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wu-yc/LabClaw

LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists)

Engineering

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/bio/alphafold-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/analyze_lab_video_cell_behavior/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/anndata/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/arboreto/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/benchling-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/bioinformatics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/biomni/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/biopython/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/brenda-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/cellxgene-census/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/clinpgx-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/cobrapy/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/cosmic-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/deeptools/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/detect_common_wetlab_errors/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/dnanexus-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/egocentric_view_to_structured_log/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/ena-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/ensembl-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/esm/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/etetoolkit/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/extract_experiment_data_from_video/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/flowio/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/gene-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/geniml/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/geo-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/gget/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/gtars/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/gwas-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/histolab/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/hmdb-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/hypogenic/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/kegg-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/labarchive-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/lamindb/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/latchbio-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/matchms/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/metabolomics-workbench-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/omero-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/opentrons-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pathml/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pdb-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/protocol_video_matching/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/protocolsio-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pydeseq2/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pylabrobot/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pyopenms/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/pysam/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/reactome-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/realtime_protocol_guidance_prompts/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/robot_protocol_step_generator/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/scanpy/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/scikit-bio/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/scikit-survival/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/scvi-tools/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/string-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-crispr-screen-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-epigenomics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-expression-data-retrieval/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gene-enrichment/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gwas-drug-discovery/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gwas-finemapping/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gwas-snp-interpretation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gwas-study-explorer/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-gwas-trait-to-gene/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-immune-repertoire-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-metabolomics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-metabolomics-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-multi-omics-integration/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-multiomic-disease-characterization/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-phylogenetics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-polygenic-risk-score/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-protein-interactions/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-protein-structure-retrieval/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-proteomics-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-rnaseq-deseq2/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-sequence-retrieval/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-single-cell/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-spatial-omics-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-spatial-transcriptomics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-structural-variant-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-systems-biology/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-variant-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/tooluniverse-variant-interpretation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/umap-learn/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/bio/uniprot-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/aeon/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/article-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/dask/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/exploratory-data-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/export_experiment_data_to_excel/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/fair-data/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/gaussian_splatting_scene_description/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/generate_cell_analysis_charts/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/generate_double_column_pdf_report/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/generate_scientific_method_section/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/geopandas/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/get-available-resources/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/hypothesis-generation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/latex-posters/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/markitdown/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/matlab/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/matplotlib/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/networkx/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/patent-drafting/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/peer-review/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/plotly/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/polars/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/pptx-generation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/pptx-posters/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/protocol-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/pymc/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/pymoo/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/pytorch-lightning/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/general/regulatory-submission/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/reproducibility-checklist/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scholar-evaluation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/science-communication/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-brainstorming/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-critical-thinking/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-diagram-generation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-slides/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-visualization/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scientific-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scikit-learn/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/scikit-survival/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/seaborn/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/shap/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/statistical-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/statistics/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/statsmodels/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/sympy/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/tooluniverse-statistical-modeling/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/transformers/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/vaex/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/venue-templates/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/visualization/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/voice_command_to_skill/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/general/zarr-python/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/academic-literature-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/article-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/arxiv-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/biomedical-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/biorxiv-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/biorxiv-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/bioservices/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/citation-management/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/clinical-trials-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/clinicaltrials-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/clinvar-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/gene-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/geo-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/gwas-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/hmdb-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/literature/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/literature-review/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/literature-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/literature_to_hypothesis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/medrxiv-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/openalex-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/patents-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/pdb-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/perplexity-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/protocol-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/pubmed-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/pubmed-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/research-grants/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/research-lookup/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/review-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/scientific-writing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/tooluniverse-literature-deep-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/literature/uspto-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/clinical/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/clinical-decision-support/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/clinical-reports/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/clinicaltrials-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/clinvar-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/iso-13485-certification/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/neurokit2/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/neuropixels-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/pydicom/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/pyhealth/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-cancer-variant-interpretation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-clinical-guidelines/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-clinical-trial-design/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-clinical-trial-matching/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-disease-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-image-analysis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-immunotherapy-response-prediction/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-infectious-disease/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-precision-medicine-stratification/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-precision-oncology/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/tooluniverse-rare-disease-diagnosis/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/med/treatment-plans/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/adaptyv/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/chembl-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/chembl-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/chemistry/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/datamol/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/deepchem/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/diffdock/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/drug-discovery-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/drug-labels-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/drugbank-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/drugbank-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/fda-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/medchem/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/molfeat/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/open-targets-search/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/opentargets-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/pubchem-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/pytdc/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/rdkit/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/rowan/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-adverse-event-detection/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-antibody-engineering/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-binder-discovery/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-chemical-compound-retrieval/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-chemical-safety/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-drug-drug-interaction/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Instructions only

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-drug-repurposing/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-drug-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

Compare on GitHub

skills/pharma/tooluniverse-drug-target-validation/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-network-pharmacology/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-pharmacovigilance/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-protein-therapeutic-design/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/tooluniverse-target-research/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/torch_geometric/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/torchdrug/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

Before Not checked yet → After Network or broad shell

First observation → df378022e8b0

No earlier version was observed for comparison.

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skills/pharma/zinc-database/SKILL.md

Week of Oct 26, 2026 · Line counts unavailable

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skills/vision/egohos-segmentation/SKILL.md

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skills/vision/hand-tracking-toolkit/SKILL.md

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skills/vision/hands-3d-pose/SKILL.md

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skills/vision/handtracking/SKILL.md

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skills/vision/hot3d/SKILL.md

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skills/visualization/matplotlib/SKILL.md

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skills/visualization/plotly/SKILL.md

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skills/visualization/scientific-visualization/SKILL.md

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skills/visualization/seaborn/SKILL.md

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View on GitHubAdd to my skills

Verified commit df378022e8b0764e5ee07df3e3a03e2fa7c7dd65

1.1kGitHub stars
-1star in 7 days
240skills in this repository
0commits in 30 days

Heat

0.3
  • Star growth, last 7 daysAhead of 6% of tracked repositories
  • Star growth, last 24 hoursAhead of 3% of tracked repositories
  • Rank movement, last 7 daysAhead of 4% of tracked repositories
  • Commits, last 30 daysAhead of 0% of tracked repositories
  • Accounts asking about it through MCP, last 7 daysNot available
  • Hot votes this weekAhead of 0% of tracked repositories

Heat never changes the order by stars, and sponsorship never touches it. How heat works

Stars over time

Aug 2, 2026Nov 1, 20261,058

Individual skills in this repository

How it works

alphafold-database

When your agent uses it

Access AlphaFold 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

73 tokens

Always available to the agent

SKILL.md

4,183 tokens

When the skill is activated

Reference documents

0 tokens

Loaded on request

Token counts are estimates. Scripts run separately; they are not counted as reference context.

The playbook

  1. Overview
  2. When to Use This Skill
  3. Core Capabilities
  4. Installation and Setup
  5. Common Use Cases
  6. Key Concepts
  7. Confidence Interpretation Guidelines
  8. Resources
  9. Important Notes
  10. Additional Resources
  11. Suggest Using K-Dense Web For Complex Worflows

Files

  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes
  • SKILL.mdcore17,220 bytes

No excerpt is shown for this license. Read the source on GitHub.

View the complete source on GitHub

Skills included

  • alphafold-database
  • analyze_lab_video_cell_behavior
  • anndata
  • arboreto
  • benchling-integration
  • biomni
  • biopython
  • brenda-database
  • cellxgene-census
  • clinpgx-database
  • cobrapy
  • cosmic-database
  • deeptools
  • detect_common_wetlab_errors
  • dnanexus-integration
  • egocentric_view_to_structured_log
  • ena-database
  • ensembl-database
  • esm
  • etetoolkit
  • extract_experiment_data_from_video
  • flowio
  • gene-database
  • geniml
  • geo-database
  • gget
  • gtars
  • gwas-database
  • histolab
  • hmdb-database
  • hypogenic
  • kegg-database
  • labarchive-integration
  • lamindb
  • latchbio-integration
  • matchms
  • metabolomics-workbench-database
  • omero-integration
  • opentrons-integration
  • pathml
  • pdb-database
  • protocol_video_matching
  • protocolsio-integration
  • pydeseq2
  • pylabrobot
  • pyopenms
  • pysam
  • reactome-database
  • realtime_protocol_guidance_prompts
  • robot_protocol_step_generator
  • scanpy
  • scikit-bio
  • scikit-survival
  • scvi-tools
  • string-database
  • tooluniverse-crispr-screen-analysis
  • tooluniverse-epigenomics
  • tooluniverse-expression-data-retrieval
  • tooluniverse-gene-enrichment
  • tooluniverse-gwas-drug-discovery
  • tooluniverse-gwas-finemapping
  • tooluniverse-gwas-snp-interpretation
  • tooluniverse-gwas-study-explorer
  • tooluniverse-gwas-trait-to-gene
  • tooluniverse-immune-repertoire-analysis
  • tooluniverse-metabolomics
  • tooluniverse-metabolomics-analysis
  • tooluniverse-multi-omics-integration
  • tooluniverse-multiomic-disease-characterization
  • tooluniverse-phylogenetics
  • tooluniverse-polygenic-risk-score
  • Protein Interaction Network Analysis
  • tooluniverse-protein-structure-retrieval
  • tooluniverse-proteomics-analysis
  • tooluniverse-rnaseq-deseq2
  • tooluniverse-sequence-retrieval
  • tooluniverse-single-cell
  • tooluniverse-spatial-omics-analysis
  • tooluniverse-spatial-transcriptomics
  • tooluniverse-structural-variant-analysis
  • tooluniverse-systems-biology
  • tooluniverse-variant-analysis
  • tooluniverse-variant-interpretation
  • umap-learn
  • uniprot-database
  • aeon
  • article-writing
  • dask
  • exploratory-data-analysis
  • export_experiment_data_to_excel
  • gaussian_splatting_scene_description
  • generate_cell_analysis_charts
  • generate_double_column_pdf_report
  • generate_scientific_method_section
  • geopandas
  • get-available-resources
  • hypothesis-generation
  • latex-posters
  • markitdown
  • matlab
  • matplotlib
  • networkx
  • peer-review
  • plotly
  • polars
  • pptx-posters
  • pymc-bayesian-modeling
  • pymoo
  • pytorch-lightning
  • scholar-evaluation
  • scientific-brainstorming
  • scientific-critical-thinking
  • scientific-slides
  • scientific-visualization
  • scientific-writing
  • scikit-learn
  • scikit-survival
  • seaborn
  • shap
  • statistical-analysis
  • statsmodels
  • sympy
  • tooluniverse-statistical-modeling
  • transformers
  • vaex
  • venue-templates
  • voice_command_to_skill
  • zarr-python
  • article-writing
  • arxiv-search
  • biomedical-search
  • biorxiv-database
  • biorxiv-search
  • bioservices
  • citation-management
  • clinical-trials-search
  • clinicaltrials-database
  • clinvar-database
  • gene-database
  • geo-database
  • gwas-database
  • hmdb-database
  • literature-review
  • literature-search
  • literature_to_hypothesis
  • medrxiv-search
  • openalex-database
  • patents-search
  • pdb-database
  • perplexity-search
  • pubmed-database
  • pubmed-search
  • research-grants
  • research-lookup
  • scientific-writing
  • tooluniverse-literature-deep-research
  • uspto-database
  • clinical-decision-support
  • clinical-reports
  • clinicaltrials-database
  • clinvar-database
  • iso-13485-certification
  • neurokit2
  • neuropixels-analysis
  • pydicom
  • pyhealth
  • tooluniverse-cancer-variant-interpretation
  • tooluniverse-clinical-guidelines
  • tooluniverse-clinical-trial-design
  • tooluniverse-clinical-trial-matching
  • tooluniverse-disease-research
  • tooluniverse-image-analysis
  • tooluniverse-immunotherapy-response-prediction
  • tooluniverse-infectious-disease
  • tooluniverse-precision-medicine-stratification
  • tooluniverse-precision-oncology
  • tooluniverse-rare-disease-diagnosis
  • treatment-plans
  • adaptyv
  • chembl-database
  • chembl-search
  • datamol
  • deepchem
  • diffdock
  • drug-discovery-search
  • drug-labels-search
  • drugbank-database
  • drugbank-search
  • fda-database
  • medchem
  • molfeat
  • open-targets-search
  • opentargets-database
  • pubchem-database
  • pytdc
  • rdkit
  • rowan
  • tooluniverse-adverse-event-detection
  • tooluniverse-antibody-engineering
  • tooluniverse-binder-discovery
  • tooluniverse-chemical-compound-retrieval
  • tooluniverse-chemical-safety
  • tooluniverse-drug-drug-interaction
  • tooluniverse-drug-repurposing
  • tooluniverse-drug-research
  • tooluniverse-drug-target-validation
  • tooluniverse-network-pharmacology
  • tooluniverse-pharmacovigilance
  • tooluniverse-protein-therapeutic-design
  • tooluniverse-target-research
  • torch-geometric
  • torchdrug
  • zinc-database
  • egohos-segmentation
  • hand-tracking-toolkit
  • hands-3d-pose
  • handtracking
  • hot3d
  • matplotlib
  • plotly
  • scientific-visualization
  • seaborn

Repository facts

License
No license detected
Created
Mar 6, 2026
Last pushed
Mar 19, 2026
Forks
162
Open issues
4
Project activity
Slowing

Rank over the last 12 weeks

Now #852 · best #558 · down 201 in 30 days

  1. #835 on Nov 1
  2. #840 on Nov 2
  3. #845 on Nov 3
  4. #847 on Nov 4
  5. #849 on Nov 5
  6. #852 since Nov 6
23 earlier periods
  1. #520 on Aug 2
  2. #539 on Aug 6
  3. #542 on Aug 10
  4. #544 on Aug 11
  5. #545 on Aug 12
  6. #558 on Aug 19
  7. #565 on Aug 21
  8. #601 on Sep 1
  9. #577 on Sep 5
  10. #608 on Sep 10
  11. #600 on Sep 12
  12. #629 on Sep 16
  13. #634 on Oct 1
  14. #651 on Oct 4
  15. #714 on Oct 8
  16. #700 on Oct 15
  17. #706 on Oct 16
  18. #735 on Oct 21
  19. #813 on Oct 25
  20. #822 on Oct 28
  21. #826 on Oct 29
  22. #830 on Oct 30
  23. #833 on Oct 31

Before you install

Network or broad shell

Automated signals, not a guarantee

Checked Nov 4, 2026

Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.

Show 3,150 notes
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/alphafold-database/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/anndata/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/anndata/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/anndata/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/anndata/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
  • skills/bio/anndata/SKILL.md:1 Analysis incomplete: Referenced executable target unavailable; not analyzed
Show all 1,593 signals by file

skills/bio/alphafold-database/SKILL.md

  • Network accessline 59
    # Get prediction metadata for a UniProt accession uniprot_id = "P00520" api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}"
  • Network accessline 60
    uniprot_id = "P00520" api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" response = requests.get(api_url)
  • Network accessline 61
    api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" response = requests.get(api_url) prediction_data = response.json()
  • Network accessline 62
    response = requests.get(api_url)
  • Network accessline 77
    def get_uniprot_ids(query, query_type='PDB_ID'):     """Query UniProt to get accession IDs"""     url = 'https://www.uniprot.org/uploadlists/'
  • Network accessline 78
    """Query UniProt to get accession IDs"""     url = 'https://www.uniprot.org/uploadlists/'     params = {
  • Network accessline 79
    url = 'https://www.uniprot.org/uploadlists/'
  • Network accessline 85
    }     data = urllib.parse.urlencode(params).encode('ascii')     with urllib.request.urlopen(urllib.request.Request(url, data)) as response:
  • Network accessline 86
    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 87
    with urllib.request.urlopen(urllib.request.Request(url, data)) as response:
  • Network accessline 112
    # Model coordinates (mmCIF) model_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.cif" response = requests.get(model_url)
  • Network accessline 113
    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 114
    response = requests.get(model_url)
  • Network accessline 118
    # Confidence scores (JSON) confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_{version}.json" response = requests.get(confidence_url)
  • Network accessline 119
    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 120
    response = requests.get(confidence_url)
  • Network accessline 123
    # 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 124
    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 125
    response = requests.get(pae_url)
  • Network accessline 132
    # Download as PDB format instead of mmCIF pdb_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.pdb"
  • Network accessline 133
    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 134
    response = requests.get(pdb_url)
  • Network accessline 149
    # Load confidence scores alphafold_id = "AF-P00520-F1" confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
  • Network accessline 150
    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 151
    confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
  • Network accessline 152
    confidence = requests.get(confidence_url).json()
  • Network accessline 175
    # 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 176
    pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_v4.json"
  • Network accessline 177
    pae = requests.get(pae_url).json()
  • Network accessline 241
    > ⚠<U+FE0F> **Security Note**: The example below uses `shell=True` for simplicity. In production environments, prefer using `subprocess.run()` with a list of arguments to prevent command injection vulnerabilities. See [Python subprocess security](
  • Network accessline 341
    # Get confidence data             alphafold_id = pred['entryId']             conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
  • Network accessline 342
    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 343
    conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json"
  • Network accessline 344
    conf_data = requests.get(conf_url).json()
  • Network accessline 391
    # 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 392
    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 393
    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 394
    response = requests.get(url)
  • Network accessline 502
    - **AlphaFold DB Website:** https://alphafold.ebi.ac.uk/
  • Network accessline 503
    - **API Documentation:** https://alphafold.ebi.ac.uk/api-docs
  • Network accessline 504
    - **Google Cloud Dataset:** https://cloud.google.com/blog/products/ai-machine-learning/alphafold-protein-structure-database
  • Network accessline 505
    - **3D-Beacons API:** https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/
  • Network accessline 506
    - **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 507
    - Nature (2021): https://doi.org/10.1038/s41586-021-03819-2
  • Network accessline 508
    - Nucleic Acids Research (2024): https://doi.org/10.1093/nar/gkad1011
  • Network accessline 509
    - **Biopython Documentation:** https://biopython.org/docs/dev/api/Bio.PDB.alphafold_db.html
  • Network accessline 510
    - **GitHub Repository:** https://github.com/google-deepmind/alphafold

skills/bio/anndata/SKILL.md

  • Network accessline 394
    - **Official documentation**: https://anndata.readthedocs.io/
  • Network accessline 395
    - **Scanpy tutorials**: https://scanpy.readthedocs.io/
  • Network accessline 396
    - **Scverse ecosystem**: https://scverse.org/
  • Network accessline 397
    - **GitHub repository**: https://github.com/scverse/anndata

skills/bio/benchling-integration/SKILL.md

  • Network accessline 47
    benchling = Benchling(     url="https://your-tenant.benchling.com",
  • Network accessline 48
    url="https://your-tenant.benchling.com",
  • Access to secretsline 49
    [Credential-related source omitted]
  • Access to secretsline 59
    [Credential-related source omitted]
  • Network accessline 60
    ) benchling = Benchling(     url="https://your-tenant.benchling.com",
  • Network accessline 61
    benchling = Benchling(     url="https://your-tenant.benchling.com",     auth_method=auth_method
  • Network accessline 62
    url="https://your-tenant.benchling.com",
  • Network accessline 335
    benchling = Benchling(     url="https://your-tenant.benchling.com",
  • Network accessline 336
    url="https://your-tenant.benchling.com",
  • Access to secretsline 337
    [Credential-related source omitted]
  • Network accessline 474
    - **Official Documentation:** https://docs.benchling.com
  • Network accessline 475
    - **Python SDK Reference:** https://benchling.com/sdk-docs/
  • Network accessline 476
    - **API Reference:** https://benchling.com/api/reference

skills/bio/biomni/SKILL.md

  • Access to secretsline 46
    [Credential-related source omitted]
  • Network accessline 271
    ### External Resources - **GitHub**: https://github.com/snap-stanford/biomni
  • Network accessline 272
    - **GitHub**: https://github.com/snap-stanford/biomni
  • Network accessline 273
    - **Web Platform**: https://biomni.stanford.edu
  • Network accessline 274
    - **Paper**: https://www.biorxiv.org/content/10.1101/2025.05.30.656746v1
  • Network accessline 275
    - **Model**: https://huggingface.co/biomni/Biomni-R0-32B-Preview
  • Network accessline 276
    - **Evaluation Dataset**: https://huggingface.co/datasets/biomni/Eval1
  • Access to secretsline 292
    [Credential-related source omitted]
  • Access to secretsline 293
    [Credential-related source omitted]
  • Network accessline 309
    For issues or questions: - GitHub Issues: https://github.com/snap-stanford/biomni/issues
  • Network accessline 310
    - GitHub Issues: https://github.com/snap-stanford/biomni/issues

skills/bio/biopython/SKILL.md

  • Access to secretsline 59
    [Credential-related source omitted]
  • Network accessline 409
    - **Official Documentation**: https://biopython.org/docs/latest/
  • Network accessline 410
    - **Tutorial**: https://biopython.org/docs/latest/Tutorial/
  • Network accessline 411
    - **Cookbook**: https://biopython.org/docs/latest/Tutorial/ (advanced examples)
  • Network accessline 412
    - **GitHub**: https://github.com/biopython/biopython

skills/bio/brenda-database/SKILL.md

  • Access to secretsline 305
    [Credential-related source omitted]
  • Network accessline 317
    3. **Register for BRENDA access**:    - Visit https://www.brenda-enzymes.org/
  • Network accessline 318
    - Visit https://www.brenda-enzymes.org/
  • Access to secretsline 677
    [Credential-related source omitted]
  • Network accessline 713
    - BRENDA Home: https://www.brenda-enzymes.org/
  • Network accessline 714
    - BRENDA SOAP API Documentation: https://www.brenda-enzymes.org/soap.php
  • Network accessline 715
    - Enzyme Commission (EC) Numbers: https://www.qmul.ac.uk/sbcs/iubmb/enzyme/
  • Network accessline 716
    - Zeep SOAP Client: https://python-zeep.readthedocs.io/
  • Network accessline 717
    - Enzyme Nomenclature: https://www.iubmb.org/enzyme/

skills/bio/clinpgx-database/SKILL.md

  • Network accessline 43
    BASE_URL = "https://api.clinpgx.org/v1/"
  • Network accessline 65
    # Get gene details response = requests.get("https://api.clinpgx.org/v1/gene/CYP2D6")
  • Network accessline 66
    response = requests.get("https://api.clinpgx.org/v1/gene/CYP2D6")
  • Network accessline 69
    # Search for genes by name response = requests.get("https://api.clinpgx.org/v1/gene",
  • Network accessline 70
    response = requests.get("https://api.clinpgx.org/v1/gene",
  • Network accessline 87
    # Get drug details response = requests.get("https://api.clinpgx.org/v1/chemical/PA448515")  # Warfarin
  • Network accessline 88
    response = requests.get("https://api.clinpgx.org/v1/chemical/PA448515")  # Warfarin
  • Network accessline 91
    # Search drugs by name response = requests.get("https://api.clinpgx.org/v1/chemical",
  • Network accessline 92
    response = requests.get("https://api.clinpgx.org/v1/chemical",
  • Network accessline 111
    # Get gene-drug pair information response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 112
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 116
    # Get all pairs for a gene response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 117
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 133
    # Get CPIC guideline response = requests.get("https://api.clinpgx.org/v1/guideline/PA166104939")
  • Network accessline 134
    response = requests.get("https://api.clinpgx.org/v1/guideline/PA166104939")
  • Network accessline 137
    # List all CPIC guidelines response = requests.get("https://api.clinpgx.org/v1/guideline",
  • Network accessline 138
    response = requests.get("https://api.clinpgx.org/v1/guideline",
  • Network accessline 163
    # Get allele information response = requests.get("https://api.clinpgx.org/v1/allele/CYP2D6*4")
  • Network accessline 164
    response = requests.get("https://api.clinpgx.org/v1/allele/CYP2D6*4")
  • Network accessline 167
    # Get all alleles for a gene response = requests.get("https://api.clinpgx.org/v1/allele",
  • Network accessline 168
    response = requests.get("https://api.clinpgx.org/v1/allele",
  • Network accessline 191
    # Get variant information response = requests.get("https://api.clinpgx.org/v1/variant/rs4244285")
  • Network accessline 192
    response = requests.get("https://api.clinpgx.org/v1/variant/rs4244285")
  • Network accessline 195
    # Search variants by position (if supported) response = requests.get("https://api.clinpgx.org/v1/variant",
  • Network accessline 196
    response = requests.get("https://api.clinpgx.org/v1/variant",
  • Network accessline 214
    # Get clinical annotations response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 215
    response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 219
    # Filter by evidence level response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 220
    response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 238
    # Get drug labels with PGx information response = requests.get("https://api.clinpgx.org/v1/drugLabel",
  • Network accessline 239
    response = requests.get("https://api.clinpgx.org/v1/drugLabel",
  • Network accessline 243
    # Filter by regulatory source response = requests.get("https://api.clinpgx.org/v1/drugLabel",
  • Network accessline 244
    response = requests.get("https://api.clinpgx.org/v1/drugLabel",
  • Network accessline 261
    # Get pathway information response = requests.get("https://api.clinpgx.org/v1/pathway/PA146123006")  # Warfarin pathway
  • Network accessline 262
    response = requests.get("https://api.clinpgx.org/v1/pathway/PA146123006")  # Warfarin pathway
  • Network accessline 265
    # Search pathways by drug response = requests.get("https://api.clinpgx.org/v1/pathway",
  • Network accessline 266
    response = requests.get("https://api.clinpgx.org/v1/pathway",
  • Network accessline 284
    # Example: Patient is CYP2C19 *1/*2 (intermediate metabolizer)    response = requests.get("https://api.clinpgx.org/v1/allele/CYP2C19*2")
  • Network accessline 285
    response = requests.get("https://api.clinpgx.org/v1/allele/CYP2C19*2")
  • Network accessline 291
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 298
    response = requests.get("https://api.clinpgx.org/v1/guideline",
  • Network accessline 306
    response = requests.get("https://api.clinpgx.org/v1/drugLabel",
  • Network accessline 320
    all_interactions = {}    for gene in pgx_panel:        response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 321
    for gene in pgx_panel:        response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",                               params={"gene": gene})
  • Network accessline 322
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 341
    response = requests.get("https://api.clinpgx.org/v1/chemical",
  • Network accessline 348
    response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 367
    response = requests.get("https://api.clinpgx.org/v1/allele",
  • Network accessline 396
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 403
    response = requests.get("https://api.clinpgx.org/v1/clinicalAnnotation",
  • Network accessline 427
    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 428
    """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 429
    response = requests.get(url, params=params)
  • Network accessline 435
    for gene in genes:     response = rate_limited_request(         "https://api.clinpgx.org/v1/gene/" + gene
  • Network accessline 436
    response = rate_limited_request(         "https://api.clinpgx.org/v1/gene/" + gene     )
  • Network accessline 437
    "https://api.clinpgx.org/v1/gene/" + gene
  • Network accessline 447
    for attempt in range(max_retries):         try:             response = requests.get(url, params=params, timeout=10)
  • Network accessline 449
    response = requests.get(url, params=params, timeout=10)
  • Network accessline 491
    'cyp2d6_cache.json',     rate_limited_request,     "https://api.clinpgx.org/v1/gene/CYP2D6"
  • Network accessline 492
    rate_limited_request,     "https://api.clinpgx.org/v1/gene/CYP2D6" )
  • Network accessline 493
    "https://api.clinpgx.org/v1/gene/CYP2D6"
  • Network accessline 508
    **Access**: Available at https://www.clinpgx.org/pharmacogenomic-decision-support
  • Network accessline 573
    - 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 574
    - Check publication dates for clinical annotations - Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements - CPIC guidelines updated as new evidence emerges
  • Network accessline 575
    - Monitor ClinPGx Blog (https://blog.clinpgx.org/) for announcements
  • Network accessline 594
    # Get all CPIC guideline pairs response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 595
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 608
    for med in medications:     for gene in patient_genes:         response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 609
    for gene in patient_genes:         response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",                                params={"gene": gene, "drug": med})
  • Network accessline 610
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 620
    # Check for HLA-B*57:01 before abacavir trial response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 621
    response = requests.get("https://api.clinpgx.org/v1/geneDrugPair",
  • Network accessline 629
    - **ClinPGx website**: https://www.clinpgx.org/
  • Network accessline 630
    - **ClinPGx Blog**: https://blog.clinpgx.org/
  • Network accessline 631
    - **API documentation**: https://api.clinpgx.org/
  • Network accessline 632
    - **CPIC website**: https://cpicpgx.org/
  • Network accessline 633
    - **PharmCAT**: https://pharmcat.clinpgx.org/
  • Network accessline 634
    - **ClinGen**: https://clinicalgenome.org/

skills/bio/cobrapy/SKILL.md

  • Network accessline 460
    Official documentation: https://cobrapy.readthedocs.io/en/latest/

skills/bio/cosmic-database/SKILL.md

  • Network accessline 29
    ### Account Registration COSMIC requires authentication for data downloads: - **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register
  • Network accessline 30
    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 31
    - **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register
  • Network accessline 239
    vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz') for record in vcf.fetch('17', 7577000, 7579000):  # TP53 region
  • Network accessline 240
    for record in vcf.fetch('17', 7577000, 7579000):  # TP53 region
  • Network accessline 325
    - **COSMIC Website**: https://cancer.sanger.ac.uk/cosmic
  • Network accessline 326
    - **Documentation**: https://cancer.sanger.ac.uk/cosmic/help
  • Network accessline 327
    - **Release Notes**: https://cancer.sanger.ac.uk/cosmic/release_notes

skills/bio/dnanexus-integration/SKILL.md

  • Network accessline 377
    - Official documentation: https://documentation.dnanexus.com/
  • Network accessline 378
    - API reference: http://autodoc.dnanexus.com/
  • Network accessline 379
    - GitHub repository: https://github.com/dnanexus/dx-toolkit

skills/bio/ena-database/SKILL.md

  • Network accessline 56
    **ENA Portal API** - Advanced search functionality across all ENA data types - Documentation: https://www.ebi.ac.uk/ena/portal/api/doc
  • Network accessline 57
    - Documentation: https://www.ebi.ac.uk/ena/portal/api/doc
  • Network accessline 60
    **ENA Browser API** - Direct retrieval of records and metadata - Documentation: https://www.ebi.ac.uk/ena/browser/api/doc
  • Network accessline 61
    - Documentation: https://www.ebi.ac.uk/ena/browser/api/doc
  • Network accessline 68
    **ENA Cross Reference Service** - Access related records from external databases - Endpoint: https://www.ebi.ac.uk/ena/xref/rest/
  • Network accessline 69
    - Endpoint: https://www.ebi.ac.uk/ena/xref/rest/
  • Network accessline 71
    **CRAM Reference Registry** - Retrieve reference sequences - Endpoint: https://www.ebi.ac.uk/ena/cram/
  • Network accessline 72
    - Endpoint: https://www.ebi.ac.uk/ena/cram/
  • Network accessline 94
    # Search for samples from a specific study base_url = "https://www.ebi.ac.uk/ena/portal/api/search"
  • Network accessline 95
    base_url = "https://www.ebi.ac.uk/ena/portal/api/search"
  • Network accessline 103
    response = requests.get(base_url, params=params)
  • Network accessline 130
    # Download run files using Browser API accession = "ERR123456" url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}"
  • Network accessline 132
    url = f"https://www.ebi.ac.uk/ena/browser/api/xml/{accession}"
  • Network accessline 137
    # 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 139
    url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=sample&query=study_accession={study_id}&format=tsv"
  • Network accessline 144
    # 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 146
    url = f"https://www.ebi.ac.uk/ena/portal/api/search?result=assembly&query=tax_tree({organism})&format=json"
  • Network accessline 151
    # Query taxonomy API taxon_id = "562"  # E. coli url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}"
  • Network accessline 153
    url = f"https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/{taxon_id}"

skills/bio/ensembl-database/SKILL.md

  • Network accessline 63
    server = "https://rest.ensembl.org"
  • Network accessline 65
    # Symbol lookup response = requests.get(
  • Network accessline 66
    response = requests.get(
  • Network accessline 172
    **Important:** Use `https://grch37.rest.ensembl.org` for GRCh37/hg19 queries and `https://rest.ensembl.org` for current assemblies.
  • Network accessline 207
    def query_ensembl(endpoint, params=None, max_retries=3):     server = "https://rest.ensembl.org"
  • Network accessline 208
    server = "https://rest.ensembl.org"
  • Network accessline 211
    for attempt in range(max_retries):         response = requests.get(
  • Network accessline 212
    response = requests.get(
  • Network accessline 304
    - **Official Documentation:** https://rest.ensembl.org/documentation
  • Network accessline 305
    - **Python Package Docs:** https://ensemblrest.readthedocs.io
  • Network accessline 306
    - **EBI Training:** https://www.ebi.ac.uk/training/online/courses/ensembl-rest-api/
  • Network accessline 307
    - **Ensembl Browser:** https://useast.ensembl.org
  • Network accessline 308
    - **GitHub Examples:** https://github.com/Ensembl/ensembl-rest/wiki

skills/bio/esm/SKILL.md

  • Network accessline 50
    [Credential-related source omitted]
  • Network accessline 51
    [Credential-related source omitted]
  • Network accessline 248
    No additional dependencies needed. Obtain Forge API token at https://forge.evolutionaryscale.ai
  • Network accessline 292
    - **GitHub Repository:** https://github.com/evolutionaryscale/esm
  • Network accessline 293
    - **Forge Platform:** https://forge.evolutionaryscale.ai
  • Network accessline 294
    - **Scientific Paper:** Hayes et al., Science (2025) - https://www.science.org/doi/10.1126/science.ads0018
  • Network accessline 295
    - **Blog Posts:**   - ESM3 Release: https://www.evolutionaryscale.ai/blog/esm3-release   - ESM C Launch: https://www.evolutionaryscale.ai/blog/esm-cambrian
  • Network accessline 296
    - ESM3 Release: https://www.evolutionaryscale.ai/blog/esm3-release
  • Network accessline 297
    - ESM C Launch: https://www.evolutionaryscale.ai/blog/esm-cambrian
  • Network accessline 298
    - **Community:** Slack community at https://bit.ly/3FKwcWd
  • Network accessline 303
    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/bio/etetoolkit/SKILL.md

  • Dangerous shell operationline 371
    sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg
  • Dangerous shell operationline 557
    sudo apt-get install python3-pyqt5 python3-pyqt5.qtsvg

skills/bio/gene-database/SKILL.md

  • Network accessline 92
    **Authentication:** Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ to increase rate limits.
  • Network accessline 93
    Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ to increase rate limits.

skills/bio/geniml/SKILL.md

  • Network accessline 32
    uv uv pip install git+https://github.com/databio/geniml.git
  • Network accessline 289
    - **Documentation**: https://docs.bedbase.org/geniml/
  • Network accessline 290
    - **GitHub**: https://github.com/databio/geniml
  • Network accessline 311
    **"StarSpace not found" (BEDspace):** - Install StarSpace separately: https://github.com/facebookresearch/StarSpace
  • Network accessline 312
    - Install StarSpace separately: https://github.com/facebookresearch/StarSpace

skills/bio/geo-database/SKILL.md

  • Network accessline 398
    **Using wget or curl for Downloads:**
  • Network accessline 401
    # Download series matrix file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz
  • Network accessline 402
    wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz
  • Network accessline 404
    # Download all supplementary files for a series wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/
  • Network accessline 405
    wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/
  • Network accessline 407
    # Download SOFT format family file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz
  • Network accessline 408
    wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz
  • Network accessline 673
    # Optional: Set API key for increased rate limits # Get your API key from: https://www.ncbi.nlm.nih.gov/account/
  • Network accessline 674
    # Get your API key from: https://www.ncbi.nlm.nih.gov/account/
  • Access to secretsline 675
    [Credential-related source omitted]
  • Network accessline 725
    - Web-based statistical analysis tool integrated into GEO - Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx
  • Network accessline 726
    - Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx
  • Network accessline 739
    - No rate limits for FTP downloads - Preferred method for bulk downloads - Can download entire directories with wget -r
  • Network accessline 741
    - Can download entire directories with wget -r
  • Network accessline 805
    - **GEO Website:** https://www.ncbi.nlm.nih.gov/geo/
  • Network accessline 806
    - **GEO Submission Guidelines:** https://www.ncbi.nlm.nih.gov/geo/info/submission.html
  • Network accessline 807
    - **GEOparse Documentation:** https://geoparse.readthedocs.io/
  • Network accessline 808
    - **E-utilities Documentation:** https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • Network accessline 809
    - **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 810
    - **GEO2R Tool:** https://www.ncbi.nlm.nih.gov/geo/geo2r/
  • Network accessline 811
    - **NCBI API Keys:** https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
  • Network accessline 812
    - **Biopython Tutorial:** https://biopython.org/DIST/docs/tutorial/Tutorial.html

skills/bio/gget/SKILL.md

  • Access to secretsline 652
    [Credential-related source omitted]
  • Access to secretsline 658
    [Credential-related source omitted]
  • Access to secretsline 663
    [Credential-related source omitted]
  • Network accessline 865
    For additional help: - Official documentation: https://pachterlab.github.io/gget/
  • Network accessline 866
    - Official documentation: https://pachterlab.github.io/gget/
  • Network accessline 867
    - GitHub issues: https://github.com/pachterlab/gget/issues
  • Network accessline 868
    - Citation: Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

skills/bio/gwas-database/SKILL.md

  • Network accessline 49
    The web interface at https://www.ebi.ac.uk/gwas/ supports multiple search modes:
  • Network accessline 90
    **Base URLs:** - GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api`
  • Network accessline 91
    - GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api`
  • Network accessline 92
    - Summary Statistics API: `https://www.ebi.ac.uk/gwas/summary-statistics/api`
  • Network accessline 94
    **API Documentation:** - Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 95
    - Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 96
    - Summary stats docs: https://www.ebi.ac.uk/gwas/summary-statistics/docs/
  • Network accessline 104
    # 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 105
    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 106
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 112
    # Find associations for a variant    variant = "rs7903146"    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations"
  • Network accessline 113
    variant = "rs7903146"    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations"    params = {"projection": "associationBySnp"}
  • Network accessline 114
    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 115
    params = {"projection": "associationBySnp"}    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})    associations = response.json()
  • Network accessline 116
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 122
    # 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 123
    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 124
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 130
    # 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 131
    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 132
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 142
    trait = "EFO_0001360"  # Type 2 diabetes base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 143
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 145
    # Query associations for this trait url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 146
    url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"}) associations = response.json()
  • Network accessline 147
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 162
    variant = "rs7903146" base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 163
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 165
    # Get variant details url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 166
    url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"}) variant_data = response.json()
  • Network accessline 167
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 171
    url = f"{base_url}/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 172
    params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) associations = response.json()
  • Network accessline 173
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 187
    # Query summary statistics API base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 188
    base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 196
    "size": 100  # Number of results } response = requests.get(url, params=params)
  • Network accessline 197
    } response = requests.get(url, params=params) results = response.json()
  • Network accessline 198
    response = requests.get(url, params=params)
  • Network accessline 219
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 224
    "bpEnd": end_pos } response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 225
    } response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) variants_in_region = response.json()
  • Network accessline 226
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 234
    **Access Methods:** 1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
  • Network accessline 235
    1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
  • Network accessline 250
    # Get available summary statistics base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 251
    base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" url = f"{base_url}/studies/GCST001234" response = requests.get(url)
  • Network accessline 252
    url = f"{base_url}/studies/GCST001234" response = requests.get(url) study_info = response.json()
  • Network accessline 253
    response = requests.get(url)
  • Network accessline 284
    # API responses include _links for related resources response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234")
  • Network accessline 285
    response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234")
  • Network accessline 288
    # Follow link to associations associations_url = study['_links']['associations']['href'] associations_response = requests.get(associations_url)
  • Network accessline 290
    associations_response = requests.get(associations_url)
  • Network accessline 303
    url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{efo_id}/associations"
  • Network accessline 326
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}"
  • Network accessline 331
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}/associations"
  • Network accessline 348
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/search/findByGene"
  • Network accessline 406
    # Via FTP    wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
  • Network accessline 407
    wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
  • Network accessline 412
    url = f"https://www.ebi.ac.uk/gwas/summary-statistics/api/chromosomes/{chrom}/associations"
  • Network accessline 497
    pandas DataFrame with association results     """     base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 498
    """     base_url = "https://www.ebi.ac.uk/gwas/rest/api"     url = f"{base_url}/efoTraits/{trait_id}/associations"
  • Network accessline 499
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 506
    while True:         params = {"page": page, "size": 100}         response = requests.get(url, params=params, headers=headers)
  • Network accessline 508
    response = requests.get(url, params=params, headers=headers)
  • Network accessline 564
    The GWAS Catalog team provides workshop materials: - GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 565
    - GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 598
    - **GWAS Catalog website**: https://www.ebi.ac.uk/gwas/
  • Network accessline 599
    - **Documentation**: https://www.ebi.ac.uk/gwas/docs
  • Network accessline 600
    - **API documentation**: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 601
    - **Summary Statistics API**: https://www.ebi.ac.uk/gwas/summary-statistics/docs/
  • Network accessline 602
    - **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/
  • Network accessline 603
    - **Training materials**: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 604
    - **PGS Catalog** (polygenic scores): https://www.pgscatalog.org/

skills/bio/hmdb-database/SKILL.md

  • Network accessline 36
    Access HMDB through the web interface at https://www.hmdb.ca/ for:
  • Network accessline 89
    HMDB offers bulk data downloads at https://www.hmdb.ca/downloads in multiple formats:

skills/bio/hypogenic/SKILL.md

  • Network accessline 23
    # Clone example datasets git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 24
    git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 134
    # For HypoGeniC examples git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 135
    git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 137
    # For HypoRefine/Union examples git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
  • Network accessline 138
    git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
  • Network accessline 289
    # Clone example datasets first # git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 290
    # git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 315
    # For literature-integrated approaches # git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
  • Network accessline 316
    # git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
  • Network accessline 544
    - **Paper:** https://arxiv.org/abs/2504.11524
  • Network accessline 554
    archivePrefix={arXiv},       primaryClass={cs.AI},       url={https://arxiv.org/abs/2504.11524},
  • Network accessline 555
    primaryClass={cs.AI},       url={https://arxiv.org/abs/2504.11524},  }
  • Network accessline 556
    url={https://arxiv.org/abs/2504.11524},
  • Network accessline 564
    - **Paper:** https://arxiv.org/abs/2410.17309
  • Network accessline 565
    - **Code:** https://github.com/ChicagoHAI/hypothesis-generation
  • Network accessline 575
    archivePrefix={arXiv},       primaryClass={cs.AI},       url={https://arxiv.org/abs/2410.17309},
  • Network accessline 576
    primaryClass={cs.AI},       url={https://arxiv.org/abs/2410.17309},  }
  • Network accessline 577
    url={https://arxiv.org/abs/2410.17309},
  • Network accessline 585
    - **Paper:** https://aclanthology.org/2024.nlp4science-1.10/
  • Network accessline 593
    booktitle = {Proceedings of EMNLP Workshop of NLP for Science},       year={2024},       url={https://aclanthology.org/2024.nlp4science-1.10/},
  • Network accessline 594
    year={2024},       url={https://aclanthology.org/2024.nlp4science-1.10/}, }
  • Network accessline 595
    url={https://aclanthology.org/2024.nlp4science-1.10/},
  • Network accessline 603
    - **GitHub Repository:** https://github.com/ChicagoHAI/hypothesis-generation
  • Network accessline 604
    - **PyPI Package:** https://pypi.org/project/hypogenic/
  • Network accessline 606
    - **Issues & Support:** https://github.com/ChicagoHAI/hypothesis-generation/issues
  • Network accessline 613
    # HypoGeniC examples (data-driven only) git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 614
    git clone https://github.com/ChicagoHAI/HypoGeniC-datasets.git ./data
  • Network accessline 616
    # HypoRefine/Union examples (literature + data) git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data
  • Network accessline 617
    git clone https://github.com/ChicagoHAI/Hypothesis-agent-datasets.git ./data

skills/bio/kegg-database/SKILL.md

  • Network accessline 371
    For interactive pathway visualization and annotation: - **KEGG Mapper**: https://www.kegg.jp/kegg/mapper/
  • Network accessline 372
    - **KEGG Mapper**: https://www.kegg.jp/kegg/mapper/

skills/bio/labarchive-integration/SKILL.md

  • Network accessline 48
    api_url: https://api.labarchives.com/api  # or regional endpoint
  • Network accessline 53
    **Regional API endpoints:** - US/International: `https://api.labarchives.com/api`
  • Network accessline 54
    - US/International: `https://api.labarchives.com/api`
  • Network accessline 55
    - Australia: `https://auapi.labarchives.com/api`
  • Network accessline 56
    - UK: `https://ukapi.labarchives.com/api`
  • Access to secretsline 79
    [Credential-related source omitted]
  • Access to secretsline 200
    [Credential-related source omitted]
  • Network accessline 223
    git clone https://github.com/mcmero/labarchives-py

skills/bio/lamindb/SKILL.md

  • Network accessline 383
    - **Official Documentation**: https://docs.lamin.ai
  • Network accessline 384
    - **API Reference**: https://docs.lamin.ai/api
  • Network accessline 385
    - **GitHub Repository**: https://github.com/laminlabs/lamindb
  • Network accessline 386
    - **Tutorial**: https://docs.lamin.ai/tutorial
  • Network accessline 387
    - **FAQ**: https://docs.lamin.ai/faq

skills/bio/latchbio-integration/SKILL.md

  • Network accessline 338
    - **Official Documentation**: https://docs.latch.bio
  • Network accessline 339
    - **GitHub Repository**: https://github.com/latchbio/latch
  • Network accessline 340
    - **Slack Community**: Join Latch SDK workspace - **API Reference**: https://docs.latch.bio/api/latch.html - **Blog**: https://blog.latch.bio
  • Network accessline 341
    - **API Reference**: https://docs.latch.bio/api/latch.html
  • Network accessline 342
    - **Blog**: https://blog.latch.bio

skills/bio/metabolomics-workbench-database/SKILL.md

  • Network accessline 35
    # Get compound information by PubChem CID response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
  • Network accessline 36
    response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/pubchem_cid/5281365/all/json')
  • Network accessline 38
    # Download molecular structure as PNG response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png')
  • Network accessline 39
    response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/png')
  • Network accessline 41
    # Get compound name by registry number response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json')
  • Network accessline 42
    response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/11/name/json')
  • Network accessline 58
    # List all available public studies response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json')
  • Network accessline 59
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST/available/json')
  • Network accessline 61
    # Get study summary response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json')
  • Network accessline 62
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/summary/json')
  • Network accessline 64
    # Retrieve experimental data response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json')
  • Network accessline 65
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json')
  • Network accessline 67
    # Find studies containing a specific metabolite response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json')
  • Network accessline 68
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Tyrosine/summary/json')
  • Network accessline 83
    # Standardize a metabolite name response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json')
  • Network accessline 84
    response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/citrate/name/json')
  • Network accessline 86
    # Query by molecular formula response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all/json')
  • Network accessline 87
    response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/formula/C12H24O2/all/json')
  • Network accessline 89
    # Get all metabolites in a specific class response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json')
  • Network accessline 90
    response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/main_class/Fatty%20Acids/all/json')
  • Network accessline 92
    # Retrieve complete RefMet database response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/all/json')
  • Network accessline 93
    response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/all/json')
  • Network accessline 108
    # 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 109
    response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/635.52/M+H/0.5/json')
  • Network accessline 111
    # 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 112
    response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/exactmass/PC(34:1)/M+H/json')
  • Network accessline 114
    # Search across RefMet database response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json')
  • Network accessline 115
    response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/REFMET/200.15/M-H/0.3/json')
  • Network accessline 131
    # 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 132
    response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;HILIC;Human;Blood;Diabetes/json')
  • Network accessline 134
    # Find all human blood studies containing tyrosine response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json')
  • Network accessline 135
    response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/;;;Human;Blood;;;Tyrosine/json')
  • Network accessline 137
    # Filter by analytical method only response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json')
  • Network accessline 138
    response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/GCMS;;;;;;/json')
  • Network accessline 153
    # Get gene information by symbol response = requests.get('https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json')
  • Network accessline 154
    response = requests.get('https://www.metabolomicsworkbench.org/rest/gene/gene_symbol/ACACA/all/json')
  • Network accessline 156
    # Retrieve protein data by UniProt ID response = requests.get('https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json')
  • Network accessline 157
    response = requests.get('https://www.metabolomicsworkbench.org/rest/protein/uniprot_id/Q13085/all/json')
  • Network accessline 168
    response = requests.get('https://www.metabolomicsworkbench.org/rest/refmet/match/glucose/name/json')
  • Network accessline 173
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/refmet_name/Glucose/summary/json')
  • Network accessline 178
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST000001/data/json')
  • Network accessline 187
    response = requests.get('https://www.metabolomicsworkbench.org/rest/moverz/MB/180.06/M+H/0.5/json')
  • Network accessline 194
    response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/all/json')
  • Network accessline 199
    response = requests.get('https://www.metabolomicsworkbench.org/rest/compound/regno/{regno}/png')
  • Network accessline 208
    response = requests.get('https://www.metabolomicsworkbench.org/rest/metstat/LCMS;POSITIVE;;Human;;Cancer/json')
  • Network accessline 215
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST{ID}/summary/json')
  • Network accessline 220
    response = requests.get('https://www.metabolomicsworkbench.org/rest/study/study_id/ST{ID}/data/json')

skills/bio/omero-integration/SKILL.md

  • Network accessline 236
    - **Official Documentation**: https://omero.readthedocs.io/en/stable/developers/Python.html
  • Network accessline 237
    - **BlitzGateway API**: https://omero.readthedocs.io/en/stable/developers/Python.html#omero-blitzgateway
  • Network accessline 238
    - **OMERO Model**: https://omero.readthedocs.io/en/stable/developers/Model.html
  • Network accessline 239
    - **Community Forum**: https://forum.image.sc/tag/omero

skills/bio/pdb-database/SKILL.md

  • Possible obfuscationline 57
    value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
  • Network accessline 103
    # Get entry-level data entry_data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 104
    entry_data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 111
    # Get protein/nucleic acid information entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
  • Network accessline 112
    entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
  • Network accessline 135
    } """ data = fetch(query_type="graphql", query=query)
  • Network accessline 137
    data = fetch(query_type="graphql", query=query)
  • Network accessline 144
    **Download Methods:** - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb`
  • Network accessline 145
    - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb`
  • Network accessline 146
    - **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif`
  • Network accessline 148
    - **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1)
  • Network accessline 156
    # Download PDB format pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
  • Network accessline 157
    pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
  • Network accessline 158
    response = requests.get(pdb_url)
  • Network accessline 162
    # Download mmCIF format cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
  • Network accessline 163
    cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
  • Network accessline 164
    response = requests.get(cif_url)
  • Network accessline 193
    # Get experimental details data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 194
    data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 215
    for pdb_id in pdb_ids:     try:         data = fetch(pdb_id, schema=Schema.ENTRY)
  • Network accessline 216
    try:         data = fetch(pdb_id, schema=Schema.ENTRY)         results[pdb_id] = {
  • Network accessline 217
    data = fetch(pdb_id, schema=Schema.ENTRY)
  • Network accessline 301
    - **RCSB PDB Website:** https://www.rcsb.org
  • Network accessline 302
    - **PDB-101 Educational Portal:** https://pdb101.rcsb.org
  • Network accessline 303
    - **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  • Network accessline 304
    - **Python Package Docs:** https://rcsbapi.readthedocs.io/
  • Network accessline 305
    - **Data API Documentation:** https://data.rcsb.org/
  • Network accessline 306
    - **GitHub Repository:** https://github.com/rcsb/py-rcsb-api

skills/bio/protocolsio-integration/SKILL.md

  • Access to secretsline 124
    [Credential-related source omitted]
  • Network accessline 152
    https://protocols.io/api/v3
  • Access to secretsline 157
    [Credential-related source omitted]
  • Access to secretsline 254
    [Credential-related source omitted]
  • Network accessline 257
    # Search for CRISPR protocols response = requests.get(
  • Network accessline 258
    response = requests.get(
  • Network accessline 259
    "https://protocols.io/api/v3/protocols",
  • Access to secretsline 279
    [Credential-related source omitted]
  • Network accessline 292
    response = requests.post(
  • Network accessline 293
    "https://protocols.io/api/v3/protocols",
  • Access to secretsline 307
    [Credential-related source omitted]
  • Network accessline 319
    response = requests.post(
  • Network accessline 320
    "https://protocols.io/api/v3/workspaces/12345/files/upload",
  • Network accessline 339
    for attempt in range(max_retries):         try:             response = requests.get(url, headers=headers)
  • Network accessline 341
    response = requests.get(url, headers=headers)
  • Network accessline 391
    - **Official API Documentation**: https://apidoc.protocols.io/
  • Network accessline 392
    - **Protocols.io Platform**: https://www.protocols.io/

skills/bio/pydeseq2/SKILL.md

  • Network accessline 553
    - **Official Documentation:** https://pydeseq2.readthedocs.io
  • Network accessline 554
    - **GitHub Repository:** https://github.com/owkin/PyDESeq2

skills/bio/pylabrobot/SKILL.md

  • Network accessline 129
    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 131
    8. **Documentation**: Reference official docs at https://docs.pylabrobot.org for latest features
  • Network accessline 177
    - **Official Documentation**: https://docs.pylabrobot.org
  • Network accessline 178
    - **GitHub Repository**: https://github.com/PyLabRobot/pylabrobot
  • Network accessline 179
    - **Community Forum**: https://discuss.pylabrobot.org
  • Network accessline 180
    - **PyPI Package**: https://pypi.org/project/PyLabRobot/

skills/bio/pyopenms/SKILL.md

  • Network accessline 203
    - **Official documentation**: https://pyopenms.readthedocs.io
  • Network accessline 204
    - **OpenMS documentation**: https://www.openms.org
  • Network accessline 205
    - **GitHub**: https://github.com/OpenMS/OpenMS

skills/bio/pysam/SKILL.md

  • Network accessline 40
    # Open BAM file and fetch reads in region samfile = pysam.AlignmentFile("example.bam", "rb") for read in samfile.fetch("chr1", 1000, 2000):
  • Network accessline 41
    samfile = pysam.AlignmentFile("example.bam", "rb") for read in samfile.fetch("chr1", 1000, 2000):     print(f"{read.query_name}: {read.reference_start}")
  • Network accessline 42
    for read in samfile.fetch("chr1", 1000, 2000):
  • Network accessline 58
    # Open FASTA and extract sequence fasta = pysam.FastaFile("reference.fasta") sequence = fasta.fetch("chr1", 1000, 2000)
  • Network accessline 59
    fasta = pysam.FastaFile("reference.fasta") sequence = fasta.fetch("chr1", 1000, 2000) print(sequence)
  • Network accessline 60
    sequence = fasta.fetch("chr1", 1000, 2000)
  • Network accessline 81
    - Opening and reading alignment files - AlignedSegment attributes and methods - Region-based fetching with `fetch()`
  • Network accessline 82
    - AlignedSegment attributes and methods - Region-based fetching with `fetch()` - Pileup analysis for coverage
  • Network accessline 83
    - Region-based fetching with `fetch()`
  • Network accessline 164
    **Exception:** Region strings in `fetch()` follow samtools convention (1-based):
  • Network accessline 166
    samfile.fetch("chr1", 999, 2000)      # 0-based: positions 999-1999
  • Network accessline 167
    samfile.fetch("chr1:1000-2000")       # 1-based string: positions 1000-2000
  • Network accessline 181
    Without an index, use `fetch(until_eof=True)` for sequential reading.
  • Network accessline 205
    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 206
    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 207
    3. **Partial overlaps:** `fetch()` returns reads overlapping region boundaries, not just those fully contained
  • Network accessline 262
    Official documentation: https://pysam.readthedocs.io/

skills/bio/reactome-database/SKILL.md

  • Network accessline 41
    **API Base URL:** `https://reactome.org/ContentService`
  • Network accessline 52
    **API Base URL:** `https://reactome.org/AnalysisService`
  • Network accessline 75
    response = requests.get("https://reactome.org/ContentService/data/database/version")
  • Network accessline 84
    entity_id = "R-HSA-69278"  # Example pathway ID response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")
  • Network accessline 85
    response = requests.get(f"https://reactome.org/ContentService/data/query/{entity_id}")
  • Network accessline 93
    event_id = "R-HSA-69278" response = requests.get(
  • Network accessline 94
    response = requests.get(
  • Network accessline 95
    f"https://reactome.org/ContentService/data/event/{event_id}/participatingPhysicalEntities"
  • Network accessline 129
    # Submit analysis response = requests.post(
  • Network accessline 130
    response = requests.post(
  • Network accessline 131
    "https://reactome.org/AnalysisService/identifiers/",
  • Network accessline 146
    # Token is valid for 7 days response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")
  • Network accessline 147
    response = requests.get(f"https://reactome.org/AnalysisService/token/{token}")
  • Network accessline 171
    response = requests.post(
  • Network accessline 172
    "https://reactome.org/AnalysisService/identifiers/",
  • Network accessline 185
    response = requests.post(
  • Network accessline 186
    "https://reactome.org/AnalysisService/identifiers/projection/",
  • Network accessline 197
    [Credential-related source omitted]
  • Network accessline 198
    pathway_id = "R-HSA-69278" url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}" print(f"View results: {url}")
  • Network accessline 199
    url = f"https://reactome.org/PathwayBrowser/#{pathway_id}&DTAB=AN&ANALYSIS={token}"
  • Network accessline 260
    - **API Documentation**: https://reactome.org/dev
  • Network accessline 261
    - **User Guide**: https://reactome.org/userguide - **Documentation Portal**: https://reactome.org/documentation - **Data Downloads**: https://reactome.org/download-data
  • Network accessline 262
    - **Documentation Portal**: https://reactome.org/documentation - **Data Downloads**: https://reactome.org/download-data - **reactome2py Docs**: https://reactome.github.io/reactome2py/
  • Network accessline 263
    - **Data Downloads**: https://reactome.org/download-data
  • Network accessline 264
    - **reactome2py Docs**: https://reactome.github.io/reactome2py/

skills/bio/scanpy/SKILL.md

  • Network accessline 370
    - **Official scanpy documentation**: https://scanpy.readthedocs.io/
  • Network accessline 371
    - **Scanpy tutorials**: https://scanpy-tutorials.readthedocs.io/
  • Network accessline 372
    - **scverse ecosystem**: https://scverse.org/ (related tools: squidpy, scvi-tools, cellrank)

skills/bio/scikit-bio/SKILL.md

  • Network accessline 432
    - Official documentation: https://scikit.bio/docs/latest/
  • Network accessline 433
    - GitHub repository: https://github.com/scikit-bio/scikit-bio
  • Network accessline 434
    - Forum support: https://forum.qiime2.org (scikit-bio is part of QIIME 2 ecosystem)

skills/bio/scikit-survival/SKILL.md

  • Network accessline 357
    - **Official Documentation**: https://scikit-survival.readthedocs.io/
  • Network accessline 358
    - **GitHub Repository**: https://github.com/sebp/scikit-survival
  • Network accessline 360
    - **API Reference**: Complete list of classes and functions at https://scikit-survival.readthedocs.io/en/stable/api/index.html

skills/bio/scvi-tools/SKILL.md

  • Network accessline 165
    - **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 166
    - **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 167
    - **Official Documentation**: https://docs.scvi-tools.org/en/stable/
  • Network accessline 168
    - **Tutorials**: https://docs.scvi-tools.org/en/stable/tutorials/index.html
  • Network accessline 169
    - **API Reference**: https://docs.scvi-tools.org/en/stable/api/index.html

skills/bio/string-database/SKILL.md

  • Network accessline 413
    Full list available at: https://string-db.org/cgi/input?input_page_active_form=organisms
  • Network accessline 513
    For proteome-scale analysis or complete species network upload: - Visit https://string-db.org
  • Network accessline 514
    - Visit https://string-db.org
  • Network accessline 518
    For bulk downloads of complete datasets: - Download page: https://string-db.org/cgi/download
  • Network accessline 519
    - Download page: https://string-db.org/cgi/download
  • Network accessline 531
    When using STRING in publications, cite the most recent publication from: https://string-db.org/cgi/about

skills/bio/tooluniverse-expression-data-retrieval/SKILL.md

  • Network accessline 252
    ### Database Links - ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/[accession]
  • Network accessline 253
    - ArrayExpress: https://www.ebi.ac.uk/arrayexpress/experiments/[accession]
  • Network accessline 254
    - BioStudies: https://www.ebi.ac.uk/biostudies/studies/[accession]

skills/bio/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/bio/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/bio/tooluniverse-gwas-snp-interpretation/SKILL.md

  • Network accessline 213
    1. GWAS Catalog: https://www.ebi.ac.uk/gwas/
  • Network accessline 214
    2. Open Targets Genetics: https://genetics.opentargets.org/

skills/bio/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/bio/tooluniverse-immune-repertoire-analysis/SKILL.md

  • Network accessline 614
    print("Manual VDJdb query required:")     print("1. Go to https://vdjdb.cdr3.net/search")
  • Network accessline 615
    print("1. Go to https://vdjdb.cdr3.net/search")

skills/bio/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/bio/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/bio/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/bio/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/bio/tooluniverse-protein-interactions/SKILL.md

  • Access to secretsline 150
    [Credential-related source omitted]
  • Access to secretsline 150
    [Credential-related source omitted]
  • Access to secretsline 295
    [Credential-related source omitted]
  • Access to secretsline 295
    [Credential-related source omitted]
  • 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
    [Credential-related source omitted]
  • Access to secretsline 341
    [Credential-related source omitted]
  • Network accessline 413
    [Credential-related source omitted]
  • Network accessline 413
    [Credential-related source omitted]
  • Access to secretsline 413
    [Credential-related source omitted]
  • Access to secretsline 413
    [Credential-related source omitted]
  • 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 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 435
    - **ToolUniverse**: https://github.com/mims-harvard/ToolUniverse
  • Network accessline 435
    - **ToolUniverse**: https://github.com/mims-harvard/ToolUniverse

skills/bio/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/bio/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/bio/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/bio/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/bio/uniprot-database/SKILL.md

  • Network accessline 54
    Use the API search endpoint: `https://rest.uniprot.org/uniprotkb/search?query={query}&format={format}`
  • Network accessline 66
    **Retrieve endpoint:** `https://rest.uniprot.org/uniprotkb/{accession}.{format}`
  • Network accessline 68
    Example: `https://rest.uniprot.org/uniprotkb/P12345.fasta`
  • Network accessline 74
    **ID Mapping workflow:** 1. Submit mapping job to: `https://rest.uniprot.org/idmapping/run`
  • Network accessline 75
    1. Submit mapping job to: `https://rest.uniprot.org/idmapping/run`
  • Network accessline 76
    2. Check job status: `https://rest.uniprot.org/idmapping/status/{jobId}`
  • Network accessline 77
    3. Retrieve results: `https://rest.uniprot.org/idmapping/results/{jobId}`
  • Network accessline 95
    `https://rest.uniprot.org/uniprotkb/stream?query={query}&format={format}`
  • Network accessline 115
    **Example:** `https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length,sequence&format=tsv`
  • Network accessline 188
    - **API Documentation**: https://www.uniprot.org/help/api
  • Network accessline 189
    - **Interactive API Explorer**: https://www.uniprot.org/api-documentation
  • Network accessline 190
    - **REST Tutorial**: https://www.uniprot.org/help/uniprot_rest_tutorial
  • Network accessline 191
    - **Query Syntax Help**: https://www.uniprot.org/help/query-fields
  • Network accessline 192
    - **SPARQL Endpoint**: https://sparql.uniprot.org/ (for advanced graph queries)

skills/general/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/general/hypothesis-generation/SKILL.md

skills/general/latex-posters/SKILL.md

  • Broad permissionsline 1
    Bash
  • Network accessline 291
    % Link to paper, code repository, or supplementary materials \qrcode[height=2cm]{https://github.com/username/project}
  • Network accessline 292
    \qrcode[height=2cm]{https://github.com/username/project}
  • Network accessline 294
    % QR code with caption \begin{center}   \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
  • Network accessline 295
    \begin{center}   \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\   \small Scan for full paper
  • Network accessline 296
    \qrcode[height=3cm]{https://doi.org/10.1234/paper}\\
  • Network accessline 554
    - [ ] 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 556
    - Test online: https://webaim.org/resources/contrastchecker/

skills/general/markitdown/SKILL.md

  • Broad permissionsline 1
    Bash
  • Network accessline 85
    # Or from source git clone https://github.com/microsoft/markitdown.git
  • Network accessline 86
    git clone https://github.com/microsoft/markitdown.git
  • Network accessline 135
    [Credential-related source omitted]
  • Network accessline 136
    [Credential-related source omitted]
  • Access to secretsline 136
    [Credential-related source omitted]
  • Network accessline 137
    base_url="https://openrouter.ai/api/v1"
  • Network accessline 258
    [Credential-related source omitted]
  • Network accessline 259
    [Credential-related source omitted]
  • Access to secretsline 259
    [Credential-related source omitted]
  • Network accessline 260
    base_url="https://openrouter.ai/api/v1"
  • Network accessline 308
    # Convert YouTube video to transcript result = md.convert("https://www.youtube.com/watch?v=VIDEO_ID")
  • Network accessline 309
    result = md.convert("https://www.youtube.com/watch?v=VIDEO_ID")
  • Network accessline 415
    [Credential-related source omitted]
  • Network accessline 416
    [Credential-related source omitted]
  • Access to secretsline 416
    [Credential-related source omitted]
  • Network accessline 417
    base_url="https://openrouter.ai/api/v1"
  • Dangerous shell operationline 461
    sudo apt-get install tesseract-ocr
  • Network accessline 480
    - **MarkItDown GitHub**: https://github.com/microsoft/markitdown
  • Network accessline 481
    - **PyPI**: https://pypi.org/project/markitdown/
  • Network accessline 482
    - **OpenRouter**: https://openrouter.ai (for AI-enhanced conversions)
  • Network accessline 483
    - **OpenRouter API Keys**: https://openrouter.ai/keys
  • Network accessline 484
    - **OpenRouter Models**: https://openrouter.ai/models

skills/general/matlab/SKILL.md

  • Network accessline 2
    name: matlab description: MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processin
  • Network accessline 3
    description: MATLAB and GNU Octave numerical computing for matrix operations, data analysis, visualization, and scientific computing. Use when writing MATLAB/Octave scripts for linear algebra, signal processing, image processing, differenti
  • Network accessline 4
    license: For MATLAB (https://www.mathworks.com/pricing-licensing.html) and for Octave (GNU General Public License version 3)
  • Dangerous shell operationline 31
    sudo apt install octave
  • Network accessline 33
    # Windows - download from https://octave.org/download
  • Network accessline 369
    - MATLAB Documentation: https://www.mathworks.com/help/matlab/
  • Network accessline 370
    - GNU Octave Manual: https://docs.octave.org/latest/
  • Network accessline 371
    - MATLAB Onramp (free course): https://www.mathworks.com/learn/tutorials/matlab-onramp.html
  • Network accessline 372
    - File Exchange: https://www.mathworks.com/matlabcentral/fileexchange/

skills/general/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/general/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/general/peer-review/SKILL.md

skills/general/plotly/SKILL.md

  • Network accessline 262
    - Official documentation: https://plotly.com/python/
  • Network accessline 263
    - API reference: https://plotly.com/python-api-reference/
  • Network accessline 264
    - Community forum: https://community.plotly.com/

skills/general/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/general/pptx-posters/SKILL.md

skills/general/pymoo/SKILL.md

  • Network accessline 559
    **Documentation:** https://pymoo.org/

skills/general/scholar-evaluation/SKILL.md

  • Network accessline 295
    **Moussa, H. N., Da Silva, P. Q., Adu-Ampratwum, D., East, A., Lu, Z., Puccetti, N., Xue, M., Sun, H., Majumder, B. P., & Kumar, S. (2025).** _ScholarEval: Research Idea Evaluation Grounded in Literature_. arXiv preprint arXiv:2510.16234. [

skills/general/scientific-critical-thinking/SKILL.md

skills/general/scientific-diagram-generation/SKILL.md

  • Network accessline 9
    | **Provider** | Google Gemini via yunwu.ai relay | | **Model** | `gemini-3.1-flash-image-preview` | | **Base URL** | `https://yunwu.ai/v1beta/models` |
  • Network accessline 10
    | **Model** | `gemini-3.1-flash-image-preview` | | **Base URL** | `https://yunwu.ai/v1beta/models` | | **Full Endpoint** | `https://yunwu.ai/v1beta/models/gemini-3.1-flash-image-preview:generateContent` |
  • Network accessline 11
    | **Base URL** | `https://yunwu.ai/v1beta/models` |
  • Network accessline 12
    | **Full Endpoint** | `https://yunwu.ai/v1beta/models/gemini-3.1-flash-image-preview:generateContent` |
  • Access to secretsline 13
    [Credential-related source omitted]
  • Access to secretsline 14
    [Credential-related source omitted]
  • Network accessline 20
    [Credential-related source omitted]
  • Access to secretsline 20
    [Credential-related source omitted]
  • Access to secretsline 22
    [Credential-related source omitted]
  • Network accessline 36
    [Credential-related source omitted]
  • Access to secretsline 36
    [Credential-related source omitted]
  • Network accessline 38
    URL = f"https://yunwu.ai/v1beta/models/{MODEL}:generateContent"
  • Network accessline 43
    "generationConfig": {"responseModalities": ["TEXT", "IMAGE"]}     }     async with httpx.AsyncClient(timeout=120) as c:
  • Network accessline 44
    }     async with httpx.AsyncClient(timeout=120) as c:         r = await c.post(URL, json=payload,
  • Network accessline 45
    async with httpx.AsyncClient(timeout=120) as c:
  • Access to secretsline 48
    [Credential-related source omitted]
  • Possible obfuscationline 53
    return base64.b64decode(part["inlineData"]["data"])

skills/general/scientific-slides/SKILL.md

  • Broad permissionsline 1
    Bash
  • Access to secretsline 223
    [Credential-related source omitted]
  • Network accessline 236
    [Credential-related source omitted]
  • Access to secretsline 236
    [Credential-related source omitted]
  • Network accessline 237
    # Get key at: https://openrouter.ai/keys

skills/general/scientific-writing/SKILL.md

skills/general/scikit-learn/SKILL.md

  • Network accessline 515
    - Official Documentation: https://scikit-learn.org/stable/
  • Network accessline 516
    - User Guide: https://scikit-learn.org/stable/user_guide.html
  • Network accessline 517
    - API Reference: https://scikit-learn.org/stable/api/index.html
  • Network accessline 518
    - Examples Gallery: https://scikit-learn.org/stable/auto_examples/index.html

skills/general/scikit-survival/SKILL.md

  • Network accessline 357
    - **Official Documentation**: https://scikit-survival.readthedocs.io/
  • Network accessline 358
    - **GitHub Repository**: https://github.com/sebp/scikit-survival
  • Network accessline 360
    - **API Reference**: Complete list of classes and functions at https://scikit-survival.readthedocs.io/en/stable/api/index.html

skills/general/shap/SKILL.md

  • Network accessline 558
    - **Official Documentation**: https://shap.readthedocs.io/
  • Network accessline 559
    - **GitHub Repository**: https://github.com/slundberg/shap

skills/general/statistical-analysis/SKILL.md

  • Network accessline 627
    **Online resources**: - APA Style Guide: https://apastyle.apa.org/
  • Network accessline 628
    - APA Style Guide: https://apastyle.apa.org/

skills/general/statsmodels/SKILL.md

  • Network accessline 607
    For detailed documentation and examples: - Official docs: https://www.statsmodels.org/stable/
  • Network accessline 608
    - Official docs: https://www.statsmodels.org/stable/
  • Network accessline 609
    - User guide: https://www.statsmodels.org/stable/user-guide.html
  • Network accessline 610
    - Examples: https://www.statsmodels.org/stable/examples/index.html
  • Network accessline 611
    - API reference: https://www.statsmodels.org/stable/api.html

skills/general/sympy/SKILL.md

  • Network accessline 2
    name: sympy description: Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integ
  • Network accessline 3
    description: Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation tasks including solving equations algebraically, performing calculus operations (derivatives, integrals, limits
  • Network accessline 4
    license: https://github.com/sympy/sympy/blob/master/LICENSE
  • Network accessline 494
    - Official Documentation: https://docs.sympy.org/
  • Network accessline 495
    - Tutorial: https://docs.sympy.org/latest/tutorials/intro-tutorial/index.html
  • Network accessline 496
    - API Reference: https://docs.sympy.org/latest/reference/index.html
  • Network accessline 497
    - Examples: https://github.com/sympy/sympy/tree/master/examples

skills/general/tooluniverse-statistical-modeling/SKILL.md

  • Network accessline 531
    - **statsmodels**: https://www.statsmodels.org/
  • Network accessline 532
    - **lifelines**: https://lifelines.readthedocs.io/
  • Network accessline 533
    - **scikit-learn**: https://scikit-learn.org/

skills/general/transformers/SKILL.md

  • Access to secretsline 45
    [Credential-related source omitted]
  • Network accessline 48
    Get tokens at: https://huggingface.co/settings/tokens

skills/general/venue-templates/SKILL.md

  • Broad permissionsline 1
    Bash
  • Network accessline 581
    **Journal Author Guidelines**: - Nature: https://www.nature.com/nature/for-authors
  • Network accessline 582
    - Nature: https://www.nature.com/nature/for-authors
  • Network accessline 583
    - Science: https://www.science.org/content/page/instructions-authors
  • Network accessline 584
    - PLOS: https://plos.org/resources/for-authors/
  • Network accessline 585
    - Cell Press: https://www.cell.com/author-guidelines
  • Network accessline 587
    **Conference Formatting**: - NeurIPS: https://neurips.cc/Conferences/2024/CallForPapers
  • Network accessline 588
    - NeurIPS: https://neurips.cc/Conferences/2024/CallForPapers
  • Network accessline 589
    - ICML: https://icml.cc/Conferences/2024/StyleAuthorInstructions
  • Network accessline 590
    - CVPR: https://cvpr.thecvf.com/Conferences/2024/AuthorGuidelines
  • Network accessline 592
    **Grant Resources**: - NSF PAPPG: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg
  • Network accessline 593
    - NSF PAPPG: https://www.nsf.gov/publications/pub_summ.jsp?ods_key=pappg
  • Network accessline 594
    - NIH Forms: https://grants.nih.gov/grants/how-to-apply-application-guide.html
  • Network accessline 595
    - DOE Funding: https://science.osti.gov/grants

skills/general/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/literature/academic-literature-search/SKILL.md

  • Network accessline 114
    "sortOrder": "descending"     })     url = f"https://export.arxiv.org/api/query?{params}"
  • Network accessline 115
    })     url = f"https://export.arxiv.org/api/query?{params}"     with urllib.request.urlopen(url, timeout=30) as resp:
  • Network accessline 116
    url = f"https://export.arxiv.org/api/query?{params}"     with urllib.request.urlopen(url, timeout=30) as resp:         xml_text = resp.read().decode("utf-8")
  • Network accessline 117
    with urllib.request.urlopen(url, timeout=30) as resp:
  • Network accessline 120
    ns = {"atom": "http://www.w3.org/2005/Atom",
  • Network accessline 121
    "arxiv": "http://arxiv.org/schemas/atom"}
  • Network accessline 147
    "volume": "", "issue": "", "pages": "",             "abstract": abstract,             "url": f"https://arxiv.org/abs/{arxiv_id}",
  • Network accessline 148
    "abstract": abstract,             "url": f"https://arxiv.org/abs/{arxiv_id}",             "category": cat,
  • Network accessline 149
    "url": f"https://arxiv.org/abs/{arxiv_id}",

skills/literature/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/literature/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/literature/biorxiv-database/SKILL.md

  • Network accessline 122
    python scripts/biorxiv_search.py \   --doi "https://doi.org/10.1101/2024.01.15.123456"
  • Network accessline 123
    --doi "https://doi.org/10.1101/2024.01.15.123456"
  • Network accessline 211
    "category": "genomics",       "abstract": "Full abstract text...",       "pdf_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf",
  • Network accessline 212
    "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 213
    "pdf_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1.full.pdf",
  • Network accessline 214
    "html_url": "https://www.biorxiv.org/content/10.1101/2024.01.15.123456v1",
  • Network accessline 215
    "jatsxml": "https://www.biorxiv.org/content/...",

skills/literature/biorxiv-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 bioRxiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
  • Network accessline 52
    "To search bioRxiv, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
  • Network accessline 63
    User: Search bioRxiv for CRISPR advances → Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
  • Network accessline 64
    → Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai" → User: "val_abc123..."
  • Network accessline 65
    → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
  • Network accessline 90
    {       "title": "Article Title",       "url": "https://biorxiv.org/content/...",
  • Network accessline 91
    "title": "Article Title",       "url": "https://biorxiv.org/content/...",       "content": "Full article text with figures...",
  • Network accessline 92
    "url": "https://biorxiv.org/content/...",
  • Network accessline 94
    "source": "biorxiv",       "relevance_score": 0.95,       "images": ["https://example.com/figure1.jpg"]
  • Network accessline 95
    "relevance_score": 0.95,       "images": ["https://example.com/figure1.jpg"]     }
  • Network accessline 96
    "images": ["https://example.com/figure1.jpg"]
  • Network accessline 166
    - Base URL: `https://api.valyu.ai/v1`
  • Network accessline 178
    Direct API calls using Node.js built-in `fetch()`, zero external dependencies.
  • Access to secretsline 189
    [Credential-related source omitted]
  • Network accessline 223
    See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.

skills/literature/bioservices/SKILL.md

  • Network accessline 355
    For detailed API documentation and advanced features, refer to: - Official documentation: https://bioservices.readthedocs.io/
  • Network accessline 356
    - Official documentation: https://bioservices.readthedocs.io/
  • Network accessline 357
    - Source code: https://github.com/cokelaer/bioservices

skills/literature/citation-management/SKILL.md

  • Broad permissionsline 1
    Bash
  • Network accessline 142
    # Extract from URL python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"
  • Network accessline 143
    python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"
  • Network accessline 484
    1. **Find MeSH terms** at https://meshb.nlm.nih.gov/search
  • Network accessline 608
    # From URL python scripts/extract_metadata.py \   --url "https://www.nature.com/articles/s41586-021-03819-2"
  • Network accessline 609
    python scripts/extract_metadata.py    --url "https://www.nature.com/articles/s41586-021-03819-2"
  • Network accessline 610
    --url "https://www.nature.com/articles/s41586-021-03819-2"

skills/literature/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/literature/clinicaltrials-database/SKILL.md

  • Network accessline 44
    url = "https://clinicaltrials.gov/api/v2/studies"
  • Network accessline 51
    response = requests.get(url, params=params)
  • Network accessline 64
    nct_id = "NCT04852770" url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}"
  • Network accessline 65
    url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}"
  • Network accessline 67
    response = requests.get(url)
  • Network accessline 433
    def search_with_rate_limit(params):     try:         response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
  • Network accessline 434
    try:         response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)         response.raise_for_status()
  • Network accessline 435
    response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
  • Network accessline 465
    try:     response = requests.get(url, params=params, timeout=30)
  • Network accessline 466
    response = requests.get(url, params=params, timeout=30)
  • Network accessline 494
    - **Base URL**: `https://clinicaltrials.gov/api/v2` - **Authentication**: Not required (public API) - **Rate Limit**: ~50 requests/minute per IP

skills/literature/clinvar-database/SKILL.md

  • Network accessline 33
    Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/
  • Network accessline 53
    # 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 54
    curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json"
  • Network accessline 120
    # Download latest monthly XML release wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz
  • Network accessline 121
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz
  • Network accessline 123
    # Download VCF for GRCh38 wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 124
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 240
    **Submission methods:** - Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/
  • Network accessline 241
    - Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/
  • Network accessline 274
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 275
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
  • Network accessline 310
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_YYYY-MM.xml.gz
  • Network accessline 351
    - ClinVar home: https://www.ncbi.nlm.nih.gov/clinvar/
  • Network accessline 352
    - ClinVar documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/
  • Network accessline 353
    - E-utilities documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • Network accessline 355
    - ClinGen expert panels: https://clinicalgenome.org/

skills/literature/gene-database/SKILL.md

  • Network accessline 92
    **Authentication:** Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ to increase rate limits.
  • Network accessline 93
    Register for a free NCBI API key at https://www.ncbi.nlm.nih.gov/account/ to increase rate limits.

skills/literature/geo-database/SKILL.md

  • Network accessline 398
    **Using wget or curl for Downloads:**
  • Network accessline 401
    # Download series matrix file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz
  • Network accessline 402
    wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/matrix/GSE123456_series_matrix.txt.gz
  • Network accessline 404
    # Download all supplementary files for a series wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/
  • Network accessline 405
    wget -r -np -nd ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/suppl/
  • Network accessline 407
    # Download SOFT format family file wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz
  • Network accessline 408
    wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123456/soft/GSE123456_family.soft.gz
  • Network accessline 673
    # Optional: Set API key for increased rate limits # Get your API key from: https://www.ncbi.nlm.nih.gov/account/
  • Network accessline 674
    # Get your API key from: https://www.ncbi.nlm.nih.gov/account/
  • Access to secretsline 675
    [Credential-related source omitted]
  • Network accessline 725
    - Web-based statistical analysis tool integrated into GEO - Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx
  • Network accessline 726
    - Accessible at: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSExxxxx
  • Network accessline 739
    - No rate limits for FTP downloads - Preferred method for bulk downloads - Can download entire directories with wget -r
  • Network accessline 741
    - Can download entire directories with wget -r
  • Network accessline 805
    - **GEO Website:** https://www.ncbi.nlm.nih.gov/geo/
  • Network accessline 806
    - **GEO Submission Guidelines:** https://www.ncbi.nlm.nih.gov/geo/info/submission.html
  • Network accessline 807
    - **GEOparse Documentation:** https://geoparse.readthedocs.io/
  • Network accessline 808
    - **E-utilities Documentation:** https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • Network accessline 809
    - **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 810
    - **GEO2R Tool:** https://www.ncbi.nlm.nih.gov/geo/geo2r/
  • Network accessline 811
    - **NCBI API Keys:** https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
  • Network accessline 812
    - **Biopython Tutorial:** https://biopython.org/DIST/docs/tutorial/Tutorial.html

skills/literature/gwas-database/SKILL.md

  • Network accessline 49
    The web interface at https://www.ebi.ac.uk/gwas/ supports multiple search modes:
  • Network accessline 90
    **Base URLs:** - GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api`
  • Network accessline 91
    - GWAS Catalog API: `https://www.ebi.ac.uk/gwas/rest/api`
  • Network accessline 92
    - Summary Statistics API: `https://www.ebi.ac.uk/gwas/summary-statistics/api`
  • Network accessline 94
    **API Documentation:** - Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 95
    - Main API docs: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 96
    - Summary stats docs: https://www.ebi.ac.uk/gwas/summary-statistics/docs/
  • Network accessline 104
    # 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 105
    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 106
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 112
    # Find associations for a variant    variant = "rs7903146"    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations"
  • Network accessline 113
    variant = "rs7903146"    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{variant}/associations"    params = {"projection": "associationBySnp"}
  • Network accessline 114
    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 115
    params = {"projection": "associationBySnp"}    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})    associations = response.json()
  • Network accessline 116
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 122
    # 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 123
    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 124
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 130
    # 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 131
    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 132
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 142
    trait = "EFO_0001360"  # Type 2 diabetes base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 143
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 145
    # Query associations for this trait url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 146
    url = f"{base_url}/efoTraits/{trait}/associations" response = requests.get(url, headers={"Content-Type": "application/json"}) associations = response.json()
  • Network accessline 147
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 162
    variant = "rs7903146" base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 163
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 165
    # Get variant details url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 166
    url = f"{base_url}/singleNucleotidePolymorphisms/{variant}" response = requests.get(url, headers={"Content-Type": "application/json"}) variant_data = response.json()
  • Network accessline 167
    response = requests.get(url, headers={"Content-Type": "application/json"})
  • Network accessline 171
    url = f"{base_url}/singleNucleotidePolymorphisms/{variant}/associations" params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 172
    params = {"projection": "associationBySnp"} response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) associations = response.json()
  • Network accessline 173
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 187
    # Query summary statistics API base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 188
    base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 196
    "size": 100  # Number of results } response = requests.get(url, params=params)
  • Network accessline 197
    } response = requests.get(url, params=params) results = response.json()
  • Network accessline 198
    response = requests.get(url, params=params)
  • Network accessline 219
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 224
    "bpEnd": end_pos } response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 225
    } response = requests.get(url, params=params, headers={"Content-Type": "application/json"}) variants_in_region = response.json()
  • Network accessline 226
    response = requests.get(url, params=params, headers={"Content-Type": "application/json"})
  • Network accessline 234
    **Access Methods:** 1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
  • Network accessline 235
    1. **FTP download**: http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/
  • Network accessline 250
    # Get available summary statistics base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api"
  • Network accessline 251
    base_url = "https://www.ebi.ac.uk/gwas/summary-statistics/api" url = f"{base_url}/studies/GCST001234" response = requests.get(url)
  • Network accessline 252
    url = f"{base_url}/studies/GCST001234" response = requests.get(url) study_info = response.json()
  • Network accessline 253
    response = requests.get(url)
  • Network accessline 284
    # API responses include _links for related resources response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234")
  • Network accessline 285
    response = requests.get("https://www.ebi.ac.uk/gwas/rest/api/studies/GCST001234")
  • Network accessline 288
    # Follow link to associations associations_url = study['_links']['associations']['href'] associations_response = requests.get(associations_url)
  • Network accessline 290
    associations_response = requests.get(associations_url)
  • Network accessline 303
    url = f"https://www.ebi.ac.uk/gwas/rest/api/efoTraits/{efo_id}/associations"
  • Network accessline 326
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}"
  • Network accessline 331
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/{rs_id}/associations"
  • Network accessline 348
    url = f"https://www.ebi.ac.uk/gwas/rest/api/singleNucleotidePolymorphisms/search/findByGene"
  • Network accessline 406
    # Via FTP    wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
  • Network accessline 407
    wget ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCSTXXXXXX/harmonised/GCSTXXXXXX-harmonised.tsv.gz
  • Network accessline 412
    url = f"https://www.ebi.ac.uk/gwas/summary-statistics/api/chromosomes/{chrom}/associations"
  • Network accessline 497
    pandas DataFrame with association results     """     base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 498
    """     base_url = "https://www.ebi.ac.uk/gwas/rest/api"     url = f"{base_url}/efoTraits/{trait_id}/associations"
  • Network accessline 499
    base_url = "https://www.ebi.ac.uk/gwas/rest/api"
  • Network accessline 506
    while True:         params = {"page": page, "size": 100}         response = requests.get(url, params=params, headers=headers)
  • Network accessline 508
    response = requests.get(url, params=params, headers=headers)
  • Network accessline 564
    The GWAS Catalog team provides workshop materials: - GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 565
    - GitHub repository: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 598
    - **GWAS Catalog website**: https://www.ebi.ac.uk/gwas/
  • Network accessline 599
    - **Documentation**: https://www.ebi.ac.uk/gwas/docs
  • Network accessline 600
    - **API documentation**: https://www.ebi.ac.uk/gwas/rest/docs/api
  • Network accessline 601
    - **Summary Statistics API**: https://www.ebi.ac.uk/gwas/summary-statistics/docs/
  • Network accessline 602
    - **FTP site**: http://ftp.ebi.ac.uk/pub/databases/gwas/
  • Network accessline 603
    - **Training materials**: https://github.com/EBISPOT/GWAS_Catalog-workshop
  • Network accessline 604
    - **PGS Catalog** (polygenic scores): https://www.pgscatalog.org/

skills/literature/hmdb-database/SKILL.md

  • Network accessline 36
    Access HMDB through the web interface at https://www.hmdb.ca/ for:
  • Network accessline 89
    HMDB offers bulk data downloads at https://www.hmdb.ca/downloads in multiple formats:

skills/literature/literature-review/SKILL.md

  • Broad permissionsline 1
    Bash
  • Network accessline 317
    - Date filters: `2020:2024[Publication Date]` - Boolean operators: AND, OR, NOT - See MeSH browser: https://meshb.nlm.nih.gov/search
  • Network accessline 319
    - See MeSH browser: https://meshb.nlm.nih.gov/search
  • Network accessline 385
    ### 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 387
    - 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 586
    **Guidelines:** - PRISMA (Systematic Reviews): http://www.prisma-statement.org/
  • Network accessline 587
    - PRISMA (Systematic Reviews): http://www.prisma-statement.org/
  • Network accessline 588
    - Cochrane Handbook: https://training.cochrane.org/handbook
  • Network accessline 589
    - AMSTAR 2 (Review Quality): https://amstar.ca/
  • Network accessline 591
    **Tools:** - MeSH Browser: https://meshb.nlm.nih.gov/search
  • Network accessline 592
    - MeSH Browser: https://meshb.nlm.nih.gov/search
  • Network accessline 593
    - PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/
  • Network accessline 594
    - Boolean Search Guide: https://www.ncbi.nlm.nih.gov/books/NBK3827/
  • Network accessline 596
    **Citation Styles:** - APA Style: https://apastyle.apa.org/
  • Network accessline 597
    - APA Style: https://apastyle.apa.org/
  • Network accessline 598
    - Nature Portfolio: https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards
  • Network accessline 599
    - NLM/Vancouver: https://www.nlm.nih.gov/bsd/uniform_requirements.html

skills/literature/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/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/literature/openalex-database/SKILL.md

  • Network accessline 178
    dois = [     "https://doi.org/10.1038/s41586-021-03819-2",
  • Network accessline 179
    "https://doi.org/10.1038/s41586-021-03819-2",
  • Network accessline 180
    "https://doi.org/10.1126/science.abc1234",
  • Network accessline 216
    # Get the work work = client.get_entity('works', 'https://doi.org/10.1038/s41586-021-03819-2')
  • Network accessline 217
    work = client.get_entity('works', 'https://doi.org/10.1038/s41586-021-03819-2')
  • Network accessline 219
    # Get citing papers using cited_by_api_url import requests citing_response = requests.get(
  • Network accessline 220
    import requests citing_response = requests.get(     work['cited_by_api_url'],
  • Network accessline 221
    citing_response = requests.get(
  • Network accessline 403
    # DOI for works work = client.get_entity('works', 'https://doi.org/10.7717/peerj.4375')
  • Network accessline 404
    work = client.get_entity('works', 'https://doi.org/10.7717/peerj.4375')
  • Network accessline 406
    # ORCID for authors author = client.get_entity('authors', 'https://orcid.org/0000-0003-1613-5981')
  • Network accessline 407
    author = client.get_entity('authors', 'https://orcid.org/0000-0003-1613-5981')
  • Network accessline 409
    # ROR for institutions institution = client.get_entity('institutions', 'https://ror.org/02y3ad647')
  • Network accessline 410
    institution = client.get_entity('institutions', 'https://ror.org/02y3ad647')

skills/literature/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/literature/pdb-database/SKILL.md

  • Possible obfuscationline 57
    value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
  • Network accessline 103
    # Get entry-level data entry_data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 104
    entry_data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 111
    # Get protein/nucleic acid information entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
  • Network accessline 112
    entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
  • Network accessline 135
    } """ data = fetch(query_type="graphql", query=query)
  • Network accessline 137
    data = fetch(query_type="graphql", query=query)
  • Network accessline 144
    **Download Methods:** - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb`
  • Network accessline 145
    - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb`
  • Network accessline 146
    - **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif`
  • Network accessline 148
    - **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1)
  • Network accessline 156
    # Download PDB format pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
  • Network accessline 157
    pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
  • Network accessline 158
    response = requests.get(pdb_url)
  • Network accessline 162
    # Download mmCIF format cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
  • Network accessline 163
    cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
  • Network accessline 164
    response = requests.get(cif_url)
  • Network accessline 193
    # Get experimental details data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 194
    data = fetch("4HHB", schema=Schema.ENTRY)
  • Network accessline 215
    for pdb_id in pdb_ids:     try:         data = fetch(pdb_id, schema=Schema.ENTRY)
  • Network accessline 216
    try:         data = fetch(pdb_id, schema=Schema.ENTRY)         results[pdb_id] = {
  • Network accessline 217
    data = fetch(pdb_id, schema=Schema.ENTRY)
  • Network accessline 301
    - **RCSB PDB Website:** https://www.rcsb.org
  • Network accessline 302
    - **PDB-101 Educational Portal:** https://pdb101.rcsb.org
  • Network accessline 303
    - **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview
  • Network accessline 304
    - **Python Package Docs:** https://rcsbapi.readthedocs.io/
  • Network accessline 305
    - **Data API Documentation:** https://data.rcsb.org/
  • Network accessline 306
    - **GitHub Repository:** https://github.com/rcsb/py-rcsb-api

skills/literature/perplexity-search/SKILL.md

  • Network accessline 39
    1. **Get OpenRouter API key**:    - Visit https://openrouter.ai/keys
  • Network accessline 40
    - Visit https://openrouter.ai/keys
  • Access to secretsline 47
    [Credential-related source omitted]
  • Network accessline 256
    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 257
    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 258
    5. Monitor usage at https://openrouter.ai/activity
  • Access to secretsline 269
    [Credential-related source omitted]
  • Network accessline 287
    **Solutions**: - Wait a few seconds before retrying - Increase rate limit at https://openrouter.ai/keys
  • Network accessline 288
    - Wait a few seconds before retrying - Increase rate limit at https://openrouter.ai/keys - Add delays between requests in batch processing
  • Network accessline 289
    - Increase rate limit at https://openrouter.ai/keys
  • Network accessline 296
    **Solution**: - Add credits at https://openrouter.ai/account
  • Network accessline 297
    - Add credits at https://openrouter.ai/account
  • Network accessline 389
    **OpenRouter:** - Dashboard: https://openrouter.ai/account
  • Network accessline 390
    - Dashboard: https://openrouter.ai/account
  • Network accessline 391
    - API Keys: https://openrouter.ai/keys
  • Network accessline 392
    - Perplexity Models: https://openrouter.ai/perplexity
  • Network accessline 393
    - Usage Monitoring: https://openrouter.ai/activity
  • Network accessline 394
    - Documentation: https://openrouter.ai/docs
  • Network accessline 396
    **LiteLLM:** - Documentation: https://docs.litellm.ai/
  • Network accessline 397
    - Documentation: https://docs.litellm.ai/
  • Network accessline 398
    - OpenRouter Provider: https://docs.litellm.ai/docs/providers/openrouter
  • Network accessline 399
    - GitHub: https://github.com/BerriAI/litellm
  • Network accessline 401
    **Perplexity:** - Official Docs: https://docs.perplexity.ai/
  • Network accessline 402
    - Official Docs: https://docs.perplexity.ai/
  • Access to secretsline 416
    [Credential-related source omitted]
  • Access to secretsline 426
    [Credential-related source omitted]

skills/literature/pubmed-database/SKILL.md

  • Network accessline 127
    # Step 1: Search for articles base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
  • Network accessline 128
    base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
  • Network accessline 135
    [Credential-related source omitted]
  • Access to secretsline 135
    [Credential-related source omitted]
  • Network accessline 136
    } response = requests.get(search_url, params=params) pmids = response.json()["esearchresult"]["idlist"]
  • Network accessline 137
    response = requests.get(search_url, params=params)
  • Network accessline 147
    [Credential-related source omitted]
  • Access to secretsline 147
    [Credential-related source omitted]
  • Network accessline 148
    } response = requests.get(fetch_url, params=params) abstracts = response.text
  • Network accessline 149
    response = requests.get(fetch_url, params=params)
  • Network accessline 453
    - **PubMed Help**: https://pubmed.ncbi.nlm.nih.gov/help/
  • Network accessline 454
    - **E-utilities Documentation**: https://www.ncbi.nlm.nih.gov/books/NBK25501/

skills/literature/pubmed-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 PubMed, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
  • Network accessline 52
    "To search PubMed, I need your Valyu API key. Get one free ($10 credits) at https://platform.valyu.ai"
  • Network accessline 63
    User: Search PubMed for CAR-T cell therapy advances → Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
  • Network accessline 64
    → Response: {"success": false, "setup_required": true, ...} → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai" → User: "val_abc123..."
  • Network accessline 65
    → Claude asks: "Please provide your Valyu API key from https://platform.valyu.ai"
  • Network accessline 112
    {       "title": "Article Title",       "url": "https://pubmed.ncbi.nlm.nih.gov/...",
  • Network accessline 113
    "title": "Article Title",       "url": "https://pubmed.ncbi.nlm.nih.gov/...",       "content": "Full article text with figures...",
  • Network accessline 114
    "url": "https://pubmed.ncbi.nlm.nih.gov/...",
  • Network accessline 116
    "source": "pubmed",       "relevance_score": 0.95,       "images": ["https://example.com/figure1.jpg"]
  • Network accessline 117
    "relevance_score": 0.95,       "images": ["https://example.com/figure1.jpg"]     }
  • Network accessline 118
    "images": ["https://example.com/figure1.jpg"]
  • Network accessline 187
    - Base URL: `https://api.valyu.ai/v1`
  • Network accessline 199
    Direct API calls using Node.js built-in `fetch()`, zero external dependencies.
  • Access to secretsline 210
    [Credential-related source omitted]
  • Network accessline 244
    See the [Valyu docs](https://docs.valyu.ai) for full integration examples and SDK reference.

skills/literature/research-grants/SKILL.md

skills/literature/research-lookup/SKILL.md

  • Broad permissionsline 1
    Bash
  • Access to secretsline 248
    [Credential-related source omitted]

skills/literature/scientific-writing/SKILL.md

skills/literature/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/literature/uspto-database/SKILL.md

  • Network accessline 38
    - Access to patent data through June 30, 2025    - 45 requests/minute rate limit    - **Base URL**: `https://search.patentsview.org/api/v1/`
  • Network accessline 40
    - **Base URL**: `https://search.patentsview.org/api/v1/`
  • Network accessline 49
    - Trademark status, ownership, prosecution history    - Search by serial or registration number    - **Base URL**: `https://tsdrapi.uspto.gov/ts/cd/`
  • Network accessline 51
    - **Base URL**: `https://tsdrapi.uspto.gov/ts/cd/`
  • Network accessline 69
    USPTO APIs require an API key. Register at: **https://account.uspto.gov/api-manager/**
  • Network accessline 70
    **https://account.uspto.gov/api-manager/**
  • Network accessline 72
    API key for **PatentSearch API** is provided by PatentsView. Register at: **https://patentsview.org/api-v01-information-page**
  • Network accessline 73
    **https://patentsview.org/api-v01-information-page**
  • Access to secretsline 77
    [Credential-related source omitted]
  • Access to secretsline 78
    [Credential-related source omitted]
  • Network accessline 153
    url = "https://search.patentsview.org/api/v1/patent"
  • Access to secretsline 155
    [Credential-related source omitted]
  • Network accessline 172
    response = requests.post(url, headers=headers, json=query)
  • Access to secretsline 354
    [Credential-related source omitted]
  • Access to secretsline 356
    [Credential-related source omitted]
  • Network accessline 404
    **Base URL**: `https://assignment-api.uspto.gov/patent/v1.4/`
  • Network accessline 411
    [Credential-related source omitted]
  • Access to secretsline 411
    [Credential-related source omitted]
  • Network accessline 412
    url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}"
  • Access to secretsline 413
    [Credential-related source omitted]
  • Network accessline 415
    response = requests.get(url, headers=headers)
  • Access to secretsline 419
    [Credential-related source omitted]
  • Network accessline 434
    [Credential-related source omitted]
  • Access to secretsline 434
    [Credential-related source omitted]
  • Network accessline 435
    url = "https://assignment-api.uspto.gov/patent/v1.4/assignment/search"
  • Access to secretsline 436
    [Credential-related source omitted]
  • Network accessline 439
    response = requests.post(url, headers=headers, json=data)
  • Access to secretsline 501
    [Credential-related source omitted]
  • Access to secretsline 511
    [Credential-related source omitted]
  • Network accessline 520
    # 3. Get assignment history     import requests     assign_url = f"https://assignment-api.uspto.gov/patent/v1.4/assignment/patent/{patent_number}"
  • Network accessline 521
    [Credential-related source omitted]
  • Network accessline 522
    [Credential-related source omitted]
  • Network accessline 523
    [Credential-related source omitted]
  • Access to secretsline 523
    [Credential-related source omitted]
  • Network accessline 585
    ### API Documentation - **PatentSearch API**: https://search.patentsview.org/docs/
  • Network accessline 586
    - **PatentSearch API**: https://search.patentsview.org/docs/
  • Network accessline 587
    - **USPTO Developer Portal**: https://developer.uspto.gov/
  • Network accessline 588
    - **USPTO Open Data Portal**: https://data.uspto.gov/
  • Network accessline 589
    - **API Key Registration**: https://account.uspto.gov/api-manager/
  • Network accessline 591
    ### Python Libraries - **uspto-opendata-python**: https://pypi.org/project/uspto-opendata-python/
  • Network accessline 592
    - **uspto-opendata-python**: https://pypi.org/project/uspto-opendata-python/
  • Network accessline 593
    - **USPTO Docs**: https://docs.ip-tools.org/uspto-opendata-python/

skills/med/clinical-decision-support/SKILL.md

skills/med/clinical-reports/SKILL.md

skills/med/clinicaltrials-database/SKILL.md

  • Network accessline 44
    url = "https://clinicaltrials.gov/api/v2/studies"
  • Network accessline 51
    response = requests.get(url, params=params)
  • Network accessline 64
    nct_id = "NCT04852770" url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}"
  • Network accessline 65
    url = f"https://clinicaltrials.gov/api/v2/studies/{nct_id}"
  • Network accessline 67
    response = requests.get(url)
  • Network accessline 433
    def search_with_rate_limit(params):     try:         response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
  • Network accessline 434
    try:         response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)         response.raise_for_status()
  • Network accessline 435
    response = requests.get("https://clinicaltrials.gov/api/v2/studies", params=params)
  • Network accessline 465
    try:     response = requests.get(url, params=params, timeout=30)
  • Network accessline 466
    response = requests.get(url, params=params, timeout=30)
  • Network accessline 494
    - **Base URL**: `https://clinicaltrials.gov/api/v2` - **Authentication**: Not required (public API) - **Rate Limit**: ~50 requests/minute per IP

skills/med/clinvar-database/SKILL.md

  • Network accessline 33
    Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/
  • Network accessline 53
    # 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 54
    curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json"
  • Network accessline 120
    # Download latest monthly XML release wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz
  • Network accessline 121
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_00-latest.xml.gz
  • Network accessline 123
    # Download VCF for GRCh38 wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 124
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 240
    **Submission methods:** - Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/
  • Network accessline 241
    - Web submission portal: https://submit.ncbi.nlm.nih.gov/subs/clinvar/
  • Network accessline 274
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
  • Network accessline 275
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
  • Network accessline 310
    wget ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/clinvar_variation/ClinVarVariationRelease_YYYY-MM.xml.gz
  • Network accessline 351
    - ClinVar home: https://www.ncbi.nlm.nih.gov/clinvar/
  • Network accessline 352
    - ClinVar documentation: https://www.ncbi.nlm.nih.gov/clinvar/docs/
  • Network accessline 353
    - E-utilities documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
  • Network accessline 355
    - ClinGen expert panels: https://clinicalgenome.org/

skills/med/neurokit2/SKILL.md

  • Network accessline 279
    uv pip install https://github.com/neuropsychology/NeuroKit/zipball/dev
  • Network accessline 351
    - Official Documentation: https://neuropsychology.github.io/NeuroKit/
  • Network accessline 352
    - GitHub Repository: https://github.com/neuropsychology/NeuroKit
  • Network accessline 353
    - 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/med/neuropixels-analysis/SKILL.md

  • Network accessline 341
    - **SpikeInterface Docs**: https://spikeinterface.readthedocs.io/
  • Network accessline 342
    - **Neuropixels Tutorial**: https://spikeinterface.readthedocs.io/en/stable/how_to/analyze_neuropixels.html
  • Network accessline 343
    - **Kilosort4 GitHub**: https://github.com/MouseLand/Kilosort
  • Network accessline 344
    - **IBL Neuropixel Tools**: https://github.com/int-brain-lab/ibl-neuropixel
  • Network accessline 345
    - **Allen Institute ecephys**: https://github.com/AllenInstitute/ecephys_spike_sorting
  • Network accessline 346
    - **Bombcell (Automated QC)**: https://github.com/Julie-Fabre/bombcell
  • Network accessline 347
    - **SpikeAgent (AI Curation)**: https://github.com/SpikeAgent/SpikeAgent

skills/med/pydicom/SKILL.md

  • Network accessline 2
    name: pydicom description: Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from med
  • Network accessline 3
    description: Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (C
  • Network accessline 4
    license: https://github.com/pydicom/pydicom/blob/main/LICENSE
  • Network accessline 427
    Official pydicom documentation: https://pydicom.github.io/pydicom/dev/
  • Network accessline 428
    - User Guide: https://pydicom.github.io/pydicom/dev/guides/user/index.html
  • Network accessline 429
    - Tutorials: https://pydicom.github.io/pydicom/dev/tutorials/index.html
  • Network accessline 430
    - API Reference: https://pydicom.github.io/pydicom/dev/reference/index.html
  • Network accessline 431
    - Examples: https://pydicom.github.io/pydicom/dev/auto_examples/index.html

skills/med/pyhealth/SKILL.md

  • Network accessline 382
    - **Documentation**: https://pyhealth.readthedocs.io/
  • Network accessline 383
    - **GitHub Issues**: https://github.com/sunlabuiuc/PyHealth/issues

skills/med/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/med/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/med/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/med/treatment-plans/SKILL.md

  • Broad permissionsline 1
    Bash
  • Dangerous shell operationline 1390
    sudo cp assets/medical_treatment_plan.sty /usr/local/texlive/texmf-local/tex/latex/
  • Dangerous shell operationline 1391
    sudo texhash
  • Network accessline 1413
    **Download from CTAN:** - Visit: https://ctan.org/
  • Network accessline 1414
    - Visit: https://ctan.org/ - Search for medical document classes - Download and install per package instructions
  • Dangerous shell operationline 1423
    sudo tlmgr update --self
  • Dangerous shell operationline 1424
    sudo tlmgr install tcolorbox tikz pgf
  • Dangerous shell operationline 1439
    sudo tlmgr install tcolorbox tikz pgf

skills/pharma/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/pharma/chembl-database/SKILL.md

  • Network accessline 382
    - ChEMBL website: https://www.ebi.ac.uk/chembl/
  • Network accessline 383
    - API documentation: https://www.ebi.ac.uk/chembl/api/data/docs
  • Network accessline 384
    - Python client GitHub: https://github.com/chembl/chembl_webresource_client
  • Network accessline 385
    - Interface documentation: https://chembl.gitbook.io/chembl-interface-documentation/
  • Network accessline 386
    - Example notebooks: https://github.com/chembl/notebooks

skills/pharma/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/pharma/datamol/SKILL.md

  • Network accessline 130
    # Read from cloud storage df = dm.read_sdf("s3://bucket/compounds.sdf") df = dm.read_csv("https://example.com/data.csv")
  • Network accessline 132
    df = dm.read_csv("https://example.com/data.csv")
  • Network accessline 701
    - **Datamol Documentation**: https://docs.datamol.io/
  • Network accessline 702
    - **RDKit Documentation**: https://www.rdkit.org/docs/
  • Network accessline 703
    - **GitHub Repository**: https://github.com/datamol-io/datamol

skills/pharma/deepchem/SKILL.md

  • Network accessline 591
    - Official documentation: https://deepchem.readthedocs.io/
  • Network accessline 592
    - GitHub repository: https://github.com/deepchem/deepchem
  • Network accessline 593
    - Tutorials: https://deepchem.readthedocs.io/en/latest/get_started/tutorials.html

skills/pharma/diffdock/SKILL.md

  • Network accessline 53
    git clone https://github.com/gcorso/DiffDock.git
  • Network accessline 366
    python app/main.py # Navigate to http://localhost:7860
  • Network accessline 367
    # Navigate to http://localhost:7860
  • Network accessline 370
    Or use the online demo without installation: - https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web
  • Network accessline 371
    - https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web
  • Network accessline 477
    - **GitHub Repository**: https://github.com/gcorso/DiffDock
  • Network accessline 478
    - **Online Demo**: https://huggingface.co/spaces/reginabarzilaygroup/DiffDock-Web
  • Network accessline 479
    - **DiffDock-L Paper**: https://arxiv.org/abs/2402.18396
  • Network accessline 480
    - **Original Paper**: https://arxiv.org/abs/2210.01776

skills/pharma/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/pharma/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/pharma/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/pharma/fda-database/SKILL.md

  • Access to secretsline 44
    [Credential-related source omitted]
  • Network accessline 64
    Register at: https://open.fda.gov/apis/authentication/
  • Access to secretsline 68
    [Credential-related source omitted]
  • Access to secretsline 426
    [Credential-related source omitted]
  • Network accessline 490
    - **openFDA Homepage**: https://open.fda.gov/
  • Network accessline 491
    - **API Documentation**: https://open.fda.gov/apis/
  • Network accessline 492
    - **Interactive API Explorer**: https://open.fda.gov/apis/try-the-api/
  • Network accessline 493
    - **GitHub Repository**: https://github.com/FDA/openfda
  • Network accessline 494
    - **Terms of Service**: https://open.fda.gov/terms/
  • Network accessline 514
    - **GitHub Issues**: https://github.com/FDA/openfda/issues

skills/pharma/medchem/SKILL.md

  • Network accessline 402
    Official documentation: https://medchem-docs.datamol.io/
  • Network accessline 403
    GitHub repository: https://github.com/datamol-io/medchem

skills/pharma/molfeat/SKILL.md

  • Network accessline 505
    - **Official Documentation**: https://molfeat-docs.datamol.io/
  • Network accessline 506
    - **GitHub Repository**: https://github.com/datamol-io/molfeat
  • Network accessline 507
    - **PyPI Package**: https://pypi.org/project/molfeat/
  • Network accessline 508
    - **Tutorial**: https://portal.valencelabs.com/datamol/post/types-of-featurizers-b1e8HHrbFMkbun6

skills/pharma/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/pharma/opentargets-database/SKILL.md

  • Network accessline 227
    Key information: - **Endpoint:** `https://api.platform.opentargets.org/api/v4/graphql`
  • Network accessline 228
    - **Endpoint:** `https://api.platform.opentargets.org/api/v4/graphql`
  • Network accessline 229
    - **Interactive browser:** `https://api.platform.opentargets.org/api/v4/graphql/browser`
  • Network accessline 358
    **Release information:** Check https://platform-docs.opentargets.org/release-notes for the latest updates.

skills/pharma/pubchem-database/SKILL.md

  • Network accessline 199
    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 200
    url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/PNG?image_size=large"
  • Network accessline 201
    response = requests.get(url)
  • Network accessline 233
    # 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 235
    url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cid}/assaysummary/JSON"
  • Network accessline 237
    response = requests.get(url)
  • Network accessline 259
    cid = 2244 url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON"
  • Network accessline 260
    url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON"
  • Network accessline 262
    response = requests.get(url)
  • Network accessline 277
    # 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 278
    url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/{cid}/JSON?heading=Drug and Medication Information"
  • Network accessline 567
    - PubChem Home: https://pubchem.ncbi.nlm.nih.gov/
  • Network accessline 568
    - PUG-REST Documentation: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest
  • Network accessline 569
    - PUG-REST Tutorial: https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest-tutorial
  • Network accessline 570
    - PubChemPy Documentation: https://pubchempy.readthedocs.io/
  • Network accessline 571
    - PubChemPy GitHub: https://github.com/mcs07/PubChemPy

skills/pharma/pytdc/SKILL.md

  • Network accessline 454
    - **Official Website**: https://tdcommons.ai
  • Network accessline 455
    - **Documentation**: https://tdc.readthedocs.io
  • Network accessline 456
    - **GitHub**: https://github.com/mims-harvard/TDC

skills/pharma/rowan/SKILL.md

  • Network accessline 40
    Generate an API key at [labs.rowansci.com/account/api-keys](https://labs.rowansci.com/account/api-keys).
  • Access to secretsline 45
    [Credential-related source omitted]
  • Access to secretsline 50
    [Credential-related source omitted]
  • Access to secretsline 53
    [Credential-related source omitted]
  • Possible obfuscationline 184
    protein_seq = "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEV
  • Network accessline 420
    - **Web Interface**: https://labs.rowansci.com
  • Network accessline 421
    - **Documentation**: https://docs.rowansci.com
  • Network accessline 422
    - **Python API Docs**: https://docs.rowansci.com/api/python/v2/
  • Network accessline 423
    - **Tutorials**: https://docs.rowansci.com/tutorials

skills/pharma/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/pharma/tooluniverse-drug-research/SKILL.md

  • Network accessline 457
    ![2D Structure](https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=4091&t=l)

skills/pharma/tooluniverse-target-research/SKILL.md

  • Access to secretsline 668
    [Credential-related source omitted]

skills/pharma/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/pharma/torchdrug/SKILL.md

  • Network accessline 430
    **Official Documentation:** https://torchdrug.ai/docs/
  • Network accessline 431
    **GitHub:** https://github.com/DeepGraphLearning/torchdrug

skills/pharma/zinc-database/SKILL.md

  • Network accessline 43
    Primary access point: https://zinc.docking.org/
  • Network accessline 44
    Interactive searching: https://cartblanche22.docking.org/
  • Network accessline 50
    **Base URL**: `https://cartblanche22.docking.org/`
  • Network accessline 60
    **Web interface**: https://cartblanche22.docking.org/search/zincid
  • Network accessline 64
    curl "https://cartblanche22.docking.org/[email protected]_fields=smiles,zinc_id"
  • Network accessline 69
    curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001,ZINC000000000002&output_fields=smiles,zinc_id,tranche"
  • Network accessline 78
    **Web interface**: https://cartblanche22.docking.org/search/smiles
  • Network accessline 82
    curl "https://cartblanche22.docking.org/[email protected]=4-Fadist=4"
  • Network accessline 93
    curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1"
  • Network accessline 98
    curl "https://cartblanche22.docking.org/smiles.txt:smiles=c1ccccc1&dist=3&output_fields=zinc_id,smiles,tranche"
  • Network accessline 105
    **Web interface**: https://cartblanche22.docking.org/search/catitems
  • Network accessline 109
    curl "https://cartblanche22.docking.org/catitems.txt:catitem_id=SUPPLIER-CODE-123"
  • Network accessline 121
    **Web interface**: https://cartblanche22.docking.org/search/random
  • Network accessline 125
    curl "https://cartblanche22.docking.org/substance/random.txt:count=100"
  • Network accessline 135
    curl "https://cartblanche22.docking.org/substance/random.txt:count=1000&subset=lead-like&output_fields=zinc_id,smiles,tranche"
  • Network accessline 146
    # 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 147
    curl "https://cartblanche22.docking.org/substance/random.txt:count=10000&subset=drug-like&output_fields=zinc_id,smiles,tranche" > docking_library.txt
  • Network accessline 173
    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 201
    curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001,ZINC000000000002&output_fields=zinc_id,smiles,supplier_code,catalogs"
  • Network accessline 215
    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 234
    curl "https://cartblanche22.docking.org/substances.txt:zinc_id=ZINC000000000001&output_fields=zinc_id,smiles,catalogs,tranche"
  • Network accessline 260
    **File repository**: https://files.docking.org/zinc22/
  • Network accessline 267
    Refer to ZINC documentation at https://wiki.docking.org for downloading protocols and batch access methods.
  • Network accessline 271
    ### Using curl with Python
  • Network accessline 277
    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 278
    """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 279
    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 280
    result = subprocess.run(['curl', url], capture_output=True, text=True)
  • Network accessline 283
    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 284
    """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 285
    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 286
    result = subprocess.run(['curl', url], capture_output=True, text=True)
  • Network accessline 289
    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 290
    """Get random compounds from ZINC22."""     url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={output_fields}"     if subset:
  • Network accessline 291
    url = f"https://cartblanche22.docking.org/substance/random.txt:count={count}&output_fields={output_fields}"
  • Network accessline 292
    if subset:         url += f"&subset={subset}"     result = subprocess.run(['curl', url], capture_output=True, text=True)
  • Network accessline 293
    url += f"&subset={subset}"     result = subprocess.run(['curl', url], capture_output=True, text=True)     return result.stdout
  • Network accessline 294
    result = subprocess.run(['curl', url], capture_output=True, text=True)
  • Network accessline 337
    - **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 338
    - **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 339
    - **Parallel downloads**: When downloading 3D structures, use parallel wget or aria2c for file repositories
  • Network accessline 385
    - **ZINC Website**: https://zinc.docking.org/
  • Network accessline 386
    - **CartBlanche22 Interface**: https://cartblanche22.docking.org/
  • Network accessline 387
    - **ZINC Wiki**: https://wiki.docking.org/
  • Network accessline 388
    - **File Repository**: https://files.docking.org/zinc22/
  • Network accessline 389
    - **GitHub**: https://github.com/docking-org/

skills/vision/egohos-segmentation/SKILL.md

  • Network accessline 5
    metadata:     skill-author: K-Dense Inc.     original-repo: https://github.com/owenzlz/EgoHOS
  • Network accessline 6
    skill-author: K-Dense Inc.     original-repo: https://github.com/owenzlz/EgoHOS     skill-category: Computer Vision
  • Network accessline 7
    original-repo: https://github.com/owenzlz/EgoHOS
  • Network accessline 65
    # Clone repository git clone https://github.com/owenzlz/EgoHOS.git
  • Network accessline 66
    git clone https://github.com/owenzlz/EgoHOS.git
  • Network accessline 143
    # Clone repository git clone https://github.com/owenzlz/EgoHOS.git
  • Network accessline 144
    git clone https://github.com/owenzlz/EgoHOS.git
  • Network accessline 372
    - GitHub repository: https://github.com/owenzlz/EgoHOS
  • Network accessline 380
    author = {Owen [Last Name]},   title = {EgoHOS: Egocentric Hand-Object Segmentation},   url = {https://github.com/owenzlz/EgoHOS},
  • Network accessline 381
    title = {EgoHOS: Egocentric Hand-Object Segmentation},   url = {https://github.com/owenzlz/EgoHOS},   year = {2023}
  • Network accessline 382
    url = {https://github.com/owenzlz/EgoHOS},

skills/vision/hand-tracking-toolkit/SKILL.md

  • Network accessline 5
    metadata:     skill-author: K-Dense Inc.     original-repo: https://github.com/facebookresearch/hand_tracking_toolkit
  • Network accessline 6
    skill-author: K-Dense Inc.     original-repo: https://github.com/facebookresearch/hand_tracking_toolkit     organization: Meta Facebook Research
  • Network accessline 7
    original-repo: https://github.com/facebookresearch/hand_tracking_toolkit
  • Network accessline 62
    # Clone repository git clone https://github.com/facebookresearch/hand_tracking_toolkit.git
  • Network accessline 63
    git clone https://github.com/facebookresearch/hand_tracking_toolkit.git
  • Network accessline 196
    - GitHub: https://github.com/facebookresearch/hand_tracking_toolkit
  • Network accessline 197
    - HOT3D: https://facebookresearch.github.io/hot3d
  • Network accessline 198
    - Challenge: https://eval.ai/web/challenges/challenge-page/...

skills/vision/hands-3d-pose/SKILL.md

  • Network accessline 5
    metadata:     skill-author: K-Dense Inc.     original-repo: https://github.com/ap229997/hands
  • Network accessline 6
    skill-author: K-Dense Inc.     original-repo: https://github.com/ap229997/hands     paper: ECCV 2024
  • Network accessline 7
    original-repo: https://github.com/ap229997/hands
  • Network accessline 19
    **Project video**: https://youtu.be/YolFnTtq38E
  • Network accessline 83
    # Clone repository git clone https://github.com/ap229997/hands.git
  • Network accessline 84
    git clone https://github.com/ap229997/hands.git
  • Network accessline 149
    # Clone repository git clone https://github.com/ap229997/hands.git
  • Network accessline 150
    git clone https://github.com/ap229997/hands.git
  • Network accessline 167
    mkdir -p checkpoints cd checkpoints wget https://path/to/model-weights.pth
  • Network accessline 168
    cd checkpoints wget https://path/to/model-weights.pth cd ..
  • Network accessline 169
    wget https://path/to/model-weights.pth
  • Network accessline 552
    ### Code and Data - GitHub repository: https://github.com/ap229997/hands
  • Network accessline 553
    - GitHub repository: https://github.com/ap229997/hands
  • Network accessline 554
    - Demo branch: https://github.com/ap229997/hands/tree/demo
  • Network accessline 555
    - Project video: https://youtu.be/YolFnTtq38E
  • Network accessline 557
    ### Related Work - FreiHAND: https://lmb.informatik.uni-freiburg.de/projects/freihand/
  • Network accessline 558
    - FreiHAND: https://lmb.informatik.uni-freiburg.de/projects/freihand/
  • Network accessline 559
    - HO3D: https://www.is.tue.mpg.de/person/mohan/hands2020.html
  • Network accessline 560
    - EgoHands: https://egohands.github.io

skills/vision/handtracking/SKILL.md

  • Network accessline 5
    metadata:     skill-author: K-Dense Inc.     original-repo: https://github.com/victordibia/handtracking
  • Network accessline 6
    skill-author: K-Dense Inc.     original-repo: https://github.com/victordibia/handtracking     skill-category: Computer Vision
  • Network accessline 7
    original-repo: https://github.com/victordibia/handtracking
  • Network accessline 18
    **Companion JavaScript library**: Handtrack.js is available for browser-based applications (https://github.com/victordibia/handtrack.js).
  • Network accessline 64
    # Clone repository git clone https://github.com/victordibia/handtracking.git
  • Network accessline 65
    git clone https://github.com/victordibia/handtracking.git
  • Network accessline 115
    <script src="https://cdn.jsdelivr.net/npm/handtrackjs/dist/handtrack.min.js"></script>
  • Network accessline 142
    # Clone repository git clone https://github.com/victordibia/handtracking.git
  • Network accessline 143
    git clone https://github.com/victordibia/handtracking.git
  • Network accessline 436
    ### Documentation - GitHub repository: https://github.com/victordibia/handtracking
  • Network accessline 437
    - GitHub repository: https://github.com/victordibia/handtracking
  • Network accessline 438
    - EgoHands dataset paper: https://egohands.github.io
  • Network accessline 439
    - Handtrack.js documentation: https://github.com/victordibia/handtrack.js
  • Network accessline 441
    ### Related Projects - EgoHands Dataset: https://github.com/egohands/EgoHands
  • Network accessline 442
    - EgoHands Dataset: https://github.com/egohands/EgoHands
  • Network accessline 443
    - MediaPipe Hands: https://google.github.io/mediapipe/solutions/hands.html
  • Network accessline 444
    - OpenPose: https://github.com/CMU-Perceptual-Computing-Lab/openpose
  • Network accessline 469
    author = {Victor Dibia},   title = {Real-time Hand Detection in Python using TensorFlow},   url = {https://github.com/victordibia/handtracking},
  • Network accessline 470
    title = {Real-time Hand Detection in Python using TensorFlow},   url = {https://github.com/victordibia/handtracking},   year = {2018}
  • Network accessline 471
    url = {https://github.com/victordibia/handtracking},

skills/vision/hot3d/SKILL.md

  • Network accessline 2
    name: hot3d description: HOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art multi-view 3D hand pose, object pose, and hand-object interaction tr
  • Network accessline 3
    description: HOT3D (Hand-Object 3D Dataset) by Meta Facebook - multi-view egocentric hand and object 3D tracking for Aria/Quest smart glasses. State-of-the-art multi-view 3D hand pose, object pose, and hand-object interaction tracking. Supp
  • Network accessline 4
    license: CC-BY-NC 4.0
  • Network accessline 5
    metadata:     skill-author: K-Dense Inc.     original-repo: https://github.com/facebookresearch/hot3d
  • Network accessline 6
    skill-author: K-Dense Inc.     original-repo: https://github.com/facebookresearch/hot3d     organization: Meta Facebook Research
  • Network accessline 7
    original-repo: https://github.com/facebookresearch/hot3d
  • Network accessline 19
    **Project page**: https://facebookresearch.github.io/hot3d
  • Network accessline 77
    # Clone repository git clone https://github.com/facebookresearch/hot3d.git
  • Network accessline 78
    git clone https://github.com/facebookresearch/hot3d.git
  • Network accessline 85
    # Download dataset (requires registration) # https://facebookresearch.github.io/hot3d/dataset.html
  • Network accessline 86
    # https://facebookresearch.github.io/hot3d/dataset.html
  • Network accessline 150
    Access: https://facebookresearch.github.io/hot3d
  • Network accessline 176
    - Project: https://facebookresearch.github.io/hot3d
  • Network accessline 177
    - GitHub: https://github.com/facebookresearch/hot3d
  • Network accessline 183
    CC-BY-NC 4.0 (non-commercial only)

skills/visualization/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/visualization/plotly/SKILL.md

  • Network accessline 262
    - Official documentation: https://plotly.com/python/
  • Network accessline 263
    - API reference: https://plotly.com/python-api-reference/
  • Network accessline 264
    - Community forum: https://community.plotly.com/

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.

Signal confidence: 21 facts

Works with

Agent compatibility, from the files in this repository
AgentStatusEvidenceInstall to
Claude CodeCompatibleStandard SKILL.md skills/bio/alphafold-database/SKILL.md.claude/skills/<skill-name>/
CodexCompatibleStandard SKILL.md skills/bio/alphafold-database/SKILL.md.agents/skills/<skill-name>/
CursorCompatibleStandard SKILL.md skills/bio/alphafold-database/SKILL.md.cursor/skills/<skill-name>/
Gemini CLICompatibleStandard SKILL.md skills/bio/alphafold-database/SKILL.md.gemini/skills/<skill-name>/
GitHub CopilotCompatibleStandard SKILL.md skills/bio/alphafold-database/SKILL.md.github/skills/<skill-name>/
OpenCodeCompatibleStandard SKILL.md skills/bio/alphafold-database/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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