@biomate/mcp-server

BioMate MCP server — exposes 19 scientific workflow tools to any MCP-compatible AI host (Claude Code, Claude Desktop, Cursor, Codex CLI).

Install

Add to your Claude Code or Claude Desktop config:

~/.mcp.json (Claude Code):

{
  "mcpServers": {
    "biomate": {
      "command": "npx",
      "args": ["-y", "@biomate/mcp-server"],
      "env": {
        "BIOMATE_API_KEY": "bm_live_your_key_here"
      }
    }
  }
}

Get your API key at dev-public.biomate.ai/account/api-keys.

Tools (19)

| Tool | Purpose | |---|---| | biomate_session | Primary: natural-language goal → full workflow execution | | search_workflow | Search 2,455 indexed workflows by natural language | | get_workflow_spec | Full parameter spec for a workflow | | run_workflow | Execute with explicit parameters | | get_run / watch_run | Status, phases, steps, outputs | | cancel_run | Cancel a running job | | list_runs | History with filters | | preview_file | Server-side preview of output files | | export_report | PDF/markdown publication report | | analyze_results | AI interpretation of findings | | explain_error | Root-cause diagnosis for failed runs | | query_database | UniProt, PDB, NCBI, ChEMBL, AlphaFold | | resolve_accession | GEO/SRA/ENA → auto-run GEO data connector | | browse_data / fetch_public_data | Browse and stage public datasets | | upload_file | Get signed S3 PUT URL for local uploads | | recall_memory | Retrieve relevant prior runs and procedures | | search_literature | PubMed, Semantic Scholar, OpenAlex |

Environment variables

| Variable | Description | |---|---| | BIOMATE_API_KEY | Personal API key (bm_live_xxx) — required | | BIOMATE_API_BASE | BioMate server URL (default: https://dev-public.biomate.ai) |

Example

> Screen aspirin and caffeine for hERG inhibition and CYP3A4 metabolism.

> Run RNA-seq differential expression on s3://bucket/exp1/ — human GRCh38, treated vs control.

> Fetch GSE183947 from GEO and run the DESeq2 pipeline.

License

MIT — this package only. BioMate platform usage governed by biomate.ai/terms.