{
  "version": 1,
  "source": "https://biorouter.ucsf.edu/baam",
  "extensions": [
    {
      "id": "cdwagent",
      "name": "CDWAgent",
      "organization": "BaranziniLab · UCSF",
      "version": "v0.5.1",
      "description": "Multimodal access to the UCSF Clinical Data Warehouse through natural language. One-call cohort building across diagnoses, medications, procedures, labs, radiology/imaging, immunizations, allergies, and vitals; clinical-notes/NLP search; read-only queries, schema discovery, and structured results. Requires UCSF network credentials (CAMPUS\\username and password).",
      "tags": [
        "UCSF",
        "MCP",
        "CDW",
        "Clinical"
      ],
      "github": "https://github.com/BaranziniLab/CDWAgent",
      "download": "https://github.com/BaranziniLab/CDWAgent/releases/download/v0.5.1-brxt/cdwagent.brxt",
      "filename": "cdwagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "ucsfomopagent",
      "name": "UCSFOMOPAgent",
      "organization": "BaranziniLab · UCSF",
      "version": "v0.2.0",
      "description": "Natural language SQL on the UCSF OMOP de-identified clinical database. Read-only access to standardized EHR data under the OMOP Common Data Model. v0.2.0 adds built-in OMOP/SQL-Server context plus concept-search, lab-finder, and live schema tools so the agent reaches the right data faster and more reliably. Requires UCSF credentials.",
      "tags": [
        "UCSF",
        "MCP",
        "OMOP",
        "EHR"
      ],
      "github": "https://github.com/BaranziniLab/UCSFOMOPAgent",
      "download": "https://github.com/BaranziniLab/UCSFOMOPAgent/releases/download/v0.2.0-brxt/ucsfomopagent.brxt",
      "filename": "ucsfomopagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "playwrightagent",
      "name": "Playwright Agent",
      "organization": "BaranziniLab · UCSF",
      "version": "v0.1.0",
      "description": "Browser automation via Microsoft's @playwright/mcp. Navigate websites, extract data, fill forms, and run web research workflows using structured accessibility snapshots. No vision model required. Requires Node.js on the host.",
      "tags": [
        "MCP",
        "Browser",
        "Automation"
      ],
      "github": "https://github.com/BaranziniLab/PlaywrightAgent",
      "download": "https://github.com/BaranziniLab/PlaywrightAgent/releases/download/v0.1.0-brxt/playwrightagent.brxt",
      "filename": "playwrightagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "spokeagent-0.4.1",
      "name": "SPOKEAgent",
      "organization": "BaranziniLab · UCSF",
      "version": "v0.4.1",
      "description": "Structure-aware access to the SPOKE biomedical knowledge graph (43M nodes): live schema introspection, entity/identifier resolution, node profiling, shortest-path finding, and guarded read-only Cypher across diseases, genes, proteins, drugs, and pathways. Includes a bundled spoke-knowledge-graph skill. Requires a SPOKEAGENT_PASSCODE (see credentials page).",
      "tags": [
        "UCSF",
        "MCP",
        "Knowledge Graph"
      ],
      "github": "https://github.com/BaranziniLab/SPOKEAgent",
      "download": "https://github.com/BaranziniLab/SPOKEAgent/releases/download/v0.4.1/spokeagent-0.4.1.brxt",
      "filename": "spokeagent-0.4.1.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "codegraphagent",
      "name": "CodeGraph Agent",
      "organization": "Broccolito · UCSF",
      "version": "v0.1.0",
      "description": "Pre-indexed code knowledge graph. Ask \"who calls X?\", \"what does Y call?\", or \"what breaks if I change Z?\" across 23 languages including R, Julia, MATLAB, Perl. Vendored fork of CodeGraph on tree-sitter.",
      "tags": [
        "MCP",
        "Code Intelligence",
        "R",
        "Tree-sitter"
      ],
      "github": "https://github.com/Broccolito/CodeGraphAgent",
      "download": "https://github.com/Broccolito/CodeGraphAgent/releases/download/v0.1.0/codegraphagent.brxt",
      "filename": "codegraphagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "bioroffice",
      "name": "BiorOffice",
      "organization": "BaranziniLab · UCSF",
      "version": "v1.0.0",
      "description": "Create, read, and edit Word (.docx), Excel (.xlsx), and PowerPoint (.pptx) files from chat. Handles headings, tables, charts, and 150+ Excel functions with live formula evaluation. Built on the open-source OfficeCLI engine, so no Microsoft Office install is needed. Ships four bundled skills for the office suite, Word, Excel, and PowerPoint.",
      "tags": [
        "MCP",
        "Office",
        "Documents",
        "Word",
        "Excel",
        "PowerPoint"
      ],
      "github": "https://github.com/BaranziniLab/BiorOffice",
      "download": "https://github.com/BaranziniLab/BiorOffice/releases/download/v1.0.0/bioroffice.brxt",
      "filename": "bioroffice.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "benchlingagent",
      "name": "BenchlingAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "Read-only and confirmation-gated MCP access to Benchling projects, registry records, notebook entries, and assay metadata for scientific workflow review.",
      "tags": [
        "MCP",
        "Benchling",
        "ELN",
        "Registry",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/BenchlingAgent",
      "download": "https://github.com/BaranziniLab/BenchlingAgent/releases/download/v0.1.0-brxt/benchlingagent.brxt",
      "filename": "benchlingagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "dnanexusagent",
      "name": "DNAnexusAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to DNAnexus project, file, app, workflow, and job metadata with guarded API calls for cloud bioinformatics runs.",
      "tags": [
        "MCP",
        "DNAnexus",
        "Cloud",
        "Workflows",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/DNAnexusAgent",
      "download": "https://github.com/BaranziniLab/DNAnexusAgent/releases/download/v0.1.0-brxt/dnanexusagent.brxt",
      "filename": "dnanexusagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "latchbioagent",
      "name": "LatchBioAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to LatchBio workspace, workflow, file, and execution metadata with guarded API request helpers for reproducible computational biology workflows.",
      "tags": [
        "MCP",
        "LatchBio",
        "Workflow",
        "Compute",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/LatchBioAgent",
      "download": "https://github.com/BaranziniLab/LatchBioAgent/releases/download/v0.1.0-brxt/latchbioagent.brxt",
      "filename": "latchbioagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "labarchivesagent",
      "name": "LabArchivesAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to LabArchives electronic lab notebook metadata and entries, with read-first notebook inspection and confirmation-gated API requests.",
      "tags": [
        "MCP",
        "LabArchives",
        "ELN",
        "Notebook",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/LabArchivesAgent",
      "download": "https://github.com/BaranziniLab/LabArchivesAgent/releases/download/v0.1.0-brxt/labarchivesagent.brxt",
      "filename": "labarchivesagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "omeroagent",
      "name": "OMEROAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access pattern for OMERO image repositories, project/dataset/image metadata, and web/API endpoint inspection for microscopy data review.",
      "tags": [
        "MCP",
        "OMERO",
        "Imaging",
        "Microscopy",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/OMEROAgent",
      "download": "https://github.com/BaranziniLab/OMEROAgent/releases/download/v0.1.0-brxt/omeroagent.brxt",
      "filename": "omeroagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "protocolsioagent",
      "name": "ProtocolsIOAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to Protocols.io public and authenticated protocol metadata for method discovery, citation, and reproducible protocol review.",
      "tags": [
        "MCP",
        "Protocols.io",
        "Methods",
        "Protocols",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ProtocolsIOAgent",
      "download": "https://github.com/BaranziniLab/ProtocolsIOAgent/releases/download/v0.1.0-brxt/protocolsioagent.brxt",
      "filename": "protocolsioagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "opennotebookagent",
      "name": "OpenNotebookAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for self-hosted or lab-hosted open-notebook systems, exposing guarded notebook entry search, retrieval, and provenance checks.",
      "tags": [
        "MCP",
        "Open Notebook",
        "Provenance",
        "Notebook",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/OpenNotebookAgent",
      "download": "https://github.com/BaranziniLab/OpenNotebookAgent/releases/download/v0.1.0-brxt/opennotebookagent.brxt",
      "filename": "opennotebookagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "modalagent",
      "name": "ModalAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP helper for Modal compute projects, deployment planning, environment validation, and guarded command/API invocation for cloud scientific jobs.",
      "tags": [
        "MCP",
        "Modal",
        "Compute",
        "Jobs",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ModalAgent",
      "download": "https://github.com/BaranziniLab/ModalAgent/releases/download/v0.1.0-brxt/modalagent.brxt",
      "filename": "modalagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "idcagent",
      "name": "IDCAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to NCI Imaging Data Commons metadata endpoints for cancer imaging cohort discovery, DICOM collection review, and reproducible image-data queries.",
      "tags": [
        "MCP",
        "IDC",
        "Cancer Imaging",
        "DICOM",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/IDCAgent",
      "download": "https://github.com/BaranziniLab/IDCAgent/releases/download/v0.1.0-brxt/idcagent.brxt",
      "filename": "idcagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "literatureagent",
      "name": "LiteratureAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access pattern for PubMed, OpenAlex, Crossref, Semantic Scholar, and literature evidence workflows, with provenance-first search and guarded API calls.",
      "tags": [
        "MCP",
        "Literature",
        "PubMed",
        "Evidence",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/LiteratureAgent",
      "download": "https://github.com/BaranziniLab/LiteratureAgent/releases/download/v0.1.0-brxt/literatureagent.brxt",
      "filename": "literatureagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "ncbiagent",
      "name": "NCBIAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access to NCBI database discovery and Entrez-style workflows for PubMed, Gene, SRA, GEO, ClinVar, dbSNP, and sequence metadata review.",
      "tags": [
        "MCP",
        "NCBI",
        "Entrez",
        "Genomics",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/NCBIAgent",
      "download": "https://github.com/BaranziniLab/NCBIAgent/releases/download/v0.1.0-brxt/ncbiagent.brxt",
      "filename": "ncbiagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "clinicalvariantagent",
      "name": "ClinicalVariantAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access pattern for variant annotation resources such as ClinVar, VEP, MyVariant, and gnomAD, with normalization and clinical-evidence review safeguards.",
      "tags": [
        "MCP",
        "ClinVar",
        "Variants",
        "Annotation",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ClinicalVariantAgent",
      "download": "https://github.com/BaranziniLab/ClinicalVariantAgent/releases/download/v0.1.0-brxt/clinicalvariantagent.brxt",
      "filename": "clinicalvariantagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "workflowrunneragent",
      "name": "WorkflowRunnerAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "Guarded MCP workflow runner for Nextflow, Snakemake, Cromwell/WDL, and CWL planning, validation, dry-run review, and confirmation-gated execution.",
      "tags": [
        "MCP",
        "Nextflow",
        "Snakemake",
        "Workflow",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/WorkflowRunnerAgent",
      "download": "https://github.com/BaranziniLab/WorkflowRunnerAgent/releases/download/v0.1.0-brxt/workflowrunneragent.brxt",
      "filename": "workflowrunneragent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "ucsfhpcagent",
      "name": "UCSFHPCAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP helper for UCSF CHPC/SLURM job planning, account inspection, file transfer checks, and confirmation-gated HPC command execution.",
      "tags": [
        "UCSF",
        "MCP",
        "HPC",
        "SLURM",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/UCSFHPCAgent",
      "download": "https://github.com/BaranziniLab/UCSFHPCAgent/releases/download/v0.1.0-brxt/ucsfhpcagent.brxt",
      "filename": "ucsfhpcagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "chemoinformaticsagent",
      "name": "ChemoinformaticsAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP helper for RDKit, PubChem, ChEMBL, SMILES/InChI normalization, molecular descriptors, and guarded local cheminformatics command planning.",
      "tags": [
        "MCP",
        "RDKit",
        "ChEMBL",
        "Molecules",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ChemoinformaticsAgent",
      "download": "https://github.com/BaranziniLab/ChemoinformaticsAgent/releases/download/v0.1.0-brxt/chemoinformaticsagent.brxt",
      "filename": "chemoinformaticsagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "proteinstructureagent",
      "name": "ProteinStructureAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP access pattern for PDB, AlphaFold, UniProt, sequence-to-structure lookup, structure metadata review, and guarded local structure-tool planning.",
      "tags": [
        "MCP",
        "PDB",
        "AlphaFold",
        "Proteins",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ProteinStructureAgent",
      "download": "https://github.com/BaranziniLab/ProteinStructureAgent/releases/download/v0.1.0-brxt/proteinstructureagent.brxt",
      "filename": "proteinstructureagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "singlecellomicsagent",
      "name": "SingleCellOmicsAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP helper for scanpy/anndata-style single-cell workflows, h5ad metadata inspection, QC planning, clustering review, and guarded local command execution.",
      "tags": [
        "MCP",
        "Single-cell",
        "Scanpy",
        "Omics",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/SingleCellOmicsAgent",
      "download": "https://github.com/BaranziniLab/SingleCellOmicsAgent/releases/download/v0.1.0-brxt/singlecellomicsagent.brxt",
      "filename": "singlecellomicsagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "opentronsagent",
      "name": "OpentronsAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Opentrons robot/run APIs, protocol metadata review, simulation planning, and guarded local Opentrons command execution.",
      "tags": [
        "MCP",
        "Opentrons",
        "Robotics",
        "Protocols",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/OpentronsAgent",
      "download": "https://github.com/BaranziniLab/OpentronsAgent/releases/download/v0.1.0-brxt/opentronsagent.brxt",
      "filename": "opentronsagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "ginkgocloudlabagent",
      "name": "GinkgoCloudLabAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Ginkgo-style cloud lab project, run, sample, and protocol metadata with guarded authenticated API calls.",
      "tags": [
        "MCP",
        "Ginkgo",
        "Cloud Lab",
        "Automation",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/GinkgoCloudLabAgent",
      "download": "https://github.com/BaranziniLab/GinkgoCloudLabAgent/releases/download/v0.1.0-brxt/ginkgocloudlabagent.brxt",
      "filename": "ginkgocloudlabagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "lamindbagent",
      "name": "LaminDBAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for LaminDB instance metadata, datasets, artifacts, collections, and guarded API/CLI planning for scientific data registries.",
      "tags": [
        "MCP",
        "LaminDB",
        "Data Registry",
        "Lineage",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/LaminDBAgent",
      "download": "https://github.com/BaranziniLab/LaminDBAgent/releases/download/v0.1.0-brxt/lamindbagent.brxt",
      "filename": "lamindbagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "cellxgenecensusagent",
      "name": "CellxGeneCensusAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for CELLxGENE Census dataset and cell metadata discovery, with guarded API calls for single-cell atlas review.",
      "tags": [
        "MCP",
        "CELLxGENE",
        "Single-cell",
        "Atlas",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/CellxGeneCensusAgent",
      "download": "https://github.com/BaranziniLab/CellxGeneCensusAgent/releases/download/v0.1.0-brxt/cellxgenecensusagent.brxt",
      "filename": "cellxgenecensusagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "depmapagent",
      "name": "DepMapAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for DepMap portal/API metadata, datasets, cell lines, genes, compounds, and cancer dependency evidence review.",
      "tags": [
        "MCP",
        "DepMap",
        "Cancer",
        "Dependencies",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/DepMapAgent",
      "download": "https://github.com/BaranziniLab/DepMapAgent/releases/download/v0.1.0-brxt/depmapagent.brxt",
      "filename": "depmapagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "primekgagent",
      "name": "PrimeKGAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for PrimeKG-style biomedical knowledge graph files and APIs, with guarded metadata lookup and graph-resource summaries.",
      "tags": [
        "MCP",
        "PrimeKG",
        "Knowledge Graph",
        "Biomedical",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/PrimeKGAgent",
      "download": "https://github.com/BaranziniLab/PrimeKGAgent/releases/download/v0.1.0-brxt/primekgagent.brxt",
      "filename": "primekgagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "zoteroagent",
      "name": "ZoteroAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Zotero libraries, collections, items, tags, and citation metadata with read-first and mutation-gated API access.",
      "tags": [
        "MCP",
        "Zotero",
        "Citations",
        "Library",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ZoteroAgent",
      "download": "https://github.com/BaranziniLab/ZoteroAgent/releases/download/v0.1.0-brxt/zoteroagent.brxt",
      "filename": "zoteroagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "markitdownagent",
      "name": "MarkItDownAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP helper for MarkItDown-style document-to-Markdown conversion planning, status checks, and guarded local conversion commands.",
      "tags": [
        "MCP",
        "MarkItDown",
        "Documents",
        "Markdown",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/MarkItDownAgent",
      "download": "https://github.com/BaranziniLab/MarkItDownAgent/releases/download/v0.1.0-brxt/markitdownagent.brxt",
      "filename": "markitdownagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "adaptyvbiofoundryagent",
      "name": "AdaptyvBioFoundryAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Adaptyv-style protein engineering design-build-test workflows, sequence libraries, experiment metadata, and result retrieval with guarded API calls.",
      "tags": [
        "MCP",
        "Adaptyv",
        "Protein Engineering",
        "Biofoundry",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/AdaptyvBioFoundryAgent",
      "download": "https://github.com/BaranziniLab/AdaptyvBioFoundryAgent/releases/download/v0.1.0-brxt/adaptyvbiofoundryagent.brxt",
      "filename": "adaptyvbiofoundryagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "structuredpapersearchagent",
      "name": "StructuredPaperSearchAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for structured paper and full-text metadata search across scholarly APIs, section-aware evidence extraction, and provenance-first literature queries.",
      "tags": [
        "MCP",
        "Papers",
        "Full Text",
        "Evidence",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/StructuredPaperSearchAgent",
      "download": "https://github.com/BaranziniLab/StructuredPaperSearchAgent/releases/download/v0.1.0-brxt/structuredpapersearchagent.brxt",
      "filename": "structuredpapersearchagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "scientificwebresearchagent",
      "name": "ScientificWebResearchAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for scientific web and deep-research workflows, web search APIs, source fetching, and provenance capture beyond scholarly APIs.",
      "tags": [
        "MCP",
        "Web Research",
        "Search",
        "Sources",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/ScientificWebResearchAgent",
      "download": "https://github.com/BaranziniLab/ScientificWebResearchAgent/releases/download/v0.1.0-brxt/scientificwebresearchagent.brxt",
      "filename": "scientificwebresearchagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "tamarindbioagent",
      "name": "TamarindBioAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Tamarind Bio-style cloud protein, structure, docking, and design workflows with guarded API calls and result provenance.",
      "tags": [
        "MCP",
        "Tamarind",
        "Protein Design",
        "Docking",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/TamarindBioAgent",
      "download": "https://github.com/BaranziniLab/TamarindBioAgent/releases/download/v0.1.0-brxt/tamarindbioagent.brxt",
      "filename": "tamarindbioagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "rowanmolecularmodelingagent",
      "name": "RowanMolecularModelingAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP adapter for Rowan-style cloud molecular modeling: conformers, pKa, docking, analogue docking, cofolding, and medicinal chemistry calculation provenance.",
      "tags": [
        "MCP",
        "Rowan",
        "Molecular Modeling",
        "MedChem",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/RowanMolecularModelingAgent",
      "download": "https://github.com/BaranziniLab/RowanMolecularModelingAgent/releases/download/v0.1.0-brxt/rowanmolecularmodelingagent.brxt",
      "filename": "rowanmolecularmodelingagent.brxt",
      "license": "Apache-2.0"
    },
    {
      "id": "unifiedpublicdatabaselookupagent",
      "name": "UnifiedPublicDatabaseLookupAgent",
      "organization": "BaranziniLab · BRXT",
      "version": "v0.1.0",
      "description": "MCP router for provenance-first public database lookups across biomedical, chemistry, materials, literature, regulatory, patent, and scientific data APIs.",
      "tags": [
        "MCP",
        "Public Databases",
        "Provenance",
        "Lookup",
        "Apache-2.0"
      ],
      "github": "https://github.com/BaranziniLab/UnifiedPublicDatabaseLookupAgent",
      "download": "https://github.com/BaranziniLab/UnifiedPublicDatabaseLookupAgent/releases/download/v0.1.0-brxt/unifiedpublicdatabaselookupagent.brxt",
      "filename": "unifiedpublicdatabaselookupagent.brxt",
      "license": "Apache-2.0"
    }
  ],
  "skills": [
    {
      "id": "scientific-research",
      "name": "Scientific Research",
      "category": "Core",
      "type": "User-invocable · /scientific-research",
      "description": "End-to-end research: scopes the question, reviews real literature, generates hypotheses, plans and verifies the analysis, then writes a cited draft. Delegates biomedical data to BioSkills and the SPOKE/CDW/OMOP extensions. It never fabricates a citation or result.",
      "tags": [
        "Research",
        "Literature",
        "Verified"
      ],
      "keywords": [
        "scientific-research",
        "auto",
        "research",
        "literature",
        "review",
        "hypothesis",
        "verification",
        "citations",
        "pubmed"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-scientific-research/scientific-research.zip",
      "filename": "scientific-research.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "empirical-research-router",
      "name": "Empirical Research Router",
      "category": "Core",
      "type": "User-invocable · /empirical-research-router",
      "description": "Stage-gated empirical research workflow: design register, data audit, identification, estimation, robustness, replication, and reporting.",
      "tags": [
        "Empirical",
        "Research",
        "Apache-2.0"
      ],
      "keywords": [
        "empirical-research-router",
        "empirical",
        "research",
        "causal",
        "inference",
        "econometrics",
        "reproducibility",
        "design",
        "register",
        "replication",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-empirical-research-router/empirical-research-router.zip",
      "filename": "empirical-research-router.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "causal-identification-gates",
      "name": "Causal Identification Gates",
      "category": "Core",
      "type": "User-invocable · /causal-identification-gates",
      "description": "Audits whether RCT, observational, IV, RDD, DiD, synthetic-control, matching, DML, or survival designs support causal language.",
      "tags": [
        "Causal",
        "Methods",
        "Apache-2.0"
      ],
      "keywords": [
        "causal-identification-gates",
        "causal",
        "inference",
        "iv",
        "rdd",
        "did",
        "synthetic",
        "control",
        "matching",
        "dml",
        "survival",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-causal-identification-gates/causal-identification-gates.zip",
      "filename": "causal-identification-gates.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "replication-package-audit",
      "name": "Replication Package Audit",
      "category": "Core",
      "type": "User-invocable · /replication-package-audit",
      "description": "Checks research packages for clean-run reproducibility, relative paths, environment capture, seeds, logs, and table/figure mapping.",
      "tags": [
        "Reproducibility",
        "Audit",
        "Apache-2.0"
      ],
      "keywords": [
        "replication-package-audit",
        "reproducibility",
        "package",
        "relative",
        "paths",
        "seeds",
        "logs",
        "environment",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-replication-package-audit/replication-package-audit.zip",
      "filename": "replication-package-audit.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "claim-evidence-integrity",
      "name": "Claim Evidence Integrity",
      "category": "Core",
      "type": "User-invocable · /claim-evidence-integrity",
      "description": "Verifies that manuscript claims, numbers, citations, figures, and tables are grounded in traceable evidence.",
      "tags": [
        "Claims",
        "Evidence",
        "Apache-2.0"
      ],
      "keywords": [
        "claim-evidence-integrity",
        "claims",
        "evidence",
        "manuscript",
        "numbers",
        "figures",
        "tables",
        "audit",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-claim-evidence-integrity/claim-evidence-integrity.zip",
      "filename": "claim-evidence-integrity.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "citation-temporal-integrity",
      "name": "Citation Temporal Integrity",
      "category": "Core",
      "type": "User-invocable · /citation-temporal-integrity",
      "description": "Confirms citations are real, relevant, current enough for the claim, and temporally valid.",
      "tags": [
        "Citations",
        "DOI",
        "Apache-2.0"
      ],
      "keywords": [
        "citation-temporal-integrity",
        "citation",
        "doi",
        "pmid",
        "openalex",
        "pubmed",
        "stale",
        "claims",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-citation-temporal-integrity/citation-temporal-integrity.zip",
      "filename": "citation-temporal-integrity.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "empirical-benchmark-harness",
      "name": "Empirical Benchmark Harness",
      "category": "Core",
      "type": "User-invocable · /empirical-benchmark-harness",
      "description": "Known-answer benchmark patterns for testing whether empirical-analysis agents avoid common causal and reproducibility failures.",
      "tags": [
        "Benchmarks",
        "Eval",
        "Apache-2.0"
      ],
      "keywords": [
        "empirical-benchmark-harness",
        "benchmark",
        "eval",
        "weak",
        "iv",
        "rdd",
        "did",
        "bad",
        "controls",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-empirical-benchmark-harness/empirical-benchmark-harness.zip",
      "filename": "empirical-benchmark-harness.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "scientific-artifacts",
      "name": "Scientific Artifacts",
      "category": "Core",
      "type": "User-invocable · /scientific-artifacts",
      "description": "Plans and verifies DOCX/PDF/PPTX/XLSX/LaTeX/scientific figure artifacts with source-to-exhibit mapping.",
      "tags": [
        "Documents",
        "Slides",
        "Apache-2.0"
      ],
      "keywords": [
        "scientific-artifacts",
        "docx",
        "pdf",
        "pptx",
        "xlsx",
        "latex",
        "figures",
        "slides",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-scientific-artifacts/scientific-artifacts.zip",
      "filename": "scientific-artifacts.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "open-science-review",
      "name": "Open Science Review",
      "category": "Core",
      "type": "User-invocable · /open-science-review",
      "description": "Reviews data/code availability, reporting checklists, protocols, ethics/privacy notes, and open-science readiness.",
      "tags": [
        "Open Science",
        "Checklist",
        "Apache-2.0"
      ],
      "keywords": [
        "open-science-review",
        "prisma",
        "consort",
        "strobe",
        "reporting",
        "checklist",
        "data",
        "code",
        "availability",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-open-science-review/open-science-review.zip",
      "filename": "open-science-review.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "scientific-data-engineering",
      "name": "Scientific Data Engineering",
      "category": "Core",
      "type": "User-invocable · /scientific-data-engineering",
      "description": "Plans scalable scientific data workflows with Polars, Dask, Zarr, TileDB, Arrow/Parquet, HDF5, and dataset versioning.",
      "tags": [
        "Data",
        "Pipelines",
        "Apache-2.0"
      ],
      "keywords": [
        "scientific-data-engineering",
        "polars",
        "dask",
        "zarr",
        "tiledb",
        "parquet",
        "hdf5",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-scientific-data-engineering/scientific-data-engineering.zip",
      "filename": "scientific-data-engineering.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "statistical-modeling-bayes",
      "name": "Statistical Modeling and Bayes",
      "category": "Core",
      "type": "User-invocable · /statistical-modeling-bayes",
      "description": "Designs and critiques statistical, Bayesian, survival, hierarchical, power, and uncertainty-reporting workflows.",
      "tags": [
        "Statistics",
        "Bayes",
        "Apache-2.0"
      ],
      "keywords": [
        "statistical-modeling-bayes",
        "pymc",
        "statsmodels",
        "survival",
        "power",
        "bayesian",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-statistical-modeling-bayes/statistical-modeling-bayes.zip",
      "filename": "statistical-modeling-bayes.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "scientific-machine-learning",
      "name": "Scientific Machine Learning",
      "category": "Core",
      "type": "User-invocable · /scientific-machine-learning",
      "description": "Plans scientific ML with leakage checks, transformers, graph neural networks, active learning, SHAP, and reproducibility gates.",
      "tags": [
        "ML",
        "Explainability",
        "Apache-2.0"
      ],
      "keywords": [
        "scientific-machine-learning",
        "transformers",
        "torch",
        "graph",
        "neural",
        "networks",
        "shap",
        "leakage",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-scientific-machine-learning/scientific-machine-learning.zip",
      "filename": "scientific-machine-learning.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "geospatial-science",
      "name": "Geospatial Science",
      "category": "Core",
      "type": "User-invocable · /geospatial-science",
      "description": "Handles geospatial analysis with CRS checks, spatial joins, rasters/vectors, maps, and spatial statistics.",
      "tags": [
        "Geospatial",
        "Maps",
        "Apache-2.0"
      ],
      "keywords": [
        "geospatial-science",
        "geopandas",
        "raster",
        "vector",
        "crs",
        "maps",
        "spatial",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-geospatial-science/geospatial-science.zip",
      "filename": "geospatial-science.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "neurophysiology-analysis",
      "name": "Neurophysiology Analysis",
      "category": "Core",
      "type": "User-invocable · /neurophysiology-analysis",
      "description": "Plans biosignal and neural-recording analysis: ECG/EDA/PPG, spike sorting, Neuropixels metadata, and peri-event QC.",
      "tags": [
        "Signals",
        "Neural",
        "Apache-2.0"
      ],
      "keywords": [
        "neurophysiology-analysis",
        "neurokit",
        "neuropixels",
        "ecg",
        "eda",
        "ppg",
        "spike",
        "sorting",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-neurophysiology-analysis/neurophysiology-analysis.zip",
      "filename": "neurophysiology-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "quantum-scientific-computing",
      "name": "Quantum Scientific Computing",
      "category": "Core",
      "type": "User-invocable · /quantum-scientific-computing",
      "description": "Routes quantum and scientific simulation work across Qiskit, Cirq, PennyLane, QuTiP, and validation checks.",
      "tags": [
        "Quantum",
        "Simulation",
        "Apache-2.0"
      ],
      "keywords": [
        "quantum-scientific-computing",
        "qiskit",
        "cirq",
        "pennylane",
        "qutip",
        "hamiltonian",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-quantum-scientific-computing/quantum-scientific-computing.zip",
      "filename": "quantum-scientific-computing.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "materials-informatics",
      "name": "Materials Informatics",
      "category": "Core",
      "type": "User-invocable · /materials-informatics",
      "description": "Guides computational materials workflows with structures, crystals, compositions, phase diagrams, and dataset provenance.",
      "tags": [
        "Materials",
        "Crystals",
        "Apache-2.0"
      ],
      "keywords": [
        "materials-informatics",
        "pymatgen",
        "crystals",
        "compositions",
        "phase",
        "diagrams",
        "descriptors",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-materials-informatics/materials-informatics.zip",
      "filename": "materials-informatics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "biomedical-imaging-pathology",
      "name": "Biomedical Imaging and Pathology",
      "category": "Core",
      "type": "User-invocable · /biomedical-imaging-pathology",
      "description": "Plans DICOM/pathology/PACS workflows with tiling, metadata, QC, cohort provenance, and privacy-safe reporting.",
      "tags": [
        "Imaging",
        "Pathology",
        "Apache-2.0"
      ],
      "keywords": [
        "biomedical-imaging-pathology",
        "dicom",
        "pathology",
        "pacs",
        "pathml",
        "histolab",
        "privacy",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-biomedical-imaging-pathology/biomedical-imaging-pathology.zip",
      "filename": "biomedical-imaging-pathology.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "citation-library-management",
      "name": "Citation Library Management",
      "category": "Core",
      "type": "User-invocable · /citation-library-management",
      "description": "Builds, cleans, verifies, and deduplicates Zotero/BibTeX/RIS/CSL citation libraries.",
      "tags": [
        "Citations",
        "Zotero",
        "Apache-2.0"
      ],
      "keywords": [
        "citation-library-management",
        "zotero",
        "bibtex",
        "ris",
        "csl",
        "doi",
        "deduplicate",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-citation-library-management/citation-library-management.zip",
      "filename": "citation-library-management.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "laboratory-automation-planning",
      "name": "Laboratory Automation Planning",
      "category": "Core",
      "type": "User-invocable · /laboratory-automation-planning",
      "description": "Plans Opentrons/cloud-lab workflows with plate maps, protocol simulation, sample metadata, and execution gates.",
      "tags": [
        "Lab Automation",
        "Protocols",
        "Apache-2.0"
      ],
      "keywords": [
        "laboratory-automation-planning",
        "opentrons",
        "ginkgo",
        "cloud",
        "lab",
        "plate",
        "maps",
        "protocols",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-laboratory-automation-planning/laboratory-automation-planning.zip",
      "filename": "laboratory-automation-planning.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "econometrics-toolkit",
      "name": "Econometrics Toolkit",
      "category": "Core",
      "type": "User-invocable · /econometrics-toolkit",
      "description": "Plans applied econometrics in Python, R, or Stata: panel data, IV, DiD, RDD, clustering, and replication tables.",
      "tags": [
        "Econometrics",
        "Causal",
        "Apache-2.0"
      ],
      "keywords": [
        "econometrics-toolkit",
        "stata",
        "r",
        "python",
        "panels",
        "fixed",
        "effects",
        "iv",
        "did",
        "rdd",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-econometrics-toolkit/econometrics-toolkit.zip",
      "filename": "econometrics-toolkit.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "systematic-review-prisma",
      "name": "Systematic Review and PRISMA",
      "category": "Core",
      "type": "User-invocable · /systematic-review-prisma",
      "description": "Runs systematic-review workflows: PICO, search strings, screening logs, PRISMA flow, extraction, risk of bias, and synthesis.",
      "tags": [
        "PRISMA",
        "Review",
        "Apache-2.0"
      ],
      "keywords": [
        "systematic-review-prisma",
        "pico",
        "screening",
        "prisma",
        "extraction",
        "risk",
        "bias",
        "evidence",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-systematic-review-prisma/systematic-review-prisma.zip",
      "filename": "systematic-review-prisma.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "taste-skill",
      "name": "Taste (Frontend Design)",
      "category": "Core",
      "type": "Auto-applied · frontend design",
      "description": "Anti-slop frontend design for landing pages, dashboards, lab tools, and paper companion sites. Reads the brief, picks a real design direction, and ships interfaces that don't look templated.",
      "tags": [
        "Design",
        "Frontend",
        "UI"
      ],
      "keywords": [
        "taste-skill",
        "design",
        "frontend",
        "ui",
        "landing",
        "page",
        "dashboard",
        "anti-slop"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-taste-skill/taste-skill.zip",
      "filename": "taste-skill.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "simulation-optimization",
      "name": "Simulation and Optimization",
      "category": "Core",
      "type": "User-invocable · /simulation-optimization",
      "description": "Plans discrete-event simulation, multi-objective optimization, sensitivity analysis, scheduling, and what-if modeling.",
      "tags": [
        "Simulation",
        "Optimization",
        "Apache-2.0"
      ],
      "keywords": [
        "simulation-optimization",
        "simpy",
        "pymoo",
        "fluidsim",
        "optimization",
        "sensitivity",
        "scheduling",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-simulation-optimization/simulation-optimization.zip",
      "filename": "simulation-optimization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "physical-science-computing",
      "name": "Physical Science Computing",
      "category": "Core",
      "type": "User-invocable · /physical-science-computing",
      "description": "Routes astronomy, physics, units, coordinate systems, spectra, numerical experiments, and physical-science workflows.",
      "tags": [
        "Physics",
        "Astronomy",
        "Apache-2.0"
      ],
      "keywords": [
        "physical-science-computing",
        "astropy",
        "physics",
        "astronomy",
        "units",
        "spectra",
        "numerical",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-physical-science-computing/physical-science-computing.zip",
      "filename": "physical-science-computing.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "metabolic-modeling-cobrapy",
      "name": "Metabolic Modeling with COBRApy",
      "category": "Core",
      "type": "User-invocable · /metabolic-modeling-cobrapy",
      "description": "Guides COBRApy/FBA metabolic modeling with GPR rules, media constraints, knockouts, objectives, and provenance.",
      "tags": [
        "Metabolism",
        "COBRApy",
        "Apache-2.0"
      ],
      "keywords": [
        "metabolic-modeling-cobrapy",
        "cobrapy",
        "fba",
        "flux",
        "balance",
        "gpr",
        "knockouts",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-metabolic-modeling-cobrapy/metabolic-modeling-cobrapy.zip",
      "filename": "metabolic-modeling-cobrapy.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "drug-discovery-benchmarks",
      "name": "Drug Discovery Benchmarks",
      "category": "Core",
      "type": "User-invocable · /drug-discovery-benchmarks",
      "description": "Plans ADMET, virtual-screening, molecular-property, scaffold-split, leakage, and assay-provenance benchmark checks.",
      "tags": [
        "Drug Discovery",
        "Benchmarks",
        "Apache-2.0"
      ],
      "keywords": [
        "drug-discovery-benchmarks",
        "pytdc",
        "torchdrug",
        "molfeat",
        "admet",
        "scaffold",
        "split",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-drug-discovery-benchmarks/drug-discovery-benchmarks.zip",
      "filename": "drug-discovery-benchmarks.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "clinical-decision-support-review",
      "name": "Clinical Decision Support Review",
      "category": "Core",
      "type": "User-invocable · /clinical-decision-support-review",
      "description": "Reviews clinical decision support, treatment plans, and reports for evidence grounding, safety scope, and no-PHI handling.",
      "tags": [
        "Clinical",
        "Safety",
        "Apache-2.0"
      ],
      "keywords": [
        "clinical-decision-support-review",
        "pyhealth",
        "treatment",
        "plans",
        "clinical",
        "reports",
        "cds",
        "no",
        "phi",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-clinical-decision-support-review/clinical-decision-support-review.zip",
      "filename": "clinical-decision-support-review.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "scientific-visual-communication",
      "name": "Scientific Visual Communication",
      "category": "Core",
      "type": "User-invocable · /scientific-visual-communication",
      "description": "Plans schematics, posters, slides, figure panels, infographics, visual abstracts, and source-to-visual traceability.",
      "tags": [
        "Visuals",
        "Posters",
        "Apache-2.0"
      ],
      "keywords": [
        "scientific-visual-communication",
        "schematics",
        "infographics",
        "posters",
        "slides",
        "visual",
        "abstracts",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-scientific-visual-communication/scientific-visual-communication.zip",
      "filename": "scientific-visual-communication.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "grant-funding-strategy",
      "name": "Grant and Funding Strategy",
      "category": "Core",
      "type": "User-invocable · /grant-funding-strategy",
      "description": "Structures research grants, specific aims, milestones, reviewer-risk responses, and funder-fit checks.",
      "tags": [
        "Grants",
        "Funding",
        "Apache-2.0"
      ],
      "keywords": [
        "grant-funding-strategy",
        "research",
        "grants",
        "specific",
        "aims",
        "milestones",
        "funder",
        "fit",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-grant-funding-strategy/grant-funding-strategy.zip",
      "filename": "grant-funding-strategy.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "regulatory-quality-systems",
      "name": "Regulatory and Quality Systems",
      "category": "Core",
      "type": "User-invocable · /regulatory-quality-systems",
      "description": "Reviews scientific software, device, and lab processes against quality, validation, traceability, and design-control gates.",
      "tags": [
        "Regulatory",
        "QMS",
        "Apache-2.0"
      ],
      "keywords": [
        "regulatory-quality-systems",
        "iso",
        "13485",
        "qms",
        "validation",
        "design",
        "controls",
        "audit",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-regulatory-quality-systems/regulatory-quality-systems.zip",
      "filename": "regulatory-quality-systems.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "gpu-compute-optimization",
      "name": "GPU Compute Optimization",
      "category": "Core",
      "type": "User-invocable · /gpu-compute-optimization",
      "description": "Plans GPU-bound training/inference, batching, profiling, memory pressure, mixed precision, and reproducible compute.",
      "tags": [
        "GPU",
        "Performance",
        "Apache-2.0"
      ],
      "keywords": [
        "gpu-compute-optimization",
        "cuda",
        "pytorch",
        "memory",
        "profiling",
        "mixed",
        "precision",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-gpu-compute-optimization/gpu-compute-optimization.zip",
      "filename": "gpu-compute-optimization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "research-evaluation-venues",
      "name": "Research Evaluation and Venues",
      "category": "Core",
      "type": "User-invocable · /research-evaluation-venues",
      "description": "Evaluates papers, scholars, venues, impact claims, reviewer fit, and publication positioning.",
      "tags": [
        "Venues",
        "Evaluation",
        "Apache-2.0"
      ],
      "keywords": [
        "research-evaluation-venues",
        "scholar",
        "evaluation",
        "venue",
        "templates",
        "journals",
        "impact",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-research-evaluation-venues/research-evaluation-venues.zip",
      "filename": "research-evaluation-venues.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "qualitative-thematic-analysis",
      "name": "Qualitative Thematic Analysis",
      "category": "Core",
      "type": "User-invocable · /qualitative-thematic-analysis",
      "description": "Plans qualitative coding, thematic analysis, codebooks, memoing, inter-rater checks, and audit trails.",
      "tags": [
        "Qualitative",
        "Codebooks",
        "Apache-2.0"
      ],
      "keywords": [
        "qualitative-thematic-analysis",
        "thematic",
        "analysis",
        "codebook",
        "interviews",
        "memoing",
        "audit",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-qualitative-thematic-analysis/qualitative-thematic-analysis.zip",
      "filename": "qualitative-thematic-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "financial-accounting-econometrics",
      "name": "Financial and Accounting Econometrics",
      "category": "Core",
      "type": "User-invocable · /financial-accounting-econometrics",
      "description": "Plans empirical finance/accounting workflows with event studies, abnormal returns, panel data, and table replication.",
      "tags": [
        "Finance",
        "Accounting",
        "Apache-2.0"
      ],
      "keywords": [
        "financial-accounting-econometrics",
        "crsp",
        "compustat",
        "event",
        "study",
        "abnormal",
        "returns",
        "accounting",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-financial-accounting-econometrics/financial-accounting-econometrics.zip",
      "filename": "financial-accounting-econometrics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "stata-research-workbench",
      "name": "Stata Research Workbench",
      "category": "Core",
      "type": "User-invocable · /stata-research-workbench",
      "description": "Plans Stata .do/.dta research workflows: audits, logs, tables, graph export, replication, and R&R updates.",
      "tags": [
        "Stata",
        "Replication",
        "Apache-2.0"
      ],
      "keywords": [
        "stata-research-workbench",
        "stata",
        "do",
        "files",
        "dta",
        "logs",
        "tables",
        "replication",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-stata-research-workbench/stata-research-workbench.zip",
      "filename": "stata-research-workbench.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "survey-weights-complex-samples",
      "name": "Survey Weights and Complex Samples",
      "category": "Core",
      "type": "User-invocable · /survey-weights-complex-samples",
      "description": "Handles complex survey designs with strata, PSUs, replicate weights, domain analysis, calibration, and weighted inference.",
      "tags": [
        "Surveys",
        "Weights",
        "Apache-2.0"
      ],
      "keywords": [
        "survey-weights-complex-samples",
        "cps",
        "acs",
        "nhanes",
        "strata",
        "psu",
        "replicate",
        "weights",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-survey-weights-complex-samples/survey-weights-complex-samples.zip",
      "filename": "survey-weights-complex-samples.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "psychometrics-sem-measurement",
      "name": "Psychometrics, SEM, and Measurement",
      "category": "Core",
      "type": "User-invocable · /psychometrics-sem-measurement",
      "description": "Plans reliability, CFA/SEM, mediation/moderation, invariance, item analysis, and APA-style measurement reporting.",
      "tags": [
        "SEM",
        "Measurement",
        "Apache-2.0"
      ],
      "keywords": [
        "psychometrics-sem-measurement",
        "reliability",
        "cfa",
        "sem",
        "mediation",
        "moderation",
        "invariance",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-psychometrics-sem-measurement/psychometrics-sem-measurement.zip",
      "filename": "psychometrics-sem-measurement.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "social-science-text-as-data",
      "name": "Social Science Text as Data",
      "category": "Core",
      "type": "User-invocable · /social-science-text-as-data",
      "description": "Plans dictionaries, topic models, embeddings, sentiment, supervised coding, LLM-label validation, and measurement-error checks.",
      "tags": [
        "Text as Data",
        "NLP",
        "Apache-2.0"
      ],
      "keywords": [
        "social-science-text-as-data",
        "topic",
        "models",
        "embeddings",
        "sentiment",
        "dictionaries",
        "llm",
        "coding",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-social-science-text-as-data/social-science-text-as-data.zip",
      "filename": "social-science-text-as-data.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "econ-finance-data-sources",
      "name": "Economics and Finance Data Sources",
      "category": "Core",
      "type": "User-invocable · /econ-finance-data-sources",
      "description": "Routes empirical econ/finance sources including WRDS, CRSP, Compustat, SEC/EDGAR, NBER, SSRN, and public datasets.",
      "tags": [
        "Data Sources",
        "Finance",
        "Apache-2.0"
      ],
      "keywords": [
        "econ-finance-data-sources",
        "wrds",
        "crsp",
        "compustat",
        "edgar",
        "nber",
        "ssrn",
        "openalex",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-econ-finance-data-sources/econ-finance-data-sources.zip",
      "filename": "econ-finance-data-sources.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "empirical-paper-submission-rr",
      "name": "Empirical Paper Submission and R&R",
      "category": "Core",
      "type": "User-invocable · /empirical-paper-submission-rr",
      "description": "Plans journal targeting, referee reports, response letters, revise-and-resubmit execution, and appendix organization.",
      "tags": [
        "R&R",
        "Submission",
        "Apache-2.0"
      ],
      "keywords": [
        "empirical-paper-submission-rr",
        "referee",
        "reports",
        "response",
        "letters",
        "journal",
        "targeting",
        "revision",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-empirical-paper-submission-rr/empirical-paper-submission-rr.zip",
      "filename": "empirical-paper-submission-rr.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "structural-economics-theory",
      "name": "Structural Economics and Theory",
      "category": "Core",
      "type": "User-invocable · /structural-economics-theory",
      "description": "Routes game theory, equilibrium, DSGE/HANK, structural IO, calibration, simulation, and identification-proof workflows.",
      "tags": [
        "Structural",
        "Theory",
        "Apache-2.0"
      ],
      "keywords": [
        "structural-economics-theory",
        "game",
        "theory",
        "dsge",
        "hank",
        "structural",
        "io",
        "equilibrium",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-structural-economics-theory/structural-economics-theory.zip",
      "filename": "structural-economics-theory.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "causal-heterogeneity-policy-learning",
      "name": "Causal Heterogeneity and Policy Learning",
      "category": "Core",
      "type": "User-invocable · /causal-heterogeneity-policy-learning",
      "description": "Plans CATE, causal forests, meta-learners, policy learning, conformal causal inference, fairness, and subgroup reporting.",
      "tags": [
        "CATE",
        "Policy",
        "Apache-2.0"
      ],
      "keywords": [
        "causal-heterogeneity-policy-learning",
        "cate",
        "causal",
        "forests",
        "meta",
        "learners",
        "policy",
        "learning",
        "fairness",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-causal-heterogeneity-policy-learning/causal-heterogeneity-policy-learning.zip",
      "filename": "causal-heterogeneity-policy-learning.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "autoskill-workflow-discovery",
      "name": "Autoskill Workflow Discovery",
      "category": "Core",
      "type": "User-invocable · /autoskill-workflow-discovery",
      "description": "Detects repeated workflows and drafts native Biorouter skills, hooks, checklist updates, or extension plans.",
      "tags": [
        "Skills",
        "Hooks",
        "Apache-2.0"
      ],
      "keywords": [
        "autoskill-workflow-discovery",
        "skill",
        "creation",
        "hooks",
        "workflow",
        "discovery",
        "repeated",
        "work",
        "guardrails",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-autoskill-workflow-discovery/autoskill-workflow-discovery.zip",
      "filename": "autoskill-workflow-discovery.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "arbor-optimization",
      "name": "Arbor Optimization",
      "category": "Core",
      "type": "User-invocable · /arbor-optimization",
      "description": "Runs evaluator-driven branch-and-prune exploration for improving research artifacts, prompts, analyses, and designs.",
      "tags": [
        "Optimization",
        "Rubrics",
        "Apache-2.0"
      ],
      "keywords": [
        "arbor-optimization",
        "evaluator",
        "optimization",
        "branch",
        "prune",
        "rubric",
        "hypothesis",
        "tree",
        "alternatives",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-arbor-optimization/arbor-optimization.zip",
      "filename": "arbor-optimization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "hugging-science-resource-discovery",
      "name": "Hugging Science Resource Discovery",
      "category": "Core",
      "type": "User-invocable · /hugging-science-resource-discovery",
      "description": "Finds and evaluates Hugging Face scientific models, datasets, Spaces, and papers with license and provenance checks.",
      "tags": [
        "Hugging Face",
        "Models",
        "Apache-2.0"
      ],
      "keywords": [
        "hugging-science-resource-discovery",
        "hugging",
        "face",
        "models",
        "datasets",
        "spaces",
        "model",
        "cards",
        "benchmark",
        "license",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-hugging-science-resource-discovery/hugging-science-resource-discovery.zip",
      "filename": "hugging-science-resource-discovery.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "molecular-dynamics",
      "name": "Molecular Dynamics",
      "category": "Core",
      "type": "User-invocable · /molecular-dynamics",
      "description": "Plans MD setup and trajectory analysis with OpenMM, GROMACS, AmberTools, MDAnalysis, MDTraj, and reproducibility checks.",
      "tags": [
        "MD",
        "OpenMM",
        "Apache-2.0"
      ],
      "keywords": [
        "molecular-dynamics",
        "openmm",
        "gromacs",
        "ambertools",
        "mdanalysis",
        "mdtraj",
        "trajectory",
        "force",
        "fields",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-molecular-dynamics/molecular-dynamics.zip",
      "filename": "molecular-dynamics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "general-time-series-forecasting",
      "name": "General Time-Series Forecasting",
      "category": "Core",
      "type": "User-invocable · /general-time-series-forecasting",
      "description": "Plans non-omics forecasting with classical models, ML, foundation models, backtesting, leakage checks, and uncertainty.",
      "tags": [
        "Forecasting",
        "Backtests",
        "Apache-2.0"
      ],
      "keywords": [
        "general-time-series-forecasting",
        "arima",
        "prophet",
        "sktime",
        "statsforecast",
        "backtesting",
        "leakage",
        "uncertainty",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-general-time-series-forecasting/general-time-series-forecasting.zip",
      "filename": "general-time-series-forecasting.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "bids-neuroimaging",
      "name": "BIDS Neuroimaging",
      "category": "Core",
      "type": "User-invocable · /bids-neuroimaging",
      "description": "Audits BIDS neuroimaging datasets, derivatives, validation, metadata, and reproducible preprocessing readiness.",
      "tags": [
        "BIDS",
        "Neuroimaging",
        "Apache-2.0"
      ],
      "keywords": [
        "bids-neuroimaging",
        "bids",
        "fmri",
        "mri",
        "eeg",
        "meg",
        "ieeg",
        "dicom",
        "fmriprep",
        "bids-validator",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-bids-neuroimaging/bids-neuroimaging.zip",
      "filename": "bids-neuroimaging.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "clinical-ai-modeling",
      "name": "Clinical AI Modeling",
      "category": "Core",
      "type": "User-invocable · /clinical-ai-modeling",
      "description": "Plans clinical AI modeling workflows with EHR cohorts, validation, bias checks, calibration, safety, and no-PHI handling.",
      "tags": [
        "Clinical AI",
        "Validation",
        "Apache-2.0"
      ],
      "keywords": [
        "clinical-ai-modeling",
        "ehr",
        "pyhealth",
        "clinical",
        "prediction",
        "calibration",
        "bias",
        "fairness",
        "no",
        "phi",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-clinical-ai-modeling/clinical-ai-modeling.zip",
      "filename": "clinical-ai-modeling.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "computational-fluid-dynamics",
      "name": "Computational Fluid Dynamics",
      "category": "Core",
      "type": "User-invocable · /computational-fluid-dynamics",
      "description": "Plans CFD workflows with meshes, boundary conditions, turbulence models, solver validation, and convergence checks.",
      "tags": [
        "CFD",
        "OpenFOAM",
        "Apache-2.0"
      ],
      "keywords": [
        "computational-fluid-dynamics",
        "cfd",
        "fluid",
        "dynamics",
        "navier",
        "stokes",
        "openfoam",
        "mesh",
        "turbulence",
        "convergence",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-computational-fluid-dynamics/computational-fluid-dynamics.zip",
      "filename": "computational-fluid-dynamics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "anti-ai-writing",
      "name": "Anti-AI Writing",
      "category": "Core",
      "type": "User-invocable · /anti-ai-writing",
      "description": "A pass/fail checklist for spotting AI writing patterns before generating prose, articles, or essays.",
      "tags": [
        "Writing"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-anti-ai-writing/anti-ai-writing.zip",
      "filename": "anti-ai-writing.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "ggplot-visualization",
      "name": "ggplot2 Visualization",
      "category": "Core",
      "type": "Auto-applied · R plotting",
      "description": "Applies ggplot2 best-practice style when writing R plotting code.",
      "tags": [
        "R",
        "ggplot2"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-ggplot-visualization/ggplot-visualization.zip",
      "filename": "ggplot-visualization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "r-scripting",
      "name": "R Scripting",
      "category": "Core",
      "type": "Auto-applied · R code",
      "description": "Applies tidyverse conventions and documentation standards when writing or reviewing R code.",
      "tags": [
        "R",
        "Tidyverse"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-r-scripting/r-scripting.zip",
      "filename": "r-scripting.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "python-scripting",
      "name": "Python Scripting",
      "category": "Core",
      "type": "Auto-applied · Python code",
      "description": "Applies Python naming, typing, error handling, and project structure conventions when writing Python code.",
      "tags": [
        "Python"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-python-scripting/python-scripting.zip",
      "filename": "python-scripting.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "ralph",
      "name": "RALPH",
      "category": "Core",
      "type": "User-invocable · /ralph",
      "description": "End-to-end planning for the Ralph autonomous agent loop. Drafts a markdown PRD from a feature idea, then converts it to prd.json. Each story is sized for one hands-off iteration.",
      "tags": [
        "Planning",
        "Automation"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-ralph/ralph.zip",
      "filename": "ralph.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "superpowers",
      "name": "Superpowers Collection",
      "category": "Core",
      "type": "13 skills · TDD, debugging, planning, more",
      "description": "Engineering discipline skills: brainstorming, TDD, systematic debugging, parallel agents, plan writing, code review, git worktrees. Workflows tested on long-running engineering tasks.",
      "tags": [
        "TDD",
        "Debugging",
        "Collection"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-superpowers/superpowers.zip",
      "filename": "superpowers.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "ucsf-hpc",
      "name": "UCSF HPC",
      "category": "Core",
      "type": "User-invocable · /ucsf-hpc",
      "description": "SSH setup, SLURM job templates (CPU/GPU/H200), file transfer, module management, and common pitfalls for the UCSF CHPC cluster.",
      "tags": [
        "UCSF",
        "HPC",
        "SLURM"
      ],
      "keywords": [],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-ucsf-hpc/ucsf-hpc.zip",
      "filename": "ucsf-hpc.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "code-review",
      "name": "Code Review",
      "category": "Developer",
      "type": "User-invocable · /code-review",
      "description": "Multi-stage, confidence-scored review of a pull request or local diff. Drops low-confidence findings and posts a formatted PR comment via gh.",
      "tags": [
        "Review",
        "Git",
        "PR"
      ],
      "keywords": [
        "code-review",
        "pull",
        "request",
        "pr",
        "gh",
        "confidence",
        "diff"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-code-review/code-review.zip",
      "filename": "code-review.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "code-simplifier",
      "name": "Code Simplifier",
      "category": "Developer",
      "type": "User-invocable · /code-simplifier",
      "description": "Simplifies recently-changed code for clarity and consistency while preserving exact behavior. Defers language style to the Python and R skills.",
      "tags": [
        "Refactor",
        "Cleanup"
      ],
      "keywords": [
        "code-simplifier",
        "refactor",
        "cleanup",
        "simplify",
        "clarity"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-code-simplifier/code-simplifier.zip",
      "filename": "code-simplifier.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "commit-commands",
      "name": "Commit Commands",
      "category": "Developer",
      "type": "User-invocable · /commit-commands",
      "description": "Three git workflows: a clean single commit; commit + push + open a PR; and cleanup of [gone] branches and their worktrees.",
      "tags": [
        "Git",
        "Commit",
        "PR"
      ],
      "keywords": [
        "commit-commands",
        "git",
        "commit",
        "push",
        "pr",
        "worktree",
        "gone",
        "branches"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-commit-commands/commit-commands.zip",
      "filename": "commit-commands.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "skill-creator",
      "name": "Skill Creator",
      "category": "Developer",
      "type": "User-invocable · /skill-creator",
      "description": "The canonical guide to authoring Biorouter skills: frontmatter, progressive disclosure, packaging, and testing.",
      "tags": [
        "Authoring",
        "Meta"
      ],
      "keywords": [
        "skill-creator",
        "authoring",
        "meta",
        "frontmatter",
        "packaging"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-skill-creator/skill-creator.zip",
      "filename": "skill-creator.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "develop-biorouter-extension",
      "name": "Develop Biorouter Extension",
      "category": "Developer",
      "type": "User-invocable · /develop-biorouter-extension",
      "description": "Step-by-step guide for building a .brxt extension: manifest, MCP server, packaging, validation, and bundled skills.",
      "tags": [
        "BRXT",
        "Extensions",
        "Apache-2.0"
      ],
      "keywords": [
        "develop-biorouter-extension",
        "brxt",
        "extension",
        "mcp",
        "manifest",
        "bundled",
        "skills",
        "packaging",
        "apache"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-develop-biorouter-extension/develop-biorouter-extension.zip",
      "filename": "develop-biorouter-extension.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "hookify",
      "name": "Hookify (Hooks)",
      "category": "Developer",
      "type": "User-invocable · /hookify",
      "description": "Turns project guardrails (warn/block rules) into real Biorouter hooks in .biorouter/hooks.yaml. A block rule stops the action; a warn rule shows a notice. Requires allow_project_hooks: true.",
      "tags": [
        "Guardrails",
        "Safety"
      ],
      "keywords": [
        "hookify",
        "guardrails",
        "warn",
        "block",
        "safety",
        "rules"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-hookify/hookify.zip",
      "filename": "hookify.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "code-modernization",
      "name": "Code Modernization",
      "category": "Developer",
      "type": "User-invocable · /code-modernization",
      "description": "Phased legacy-modernization workflow (preflight, assess, map, extract rules, brief, transform, harden, status) for COBOL, legacy Java/C++, and monoliths.",
      "tags": [
        "Legacy",
        "Migration"
      ],
      "keywords": [
        "code-modernization",
        "legacy",
        "migration",
        "cobol",
        "monolith",
        "refactor"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-code-modernization/code-modernization.zip",
      "filename": "code-modernization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "playground",
      "name": "Playground",
      "category": "Developer",
      "type": "User-invocable · /playground",
      "description": "Generates self-contained single-file interactive HTML playgrounds for configuring something visually, then copying out a ready-to-use prompt.",
      "tags": [
        "HTML",
        "Interactive"
      ],
      "keywords": [
        "playground",
        "interactive",
        "html",
        "explorer",
        "controls",
        "preview"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-playground/playground.zip",
      "filename": "playground.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "frontend-design",
      "name": "Frontend Design",
      "category": "Developer",
      "type": "Auto-applied · frontend work",
      "description": "Anthropic's anti-slop frontend guidance for distinctive, production-grade UIs. Complements the Taste skill above.",
      "tags": [
        "Design",
        "Frontend"
      ],
      "keywords": [
        "frontend-design",
        "ui",
        "anti-slop",
        "aesthetic",
        "css",
        "design"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-frontend-design/frontend-design.zip",
      "filename": "frontend-design.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "alignment",
      "name": "Alignment",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "Multiple sequence alignment and pairwise alignment.",
      "tags": [
        "MAFFT",
        "Biopython",
        "Foldseek"
      ],
      "keywords": [
        "alignment",
        "mafft",
        "biopython",
        "foldseek"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-alignment/alignment.zip",
      "filename": "alignment.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "alignment-files",
      "name": "Alignment Files",
      "category": "Biomedical",
      "type": "10 skills · auto-applied",
      "description": "SAM/BAM/CRAM manipulation, sorting, indexing, dedup, and stats.",
      "tags": [
        "samtools",
        "pysam",
        "BAM"
      ],
      "keywords": [
        "alignment-files",
        "samtools",
        "pysam",
        "bam"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-alignment-files/alignment-files.zip",
      "filename": "alignment-files.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "alternative-splicing",
      "name": "Alternative Splicing",
      "category": "Biomedical",
      "type": "9 skills · auto-applied",
      "description": "RNA isoform and splice-junction analysis from short- and long-read data.",
      "tags": [
        "rMATS",
        "SUPPA2",
        "isoforms"
      ],
      "keywords": [
        "alternative-splicing",
        "rmats",
        "suppa2",
        "isoforms"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-alternative-splicing/alternative-splicing.zip",
      "filename": "alternative-splicing.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "atac-seq",
      "name": "ATAC-seq",
      "category": "Biomedical",
      "type": "12 skills · auto-applied",
      "description": "Chromatin accessibility, peak calling, footprinting, and deep-learning ATAC.",
      "tags": [
        "MACS3",
        "TOBIAS",
        "chromBPNet"
      ],
      "keywords": [
        "atac-seq",
        "macs3",
        "tobias",
        "chrombpnet"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-atac-seq/atac-seq.zip",
      "filename": "atac-seq.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "causal-genomics",
      "name": "Causal Genomics",
      "category": "Biomedical",
      "type": "11 skills · auto-applied",
      "description": "Mendelian randomization, colocalization, fine-mapping, and TWAS.",
      "tags": [
        "MR",
        "coloc",
        "TWAS"
      ],
      "keywords": [
        "causal-genomics",
        "mr",
        "coloc",
        "twas"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-causal-genomics/causal-genomics.zip",
      "filename": "causal-genomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "chemoinformatics",
      "name": "Chemoinformatics",
      "category": "Biomedical",
      "type": "9 skills · auto-applied",
      "description": "Molecular structure handling, descriptors, and drug-discovery utilities.",
      "tags": [
        "RDKit",
        "SMILES"
      ],
      "keywords": [
        "chemoinformatics",
        "rdkit",
        "smiles"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-chemoinformatics/chemoinformatics.zip",
      "filename": "chemoinformatics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "chip-seq",
      "name": "ChIP-seq",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "Transcription-factor and histone-mark peak calling and differential binding.",
      "tags": [
        "MACS2",
        "ChIPseeker"
      ],
      "keywords": [
        "chip-seq",
        "macs2",
        "chipseeker"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-chip-seq/chip-seq.zip",
      "filename": "chip-seq.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "clinical-biostatistics",
      "name": "Clinical Biostatistics",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "Survival, mixed models, and clinical-trial statistical analysis.",
      "tags": [
        "survival",
        "R",
        "lme4"
      ],
      "keywords": [
        "clinical-biostatistics",
        "survival",
        "r",
        "lme4"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-clinical-biostatistics/clinical-biostatistics.zip",
      "filename": "clinical-biostatistics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "clinical-databases",
      "name": "Clinical Databases",
      "category": "Biomedical",
      "type": "10 skills · auto-applied",
      "description": "ClinVar, OMIM, COSMIC, gnomAD, and phenotype DB queries.",
      "tags": [
        "ClinVar",
        "OMIM",
        "gnomAD"
      ],
      "keywords": [
        "clinical-databases",
        "clinvar",
        "omim",
        "gnomad"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-clinical-databases/clinical-databases.zip",
      "filename": "clinical-databases.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "clip-seq",
      "name": "CLIP-seq",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Protein–RNA interaction mapping from iCLIP/eCLIP/PAR-CLIP data.",
      "tags": [
        "PureCLIP",
        "eCLIP"
      ],
      "keywords": [
        "clip-seq",
        "pureclip",
        "eclip"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-clip-seq/clip-seq.zip",
      "filename": "clip-seq.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "comparative-genomics",
      "name": "Comparative Genomics",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Cross-species synteny, orthology, and selection scans.",
      "tags": [
        "OrthoFinder",
        "synteny"
      ],
      "keywords": [
        "comparative-genomics",
        "orthofinder",
        "synteny"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-comparative-genomics/comparative-genomics.zip",
      "filename": "comparative-genomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "copy-number",
      "name": "Copy Number",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "CNV detection, visualization, and segmentation.",
      "tags": [
        "CNVkit",
        "GATK CNV"
      ],
      "keywords": [
        "copy-number",
        "cnvkit",
        "gatk",
        "cnv"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-copy-number/copy-number.zip",
      "filename": "copy-number.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "crispr-screens",
      "name": "CRISPR Screens",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "Pooled screen counting, MAGeCK analysis, and hit prioritization.",
      "tags": [
        "MAGeCK",
        "screens"
      ],
      "keywords": [
        "crispr-screens",
        "mageck",
        "screens"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-crispr-screens/crispr-screens.zip",
      "filename": "crispr-screens.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "data-visualization",
      "name": "Data Visualization",
      "category": "Biomedical",
      "type": "13 skills · auto-applied",
      "description": "Publication-quality plots: heatmaps, volcano, Manhattan, dimplots.",
      "tags": [
        "ggplot2",
        "matplotlib",
        "ComplexHeatmap"
      ],
      "keywords": [
        "data-visualization",
        "ggplot2",
        "matplotlib",
        "complexheatmap"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-data-visualization/data-visualization.zip",
      "filename": "data-visualization.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "database-access",
      "name": "Database Access",
      "category": "Biomedical",
      "type": "12 skills · auto-applied",
      "description": "NCBI, UniProt, Ensembl, and biological database APIs.",
      "tags": [
        "Entrez",
        "UniProt",
        "Ensembl"
      ],
      "keywords": [
        "database-access",
        "entrez",
        "uniprot",
        "ensembl"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-database-access/database-access.zip",
      "filename": "database-access.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "differential-expression",
      "name": "Differential Expression",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "RNA-seq DE testing with DESeq2, edgeR, and limma-voom.",
      "tags": [
        "DESeq2",
        "edgeR",
        "limma"
      ],
      "keywords": [
        "differential-expression",
        "deseq2",
        "edger",
        "limma"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-differential-expression/differential-expression.zip",
      "filename": "differential-expression.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "ecological-genomics",
      "name": "Ecological Genomics",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "Environmental DNA, ecological population genomics, and biodiversity.",
      "tags": [
        "eDNA",
        "popgen"
      ],
      "keywords": [
        "ecological-genomics",
        "edna",
        "popgen"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-ecological-genomics/ecological-genomics.zip",
      "filename": "ecological-genomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "epidemiological-genomics",
      "name": "Epidemiological Genomics",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Pathogen typing, outbreak phylogeography, and surveillance.",
      "tags": [
        "Nextstrain",
        "pathogens"
      ],
      "keywords": [
        "epidemiological-genomics",
        "nextstrain",
        "pathogens"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-epidemiological-genomics/epidemiological-genomics.zip",
      "filename": "epidemiological-genomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "epitranscriptomics",
      "name": "Epitranscriptomics",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "m6A and other RNA modification detection from sequencing.",
      "tags": [
        "m6A",
        "RNA mods"
      ],
      "keywords": [
        "epitranscriptomics",
        "m6a",
        "rna",
        "mods"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-epitranscriptomics/epitranscriptomics.zip",
      "filename": "epitranscriptomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "experimental-design",
      "name": "Experimental Design",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Power analysis and sample-size calculation for omics studies.",
      "tags": [
        "power",
        "design"
      ],
      "keywords": [
        "experimental-design",
        "power",
        "design"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-experimental-design/experimental-design.zip",
      "filename": "experimental-design.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "expression-matrix",
      "name": "Expression Matrix",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Count normalization, gene ID mapping, and matrix QC.",
      "tags": [
        "TPM",
        "mygene"
      ],
      "keywords": [
        "expression-matrix",
        "tpm",
        "mygene"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-expression-matrix/expression-matrix.zip",
      "filename": "expression-matrix.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "flow-cytometry",
      "name": "Flow Cytometry",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "FCS parsing, gating, and high-dimensional cytometry analysis.",
      "tags": [
        "flowCore",
        "FlowSOM"
      ],
      "keywords": [
        "flow-cytometry",
        "flowcore",
        "flowsom"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-flow-cytometry/flow-cytometry.zip",
      "filename": "flow-cytometry.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "gene-regulatory-networks",
      "name": "Gene Regulatory Networks",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "TF–target network inference from expression and chromatin data.",
      "tags": [
        "SCENIC",
        "GRNBoost2"
      ],
      "keywords": [
        "gene-regulatory-networks",
        "scenic",
        "grnboost2"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-gene-regulatory-networks/gene-regulatory-networks.zip",
      "filename": "gene-regulatory-networks.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "genome-annotation",
      "name": "Genome Annotation",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "Gene prediction, repeat masking, and functional annotation.",
      "tags": [
        "AUGUSTUS",
        "InterProScan"
      ],
      "keywords": [
        "genome-annotation",
        "augustus",
        "interproscan"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-genome-annotation/genome-annotation.zip",
      "filename": "genome-annotation.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "genome-assembly",
      "name": "Genome Assembly",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "De novo assembly, polishing, and assembly QC.",
      "tags": [
        "Flye",
        "hifiasm",
        "QUAST"
      ],
      "keywords": [
        "genome-assembly",
        "flye",
        "hifiasm",
        "quast"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-genome-assembly/genome-assembly.zip",
      "filename": "genome-assembly.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "genome-engineering",
      "name": "Genome Engineering",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "CRISPR guide design, off-target prediction, and editing analysis.",
      "tags": [
        "CRISPOR",
        "Cas9"
      ],
      "keywords": [
        "genome-engineering",
        "crispor",
        "cas9"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-genome-engineering/genome-engineering.zip",
      "filename": "genome-engineering.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "genome-intervals",
      "name": "Genome Intervals",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "BED/GTF arithmetic, overlap, and feature manipulation.",
      "tags": [
        "bedtools",
        "pybedtools"
      ],
      "keywords": [
        "genome-intervals",
        "bedtools",
        "pybedtools"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-genome-intervals/genome-intervals.zip",
      "filename": "genome-intervals.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "hi-c-analysis",
      "name": "Hi-C Analysis",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "3D chromatin contacts, TAD calling, and loop detection.",
      "tags": [
        "cooler",
        "HiC-Pro"
      ],
      "keywords": [
        "hi-c-analysis",
        "cooler",
        "hic-pro"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-hi-c-analysis/hi-c-analysis.zip",
      "filename": "hi-c-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "imaging-mass-cytometry",
      "name": "Imaging Mass Cytometry",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "Single-cell spatial proteomics from IMC and MIBI data.",
      "tags": [
        "IMC",
        "Steinbock"
      ],
      "keywords": [
        "imaging-mass-cytometry",
        "imc",
        "steinbock"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-imaging-mass-cytometry/imaging-mass-cytometry.zip",
      "filename": "imaging-mass-cytometry.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "immunoinformatics",
      "name": "Immunoinformatics",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "MHC binding, neoantigen prediction, and HLA typing.",
      "tags": [
        "NetMHC",
        "HLA"
      ],
      "keywords": [
        "immunoinformatics",
        "netmhc",
        "hla"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-immunoinformatics/immunoinformatics.zip",
      "filename": "immunoinformatics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "liquid-biopsy",
      "name": "Liquid Biopsy",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "Cell-free DNA fragmentomics, tumor fraction, and methylation cfDNA.",
      "tags": [
        "cfDNA",
        "ichorCNA"
      ],
      "keywords": [
        "liquid-biopsy",
        "cfdna",
        "ichorcna"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-liquid-biopsy/liquid-biopsy.zip",
      "filename": "liquid-biopsy.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "long-read-sequencing",
      "name": "Long-read Sequencing",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "ONT and PacBio basecalling, alignment, and structural-variant workflows.",
      "tags": [
        "Nanopore",
        "PacBio",
        "minimap2"
      ],
      "keywords": [
        "long-read-sequencing",
        "nanopore",
        "pacbio",
        "minimap2"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-long-read-sequencing/long-read-sequencing.zip",
      "filename": "long-read-sequencing.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "machine-learning",
      "name": "Machine Learning",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "Biomarker discovery, model training, and cross-validation pipelines.",
      "tags": [
        "scikit-learn",
        "ML"
      ],
      "keywords": [
        "machine-learning",
        "scikit-learn",
        "ml"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-machine-learning/machine-learning.zip",
      "filename": "machine-learning.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "metabolomics",
      "name": "Metabolomics",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "Mass-spec metabolite identification, alignment, and quantification.",
      "tags": [
        "XCMS",
        "MetaboAnalyst"
      ],
      "keywords": [
        "metabolomics",
        "xcms",
        "metaboanalyst"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-metabolomics/metabolomics.zip",
      "filename": "metabolomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "metagenomics",
      "name": "Metagenomics",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "Shotgun microbial profiling, assembly, and binning.",
      "tags": [
        "Kraken2",
        "MetaPhlAn"
      ],
      "keywords": [
        "metagenomics",
        "kraken2",
        "metaphlan"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-metagenomics/metagenomics.zip",
      "filename": "metagenomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "methylation-analysis",
      "name": "Methylation Analysis",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Bisulfite alignment and differential methylation testing.",
      "tags": [
        "Bismark",
        "methylKit"
      ],
      "keywords": [
        "methylation-analysis",
        "bismark",
        "methylkit"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-methylation-analysis/methylation-analysis.zip",
      "filename": "methylation-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "microbiome",
      "name": "Microbiome",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "16S rRNA amplicon and microbiota community profiling.",
      "tags": [
        "QIIME2",
        "DADA2"
      ],
      "keywords": [
        "microbiome",
        "qiime2",
        "dada2"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-microbiome/microbiome.zip",
      "filename": "microbiome.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "multi-omics-integration",
      "name": "Multi-omics Integration",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Cross-modality fusion: MOFA, DIABLO, WNN, totalVI.",
      "tags": [
        "MOFA",
        "DIABLO"
      ],
      "keywords": [
        "multi-omics-integration",
        "mofa",
        "diablo"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-multi-omics-integration/multi-omics-integration.zip",
      "filename": "multi-omics-integration.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "pathway-analysis",
      "name": "Pathway Analysis",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "GO, KEGG, Reactome, and GSEA enrichment testing.",
      "tags": [
        "clusterProfiler",
        "GSEA"
      ],
      "keywords": [
        "pathway-analysis",
        "clusterprofiler",
        "gsea"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-pathway-analysis/pathway-analysis.zip",
      "filename": "pathway-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "phasing-imputation",
      "name": "Phasing & Imputation",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Haplotype phasing and genotype imputation with SHAPEIT and Beagle.",
      "tags": [
        "SHAPEIT",
        "Beagle"
      ],
      "keywords": [
        "phasing-imputation",
        "shapeit",
        "beagle"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-phasing-imputation/phasing-imputation.zip",
      "filename": "phasing-imputation.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "phylogenetics",
      "name": "Phylogenetics",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "Tree construction with IQ-TREE, RAxML, BEAST, and ancestral state.",
      "tags": [
        "IQ-TREE",
        "BEAST"
      ],
      "keywords": [
        "phylogenetics",
        "iq-tree",
        "beast"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-phylogenetics/phylogenetics.zip",
      "filename": "phylogenetics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "population-genetics",
      "name": "Population Genetics",
      "category": "Biomedical",
      "type": "6 skills · auto-applied",
      "description": "GWAS, population structure, LD, and selection scans.",
      "tags": [
        "PLINK",
        "GWAS"
      ],
      "keywords": [
        "population-genetics",
        "plink",
        "gwas"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-population-genetics/population-genetics.zip",
      "filename": "population-genetics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "primer-design",
      "name": "Primer Design",
      "category": "Biomedical",
      "type": "3 skills · auto-applied",
      "description": "PCR and qPCR primer generation with Primer3 and primerBLAST.",
      "tags": [
        "Primer3",
        "qPCR"
      ],
      "keywords": [
        "primer-design",
        "primer3",
        "qpcr"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-primer-design/primer-design.zip",
      "filename": "primer-design.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "proteomics",
      "name": "Proteomics",
      "category": "Biomedical",
      "type": "9 skills · auto-applied",
      "description": "Mass-spec quantification and protein abundance pipelines.",
      "tags": [
        "MaxQuant",
        "FragPipe"
      ],
      "keywords": [
        "proteomics",
        "maxquant",
        "fragpipe"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-proteomics/proteomics.zip",
      "filename": "proteomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "read-alignment",
      "name": "Read Alignment",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Short-read mapping with BWA-MEM2, Bowtie2, STAR, HISAT2.",
      "tags": [
        "BWA-MEM2",
        "STAR"
      ],
      "keywords": [
        "read-alignment",
        "bwa-mem2",
        "star"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-read-alignment/read-alignment.zip",
      "filename": "read-alignment.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "read-qc",
      "name": "Read QC",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "FastQC, fastp, trimming, and contamination screening.",
      "tags": [
        "FastQC",
        "fastp",
        "Kraken2"
      ],
      "keywords": [
        "read-qc",
        "fastqc",
        "fastp",
        "kraken2"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-read-qc/read-qc.zip",
      "filename": "read-qc.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "reporting",
      "name": "Reporting",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Reproducible HTML, Quarto, and R Markdown reports.",
      "tags": [
        "Quarto",
        "RMarkdown"
      ],
      "keywords": [
        "reporting",
        "quarto",
        "rmarkdown"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-reporting/reporting.zip",
      "filename": "reporting.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "restriction-analysis",
      "name": "Restriction Analysis",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Restriction-enzyme mapping and digestion prediction.",
      "tags": [
        "REBASE",
        "digestion"
      ],
      "keywords": [
        "restriction-analysis",
        "rebase",
        "digestion"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-restriction-analysis/restriction-analysis.zip",
      "filename": "restriction-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "ribo-seq",
      "name": "Ribo-seq",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Ribosome profiling and translation-efficiency analysis.",
      "tags": [
        "riboWaltz",
        "Ribo-TISH"
      ],
      "keywords": [
        "ribo-seq",
        "ribowaltz",
        "ribo-tish"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-ribo-seq/ribo-seq.zip",
      "filename": "ribo-seq.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "rna-quantification",
      "name": "RNA Quantification",
      "category": "Biomedical",
      "type": "4 skills · auto-applied",
      "description": "Gene and transcript abundance with Salmon, kallisto, RSEM.",
      "tags": [
        "Salmon",
        "kallisto"
      ],
      "keywords": [
        "rna-quantification",
        "salmon",
        "kallisto"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-rna-quantification/rna-quantification.zip",
      "filename": "rna-quantification.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "rna-structure",
      "name": "RNA Structure",
      "category": "Biomedical",
      "type": "3 skills · auto-applied",
      "description": "Secondary-structure prediction with RNAfold, IPknot.",
      "tags": [
        "RNAfold",
        "ViennaRNA"
      ],
      "keywords": [
        "rna-structure",
        "rnafold",
        "viennarna"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-rna-structure/rna-structure.zip",
      "filename": "rna-structure.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "sequence-io",
      "name": "Sequence I/O",
      "category": "Biomedical",
      "type": "9 skills · auto-applied",
      "description": "FASTA/FASTQ parsing, conversion, and indexing.",
      "tags": [
        "Biopython",
        "seqkit"
      ],
      "keywords": [
        "sequence-io",
        "biopython",
        "seqkit"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-sequence-io/sequence-io.zip",
      "filename": "sequence-io.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "sequence-manipulation",
      "name": "Sequence Manipulation",
      "category": "Biomedical",
      "type": "7 skills · auto-applied",
      "description": "Transcription, translation, ORF finding, and motif search.",
      "tags": [
        "Biopython",
        "EMBOSS"
      ],
      "keywords": [
        "sequence-manipulation",
        "biopython",
        "emboss"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-sequence-manipulation/sequence-manipulation.zip",
      "filename": "sequence-manipulation.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "single-cell",
      "name": "Single-cell",
      "category": "Biomedical",
      "type": "14 skills · auto-applied",
      "description": "scRNA-seq clustering, annotation, trajectory, and integration.",
      "tags": [
        "Scanpy",
        "Seurat",
        "scVI"
      ],
      "keywords": [
        "single-cell",
        "scanpy",
        "seurat",
        "scvi"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-single-cell/single-cell.zip",
      "filename": "single-cell.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "small-rna-seq",
      "name": "Small RNA-seq",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "miRNA, piRNA, and small-RNA quantification.",
      "tags": [
        "miRDeep2",
        "isomiRs"
      ],
      "keywords": [
        "small-rna-seq",
        "mirdeep2",
        "isomirs"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-small-rna-seq/small-rna-seq.zip",
      "filename": "small-rna-seq.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "spatial-transcriptomics",
      "name": "Spatial Transcriptomics",
      "category": "Biomedical",
      "type": "11 skills · auto-applied",
      "description": "Visium, Slide-seq, and high-resolution tissue expression.",
      "tags": [
        "Visium",
        "Squidpy"
      ],
      "keywords": [
        "spatial-transcriptomics",
        "visium",
        "squidpy"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-spatial-transcriptomics/spatial-transcriptomics.zip",
      "filename": "spatial-transcriptomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "structural-biology",
      "name": "Structural Biology",
      "category": "Biomedical",
      "type": "8 skills · auto-applied",
      "description": "PDB parsing, AlphaFold, ESMFold, and structure analysis.",
      "tags": [
        "AlphaFold",
        "PyMOL"
      ],
      "keywords": [
        "structural-biology",
        "alphafold",
        "pymol"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-structural-biology/structural-biology.zip",
      "filename": "structural-biology.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "systems-biology",
      "name": "Systems Biology",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Metabolic flux balance, kinetic modelling, network analysis.",
      "tags": [
        "COBRApy",
        "FBA"
      ],
      "keywords": [
        "systems-biology",
        "cobrapy",
        "fba"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-systems-biology/systems-biology.zip",
      "filename": "systems-biology.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "tcr-bcr-analysis",
      "name": "TCR/BCR Analysis",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Immune-receptor repertoire profiling and clonal-family analysis.",
      "tags": [
        "MiXCR",
        "scirpy"
      ],
      "keywords": [
        "tcr-bcr-analysis",
        "mixcr",
        "scirpy"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-tcr-bcr-analysis/tcr-bcr-analysis.zip",
      "filename": "tcr-bcr-analysis.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "temporal-genomics",
      "name": "Temporal Genomics",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Time-series and circadian expression analysis.",
      "tags": [
        "MetaCycle",
        "JTK_CYCLE"
      ],
      "keywords": [
        "temporal-genomics",
        "metacycle",
        "jtk_cycle"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-temporal-genomics/temporal-genomics.zip",
      "filename": "temporal-genomics.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "variant-calling",
      "name": "Variant Calling",
      "category": "Biomedical",
      "type": "13 skills · auto-applied",
      "description": "SNPs, indels, SVs with GATK, DeepVariant, Manta, Delly.",
      "tags": [
        "GATK",
        "DeepVariant",
        "Manta"
      ],
      "keywords": [
        "variant-calling",
        "gatk",
        "deepvariant",
        "manta"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-variant-calling/variant-calling.zip",
      "filename": "variant-calling.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "workflow-management",
      "name": "Workflow Management",
      "category": "Biomedical",
      "type": "5 skills · auto-applied",
      "description": "Snakemake, Nextflow, CWL, WDL pipeline scaffolding.",
      "tags": [
        "Snakemake",
        "Nextflow"
      ],
      "keywords": [
        "workflow-management",
        "snakemake",
        "nextflow"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-workflow-management/workflow-management.zip",
      "filename": "workflow-management.zip",
      "license": "Apache-2.0"
    },
    {
      "id": "workflows",
      "name": "End-to-end Workflows",
      "category": "Biomedical",
      "type": "41 skills · auto-applied",
      "description": "Ready-to-run analysis pipelines combining multiple skills.",
      "tags": [
        "Pipelines",
        "End-to-end"
      ],
      "keywords": [
        "workflows",
        "pipelines",
        "end-to-end"
      ],
      "download": "https://github.com/BaranziniLab/biorouter-skills/releases/download/skill-workflows/workflows.zip",
      "filename": "workflows.zip",
      "license": "Apache-2.0"
    }
  ]
}