skills/claude-scientific-skills
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97d79018702c4f4f7b573846579e241a3d571000
claude-scientific-skills/scientific-skills
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Clayton Young 97d7901870 feat(skill): add markdown-mermaid-writing skill with source format philosophy 
New skill establishing markdown + Mermaid diagrams as the default and
canonical documentation format for all scientific skill outputs.

Core principle (from K-Dense Discord, 2026-02-19): Mermaid in markdown
is the source of truth — text-based, version-controlled, token-efficient,
universally renderable. Python/AI images are downstream conversions only.

SKILL.md includes:
- Full 'source format' philosophy with three-phase workflow diagram
- 24-entry diagram type selection table with links to each guide
- 9-entry document template index
- Per-skill integration guides (scientific-schematics, scientific-writing,
  literature-review, and any other output-producing skill)
- Quality checklist for finalizing documents from any skill
- Full attribution for ported Apache-2.0 content

Originated from conversation between Clayton Young (Boreal Bytes) and the
K-Dense team regarding documentation standards for shared scientific skills.
2026-02-23 07:43:04 -05:00
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adaptyv
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
aeon
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
alphafold-database
Merge pull request #30 from marovole/fix/shell-command-injection-docs
2026-01-08 08:53:35 -08:00
anndata
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
arboreto
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
astropy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
benchling-integration
Clean description fields
2026-01-05 14:29:10 -08:00
biopython
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
biorxiv-database
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
bioservices
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
brenda-database
Clean description fields
2026-01-05 14:29:10 -08:00
cellxgene-census
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
chembl-database
Clean description fields
2026-01-05 14:29:10 -08:00
cirq
Clean description fields
2026-01-05 14:29:10 -08:00
citation-management
Enhance citation management and literature review guidelines
2026-01-05 13:01:10 -08:00
clinical-decision-support
Clean description fields
2026-01-05 14:29:10 -08:00
clinical-reports
Clean description fields
2026-01-05 14:29:10 -08:00
clinicaltrials-database
Clean description fields
2026-01-05 14:29:10 -08:00
clinpgx-database
Clean description fields
2026-01-05 14:29:10 -08:00
clinvar-database
Clean description fields
2026-01-05 14:29:10 -08:00
cobrapy
Clean description fields
2026-01-05 14:29:10 -08:00
cosmic-database
Clean description fields
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dask
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
datacommons-client
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
datamol
Clean description fields
2026-01-05 14:29:10 -08:00
deepchem
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
deeptools
Clean description fields
2026-01-05 14:29:10 -08:00
denario
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
diffdock
Clean description fields
2026-01-05 14:29:10 -08:00
dnanexus-integration
Clean description fields
2026-01-05 14:29:10 -08:00
document-skills
Clean description fields
2026-01-05 14:29:10 -08:00
drugbank-database
Add suggestion to use K-Dense Web for complicated workflows.
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ena-database
Clean description fields
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ensembl-database
Clean description fields
2026-01-05 14:29:10 -08:00
esm
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
etetoolkit
Clean description fields
2026-01-05 14:29:10 -08:00
exploratory-data-analysis
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
fda-database
Clean description fields
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flowio
Clean description fields
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fluidsim
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
fred-economic-data
Add support for economic data form the Federal Reserve using FRED
2026-01-27 10:41:40 -08:00
gene-database
Clean description fields
2026-01-05 14:29:10 -08:00
generate-image
Clean description fields
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geniml
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
geo-database
Clean description fields
2026-01-05 14:29:10 -08:00
geopandas
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
get-available-resources
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
gget
Fix description formatting in SKILL.md
2026-01-07 15:15:18 +08:00
gtars
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
gwas-database
Clean description fields
2026-01-05 14:29:10 -08:00
histolab
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
hmdb-database
Clean description fields
2026-01-05 14:29:10 -08:00
hypogenic
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
hypothesis-generation
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
imaging-data-commons
update to v1.3.1
2026-02-11 09:42:22 -05:00
infographics
Add infographics skill for creating visual data representations
2026-02-03 17:03:44 -08:00
iso-13485-certification
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
kegg-database
Clean description fields
2026-01-05 14:29:10 -08:00
labarchive-integration
Clean description fields
2026-01-05 14:29:10 -08:00
lamindb
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
latchbio-integration
Clean description fields
2026-01-05 14:29:10 -08:00
latex-posters
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
literature-review
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
markdown-mermaid-writing
feat(skill): add markdown-mermaid-writing skill with source format philosophy
2026-02-23 07:43:04 -05:00
market-research-reports
Clean description fields
2026-01-05 14:29:10 -08:00
markitdown
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
matchms
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
matlab
Support for writing and executing MATLAB/Octave scripts
2026-01-05 10:15:22 -08:00
matplotlib
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
medchem
Clean description fields
2026-01-05 14:29:10 -08:00
metabolomics-workbench-database
Clean description fields
2026-01-05 14:29:10 -08:00
modal
fix(security): replace shell=True with safe subprocess patterns in documentation
2026-01-08 15:05:30 +08:00
molfeat
Clean description fields
2026-01-05 14:29:10 -08:00
networkx
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
neurokit2
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
neuropixels-analysis
Replace all instances of Sonnet to Opus
2026-01-21 09:16:34 -05:00
offer-k-dense-web
Add K-Dense Web skill
2026-01-05 18:20:10 -08:00
omero-integration
Clean description fields
2026-01-05 14:29:10 -08:00
openalex-database
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
opentargets-database
Clean description fields
2026-01-05 14:29:10 -08:00
opentrons-integration
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
paper-2-web
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pathml
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pdb-database
Clean description fields
2026-01-05 14:29:10 -08:00
peer-review
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pennylane
Disambiguate descriptions
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perplexity-search
Clean description fields
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plotly
Disambiguate descriptions
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polars
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pptx-posters
Merge branch 'main' into fix-writing-skills
2026-01-05 15:46:55 -08:00
protocolsio-integration
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pubchem-database
Clean description fields
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pubmed-database
Clean description fields
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pufferlib
Disambiguate descriptions
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pydeseq2
Clean description fields
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pydicom
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pyhealth
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
pylabrobot
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pymatgen
Clean description fields
2026-01-05 14:29:10 -08:00
pymc
Clean description fields
2026-01-05 14:29:10 -08:00
pymoo
Clean description fields
2026-01-05 14:29:10 -08:00
pyopenms
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
pysam
Clean description fields
2026-01-05 14:29:10 -08:00
pytdc
Clean description fields
2026-01-05 14:29:10 -08:00
pytorch-lightning
Clean description fields
2026-01-05 14:29:10 -08:00
qiskit
Clean description fields
2026-01-05 14:29:10 -08:00
qutip
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
rdkit
refactor(rdkit): update fingerprint generation to use rdFingerprintGenerator API
2026-01-26 20:25:28 +08:00
reactome-database
Clean description fields
2026-01-05 14:29:10 -08:00
research-grants
Clean description fields
2026-01-05 14:29:10 -08:00
research-lookup
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
rowan
Add support for Rowan computational platform that provides a suite of design and simulation tools for chemical R&D
2026-01-12 13:22:43 -08:00
scanpy
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
scholar-evaluation
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scientific-brainstorming
Clean description fields
2026-01-05 14:29:10 -08:00
scientific-critical-thinking
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
scientific-schematics
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
scientific-slides
Clean description fields
2026-01-05 14:29:10 -08:00
scientific-visualization
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
scientific-writing
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
scikit-bio
Clean description fields
2026-01-05 14:29:10 -08:00
scikit-learn
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scikit-survival
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
scvi-tools
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
seaborn
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
shap
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
simpy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
stable-baselines3
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
statistical-analysis
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
statsmodels
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
string-database
Clean description fields
2026-01-05 14:29:10 -08:00
sympy
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
torch_geometric
Clean description fields
2026-01-05 14:29:10 -08:00
torchdrug
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
transformers
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
treatment-plans
Clean description fields
2026-01-05 14:29:10 -08:00
umap-learn
Clean description fields
2026-01-05 14:29:10 -08:00
uniprot-database
Clean description fields
2026-01-05 14:29:10 -08:00
uspto-database
Add patentsview api key for patent search api
2026-01-08 22:38:59 -08:00
vaex
Clean description fields
2026-01-05 14:29:10 -08:00
venue-templates
Enhance citation management and literature review guidelines
2026-01-05 13:01:10 -08:00
zarr-python
Clean description fields
2026-01-05 14:29:10 -08:00
zinc-database
Clean description fields
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