{"_id":"@biomate/mcp-server","name":"@biomate/mcp-server","dist-tags":{"latest":"0.1.0"},"versions":{"0.1.0":{"name":"@biomate/mcp-server","version":"0.1.0","description":"BioMate MCP server — exposes 19 scientific workflow tools (RNA-seq, ADMET, WGS, CryoEM, proteomics, drug discovery) to any MCP-compatible AI host via stdio.","type":"module","bin":{"biomate-mcp-server":"dist/index.js"},"main":"./dist/index.js","scripts":{"build":"tsc && cp src/tools_manifest.json dist/tools_manifest.json","prepublishOnly":"npm run build"},"keywords":["biomate","mcp","bioinformatics","claude","cursor","rna-seq","genomics","drug-discovery"],"author":{"name":"BioMate AI","email":"support@biomate.ai"},"license":"MIT","repository":{"type":"git","url":"git+https://github.com/bioMate-AI/biomate-connector.git","directory":"connectors/mcp-server"},"engines":{"node":">=18"},"dependencies":{"@modelcontextprotocol/sdk":"^1.0.0"},"devDependencies":{"@types/node":"^20.0.0","typescript":"^5.4.0"},"publishConfig":{"access":"public"},"_id":"@biomate/mcp-server@0.1.0","gitHead":"9d5560530f9eae40f60f3c18e6efd68e3d9dd7e7","types":"./dist/index.d.ts","bugs":{"url":"https://github.com/bioMate-AI/biomate-connector/issues"},"homepage":"https://github.com/bioMate-AI/biomate-connector#readme","_nodeVersion":"22.18.0","_npmVersion":"10.9.3","dist":{"integrity":"sha512-Yx8qydvC+PaInogW3eCD6zH1Ex6xkcNcsyaoq9Amyyo5NK+BtplHHJOoBTJhCTEguC3Ao8823i9bSWHZdZ8aqw==","shasum":"0e34878af00e4e8eb8c7305aedf0f44e7b76a11a","tarball":"https://registry.npmjs.org/@biomate/mcp-server/-/mcp-server-0.1.0.tgz","fileCount":5,"unpackedSize":110251,"signatures":[{"keyid":"SHA256:DhQ8wR5APBvFHLF/+Tc+AYvPOdTpcIDqOhxsBHRwC7U","sig":"MEYCIQD3Pz9OFnEE/5BlHfrcShErPidp9tMz7S9rvPiLAFOkFAIhAMYmbVqHd68e0vDNSlHXkpkE3eneMMfx/9GURq1fu1gg"}]},"_npmUser":{"name":"biomate","email":"yaoyun.zhang@biomate.ai"},"directories":{},"maintainers":[{"name":"biomate","email":"yaoyun.zhang@biomate.ai"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages-npm-production","tmp":"tmp/mcp-server_0.1.0_1784652266591_0.8167250659393817"},"_hasShrinkwrap":false}},"time":{"created":"2026-07-21T16:44:26.463Z","0.1.0":"2026-07-21T16:44:26.739Z","modified":"2026-07-21T16:44:26.930Z"},"maintainers":[{"name":"biomate","email":"yaoyun.zhang@biomate.ai"}],"description":"BioMate MCP server — exposes 19 scientific workflow tools (RNA-seq, ADMET, WGS, CryoEM, proteomics, drug discovery) to any MCP-compatible AI host via stdio.","homepage":"https://github.com/bioMate-AI/biomate-connector#readme","keywords":["biomate","mcp","bioinformatics","claude","cursor","rna-seq","genomics","drug-discovery"],"repository":{"type":"git","url":"git+https://github.com/bioMate-AI/biomate-connector.git","directory":"connectors/mcp-server"},"author":{"name":"BioMate AI","email":"support@biomate.ai"},"bugs":{"url":"https://github.com/bioMate-AI/biomate-connector/issues"},"license":"MIT","readme":"# @biomate/mcp-server\n\nBioMate MCP server — exposes 19 scientific workflow tools to any MCP-compatible AI host (Claude Code, Claude Desktop, Cursor, Codex CLI).\n\n## Install\n\nAdd to your Claude Code or Claude Desktop config:\n\n**`~/.mcp.json`** (Claude Code):\n```json\n{\n  \"mcpServers\": {\n    \"biomate\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"@biomate/mcp-server\"],\n      \"env\": {\n        \"BIOMATE_API_KEY\": \"bm_live_your_key_here\"\n      }\n    }\n  }\n}\n```\n\nGet your API key at **[dev-public.biomate.ai/account/api-keys](https://dev-public.biomate.ai/account/api-keys)**.\n\n## Tools (19)\n\n| Tool | Purpose |\n|---|---|\n| `biomate_session` | Primary: natural-language goal → full workflow execution |\n| `search_workflow` | Search 2,455 indexed workflows by natural language |\n| `get_workflow_spec` | Full parameter spec for a workflow |\n| `run_workflow` | Execute with explicit parameters |\n| `get_run` / `watch_run` | Status, phases, steps, outputs |\n| `cancel_run` | Cancel a running job |\n| `list_runs` | History with filters |\n| `preview_file` | Server-side preview of output files |\n| `export_report` | PDF/markdown publication report |\n| `analyze_results` | AI interpretation of findings |\n| `explain_error` | Root-cause diagnosis for failed runs |\n| `query_database` | UniProt, PDB, NCBI, ChEMBL, AlphaFold |\n| `resolve_accession` | GEO/SRA/ENA → auto-run GEO data connector |\n| `browse_data` / `fetch_public_data` | Browse and stage public datasets |\n| `upload_file` | Get signed S3 PUT URL for local uploads |\n| `recall_memory` | Retrieve relevant prior runs and procedures |\n| `search_literature` | PubMed, Semantic Scholar, OpenAlex |\n\n## Environment variables\n\n| Variable | Description |\n|---|---|\n| `BIOMATE_API_KEY` | Personal API key (`bm_live_xxx`) — required |\n| `BIOMATE_API_BASE` | BioMate server URL (default: `https://dev-public.biomate.ai`) |\n\n## Example\n\n```\n> Screen aspirin and caffeine for hERG inhibition and CYP3A4 metabolism.\n```\n\n```\n> Run RNA-seq differential expression on s3://bucket/exp1/ — human GRCh38, treated vs control.\n```\n\n```\n> Fetch GSE183947 from GEO and run the DESeq2 pipeline.\n```\n\n## License\n\nMIT — this package only. BioMate platform usage governed by [biomate.ai/terms](https://biomate.ai/terms).\n","readmeFilename":"README.md","_rev":"1-6d1fef1cc90671b2daee8854e66f7ec3"}