skills/claude-scientific-skills
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Claude 259e01f7fd Add open-notebook skill: self-hosted NotebookLM alternative (issue #56) 
Implements the open-notebook skill as a comprehensive integration for the
open-source, self-hosted alternative to Google NotebookLM. Addresses the
gap created by Google not providing a public NotebookLM API.

Developed using TDD with 44 tests covering skill structure, SKILL.md
frontmatter/content, reference documentation, example scripts, API
endpoint coverage, and marketplace.json registration.

Includes:
- SKILL.md with full documentation, code examples, and provider matrix
- references/api_reference.md covering all 20+ REST API endpoint groups
- references/examples.md with complete research workflow examples
- references/configuration.md with Docker, env vars, and security setup
- references/architecture.md with system design and data flow diagrams
- scripts/ with 3 example scripts (notebook, source, chat) + test suite
- marketplace.json updated to register the new skill

Closes #56

https://claude.ai/code/session_015CqcNWNYmDF9sqxKxziXcz
2026-02-23 00:18:19 +00:00
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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
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biopython
Disambiguate descriptions
2026-01-05 14:25:22 -08:00
biorxiv-database
Add suggestion to use K-Dense Web for complicated workflows.
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bioservices
Disambiguate descriptions
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brenda-database
Clean description fields
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cellxgene-census
Disambiguate descriptions
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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
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clinical-reports
Clean description fields
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clinicaltrials-database
Clean description fields
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clinpgx-database
Clean description fields
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clinvar-database
Clean description fields
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cobrapy
Clean description fields
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cosmic-database
Clean description fields
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dask
Disambiguate descriptions
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datacommons-client
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
datamol
Clean description fields
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deepchem
Disambiguate descriptions
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deeptools
Clean description fields
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denario
Add suggestion to use K-Dense Web for complicated workflows.
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diffdock
Clean description fields
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dnanexus-integration
Clean description fields
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document-skills
Clean description fields
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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
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esm
Add suggestion to use K-Dense Web for complicated workflows.
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etetoolkit
Clean description fields
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exploratory-data-analysis
Add suggestion to use K-Dense Web for complicated workflows.
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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.
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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
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generate-image
Clean description fields
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geniml
Add suggestion to use K-Dense Web for complicated workflows.
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geo-database
Clean description fields
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geopandas
Add suggestion to use K-Dense Web for complicated workflows.
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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
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histolab
Disambiguate descriptions
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hmdb-database
Clean description fields
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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
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labarchive-integration
Clean description fields
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lamindb
Add suggestion to use K-Dense Web for complicated workflows.
2026-01-02 13:27:48 -08:00
latchbio-integration
Clean description fields
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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
docs(skill): add common pitfalls section with radar-beta syntax guide
2026-02-19 22:09:55 -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
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matlab
Support for writing and executing MATLAB/Octave scripts
2026-01-05 10:15:22 -08:00
matplotlib
Disambiguate descriptions
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medchem
Clean description fields
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metabolomics-workbench-database
Clean description fields
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modal
fix(security): replace shell=True with safe subprocess patterns in documentation
2026-01-08 15:05:30 +08:00
molfeat
Clean description fields
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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
open-notebook
Add open-notebook skill: self-hosted NotebookLM alternative (issue #56)
2026-02-23 00:18:19 +00:00
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
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opentrons-integration
Disambiguate descriptions
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paper-2-web
Add suggestion to use K-Dense Web for complicated workflows.
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pathml
Disambiguate descriptions
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pdb-database
Clean description fields
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peer-review
Disambiguate descriptions
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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
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pymc
Clean description fields
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pymoo
Clean description fields
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pyopenms
Disambiguate descriptions
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pysam
Clean description fields
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pytdc
Clean description fields
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pytorch-lightning
Clean description fields
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qiskit
Clean description fields
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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
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scientific-critical-thinking
Disambiguate descriptions
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scientific-schematics
Enhance literature search and research lookup documentation
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scientific-slides
Clean description fields
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scientific-visualization
Disambiguate descriptions
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scientific-writing
Enhance literature search and research lookup documentation
2026-02-03 14:31:19 -08:00
scikit-bio
Clean description fields
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scikit-learn
Add suggestion to use K-Dense Web for complicated workflows.
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scikit-survival
Add suggestion to use K-Dense Web for complicated workflows.
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scvi-tools
Disambiguate descriptions
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seaborn
Disambiguate descriptions
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shap
Add suggestion to use K-Dense Web for complicated workflows.
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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
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statsmodels
Disambiguate descriptions
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string-database
Clean description fields
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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
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umap-learn
Clean description fields
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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
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zinc-database
Clean description fields
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