TobiasBlask/open-paper-machine

scientific-skills/citation-management/SKILL.md

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  # Extract from URL python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"

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  python scripts/extract_metadata.py --url "https://www.nature.com/articles/s41586-021-03819-2"

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  1. **Find MeSH terms** at https://meshb.nlm.nih.gov/search

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  # From URL python scripts/extract_metadata.py \   --url "https://www.nature.com/articles/s41586-021-03819-2"

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  python scripts/extract_metadata.py    --url "https://www.nature.com/articles/s41586-021-03819-2"

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  --url "https://www.nature.com/articles/s41586-021-03819-2"

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  **Search Engines**: - Google Scholar: https://scholar.google.com/

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  - Google Scholar: https://scholar.google.com/

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  - PubMed: https://pubmed.ncbi.nlm.nih.gov/

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  - PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/

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  **Metadata APIs**: - CrossRef API: https://api.crossref.org/

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  - CrossRef API: https://api.crossref.org/

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  - PubMed E-utilities: https://www.ncbi.nlm.nih.gov/books/NBK25501/

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  - arXiv API: https://arxiv.org/help/api/

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  - DataCite API: https://api.datacite.org/

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  **Tools and Validators**: - MeSH Browser: https://meshb.nlm.nih.gov/search

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  - MeSH Browser: https://meshb.nlm.nih.gov/search

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  - DOI Resolver: https://doi.org/

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  - BibTeX Format: http://www.bibtex.org/Format/

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  **Citation Styles**: - BibTeX documentation: http://www.bibtex.org/

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  - BibTeX documentation: http://www.bibtex.org/

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  - LaTeX bibliography management: https://www.overleaf.com/learn/latex/Bibliography_management

scientific-skills/citation-management/assets/bibtex_template.bib

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  pages     = {5998--6008},   address   = {Long Beach, CA},   url       = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html}

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  address   = {Long Beach, CA},   url       = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html} }

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  url       = {https://proceedings.neurips.cc/paper/2017/hash/3f5ee243547dee91fbd053c1c4a845aa-Abstract.html}

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  year         = {2021},   howpublished = {Database},   url          = {https://alphafold.ebi.ac.uk/},

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  howpublished = {Database},   url          = {https://alphafold.ebi.ac.uk/},   doi          = {10.1093/nar/gkab1061},

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  url          = {https://alphafold.ebi.ac.uk/},

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  year         = {2010},   howpublished = {Software},   url          = {https://pandas.pydata.org/},

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  howpublished = {Software},   url          = {https://pandas.pydata.org/},   note         = {Python Data Analysis Library}

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  url          = {https://pandas.pydata.org/},

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  year         = {2024},   howpublished = {Website},   url          = {https://pubmed.ncbi.nlm.nih.gov/},

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  howpublished = {Website},   url          = {https://pubmed.ncbi.nlm.nih.gov/},   note         = {Accessed: 2024-01-15}

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  url          = {https://pubmed.ncbi.nlm.nih.gov/},

scientific-skills/citation-management/assets/citation_checklist.md

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  - [ ] All DOIs are properly formatted (10.XXXX/...) - [ ] DOIs resolve correctly to the article - [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")

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  - [ ] DOIs resolve correctly to the article - [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/") - [ ] Metadata from CrossRef matches your BibTeX entry

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  - [ ] No DOI prefix in the BibTeX field (no "doi:" or "https://doi.org/")

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  - [ ] Ampersands in author lists (Smith & Jones → Smith and Jones) - [ ] Unprotected acronyms in titles (DNA → {DNA}) - [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)

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  - [ ] DOI includes URL prefix (https://doi.org/10.xxx → 10.xxx)

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  # Find correct DOI # Option 1: Search CrossRef # https://www.crossref.org/

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  # https://www.crossref.org/

scientific-skills/citation-management/references/bibtex_formatting.md

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  year         = {2024},   howpublished = {GitHub},   url          = {https://github.com/user/repo},

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  howpublished = {GitHub},   url          = {https://github.com/user/repo},   note         = {Version 2.0}

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  url          = {https://github.com/user/repo},

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  author = {{Organization Name}},   title  = {Page Title},   url    = {https://example.com/page},

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  title  = {Page Title},   url    = {https://example.com/page},   year   = {2024},

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  url    = {https://example.com/page},

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  doi = {https://doi.org/10.1038/s41586-021-03819-2}  % Don't include URL

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  url = {https://www.example.com/article}

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  % Don't include both if DOI URL is same as url doi = {10.1038/nature12345} url = {https://doi.org/10.1038/nature12345}  % Redundant!

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  url = {https://doi.org/10.1038/nature12345}  % Redundant!

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  doi = {https://doi.org/10.1038/nature12345}

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  year         = {2021},   howpublished = {Database},   url          = {https://alphafold.ebi.ac.uk/},

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  howpublished = {Database},   url          = {https://alphafold.ebi.ac.uk/},   doi          = {10.1093/nar/gkab1061}

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  url          = {https://alphafold.ebi.ac.uk/},

scientific-skills/citation-management/references/citation_validation.md

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  **DOI resolution**: - DOI should resolve via https://doi.org/

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  - DOI should resolve via https://doi.org/

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  **Manual check**: 1. Copy DOI from BibTeX 2. Visit https://doi.org/10.1038/nature12345

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  1. Copy DOI from BibTeX 2. Visit https://doi.org/10.1038/nature12345 3. Verify it redirects to correct article

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  2. Visit https://doi.org/10.1038/nature12345

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  url = {https://www.nature.com/articles/nature12345}

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  url = {https://arxiv.org/abs/2103.14030}

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  url = {http://...}  % HTTP instead of HTTPS

scientific-skills/citation-management/references/metadata_extraction.md

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  **Base URL**: `https://api.crossref.org/works/`

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  GET https://api.crossref.org/works/10.1038/s41586-021-03819-2

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  **Base URL**: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`

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  GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?

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  **Base URL**: `http://export.arxiv.org/api/query`

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  GET http://export.arxiv.org/api/query?id_list=2103.14030

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  <entry>   <id>http://arxiv.org/abs/2103.14030v2</id>

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  <id>http://arxiv.org/abs/2103.14030v2</id>

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  <summary>Abstract text here...</summary>   <arxiv:doi>10.1038/s41586-021-03819-2</arxiv:doi>   <category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/>

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  <arxiv:doi>10.1038/s41586-021-03819-2</arxiv:doi>   <category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/>   <category term="cs.LG" scheme="http://arxiv.org/schemas/atom"/>

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  <category term="q-bio.BM" scheme="http://arxiv.org/schemas/atom"/>

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  <category term="cs.LG" scheme="http://arxiv.org/schemas/atom"/>

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  **Base URL**: `https://api.datacite.org/dois/`

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  GET https://api.datacite.org/dois/10.5281/zenodo.1234567

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  year         = {2021},   howpublished = {Software},   url          = {https://alphafold.ebi.ac.uk/},

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  howpublished = {Software},   url          = {https://alphafold.ebi.ac.uk/},   doi          = {10.5281/zenodo.5123456}

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  url          = {https://alphafold.ebi.ac.uk/},

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  python scripts/extract_metadata.py \   --url "https://www.nature.com/articles/s41586-021-03819-2"

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  --url "https://www.nature.com/articles/s41586-021-03819-2"

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  # DOI URLs https://doi.org/10.1038/nature12345

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  https://doi.org/10.1038/nature12345

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  https://dx.doi.org/10.1126/science.abc123

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  https://www.nature.com/articles/s41586-021-03819-2

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  # PubMed URLs https://pubmed.ncbi.nlm.nih.gov/34265844/

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  https://pubmed.ncbi.nlm.nih.gov/34265844/

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  https://www.ncbi.nlm.nih.gov/pubmed/34265844

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  # arXiv URLs https://arxiv.org/abs/2103.14030

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  https://arxiv.org/abs/2103.14030

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  https://arxiv.org/pdf/2103.14030.pdf

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  #   34265844 #   2103.14030 #   https://doi.org/10.1126/science.abc123

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  #   https://doi.org/10.1126/science.abc123

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  volume  = {123},   pages   = {45--67},   url     = {https://stable-url-here},

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  pages   = {45--67},   url     = {https://stable-url-here},   note    = {PMID: 12345678}

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  url     = {https://stable-url-here},

scientific-skills/citation-management/references/pubmed_search.md

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  **MeSH Browser**: https://meshb.nlm.nih.gov/search

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  **Access**: https://pubmed.ncbi.nlm.nih.gov/advanced/

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  **Base URL**: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`

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  **Get API key**: https://www.ncbi.nlm.nih.gov/account/

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  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?

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  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?

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  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?

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  https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?

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  **Get API key**: 1. Create NCBI account: https://www.ncbi.nlm.nih.gov/account/

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  1. Create NCBI account: https://www.ncbi.nlm.nih.gov/account/

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scientific-skills/citation-management/scripts/doi_to_bibtex.py

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  #!/usr/bin/env python3

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  def __init__(self):         self.session = requests.Session()

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  self.session = requests.Session()

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  doi = doi.strip()         if doi.startswith('https://doi.org/'):

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  if doi.startswith('https://doi.org/'):

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  doi = doi.replace('https://doi.org/', '')

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  elif doi.startswith('http://doi.org/'):

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  doi = doi.replace('http://doi.org/', '')

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  url = f'https://doi.org/{doi}'

scientific-skills/citation-management/scripts/extract_metadata.py

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  #!/usr/bin/env python3

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  self.session = requests.Session()

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  url = f'https://api.crossref.org/works/{doi}'

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  'pages': message.get('page', ''),                     'publisher': message.get('publisher', ''),                     'url': f'https://doi.org/{doi}'

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  'publisher': message.get('publisher', ''),                     'url': f'https://doi.org/{doi}'                 }

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  'url': f'https://doi.org/{doi}'

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  url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi'

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  [Credential-related source omitted]

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  url = 'http://export.arxiv.org/api/query'

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  root = ET.fromstring(response.content)                 ns = {'atom': 'http://www.w3.org/2005/Atom', 'arxiv': 'http://arxiv.org/schemas/atom'}

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  ns = {'atom': 'http://www.w3.org/2005/Atom', 'arxiv': 'http://arxiv.org/schemas/atom'}

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  'journal_ref': journal_ref,                     'abstract': entry.findtext('atom:summary', '', ns).strip().replace('\n', ' '),                     'url': f'https://arxiv.org/abs/{arxiv_id}'

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  'abstract': entry.findtext('atom:summary', '', ns).strip().replace('\n', ' '),                     'url': f'https://arxiv.org/abs/{arxiv_id}'                 }

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  'url': f'https://arxiv.org/abs/{arxiv_id}'

scientific-skills/citation-management/scripts/format_bibtex.py

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  #!/usr/bin/env python3

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  if 'doi' in fields:             doi = fields['doi']             doi = doi.replace('https://doi.org/', '')

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  doi = fields['doi']             doi = doi.replace('https://doi.org/', '')             doi = doi.replace('http://doi.org/', '')

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  doi = doi.replace('https://doi.org/', '')

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  doi = doi.replace('http://doi.org/', '')

scientific-skills/citation-management/scripts/search_google_scholar.py

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  #!/usr/bin/env python3

scientific-skills/citation-management/scripts/search_pubmed.py

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  #!/usr/bin/env python3

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  self.email = email or os.getenv('NCBI_EMAIL', '')         self.base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'         self.session = requests.Session()

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  self.base_url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'

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  self.session = requests.Session()

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scientific-skills/citation-management/scripts/validate_citations.py

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  #!/usr/bin/env python3

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  def __init__(self):         self.session = requests.Session()

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  self.session = requests.Session()

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  try:             url = f'https://doi.org/{doi}'

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  url = f'https://doi.org/{doi}'

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  crossref_url = f'https://api.crossref.org/works/{doi}'

scientific-skills/consciousness-council/SKILL.md

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  Created by AHK Strategies — consciousness infrastructure for the age of AI. Learn more: https://ahkstrategies.net

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  Learn more: https://ahkstrategies.net

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  Powered by the Mind Council architecture from TheMindBook: https://themindbook.app

scientific-skills/exploratory-data-analysis/references/chemistry_molecular_formats.md

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  ### .nc / .netcdf - Amber NetCDF Trajectory

scientific-skills/exploratory-data-analysis/references/general_scientific_formats.md

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  ### .nc / .netcdf - Network Common Data Form

scientific-skills/exploratory-data-analysis/scripts/eda_analyzer.py

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  #!/usr/bin/env python3

scientific-skills/get-available-resources/scripts/detect_resources.py

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  #!/usr/bin/env python3

scientific-skills/hypothesis-generation/SKILL.md

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scientific-skills/hypothesis-generation/references/literature_search_strategies.md

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  **Example searches:** - `https://pubmed.ncbi.nlm.nih.gov/?term=wound+healing+diabetes+review`

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  - `https://pubmed.ncbi.nlm.nih.gov/?term=wound+healing+diabetes+review`

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  - `https://pubmed.ncbi.nlm.nih.gov/?term=gut+microbiome+cognition+systematic+review`

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  https://pubmed.ncbi.nlm.nih.gov/?term=(mechanism+OR+pathway)+AND+[phenomenon]+AND+(molecular+OR+cellular)

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  https://pubmed.ncbi.nlm.nih.gov/?term=[exposure]+AND+[outcome]+AND+(randomized+controlled+trial+OR+cohort+study)

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  https://pubmed.ncbi.nlm.nih.gov/?term=[biomarker]+AND+[disease]+AND+(association+OR+correlation+OR+prediction)

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  https://pubmed.ncbi.nlm.nih.gov/?term=[intervention]+AND+[condition]+AND+(efficacy+OR+effectiveness+OR+clinical+trial)

scientific-skills/literature-review/SKILL.md

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  - Date filters: `2020:2024[Publication Date]` - Boolean operators: AND, OR, NOT - See MeSH browser: https://meshb.nlm.nih.gov/search

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  - See MeSH browser: https://meshb.nlm.nih.gov/search

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  ### 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

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  - Reference: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Title. *Journal*, *22*(4), 301-318. https://doi.org/10.xxx/yyy

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  **Guidelines:** - PRISMA (Systematic Reviews): http://www.prisma-statement.org/

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  - PRISMA (Systematic Reviews): http://www.prisma-statement.org/

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  - Cochrane Handbook: https://training.cochrane.org/handbook

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  - AMSTAR 2 (Review Quality): https://amstar.ca/

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  **Tools:** - MeSH Browser: https://meshb.nlm.nih.gov/search

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  - MeSH Browser: https://meshb.nlm.nih.gov/search

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  - PubMed Advanced Search: https://pubmed.ncbi.nlm.nih.gov/advanced/

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  - Boolean Search Guide: https://www.ncbi.nlm.nih.gov/books/NBK3827/

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  **Citation Styles:** - APA Style: https://apastyle.apa.org/

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  - APA Style: https://apastyle.apa.org/

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  - Nature Portfolio: https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards

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  - NLM/Vancouver: https://www.nlm.nih.gov/bsd/uniform_requirements.html

scientific-skills/literature-review/assets/review_template.md

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  APA: Author, A. A., & Author, B. B. (Year). Title. *Journal*, *volume*(issue), pages. https://doi.org/xx.xxxx

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  **Resources:** - PRISMA 2020: http://prisma-statement.org/

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  - PRISMA 2020: http://prisma-statement.org/

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  - PROSPERO: https://www.crd.york.ac.uk/prospero/

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  - Cochrane Handbook: https://training.cochrane.org/handbook

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  - GRADE: https://www.gradeworkinggroup.org/

scientific-skills/literature-review/references/citation_styles.md

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  **Format**: Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. *Title of Periodical*, *volume*(issue), page range. https://doi.org/xx.xxx/yyyy

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  **Example**: Smith, J. D., Johnson, M. L., & Williams, K. R. (2023). Machine learning approaches in drug discovery. *Nature Reviews Drug Discovery*, *22*(4), 301-318. https://doi.org/10.1038/nrd.2023.001

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  **Format**: Author, A. A. (Year). *Title of work: Capital letter also for subtitle*. Publisher Name. https://doi.org/xxxx

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  **Format**: Author, A. A., & Author, B. B. (Year). Title of preprint. *Repository Name*. https://doi.org/xxxx

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  **Example**: Zhang, Y., Chen, L., & Wang, H. (2024). Novel therapeutic targets in Alzheimer's disease. *bioRxiv*. https://doi.org/10.1101/2024.01.001

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  **Format**: Author, A. A. (Year, Month day-day). Title of paper. In E. E. Editor (Ed.), *Title of conference proceedings* (pp. xx-xx). Publisher. https://doi.org/xxxx

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  **Example**: Zhang, Y. et al. Novel therapeutic targets in Alzheimer's disease. *bioRxiv* https://doi.org/10.1101/2024.01.001 (2024).

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  **Format**: Author, First Name Middle Initial. Year. "Article Title." *Journal Title* volume, no. issue (Month): page range. https://doi.org/xxxx.

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  **Example**: Smith, John D., Mary L. Johnson, and Karen R. Williams. 2023. "Machine Learning Approaches in Drug Discovery." *Nature Reviews Drug Discovery* 22, no. 4 (April): 301-318. https://doi.org/10.1038/nrd.2023.001.

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  1. **Always verify DOIs**: Use the verify_citations.py script to check all DOIs 2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)

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  2. **Format as URLs**: https://doi.org/10.xxxx/yyyy (preferred over doi:10.xxxx/yyyy)

scientific-skills/literature-review/references/database_strategies.md

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  ### MeSH Browser https://meshb.nlm.nih.gov/search

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  https://meshb.nlm.nih.gov/search

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  ### Boolean Search Tutorial https://www.ncbi.nlm.nih.gov/books/NBK3827/

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  https://www.ncbi.nlm.nih.gov/books/NBK3827/

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  ### PRISMA Guidelines Preferred Reporting Items for Systematic Reviews and Meta-Analyses: http://www.prisma-statement.org/

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  http://www.prisma-statement.org/

scientific-skills/literature-review/scripts/generate_pdf.py

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  #!/usr/bin/env python3

scientific-skills/literature-review/scripts/search_databases.py

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  #!/usr/bin/env python3

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  if result.get('doi'):                 md += f"**DOI**: [{result['doi']}](https://doi.org/{result['doi']})\n\n"

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  md += f"**DOI**: [{result['doi']}](https://doi.org/{result['doi']})\n\n"

scientific-skills/literature-review/scripts/verify_citations.py

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  #!/usr/bin/env python3

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  class CitationVerifier:     def __init__(self):         self.session = requests.Session()

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  def __init__(self):         self.session = requests.Session()         self.session.headers.update({

• Network accessline 16

  self.session = requests.Session()

• Network accessline 31

  try:             url = f"https://doi.org/api/handles/{doi}"

• Network accessline 32

  url = f"https://doi.org/api/handles/{doi}"

• Network accessline 46

  try:             url = f"https://api.crossref.org/works/{doi}"

• Network accessline 47

  url = f"https://api.crossref.org/works/{doi}"

• Network accessline 155

  citation += f", {pages}"         if doi:             citation += f". https://doi.org/{doi}"

• Network accessline 157

  citation += f". https://doi.org/{doi}"

scientific-skills/markdown-mermaid-writing/SKILL.md

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  Read Write Edit Bash

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  metadata:   skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes)   skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project

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  skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes)   skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project   skill-version: "1.0.0"

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  skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project

• Network accessline 317

  - **Source**: https://github.com/SuperiorByteWorks-LLC/agent-project

• Network accessline 325

  [^1]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

• Network accessline 327

  [^2]: Mermaid. "Mermaid Diagramming and Charting Tool." https://mermaid.js.org/

scientific-skills/markdown-mermaid-writing/assets/examples/example-research-report.md

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  [^1]: Ran, F.A. et al. (2013). "Genome engineering using the CRISPR-Cas9 system." _Nature Protocols_, 8(11), 2281–2308. https://doi.org/10.1038/nprot.2013.143

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  [^2]: ATCC. (2024). "Cell Line Authentication and Quality Control." https://www.atcc.org/resources/technical-documents/cell-line-authentication

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  [^3]: Moreno-Mateos, M.A. et al. (2015). "CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo." _Nature Methods_, 12(10), 982–988. https://doi.org/10.1038/nmeth.3543

• Network accessline 221

  [^4]: Molla, K.A. & Yang, Y. (2019). "CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical Applications." _Trends in Biotechnology_, 37(10), 1121–1142. https://doi.org/10.1016/j.tibtech.2019.03.008

scientific-skills/markdown-mermaid-writing/references/diagrams/architecture.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/block.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/c4.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/class.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/complex_examples.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/er.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

• Access to secretsline 125

  [Credential-related source omitted]

• Access to secretsline 207

  [Credential-related source omitted]

scientific-skills/markdown-mermaid-writing/references/diagrams/flowchart.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/gantt.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/git_graph.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/kanban.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/mindmap.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/packet.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/pie.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/quadrant.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/radar.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/requirement.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/sankey.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/sequence.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/state.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/timeline.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/treemap.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/user_journey.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/xy_chart.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/diagrams/zenuml.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/references/markdown_style_guide.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  - **Meaningful link text** — `[Mermaid Style Guide]` not `[click here]` or `[link]` - **Relative paths** for internal links — `[Guide](./README.md)` not absolute URLs - **Full URLs** for external links — always `https://`

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  - **Full URLs** for external links — always `https://`

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  [^1]: Gruber, J. (2004). "Markdown." _Daring Fireball_. https://daringfireball.net/projects/markdown/

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  [^2]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

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  [^N]: Author/Org. (Year). "Title." *Publication*. https://full-url

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  [mermaid-docs]: https://mermaid.js.org/ 'Mermaid Documentation'

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  - Transition to next topic - **Bold** emphasis works inside details - [Links](https://example.com) work too

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  - [Links](https://example.com) work too

• Possible obfuscationline 529

  <U+200E>```mermaid

• Possible obfuscationline 543

  <U+200E>```

• Network accessline 677

  [^1]: Stack Overflow. (2024). "Developer Survey Results." https://survey.stackoverflow.co/2024

• Network accessline 733

  - [GitHub Flavored Markdown Spec](https://github.github.com/gfm/) · [Mermaid Style Guide](mermaid_style_guide.md) · [GitHub Basic Formatting](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatti

scientific-skills/markdown-mermaid-writing/references/mermaid_style_guide.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  1. **GitHub:** Push to branch → toggle Profile → Settings → Appearance → Theme 2. **VS Code:** "Markdown Preview Mermaid Support" extension → `Cmd/Ctrl + Shift + V` 3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggl

• Network accessline 449

  2. **VS Code:** "Markdown Preview Mermaid Support" extension → `Cmd/Ctrl + Shift + V` 3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggle themes 4. **Screen reader:** Verify `accTitle`/`accDescr` announced (VoiceOve

• Network accessline 450

  3. **Live editor:** [mermaid.live](https://mermaid.live/) — paste and toggle themes

• Network accessline 457

  - [Markdown Style Guide](markdown_style_guide.md) — Formatting, citations, and document structure for the markdown that wraps your diagrams - [Mermaid Docs](https://mermaid.js.org/) · [Live Editor](https://mermaid.live/) · [Accessibility](h

• Network accessline 458

  - [Mermaid Docs](https://mermaid.js.org/) · [Live Editor](https://mermaid.live/) · [Accessibility](https://mermaid.js.org/config/accessibility.html) · [GitHub Support](https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/)

scientific-skills/markdown-mermaid-writing/templates/decision_record.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  - [Related ADR or RFC](../adr/ADR-001-agent-optimized-documentation-system.md) - [External documentation or benchmark](https://example.com)

• Network accessline 198

  - [External documentation or benchmark](https://example.com)

scientific-skills/markdown-mermaid-writing/templates/how_to_guide.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  | Requirement      | Version     | Verify with           | Install link                         | | ---------------- | ----------- | --------------------- | ------------------------------------ | | [Tool/Runtime]   | ≥ [version] | `[command

• Network accessline 72

  | ---------------- | ----------- | --------------------- | ------------------------------------ | | [Tool/Runtime]   | ≥ [version] | `[command] --version` | [Install guide](https://example.com) | | [Dependency]     | ≥ [version] | `[command

• Network accessline 73

  | [Tool/Runtime]   | ≥ [version] | `[command] --version` | [Install guide](https://example.com) |

• Network accessline 74

  | [Dependency]     | ≥ [version] | `[command] --version` | [Install guide](https://example.com) |

• Network accessline 75

  | [Account/Access] | —           | [How to verify]       | [Sign up](https://example.com)       |

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  - [Official documentation](https://example.com) — [Which section is most relevant]

• Network accessline 271

  - [Source repository](https://github.com/SuperiorByteWorks-LLC) — [For bug reports and contributions]

scientific-skills/markdown-mermaid-writing/templates/issue.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

• Network accessline 180

  - [Related issues](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Relevant documentation](https://example.com)

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  - [Relevant documentation](https://example.com)

• Network accessline 182

  - [Monitoring dashboard or alert](https://example.com)

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  - [User feedback or support tickets](https://example.com) - [Competitive analysis](https://example.com) - [Related feature requests](../../docs/project/issues/issue-00000001-agentic-documentation-system.md)

• Network accessline 297

  - [Competitive analysis](https://example.com) - [Related feature requests](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Design document or ADR](../adr/ADR-001-agent-optimized-documentation-system.md)

scientific-skills/markdown-mermaid-writing/templates/kanban.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

scientific-skills/markdown-mermaid-writing/templates/presentation.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  [^1]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  - [Resource title](https://example.com) — Why this is useful

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  - [Resource title](https://example.com) — What it provides

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  - [Tool name](https://example.com) — Purpose and how to access

scientific-skills/markdown-mermaid-writing/templates/project_documentation.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  [![Build Status](https://img.shields.io/badge/build-passing-brightgreen)]() [![License](https://img.shields.io/badge/license-MIT-blue)]()

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  # Clone the repository git clone https://github.com/[org]/[repo].git

• Network accessline 68

  git clone https://github.com/[org]/[repo].git

• Access to secretsline 75

  [Credential-related source omitted]

• Access to secretsline 76

  [Credential-related source omitted]

• Network accessline 85

  curl http://localhost:[port]/health

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  # Fork and clone git clone https://github.com/[your-fork]/[repo].git

• Network accessline 375

  git clone https://github.com/[your-fork]/[repo].git

• Network accessline 406

  - [Official framework docs](https://example.com) — [What version and which sections are most relevant]

• Network accessline 407

  - [API specification](https://example.com) — [OpenAPI/Swagger link if applicable]

scientific-skills/markdown-mermaid-writing/templates/pull_request.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  - **Naming:** `pr-` + PR number zero-padded to 8 digits + `-` + short lowercase hyphenated description - **Cross-reference:** Link to the live PR in the metadata table - **GitHub PR body:** Use only the full branch URL to this file (for exa

• Network accessline 30

  - **GitHub PR body:** Use only the full branch URL to this file (for example, `https://github.com/<org>/<repo>/blob/<branch>/docs/project/pr/pr-00000123-fix-auth-timeout.md`)

• Network accessline 313

  - [Design document or ADR](../adr/ADR-001-agent-optimized-documentation-system.md) - [Related issue](../../docs/project/issues/issue-00000001-agentic-documentation-system.md) - [Relevant documentation](https://example.com)

• Network accessline 315

  - [Relevant documentation](https://example.com)

scientific-skills/markdown-mermaid-writing/templates/research_paper.md

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  <!-- Source: https://github.com/SuperiorByteWorks-LLC/agent-project | License: Apache-2.0 | Author: Clayton Young / Superior Byte Works, LLC (Boreal Bytes) -->

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  [^1]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^2]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^3]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^4]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^5]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^6]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

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  [^7]: [Author/Org]. ([Year]). "[Title]." _[Publication]_. <https://example.com>

scientific-skills/matplotlib/SKILL.md

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  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/

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  - 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

scientific-skills/matplotlib/references/api_reference.md

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  **Named colors:** - `'steelblue'`, `'coral'`, `'teal'`, etc. - See full list: https://matplotlib.org/stable/gallery/color/named_colors.html

• Network accessline 175

  - See full list: https://matplotlib.org/stable/gallery/color/named_colors.html

scientific-skills/matplotlib/scripts/plot_template.py

• Executable scriptline 1

  #!/usr/bin/env python3

scientific-skills/matplotlib/scripts/style_configurator.py

• Executable scriptline 1

  #!/usr/bin/env python3

scientific-skills/networkx/SKILL.md

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  - **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

scientific-skills/peer-review/SKILL.md

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  Read Write Edit Bash

scientific-skills/peer-review/references/reporting_standards.md

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  **Reference:** http://www.consort-statement.org/

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  **Reference:** https://www.strobe-statement.org/

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  **Reference:** http://www.prisma-statement.org/

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  **Reference:** https://www.spirit-statement.org/

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  **Reference:** https://www.care-statement.org/

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  **Reference:** https://arriveguidelines.org/

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  **Reference:** http://fged.org/projects/miame/

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  **Reference:** https://gensc.org/

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  **Reference:** https://www.wwpdb.org/

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  **Reference:** http://www.psidev.info/

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  **Reference:** https://www.humanbrainmapping.org/cobidas

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  **Reference:** http://flowcyt.org/

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  **Reference:** https://www.miappe.org/

scientific-skills/plotly/SKILL.md

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  - 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/

scientific-skills/pyzotero/SKILL.md

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  Read Write Edit Bash

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  Pyzotero is a Python wrapper for the [Zotero API v3](https://www.zotero.org/support/dev/web_api/v3/start). Use it to programmatically manage Zotero libraries: read items and collections, create and update references, upload attachments, man

• Network accessline 16

  **Required credentials** — get from https://www.zotero.org/settings/keys:

• Network accessline 17

  - **User ID**: shown as "Your userID for use in API calls" - **API Key**: create at https://www.zotero.org/settings/keys/new - **Library ID**: for group libraries, the integer after `/groups/` in the group URL

• Network accessline 18

  - **API Key**: create at https://www.zotero.org/settings/keys/new

• Access to secretsline 24

  [Credential-related source omitted]

• Access to secretsline 43

  [Credential-related source omitted]

scientific-skills/pyzotero/references/authentication.md

• Network accessline 5

  Obtain from https://www.zotero.org/settings/keys:

• Network accessline 9

  | **User ID** | "Your userID for use in API calls" section | | **API Key** | Create new key at /settings/keys/new | | **Group Library ID** | Integer after `/groups/` in group URL (e.g. `https://www.zotero.org/groups/169947`) |

• Network accessline 11

  | **Group Library ID** | Integer after `/groups/` in group URL (e.g. `https://www.zotero.org/groups/169947`) |

• Access to secretsline 18

  [Credential-related source omitted]

• Access to secretsline 31

  [Credential-related source omitted]

• Access to secretsline 32

  [Credential-related source omitted]

• Access to secretsline 33

  [Credential-related source omitted]

• Access to secretsline 64

  [Credential-related source omitted]

• Network accessline 86

  When creating an API key at https://www.zotero.org/settings/keys/new, choose appropriate permissions:

scientific-skills/pyzotero/references/exports.md