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BioMCP-TS

Biomedical MCP server: genes, variants, trials, literature, patents, optional SQL/R/biowasm tools.

TypeScript

★ 12 stars Last pushed 2026-09-24 License: Apache-2.0

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Review any command before running it. Package names and URLs come from the server's own registry entry.

Package (npm 1.4.3)

npx -y biomcp@1.4.3

Or add to your MCP client config:

{
  "mcpServers": {
    "biomcp-ts": {
      "command": "npx",
      "args": [
        "-y",
        "biomcp@1.4.3"
      ],
      "env": {
        "ANALYSIS_BIOWASM": "<YOUR_VALUE>",
        "ANALYSIS_R": "<YOUR_VALUE>",
        "DB_TYPE": "<YOUR_VALUE>",
        "NCBI_API_KEY": "<YOUR_VALUE>",
        "S2_API_KEY": "<YOUR_VALUE>",
        "OPENFDA_API_KEY": "<YOUR_VALUE>",
        "ONCOKB_TOKEN": "<YOUR_VALUE>",
        "DISGENET_API_KEY": "<YOUR_VALUE>"
      }
    }
  }
}

ANALYSIS_BIOWASM — Set to 1 to enable the samtools/bedtools/bcftools biowasm analysis tools
ANALYSIS_R — Set to 1 to enable the R/Bioconductor analysis tools (requires the webr peer dependency; use the pinned one-shot client command)
DB_TYPE — Set to mysql or sqlite to enable the read-only SQL database tools
NCBI_API_KEY secret — Higher NCBI E-utilities rate limits (3 -> 10 req/s)
S2_API_KEY secret — Higher Semantic Scholar rate limits
OPENFDA_API_KEY secret — Higher OpenFDA rate limits
ONCOKB_TOKEN secret — Required by the variant_oncokb tool (OncoKB annotations)
DISGENET_API_KEY secret — Required for DisGeNET disease-gene associations