diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json index b1362a4..f1c61d5 100644 --- a/.claude-plugin/marketplace.json +++ b/.claude-plugin/marketplace.json @@ -2,172 +2,137 @@ { "name": "claude-scientific-skills", "owner": { - "name": "Timothy Kassis", - "email": "timothy.kassis@k-dense.ai" + "name": "K-Dense Inc.", + "email": "contact@k-dense.ai" }, "metadata": { "description": "Claude scientific skills from K-Dense Inc", - "version": "1.80.0" + "version": "2.0.0" }, "plugins": [ { - "name": "scientific-packages", - "description": "Collection of python scientific packages", + "name": "scientific-skills", + "description": "Collection of scientific skills", "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/denario", - "./scientific-packages/datamol", - "./scientific-packages/deepchem", - "./scientific-packages/deeptools", - "./scientific-packages/diffdock", - "./scientific-packages/esm", - "./scientific-packages/etetoolkit", - "./scientific-packages/flowio", - "./scientific-packages/geniml", - "./scientific-packages/gget", - "./scientific-packages/gtars", - "./scientific-packages/hypogenic", - "./scientific-packages/histolab", - "./scientific-packages/lamindb", - "./scientific-packages/markitdown", - "./scientific-packages/matchms", - "./scientific-packages/matplotlib", - "./scientific-packages/medchem", - "./scientific-packages/modal", - "./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/pufferlib", - "./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/stable-baselines3", - "./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" + "./scientific-skills/aeon", + "./scientific-skills/anndata", + "./scientific-skills/arboreto", + "./scientific-skills/astropy", + "./scientific-skills/biomni", + "./scientific-skills/biopython", + "./scientific-skills/bioservices", + "./scientific-skills/cellxgene-census", + "./scientific-skills/cobrapy", + "./scientific-skills/dask", + "./scientific-skills/datacommons-client", + "./scientific-skills/denario", + "./scientific-skills/datamol", + "./scientific-skills/deepchem", + "./scientific-skills/deeptools", + "./scientific-skills/diffdock", + "./scientific-skills/esm", + "./scientific-skills/etetoolkit", + "./scientific-skills/flowio", + "./scientific-skills/geniml", + "./scientific-skills/gget", + "./scientific-skills/gtars", + "./scientific-skills/hypogenic", + "./scientific-skills/histolab", + "./scientific-skills/lamindb", + "./scientific-skills/markitdown", + "./scientific-skills/matchms", + "./scientific-skills/matplotlib", + "./scientific-skills/medchem", + "./scientific-skills/modal", + "./scientific-skills/molfeat", + "./scientific-skills/neurokit2", + "./scientific-skills/networkx", + "./scientific-skills/paper-2-web", + "./scientific-skills/pathml", + "./scientific-skills/polars", + "./scientific-skills/pydeseq2", + "./scientific-skills/pydicom", + "./scientific-skills/pyhealth", + "./scientific-skills/pymatgen", + "./scientific-skills/pymc", + "./scientific-skills/pylabrobot", + "./scientific-skills/pymoo", + "./scientific-skills/pufferlib", + "./scientific-skills/pyopenms", + "./scientific-skills/pysam", + "./scientific-skills/pytdc", + "./scientific-skills/pytorch-lightning", + "./scientific-skills/rdkit", + "./scientific-skills/reportlab", + "./scientific-skills/scanpy", + "./scientific-skills/scvi-tools", + "./scientific-skills/scikit-bio", + "./scientific-skills/scikit-learn", + "./scientific-skills/scikit-survival", + "./scientific-skills/seaborn", + "./scientific-skills/shap", + "./scientific-skills/simpy", + "./scientific-skills/stable-baselines3", + "./scientific-skills/statsmodels", + "./scientific-skills/sympy", + "./scientific-skills/torch_geometric", + "./scientific-skills/torchdrug", + "./scientific-skills/tooluniverse", + "./scientific-skills/transformers", + "./scientific-skills/umap-learn", + "./scientific-skills/vaex", + "./scientific-skills/zarr-python", + "./scientific-skills/alphafold-database", + "./scientific-skills/biorxiv-database", + "./scientific-skills/chembl-database", + "./scientific-skills/clinpgx-database", + "./scientific-skills/clinvar-database", + "./scientific-skills/clinicaltrials-database", + "./scientific-skills/cosmic-database", + "./scientific-skills/drugbank-database", + "./scientific-skills/ena-database", + "./scientific-skills/ensembl-database", + "./scientific-skills/fda-database", + "./scientific-skills/gene-database", + "./scientific-skills/geo-database", + "./scientific-skills/gwas-database", + "./scientific-skills/hmdb-database", + "./scientific-skills/kegg-database", + "./scientific-skills/metabolomics-workbench-database", + "./scientific-skills/opentargets-database", + "./scientific-skills/pdb-database", + "./scientific-skills/pubchem-database", + "./scientific-skills/pubmed-database", + "./scientific-skills/reactome-database", + "./scientific-skills/string-database", + "./scientific-skills/uniprot-database", + "./scientific-skills/uspto-database", + "./scientific-skills/zinc-database", + "./scientific-skills/exploratory-data-analysis", + "./scientific-skills/hypothesis-generation", + "./scientific-skills/literature-review", + "./scientific-skills/peer-review", + "./scientific-skills/scholar-evaluation", + "./scientific-skills/scientific-brainstorming", + "./scientific-skills/scientific-critical-thinking", + "./scientific-skills/scientific-writing", + "./scientific-skills/statistical-analysis", + "./scientific-skills/scientific-visualization", + "./scientific-skills/document-skills/docx", + "./scientific-skills/document-skills/pdf", + "./scientific-skills/document-skills/pptx", + "./scientific-skills/document-skills/xlsx", + "./scientific-skills/benchling-integration", + "./scientific-skills/dnanexus-integration", + "./scientific-skills/labarchive-integration", + "./scientific-skills/latchbio-integration", + "./scientific-skills/omero-integration", + "./scientific-skills/opentrons-integration", + "./scientific-skills/protocolsio-integration", + "./scientific-skills/get-available-resources" ] - }, - { - "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 } ] -} +} \ No newline at end of file