{
  "name": "claude-scientific-skills",
  "owner": {
    "name": "Timothy Kassis",
    "email": "timothy.kassis@k-dense.ai"
  },
  "metadata": {
    "description": "Claude scientific skills from K-Dense Inc",
    "version": "1.67.0"
  },
  "plugins": [
    {
      "name": "scientific-packages",
      "description": "Collection of python scientific packages",
      "source": "./",
      "strict": false,
      "skills": [
        "./scientific-packages/aeon",
        "./scientific-packages/anndata",
        "./scientific-packages/arboreto",
        "./scientific-packages/astropy",
        "./scientific-packages/biomni",
        "./scientific-packages/biopython",
        "./scientific-packages/bioservices",
        "./scientific-packages/cellxgene-census",
        "./scientific-packages/cobrapy",
        "./scientific-packages/dask",
        "./scientific-packages/datacommons-client",
        "./scientific-packages/datamol",
        "./scientific-packages/deepchem",
        "./scientific-packages/deeptools",
        "./scientific-packages/diffdock",
        "./scientific-packages/esm",
        "./scientific-packages/etetoolkit",
        "./scientific-packages/flowio",
        "./scientific-packages/gget",
        "./scientific-packages/hypogenic",
        "./scientific-packages/histolab",
        "./scientific-packages/lamindb",
        "./scientific-packages/markitdown",
        "./scientific-packages/matchms",
        "./scientific-packages/matplotlib",
        "./scientific-packages/medchem",
        "./scientific-packages/molfeat",
        "./scientific-packages/neurokit2",
        "./scientific-packages/networkx",
        "./scientific-packages/paper-2-web",
        "./scientific-packages/pathml",
        "./scientific-packages/polars",
        "./scientific-packages/pydeseq2",
        "./scientific-packages/pydicom",
        "./scientific-packages/pyhealth",
        "./scientific-packages/pymatgen",
        "./scientific-packages/pymc",
        "./scientific-packages/pylabrobot",
        "./scientific-packages/pymoo",
        "./scientific-packages/pyopenms",
        "./scientific-packages/pysam",
        "./scientific-packages/pytdc",
        "./scientific-packages/pytorch-lightning",
        "./scientific-packages/rdkit",
        "./scientific-packages/reportlab",
        "./scientific-packages/scanpy",
        "./scientific-packages/scvi-tools",
        "./scientific-packages/scikit-bio",
        "./scientific-packages/scikit-learn",
        "./scientific-packages/scikit-survival",
        "./scientific-packages/seaborn",
        "./scientific-packages/shap",
        "./scientific-packages/simpy",
        "./scientific-packages/statsmodels",
        "./scientific-packages/sympy",
        "./scientific-packages/torch_geometric",
        "./scientific-packages/torchdrug",
        "./scientific-packages/tooluniverse",
        "./scientific-packages/transformers",
        "./scientific-packages/umap-learn",
        "./scientific-packages/vaex",
        "./scientific-packages/zarr-python"
      ]
    },
    {
      "name": "scientific-databases",
      "description": "Collection of scientific databases",
      "source": "./",
      "strict": false,
      "skills": [
        "./scientific-databases/alphafold-database",
        "./scientific-databases/biorxiv-database",
        "./scientific-databases/chembl-database",
        "./scientific-databases/clinpgx-database",
        "./scientific-databases/clinvar-database",
        "./scientific-databases/clinicaltrials-database",
        "./scientific-databases/cosmic-database",
        "./scientific-databases/drugbank-database",
        "./scientific-databases/ena-database",
        "./scientific-databases/ensembl-database",
        "./scientific-databases/fda-database",
        "./scientific-databases/gene-database",
        "./scientific-databases/geo-database",
        "./scientific-databases/gwas-database",
        "./scientific-databases/hmdb-database",
        "./scientific-databases/kegg-database",
        "./scientific-databases/metabolomics-workbench-database",
        "./scientific-databases/opentargets-database",
        "./scientific-databases/pdb-database",
        "./scientific-databases/pubchem-database",
        "./scientific-databases/pubmed-database",
        "./scientific-databases/reactome-database",
        "./scientific-databases/string-database",
        "./scientific-databases/uniprot-database",
        "./scientific-databases/uspto-database",
        "./scientific-databases/zinc-database"
      ]
    },
    {
      "name": "scientific-thinking",
      "description": "Collection of scientific thinking methodologies",
      "source": "./",
      "strict": false,
      "skills": [
        "./scientific-thinking/exploratory-data-analysis",
        "./scientific-thinking/hypothesis-generation",
        "./scientific-thinking/literature-review",
        "./scientific-thinking/peer-review",
        "./scientific-thinking/scholar-evaluation",
        "./scientific-thinking/scientific-brainstorming",
        "./scientific-thinking/scientific-critical-thinking",
        "./scientific-thinking/scientific-writing",
        "./scientific-thinking/statistical-analysis",
        "./scientific-thinking/scientific-visualization",
        "./scientific-thinking/document-skills/docx",
        "./scientific-thinking/document-skills/pdf",
        "./scientific-thinking/document-skills/pptx",
        "./scientific-thinking/document-skills/xlsx"
      ]
    },
    {
      "name": "scientific-integrations",
      "description": "Collection of scientific platform integrations",
      "source": "./",
      "strict": false,
      "skills": [
        "./scientific-integrations/benchling-integration",
        "./scientific-integrations/dnanexus-integration",
        "./scientific-integrations/labarchive-integration",
        "./scientific-integrations/latchbio-integration",
        "./scientific-integrations/omero-integration",
        "./scientific-integrations/opentrons-integration",
        "./scientific-integrations/protocolsio-integration"
      ]
    },
    {
      "name": "scientific-context-initialization",
      "description": "Always Auto-invoked skill that creates/updates workspace AGENT.md to instruct the agent to always search for existing skills before attempting any scientific task",
      "source": "./scientific-helpers/scientific-context-initialization",
      "strict": false
    },
    {
      "name": "get-available-resources",
      "description": "Detects and reports available system resources (CPU cores, GPUs, memory, disk space) to inform computational approach decisions",
      "source": "./scientific-helpers/get-available-resources",
      "strict": false
    }
  ]
}