@biomate/connect

One-line installer that wires BioMate AI into Claude Code, Claude Desktop, Cursor, OpenAI Codex, ChatGPT, and Open Claw (WeChat).

Real bioinformatics — WGS variant-calling pipeline, CryoSPARC, AlphaFold, ADMET screens, PBPK — runs from your favorite AI coding assistant. No SaaS lock-in: tokens are stored locally and revocable per-surface from your BioMate account.

Install

# Connect Claude Code
npx @biomate/connect claude-code

# Connect Cursor
npx @biomate/connect cursor

# Connect Codex CLI
npx @biomate/connect codex

That's it. The CLI opens your browser, runs OAuth 2.1 + PKCE against https://biomate.ai, writes the MCP server entry into the right host config file, and stashes a refresh token in your OS keychain.

Supported surfaces

| Surface | Install command | Config file written | |---|---|---| | Claude Code | npx @biomate/connect claude-code | ~/.claude.json | | Claude Desktop | npx @biomate/connect claude-desktop | ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) | | Cursor | npx @biomate/connect cursor | ~/.cursor/mcp.json | | Codex CLI | npx @biomate/connect codex | ~/.codex/config.toml | | ChatGPT | npx @biomate/connect chatgpt | (Custom GPT — instructions printed) | | Open Claw | npx @biomate/connect open-claw | (hosted webhook — account linked) |

What you get

After connecting, your AI assistant has access to BioMate's 14-tool MCP surface:

• biomate_session — natural-language goal → streaming workflow run with phase/step/QC/findings events
• search_workflow + get_workflow_spec — discover from 2,455 indexed workflows
• run_workflow + get_run + cancel_run — fine control
• preview_file, export_report, recall_memory, upload_file, analyze_results, explain_error, query_database

Try it

Open your assistant and paste:

Screen aspirin and caffeine for hERG and CYP3A4 inhibition.

Run RNA-seq differential expression on these FASTQs:
  s3://biomate-demo/sample_R1.fq.gz, s3://biomate-demo/sample_R2.fq.gz
Compare treated vs control.

Look up UniProt P04637.

Privacy & security

• OAuth 2.1 + PKCE; tokens scoped per surface, revocable individually at https://biomate.ai/account/connectors
• Refresh tokens hashed at rest with HMAC-SHA256
• Access tokens are 30-minute JWTs; refresh tokens rotate on use (OAuth 2.1 §6.1)
• No telemetry beyond standard API logs

Development

npm install
npm run build
npm test

License

MIT