sleep/deep-sleep-improvement - Network accessline 96
- Reduce night awakenings: https://wellally.tech/knowledge-base/sleep/reduce-night-awakenings - Network accessline 97
- Sleep continuity: https://wellally.tech/knowledge-base/sleep/sleep-continuity - Network accessline 99
**Daytime Sleepiness** - Daytime sleepiness causes: https://wellally.tech/knowledge-base/sleep/daytime-sleepiness-causes - Network accessline 100
- Daytime sleepiness causes: https://wellally.tech/knowledge-base/sleep/daytime-sleepiness-causes - Network accessline 101
- Improve night sleep: https://wellally.tech/knowledge-base/sleep/improve-night-sleep - Network accessline 102
- Nap guidelines: https://wellally.tech/knowledge-base/sleep/nap-guidelines - Network accessline 106
**Adults** - Adult sleep needs: https://wellally.tech/knowledge-base/sleep/adult-sleep-needs - Network accessline 107
- Adult sleep needs: https://wellally.tech/knowledge-base/sleep/adult-sleep-needs - Network accessline 108
- Work-sleep balance: https://wellally.tech/knowledge-base/sleep/work-sleep-balance - Network accessline 109
- Stress and sleep: https://wellally.tech/knowledge-base/sleep/stress-sleep - Network accessline 111
**Older Adults** - Senior sleep changes: https://wellally.tech/knowledge-base/sleep/senior-sleep-changes - Network accessline 112
- Senior sleep changes: https://wellally.tech/knowledge-base/sleep/senior-sleep-changes - Network accessline 113
- Senior sleep tips: https://wellally.tech/knowledge-base/sleep/senior-sleep-tips - Network accessline 114
- Sleep medication precautions: https://wellally.tech/knowledge-base/sleep/senior-sleep-medication - Network accessline 116
**Children and Adolescents** - Child sleep needs: https://wellally.tech/knowledge-base/sleep/child-sleep-needs - Network accessline 117
- Child sleep needs: https://wellally.tech/knowledge-base/sleep/child-sleep-needs - Network accessline 118
- Teen sleep: https://wellally.tech/knowledge-base/sleep/teen-sleep - Network accessline 119
- Establishing sleep habits: https://wellally.tech/knowledge-base/sleep/sleep-habits-children - Network accessline 321
- [Sleep Data Analysis](https://wellally.tech/blog/sleep-data-analysis) - Network accessline 322
- [Sleep and Mental Health](https://wellally.tech/blog/sleep-mental-health) - Network accessline 326
- National Sleep Foundation: https://www.thensf.org/ - Network accessline 327
- American Academy of Sleep Medicine: https://aasm.org/ - Network accessline 328
- Chinese Sleep Research Society: http://www.csre.org.cn/
skills/wikipedia-search/SKILL.md
- Network accessline 87
"title": "Quantum computing", "description": "Study of computers based on quantum phenomena", "url": "https://en.wikipedia.org/wiki/Quantum_computing" - Network accessline 88
"description": "Study of computers based on quantum phenomena", "url": "https://en.wikipedia.org/wiki/Quantum_computing" }, - Network accessline 89
"url": "https://en.wikipedia.org/wiki/Quantum_computing" - Network accessline 115
"title": "Albert Einstein", "exists": true, "url": "https://en.wikipedia.org/wiki/Albert_Einstein", - Network accessline 116
"exists": true, "url": "https://en.wikipedia.org/wiki/Albert_Einstein", "summary": "Albert Einstein was a German-born theoretical physicist...", - Network accessline 117
"url": "https://en.wikipedia.org/wiki/Albert_Einstein", - Network accessline 135
"title": "Machine learning", "exists": true, "url": "https://en.wikipedia.org/wiki/Machine_learning", - Network accessline 136
"exists": true, "url": "https://en.wikipedia.org/wiki/Machine_learning", "summary": "Machine learning is a field of study in artificial intelligence...", - Network accessline 137
"url": "https://en.wikipedia.org/wiki/Machine_learning", - Network accessline 192
"title": "Page Title", "description": "Brief description", "url": "https://en.wikipedia.org/wiki/Page_Title" - Network accessline 193
"description": "Brief description", "url": "https://en.wikipedia.org/wiki/Page_Title" } - Network accessline 194
"url": "https://en.wikipedia.org/wiki/Page_Title" - Network accessline 205
"title": "Article Title", "exists": true, "url": "https://en.wikipedia.org/wiki/Article_Title", - Network accessline 206
"exists": true, "url": "https://en.wikipedia.org/wiki/Article_Title", "summary": "Summary text...", - Network accessline 207
"url": "https://en.wikipedia.org/wiki/Article_Title", - Network accessline 217
"title": "Article Title", "exists": true, "url": "https://en.wikipedia.org/wiki/Article_Title", - Network accessline 218
"exists": true, "url": "https://en.wikipedia.org/wiki/Article_Title", "summary": "Summary text...", - Network accessline 219
"url": "https://en.wikipedia.org/wiki/Article_Title", - Network accessline 287
Source: - [Python (programming language) - Wikipedia](https://en.wikipedia.org/wiki/Python_(programming_language)) - Network accessline 288
- [Python (programming language) - Wikipedia](https://en.wikipedia.org/wiki/Python_(programming_language)) - Network accessline 472
- [Wikipedia API Documentation](https://www.mediawiki.org/wiki/API:Main_page) — Official MediaWiki API docs - Network accessline 473
- [Wikipedia-API Python Library](https://github.com/martin-majlis/Wikipedia-API) — Upstream library documentation
skills/wikipedia-search/scripts/wiki.py
skills/wikipedia-search/setup.sh
- Executable scriptline 1
#!/bin/bash
skills/writing-skills/anthropic-best-practices.md
- Network accessline 13
The [context window](https://platform.claude.com/docs/en/build-with-claude/context-windows) is a public good. Your Skill shares the context window with everything else Claude needs to know, including: - Network accessline 249
<img src="https://mintcdn.com/anthropic-claude-docs/4Bny2bjzuGBK7o00/images/agent-skills-simple-file.png?fit=max&auto=format&n=4Bny2bjzuGBK7o00&q=85&s=87782ff239b297d9a9e8e1b72ed72db9" alt="Simple SKILL.md file showing YAML frontmatter and - Network accessline 253
<img src="https://mintcdn.com/anthropic-claude-docs/4Bny2bjzuGBK7o00/images/agent-skills-bundling-content.png?fit=max&auto=format&n=4Bny2bjzuGBK7o00&q=85&s=a5e0aa41e3d53985a7e3e43668a33ea3" alt="Bundling additional reference files like refe - Network accessline 919
<img src="https://mintcdn.com/anthropic-claude-docs/4Bny2bjzuGBK7o00/images/agent-skills-executable-scripts.png?fit=max&auto=format&n=4Bny2bjzuGBK7o00&q=85&s=4bbc45f2c2e0bee9f2f0d5da669bad00" alt="Bundling executable scripts alongside instr
skills/writing-skills/render-graphs.js
- Executable scriptline 1
#!/usr/bin/env node
skills/xlsx-official/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/xlsx-official/recalc.py
- Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 35
macro_content = '''<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" scr - Network accessline 36
<!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic"> Sub RecalculateAndSave() - Network accessline 37
<script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic">
skills/xlsx/LICENSE.txt
- Network accessline 6
exists, use is governed by Anthropic's Consumer Terms of Service or Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms - Network accessline 7
Commercial Terms of Service, as applicable: https://www.anthropic.com/legal/consumer-terms https://www.anthropic.com/legal/commercial-terms - Network accessline 8
https://www.anthropic.com/legal/consumer-terms - Network accessline 9
https://www.anthropic.com/legal/commercial-terms
skills/xlsx/scripts/office/helpers/__init__.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/helpers/merge_runs.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/helpers/simplify_redlines.py
skills/xlsx/scripts/office/pack.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 6
xmlns:cdr="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 9
elementFormDefault="qualified" attributeFormDefault="unqualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" schemaLocation="dml-chartDrawing.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 15
schemaLocation="dml-chartDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/chartDrawing" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 8
elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 12
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
xmlns="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 11
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" schemaLocation="dml-diagram.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/diagram" - Network accessline 13
schemaLocation="dml-diagram.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" schemaLocation="dml-chart.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/chart" - Network accessline 15
schemaLocation="dml-chart.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" schemaLocation="dml-picture.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 17
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas" schemaLocation="dml-lockedCanvas.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/lockedCanvas"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 4
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" elementFormDefault="qualified" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/picture"> - Network accessline 6
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 5
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 7
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 9
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> - Network accessline 10
<xsd:import schemaLocation="shared-relationshipReference.xsd" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/> <xsd:element name="from" type="CT_Marker"/> - Network accessline 11
namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"/>
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 4
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 5
xmlns:dpct="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 9
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 11
schemaLocation="dml-main.xsd"/> <xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 12
<xsd:import schemaLocation="wml.xsd" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 13
namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/picture" - Network accessline 15
schemaLocation="dml-picture.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 16
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 4
xmlns:p="http://schemas.openxmlformats.org/presentationml/2006/main" - Network accessline 5
xmlns:a="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 6
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 7
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 8
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 9
targetNamespace="http://schemas.openxmlformats.org/presentationml/2006/main"> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 11
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="dml-main.xsd"/> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" - Network accessline 13
schemaLocation="dml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/characteristics" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/characteristics"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/bibliography" - Network accessline 6
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/customXml" - Network accessline 6
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/custom-properties" - Network accessline 7
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 8
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 9
schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 10
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 4
xmlns:vt="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/extended-properties" - Network accessline 6
elementFormDefault="qualified" blockDefault="#all"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" schemaLocation="shared-documentPropertiesVariantTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/docPropsVTypes" - Network accessline 6
blockDefault="#all" elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/ - Network accessline 8
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/math"> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 10
schemaLocation="wml.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/> <xsd:simpleType name="ST_Integer255"> - Network accessline 13
<xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="xml.xsd"/>
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" blockDefault="#all"> - Network accessline 6
targetNamespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:xdr="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 6
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
targetNamespace="http://schemas.openxmlformats.org/spreadsheetml/2006/main" - Network accessline 8
elementFormDefault="qualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing" schemaLocation="dml-spreadsheetDrawing.xsd"/> - Network accessline 14
namespace="http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="urn:schemas-microsoft-com:vml" - Network accessline 3
xmlns:pvml="urn:schemas-microsoft-com:office:powerpoint" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 4
xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:w10="urn:schemas-microsoft-com:office:word" - Network accessline 5
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 6
xmlns:w10="urn:schemas-microsoft-com:office:word" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:x="urn:schemas-microsoft-com:office:excel" - Network accessline 7
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:vml" elementFormDefault="qualified" - Network accessline 9
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 12
<xsd:import namespace="urn:schemas-microsoft-com:office:office" schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 13
schemaLocation="vml-officeDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="wml.xsd"/> - Network accessline 14
<xsd:import namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 16
<xsd:import namespace="urn:schemas-microsoft-com:office:word" schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 17
schemaLocation="vml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 18
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 22
<xsd:import namespace="urn:schemas-microsoft-com:office:powerpoint" schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 23
schemaLocation="vml-presentationDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 24
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:office" xmlns:v="urn:schemas-microsoft-com:vml" xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedT - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 7
attributeFormDefault="unqualified"> <xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 8
<xsd:import namespace="urn:schemas-microsoft-com:vml" schemaLocation="vml-main.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 9
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 10
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 11
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns="urn:schemas-microsoft-com:office:excel" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" - Network accessline 4
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 5
targetNamespace="urn:schemas-microsoft-com:office:excel" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 6
attributeFormDefault="unqualified"> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 7
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes"
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 2
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 3
xmlns:m="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 4
xmlns:r="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 5
xmlns:sl="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 6
xmlns:wp="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 7
xmlns="http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 8
xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 9
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 10
elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> <xsd:import namespace="http://schemas.openxmlformats.org/markup-compatib - Network accessline 11
targetNamespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main"> - Network accessline 12
<xsd:import namespace="http://schemas.openxmlformats.org/markup-compatibility/2006" schemaLocation="../mce/mc.xsd"/> - Network accessline 13
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing" - Network accessline 14
schemaLocation="dml-wordprocessingDrawing.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" schemaLocation="shared-math.xsd"/> - Network accessline 15
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/math" - Network accessline 16
schemaLocation="shared-math.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="shared-relationshipReference.xsd"/> - Network accessline 17
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 18
schemaLocation="shared-relationshipReference.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="shared-commonSimpleTypes.xsd"/> - Network accessline 19
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" - Network accessline 20
schemaLocation="shared-commonSimpleTypes.xsd"/> <xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" schemaLocation="shared-customXmlSchemaProperties.xsd"/> - Network accessline 21
<xsd:import namespace="http://schemas.openxmlformats.org/schemaLibrary/2006/main" - Network accessline 22
schemaLocation="shared-customXmlSchemaProperties.xsd"/> <xsd:import namespace="http://www.w3.org/XML/1998/namespace"/> <xsd:complexType name="CT_Empty"/> - Network accessline 23
<xsd:import namespace="http://www.w3.org/XML/1998/namespace"/>
skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd
- Network accessline 1
<?xml version='1.0'?> <xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 2
<xs:schema targetNamespace="http://www.w3.org/XML/1998/namespace" xmlns:xs="http://www.w3.org/2001/XMLSchema" xml:lang="en"> - Network accessline 4
<xs:annotation> <xs:documentation> See http://www.w3.org/XML/1998/namespace.html and - Network accessline 5
<xs:documentation> See http://www.w3.org/XML/1998/namespace.html and http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 6
See http://www.w3.org/XML/1998/namespace.html and - Network accessline 7
http://www.w3.org/TR/REC-xml for information about this namespace. - Network accessline 55
<schema . . .> . . . <import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 56
. . . <import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 57
<import namespace="http://www.w3.org/XML/1998/namespace" - Network accessline 58
schemaLocation="http://www.w3.org/2001/03/xml.xsd"/> - Network accessline 72
<xs:documentation>In keeping with the XML Schema WG's standard versioning policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. - Network accessline 73
policy, this schema document will persist at http://www.w3.org/2001/03/xml.xsd. At the date of issue it can also be found at - Network accessline 74
http://www.w3.org/2001/03/xml.xsd. - Network accessline 75
At the date of issue it can also be found at http://www.w3.org/2001/xml.xsd. The schema document at that URI may however change in the future, - Network accessline 76
http://www.w3.org/2001/xml.xsd. - Network accessline 79
itself. In other words, if the XML Schema namespace changes, the version of this document at http://www.w3.org/2001/xml.xsd will change - Network accessline 80
of this document at http://www.w3.org/2001/xml.xsd will change accordingly; the version at - Network accessline 81
http://www.w3.org/2001/xml.xsd will change - Network accessline 82
accordingly; the version at http://www.w3.org/2001/03/xml.xsd will not change. </xs:documentation> - Network accessline 83
http://www.w3.org/2001/03/xml.xsd will not change. - Network accessline 103
<xs:attribute name="base" type="xs:anyURI"> <xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for - Network accessline 104
<xs:annotation> <xs:documentation>See http://www.w3.org/TR/xmlbase/ for information about this attribute.</xs:documentation> - Network accessline 105
<xs:documentation>See http://www.w3.org/TR/xmlbase/ for
skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 2
<xs:schema xmlns="http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 3
xmlns:xs="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/content-types"
skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8"?> <xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 2
<xs:schema targetNamespace="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 3
xmlns="http://schemas.openxmlformats.org/package/2006/metadata/core-properties" - Network accessline 4
xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/" - Network accessline 5
xmlns:dcterms="http://purl.org/dc/terms/" elementFormDefault="qualified" blockDefault="#all"> - Network accessline 7
<xs:import namespace="http://purl.org/dc/elements/1.1/" - Network accessline 8
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dc.xsd"/> - Network accessline 9
<xs:import namespace="http://purl.org/dc/terms/" - Network accessline 10
schemaLocation="http://dublincore.org/schemas/xmls/qdc/2003/04/02/dcterms.xsd"/> - Network accessline 11
<xs:import id="xml" namespace="http://www.w3.org/XML/1998/namespace"/>
skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd
- Network accessline 1
<?xml version="1.0" encoding="UTF-8"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/digital-signature" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/digital-signature"
skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd
- Network accessline 1
<U+FEFF><?xml version="1.0" encoding="UTF-8" standalone="no"?> <xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 2
<xsd:schema xmlns="http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 3
xmlns:xsd="http://www.w3.org/2001/XMLSchema" - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/package/2006/relationships"
skills/xlsx/scripts/office/schemas/mce/mc.xsd
- Network accessline 1
<?xml version="1.0" encoding="utf-8"?> <xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 2
<xsd:schema xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 3
attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 4
targetNamespace="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 5
xmlns:xsd="http://www.w3.org/2001/XMLSchema"> - Network accessline 7
<!-- This XSD is a modified version of the one found at: https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 9
https://github.com/plutext/docx4j/blob/master/xsd/mce/markup-compatibility-2006-MINIMAL.xsd - Network accessline 15
<w:document xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 16
xmlns:mc="http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 17
xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns:r="http://schemas.op - Network accessline 2
<!-- <xsd:import id="rel" namespace="http://schemas.openxmlformats.org/officeDocument/2006/relationships" schemaLocation="orel.xsd"/> --> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<!-- <xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartbasetypes.xsd"/> - Network accessline 5
<xsd:import namespace="http://schemas.openxmlformats.org/drawingml/2006/main" schemaLocation="oartsplineproperties.xsd"/> -->
skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" elementFormDefault="qualified" att - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 3
<xsd:import namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w="http://schemas.openxmlformats.org/wordprocessingml/2006/main" xmlns:s="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" xmlns:w16="http://schemas.microsoft. - Network accessline 2
<xsd:import id="w16" namespace="http://schemas.microsoft.com/office/word/2018/wordml" schemaLocation="wml-2018.xsd"/> - Network accessline 3
<xsd:import id="w" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/> - Network accessline 4
<xsd:import id="s" namespace="http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes" schemaLocation="../ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd"/>
skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd
- Network accessline 1
<xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:w12="http://schemas.openxmlformats.org/wordprocessingml/2006/main" elementFormDefault="qualified" attributeFormDefault="qualified" blockDefault="#all" xmlns="http://schemas.micr - Network accessline 2
<xsd:import id="w12" namespace="http://schemas.openxmlformats.org/wordprocessingml/2006/main" schemaLocation="../ISO-IEC29500-4_2016/wml.xsd"/>
skills/xlsx/scripts/office/soffice.py
- Executable scriptline 1
Executable file - Access to secretsline 25
[Credential-related source omitted] - Network accessline 44
def _needs_shim() -> bool: try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) - Network accessline 45
try: s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM) s.close() - Network accessline 46
s = socket.socket(socket.AF_UNIX, socket.SOCK_STREAM)
skills/xlsx/scripts/office/unpack.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/validate.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/validators/__init__.py
- Executable scriptline 1
Executable file
skills/xlsx/scripts/office/validators/base.py
- Executable scriptline 1
Executable file - Network accessline 61
MC_NAMESPACE = "http://schemas.openxmlformats.org/markup-compatibility/2006" - Network accessline 62
XML_NAMESPACE = "http://www.w3.org/XML/1998/namespace" - Network accessline 64
PACKAGE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 65
"http://schemas.openxmlformats.org/package/2006/relationships" - Network accessline 66
) OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 67
OFFICE_RELATIONSHIPS_NAMESPACE = ( "http://schemas.openxmlformats.org/officeDocument/2006/relationships" ) - Network accessline 68
"http://schemas.openxmlformats.org/officeDocument/2006/relationships" - Network accessline 69
) CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 70
CONTENT_TYPES_NAMESPACE = ( "http://schemas.openxmlformats.org/package/2006/content-types" ) - Network accessline 71
"http://schemas.openxmlformats.org/package/2006/content-types" - Network accessline 76
OOXML_NAMESPACES = { "http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 77
"http://schemas.openxmlformats.org/officeDocument/2006/math", - Network accessline 78
"http://schemas.openxmlformats.org/officeDocument/2006/relationships", - Network accessline 79
"http://schemas.openxmlformats.org/schemaLibrary/2006/main", - Network accessline 80
"http://schemas.openxmlformats.org/drawingml/2006/main", - Network accessline 81
"http://schemas.openxmlformats.org/drawingml/2006/chart", - Network accessline 82
"http://schemas.openxmlformats.org/drawingml/2006/chartDrawing", - Network accessline 83
"http://schemas.openxmlformats.org/drawingml/2006/diagram", - Network accessline 84
"http://schemas.openxmlformats.org/drawingml/2006/picture", - Network accessline 85
"http://schemas.openxmlformats.org/drawingml/2006/spreadsheetDrawing", - Network accessline 86
"http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing", - Network accessline 87
"http://schemas.openxmlformats.org/wordprocessingml/2006/main", - Network accessline 88
"http://schemas.openxmlformats.org/presentationml/2006/main", - Network accessline 89
"http://schemas.openxmlformats.org/spreadsheetml/2006/main", - Network accessline 90
"http://schemas.openxmlformats.org/officeDocument/2006/sharedTypes", - Network accessline 91
"http://www.w3.org/XML/1998/namespace",
skills/xlsx/scripts/office/validators/docx.py
- Executable scriptline 1
Executable file - Network accessline 18
WORD_2006_NAMESPACE = "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 19
W14_NAMESPACE = "http://schemas.microsoft.com/office/word/2010/wordml" - Network accessline 20
W16CID_NAMESPACE = "http://schemas.microsoft.com/office/word/2016/wordml/cid"
skills/xlsx/scripts/office/validators/pptx.py
skills/xlsx/scripts/office/validators/redlining.py
- Executable scriptline 1
Executable file - Network accessline 17
self.author = author self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" - Network accessline 18
self.namespaces = { "w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main" } - Network accessline 19
"w": "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
skills/xlsx/scripts/recalc.py
- Executable scriptline 1
Executable file - Network accessline 21
RECALCULATE_MACRO = """<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" - Network accessline 22
<!DOCTYPE script:module PUBLIC "-//OpenOffice.org//DTD OfficeDocument 1.0//EN" "module.dtd"> <script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic"> Sub RecalculateAndSave() - Network accessline 23
<script:module xmlns:script="http://openoffice.org/2000/script" script:name="Module1" script:language="StarBasic">
skills/zarr-python/SKILL.md
- Network accessline 768
- **Official Documentation**: https://zarr.readthedocs.io/ - Network accessline 769
- **Zarr Specifications**: https://zarr-specs.readthedocs.io/ - Network accessline 770
- **GitHub Repository**: https://github.com/zarr-developers/zarr-python - Network accessline 771
- **Community Chat**: https://gitter.im/zarr-developers/community - Network accessline 773
**Related Libraries**: - **Xarray**: https://docs.xarray.dev/ (labeled arrays) - Network accessline 774
- **Xarray**: https://docs.xarray.dev/ (labeled arrays) - Network accessline 775
- **Dask**: https://docs.dask.org/ (parallel computing) - Network accessline 776
- **NumCodecs**: https://numcodecs.readthedocs.io/ (compression codecs)
skills/zinc-database/SKILL.md
- Network accessline 40
Primary access point: https://zinc.docking.org/ - Network accessline 41
Interactive searching: https://cartblanche22.docking.org/ - Network accessline 47
**Base URL**: `https://cartblanche22.docking.org/` - Network accessline 57
**Web interface**: https://cartblanche22.docking.org/search/zincid - Network accessline 61
curl "https://cartblanche22.docking.org/[email protected]_fields=smiles,zinc_id" - Network accessline 66
curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001,ZINC000000000002&output_fields=smiles,zinc_id,tranche" - Network accessline 75
**Web interface**: https://cartblanche22.docking.org/search/smiles - Network accessline 79
curl "https://cartblanche22.docking.org/[email protected]=4-Fadist=4" - Network accessline 90
curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1" - Network accessline 95
curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1&dist=3&output_fields=zinc_id,smiles,tranche" - Network accessline 102
**Web interface**: https://cartblanche22.docking.org/search/catitems - Network accessline 106
curl "https://cartblanche22.docking.org/catitems.txt:catitem_id=SUPPLIER-CODE-123" - Network accessline 118
**Web interface**: https://cartblanche22.docking.org/search/random - Network accessline 122
curl "https://cartblanche22.docking.org/substance/random.txt:count=100" - Network accessline 132
curl "https://cartblanche22.docking.org/substance/random.txt:count=1000&subset=lead-like&output_fields=zinc_id,smiles,tranche" - Network accessline 143
# Example: Get drug-like compounds with specific LogP and MW curl "https://cartblanche22.docking.org/substance/random.txt:count=10000&subset=drug-like&output_fields=zinc_id,smiles,tranche" > docking_library.txt - Network accessline 144
curl "https://cartblanche22.docking.org/substance/random.txt:count=10000&subset=drug-like&output_fields=zinc_id,smiles,tranche" > docking_library.txt - Network accessline 170
curl "https://cartblanche22.docking.org/smiles.txt:smiles=CC(C)Cc1ccc(cc1)C(C)C(=O)O&dist=5&output_fields=zinc_id,smiles,catalogs" > analogs.txt - Network accessline 198
curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001,ZINC000000000002&output_fields=zinc_id,smiles,supplier_code,catalogs" - Network accessline 212
curl "https://cartblanche22.docking.org/substance/random.txt:count=5000&subset=lead-like&output_fields=zinc_id,smiles,tranche" > chemical_space_sample.txt - Network accessline 231
curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001&output_fields=zinc_id,smiles,catalogs,tranche" - Network accessline 257
**File repository**: https://files.docking.org/zinc22/ - Network accessline 264
Refer to ZINC documentation at https://wiki.docking.org for downloading protocols and batch access methods. - Network accessline 268
### Using curl with Python - Network accessline 274
def query_zinc_by_id(zinc_id, output_fields="zinc_id,smiles,catalogs"): """Query ZINC22 by ZINC ID.""" url = f"https://cartblanche22.docking.org/[email protected]_id={zinc_id}&output_fields={output_fields}" - Network accessline 275
"""Query ZINC22 by ZINC ID.""" url = f"https://cartblanche22.docking.org/[email protected]_id={zinc_id}&output_fields={output_fields}" result = subprocess.run(['curl', url], capture_output=True, text=True) - Network accessline 276
url = f"https://cartblanche22.docking.org/[email protected]_id={zinc_id}&output_fields={output_fields}" result = subprocess.run(['curl', url], capture_output=True, text=True) return result.stdout - Network accessline 277
result = subprocess.run(['curl', url], capture_output=True, text=True) - Network accessline 280
def search_by_smiles(smiles, dist=0, adist=0, output_fields="zinc_id,smiles"): """Search ZINC22 by SMILES with optional distance parameters.""" url = f"https://cartblanche22.docking.org/smiles.txt:smiles={smiles}&dist={dist}&adist={ - Network accessline 281
"""Search ZINC22 by SMILES with optional distance parameters.""" url = f"https://cartblanche22.docking.org/smiles.txt:smiles={smiles}&dist={dist}&adist={adist}&output_fields={output_fields}" result = subprocess.run(['curl', url], ca - Network accessline 282
url = f"https://cartblanche22.docking.org/smiles.txt:smiles={smiles}&dist={dist}&adist={adist}&output_fields={output_fields}" result = subprocess.run(['curl', url], capture_output=True, text=True) return result.stdout - Network accessline 283
result = subprocess.run(['curl', url], capture_output=True, text=True) - Network accessline 286
def get_random_compounds(count=100, subset=None, output_fields="zinc_id,smiles,tranche"): """Get random compounds from ZINC22.""" url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={output_fie - Network accessline 287
"""Get random compounds from ZINC22.""" url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={output_fields}" if subset: - Network accessline 288
url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={output_fields}" - Network accessline 289
if subset: url += f"&subset={subset}" result = subprocess.run(['curl', url], capture_output=True, text=True) - Network accessline 290
url += f"&subset={subset}" result = subprocess.run(['curl', url], capture_output=True, text=True) return result.stdout - Network accessline 291
result = subprocess.run(['curl', url], capture_output=True, text=True) - Network accessline 334
- **Rate limiting**: Respect server resources; avoid rapid consecutive requests - **Caching**: Store frequently accessed compounds locally - **Parallel downloads**: When downloading 3D structures, use parallel wget or aria2c for file reposi - Network accessline 335
- **Caching**: Store frequently accessed compounds locally - **Parallel downloads**: When downloading 3D structures, use parallel wget or aria2c for file repositories - **Subset filtering**: Use lead-like, drug-like, or fragment subsets to - Network accessline 336
- **Parallel downloads**: When downloading 3D structures, use parallel wget or aria2c for file repositories - Network accessline 382
- **ZINC Website**: https://zinc.docking.org/ - Network accessline 383
- **CartBlanche22 Interface**: https://cartblanche22.docking.org/ - Network accessline 384
- **ZINC Wiki**: https://wiki.docking.org/ - Network accessline 385
- **File Repository**: https://files.docking.org/zinc22/ - Network accessline 386
- **GitHub**: https://github.com/docking-org/
skills/zinc-database/references/api_reference.md
- Network accessline 9
### ZINC22 (Current) - **CartBlanche22 API**: `https://cartblanche22.docking.org/` - Network accessline 10
- **CartBlanche22 API**: `https://cartblanche22.docking.org/` - Network accessline 11
- **File Repository**: `https://files.docking.org/zinc22/` - Network accessline 12
- **Main Website**: `https://zinc.docking.org/` - Network accessline 14
### ZINC20 (Maintained) - **API**: `https://zinc20.docking.org/` - Network accessline 15
- **API**: `https://zinc20.docking.org/` - Network accessline 16
- **File Repository**: `https://files.docking.org/zinc20/` - Network accessline 18
### Documentation - **Wiki**: `https://wiki.docking.org/` - Network accessline 19
- **Wiki**: `https://wiki.docking.org/` - Network accessline 20
- **GitHub**: `https://github.com/docking-org/` - Network accessline 36
https://cartblanche22.docking.org/substances.txt:zinc_id={ZINC_ID}&output_fields={FIELDS} - Network accessline 43
curl "https://cartblanche22.docking.org/[email protected]_fields=zinc_id,smiles,catalogs" - Network accessline 48
curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001,ZINC000000000002,ZINC000000000003&output_fields=zinc_id,smiles,tranche" - Network accessline 53
# Create file with ZINC IDs (one per line or comma-separated) curl -X POST "https://cartblanche22.docking.org/substances.txt?output_fields=zinc_id,smiles" \ - Network accessline 54
curl -X POST "https://cartblanche22.docking.org/substances.txt?output_fields=zinc_id,smiles" \ - Network accessline 79
https://cartblanche22.docking.org/smiles.txt:smiles={SMILES}&dist={DIST}&adist={ADIST}&output_fields={FIELDS} - Network accessline 86
curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1&output_fields=zinc_id,smiles" - Network accessline 91
curl "https://cartblanche22.docking.org/smiles.txt:smiles=CC(C)Cc1ccc(cc1)C(C)C(=O)O&dist=3&output_fields=zinc_id,smiles,catalogs" - Network accessline 96
curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1&dist=5&adist=5&output_fields=zinc_id,smiles,tranche" - Network accessline 101
# Original: CC(=O)Oc1ccccc1C(=O)O # Encoded: CC%28%3DO%29Oc1ccccc1C%28%3DO%29O curl "https://cartblanche22.docking.org/smiles.txt:smiles=CC%28%3DO%29Oc1ccccc1C%28%3DO%29O&dist=2" - Network accessline 103
curl "https://cartblanche22.docking.org/smiles.txt:smiles=CC%28%3DO%29Oc1ccccc1C%28%3DO%29O&dist=2" - Network accessline 124
https://cartblanche22.docking.org/catitems.txt:catitem_id={SUPPLIER_CODE}&output_fields={FIELDS} - Network accessline 129
curl "https://cartblanche22.docking.org/catitems.txt:catitem_id=SUPPLIER-12345&output_fields=zinc_id,smiles,supplier_code,catalogs" - Network accessline 145
https://cartblanche22.docking.org/substance/random.txt:count={COUNT}&subset={SUBSET}&output_fields={FIELDS} - Network accessline 152
curl "https://cartblanche22.docking.org/substance/random.txt" - Network accessline 157
curl "https://cartblanche22.docking.org/substance/random.txt:count=1000&subset=lead-like&output_fields=zinc_id,smiles,tranche" - Network accessline 162
curl "https://cartblanche22.docking.org/substance/random.txt:count=5000&subset=drug-like&output_fields=zinc_id,smiles" - Network accessline 167
curl "https://cartblanche22.docking.org/substance/random.txt:count=500&subset=fragment&output_fields=zinc_id,smiles,tranche" - Network accessline 206
curl "https://cartblanche22.docking.org/[email protected]_fields=zinc_id,smiles" - Network accessline 211
curl "https://cartblanche22.docking.org/[email protected]_fields=zinc_id,smiles,tranche,catalogs" - Network accessline 282
# Download all compounds in a specific tranche wget https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 283
wget https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 293
https://files.docking.org/zinc22/ - Network accessline 316
wget https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 321
# Create URL list cat > tranche_urls.txt <<EOF https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 322
cat > tranche_urls.txt <<EOF https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 323
https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 324
https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 325
https://files.docking.org/zinc22/H05/H05P040M400-0.db2.gz - Network accessline 334
wget -r -np -nH --cut-dirs=1 -A "*.db2.gz" \ - Network accessline 335
https://files.docking.org/zinc22/H05/ - Network accessline 381
# Structure search if smiles: url = f"https://cartblanche22.docking.org/smiles.txt:smiles={smiles}&dist={dist}&output_fields={fields_str}" - Network accessline 383
url = f"https://cartblanche22.docking.org/smiles.txt:smiles={smiles}&dist={dist}&output_fields={fields_str}" - Network accessline 386
elif zinc_ids: zinc_ids_str = ','.join(zinc_ids) url = f"https://cartblanche22.docking.org/substances.txt:zinc_id={zinc_ids_str}&output_fields={fields_str}" - Network accessline 388
url = f"https://cartblanche22.docking.org/substances.txt:zinc_id={zinc_ids_str}&output_fields={fields_str}" - Network accessline 390
# Random sampling elif count: url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={fields_str}" - Network accessline 391
elif count: url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={fields_str}" if subset: - Network accessline 392
url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={fields_str}" - Network accessline 399
# Execute query result = subprocess.run(['curl', '-s', url], - Network accessline 400
result = subprocess.run(['curl', '-s', url], - Network accessline 528
try: result = subprocess.run( ['curl', '-s', '--max-time', str(timeout), url], - Network accessline 529
result = subprocess.run( ['curl', '-s', '--max-time', str(timeout), url], capture_output=True, - Network accessline 557
# 1. Download tranche files wget https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 558
wget https://files.docking.org/zinc22/H05/H05P035M400-0.db2.gz - Network accessline 570
# 1. Download MOL2 format wget https://files.docking.org/zinc22/H05/H05P035M400-0.mol2.gz - Network accessline 571
wget https://files.docking.org/zinc22/H05/H05P035M400-0.mol2.gz - Network accessline 653
result = subprocess.run(['curl', '-v', url], - Network accessline 685
- **ZINC Wiki**: https://wiki.docking.org/ - Network accessline 686
- **ZINC22 Documentation**: https://wiki.docking.org/index.php/Category:ZINC22 - Network accessline 687
- **ZINC API Guide**: https://wiki.docking.org/index.php/ZINC_api - Network accessline 688
- **File Access Guide**: https://wiki.docking.org/index.php/ZINC22:Getting_started
How the signals fit together
Facts from a static read of the files at the pinned commit. They describe what the code does, not why.
Some files could not be read; the facts below still hold.
Declared and executed: 4 facts
- Allows Bash without restrictions, though it has no scripts or shell blocksadhd-daily-planner/SKILL.md:5High confidence
- Contacts cpc2.gao-lab.org, which SKILL.md, the README and the plugin manifest do not mentionbio-isoform-switching/examples/isoform_switch_analysis.R:61High confidence
- Contacts iupred2a.elte.hu, which SKILL.md, the README and the plugin manifest do not mentionbio-isoform-switching/examples/isoform_switch_analysis.R:64High confidence
- Contacts hmdb.ca, which SKILL.md, the README and the plugin manifest do not mentionbio-metabolomics-metabolite-annotation/examples/annotate_features.py:6High confidence
Signal confidence: 496 facts
- Access to secrets in code of the SKILL.mdadaptyv/SKILL.md:24High confidence
- Access to secrets in code of the SKILL.mdadaptyv/SKILL.md:30High confidence
- Access to secrets in code of the SKILL.md: a variable, placeholder or call, not a stored valueadaptyv/SKILL.md:52Low confidence
- Network access in code of the SKILL.mdadaptyv/SKILL.md:53High confidence
- Network access in code of the SKILL.mdadaptyv/SKILL.md:61High confidence
- Network access in code of the SKILL.mdadaptyv/SKILL.md:67High confidence
- Network access in code of documentationadaptyv/reference/api_reference.md:6Low confidence
- Access to secrets in code of documentation: a variable, placeholder or call, not a stored valueadaptyv/reference/api_reference.md:14Low confidence
- Access to secrets in code of documentation: a variable, placeholder or call, not a stored valueadaptyv/reference/examples.md:16Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:17Low confidence
- Access to secrets in code of documentationadaptyv/reference/examples.md:21Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:28Low confidence
- Access to secrets in code of documentationadaptyv/reference/examples.md:42Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:79Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:129Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:185Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:201Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:221Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:263Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:338Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:479Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:528Low confidence
- Network access in code of documentationadaptyv/reference/examples.md:777Low confidence
- Network access in code of documentationadaptyv/reference/protein_optimization.md:77Low confidence
- Network access in code of documentationadaptyv/reference/protein_optimization.md:84Low confidence
- Network access in code of documentationadaptyv/reference/protein_optimization.md:599Low confidence
- Network access in code of documentationadaptyv/reference/protein_optimization.md:600Low confidence
- Broad permissions in the frontmatter of the SKILL.mdadhd-daily-planner/SKILL.md:5High confidence
- Network access in code of the SKILL.mdagent-browser/SKILL.md:108High confidence
- Network access in code of the SKILL.mdagent-browser/SKILL.md:118High confidence
- Dangerous shell operation in code of the SKILL.mdagent-browser/SKILL.md:134High confidence
- Network access in code of the SKILL.mdagent-browser/SKILL.md:140High confidence
- Network access in code of the SKILL.mdagent-browser/SKILL.md:154High confidence
- Executable script in a comment of a file that runsagentd-drug-discovery/agent_d.py:1Low confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:58High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:59High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:76High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:84High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:110High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:111High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:116High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:117High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:121High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:122High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:130High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:131High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:148High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:149High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:173High confidence
- Network access in code of the SKILL.mdalphafold-database/SKILL.md:174High confidence
and 446 more
Only the first 500 facts are listed.
Works with
| Agent | Status | Evidence | Install to |
|---|---|---|---|
| Claude Code | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .claude/skills/<skill-name>/ |
| Codex | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .agents/skills/<skill-name>/ |
| Cursor | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .cursor/skills/<skill-name>/ |
| Gemini CLI | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .gemini/skills/<skill-name>/ |
| GitHub Copilot | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .github/skills/<skill-name>/ |
| OpenCode | Compatible | Standard SKILL.md skills/adaptyv/SKILL.md | .opencode/skills/<skill-name>/ |
- Native The repository ships a manifest, folder or frontmatter field for this agent.
- Compatible A standard SKILL.md that this agent can read.
- Unknown No evidence either way.
Derived automatically from paths, manifests and frontmatter. Not tested on each agent.
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