Connect BioMate to the AI tools you already use — Claude Code, Claude Desktop, Cursor, Codex, ChatGPT, Slack, and WeChat — and run real bioinformatics pipelines without leaving your chat window. Also connect your lab instruments (Illumina, Nanopore, CryoEM, LC-MS, and more) so data flows automatically into the right pipeline the moment a run finishes.
> Screen aspirin and caffeine for hERG inhibition and CYP3A4 metabolism.
> Run RNA-seq differential expression on s3://my-bucket/fastqs/, treated vs control.
> Refine this cryo-EM stack with CryoSPARC homogeneous refinement, C2 symmetry.
BioMate finds the right pipeline from 2,455 indexed workflows, fills the parameters, launches on BioMate cloud, and streams live progress back to your assistant. No copy-pasting commands. No waiting for a dashboard to refresh.
npx @biomate/connect claude-codePick your surface, authenticate once via your browser, and you're done. The CLI writes the MCP config for you and stores your token in the OS keychain.
| Surface | Command |
|---|---|
| Claude Code | npx @biomate/connect claude-code |
| Claude Desktop | npx @biomate/connect claude-desktop |
| Cursor | npx @biomate/connect cursor |
| Codex CLI | npx @biomate/connect codex |
| ChatGPT | See connectors/chatgpt/INSTALL.md |
| Slack | See connectors/slack/README.md |
| WeChat / Open Claw | npx @biomate/connect open-claw |
connectors/ Per-surface install guides, MCP config snippets, and the @biomate/connect CLI
lab_instruments/ Lab instrument connectors (Illumina, Nanopore, CryoEM, LC-MS, and 6 more)
oauth_server/ OAuth 2.1 + PKCE authorization server (self-hostable)
mcp/ Shared MCP tools manifest and server — the single source of truth for all surfaces
skills/biomate/ Claude Skill bundle for the Anthropic Skills gallery
tests/ Connector test suites (offline sandbox + live API + 68 lab instrument checks)
Connect physical instruments so raw data is routed automatically to the right BioMate workflow the moment a run finishes — no manual upload, no copy-pasting paths.
| Instrument | File | Trigger |
|---|---|---|
| Illumina BaseSpace | lab_instruments/illumina_basespace_connector.py |
New run via BaseSpace API |
| Oxford Nanopore MinKNOW | lab_instruments/nanopore_minknow_connector.py |
Run complete via MinKNOW HTTP API |
| CryoEM EPU | lab_instruments/cryoem_instrument_connector.py |
New .mrc/.mrcs micrographs in output dir |
| LC-MS | lab_instruments/lcms_connector.py |
New .raw/.d/.wiff files (Thermo, Bruker, Waters, SCIEX) |
| Flow Cytometer | lab_instruments/flow_cytometer_connector.py |
New .fcs files (BD, Beckman, Sony) |
| qPCR | lab_instruments/qpcr_connector.py |
New .eds (QuantStudio) or .pcrd (Bio-Rad CFX) |
| Plate Reader | lab_instruments/plate_reader_connector.py |
New .xlsx exports (BioTek, Molecular Devices) |
| Opentrons OT-2/Flex | lab_instruments/opentrons_connector.py |
Protocol complete via robot HTTP API |
| Benchling ELN | lab_instruments/benchling_connector.py |
New entry or assay result via Benchling API |
| SiLA2 devices | lab_instruments/sila2_adapter.py |
gRPC events (Hamilton, Sartorius, etc.) |
Quick start — copy config.example.yaml (in lab_instruments/), fill in your instrument details, and run:
pip install -r requirements.txt
python3 lab_instruments/instrument_watcher.py --config config.yamlBioMate exposes 17 tools across three tiers.
| Tool | What it does |
|---|---|
biomate_session |
The main one. Describe your goal; BioMate picks the workflow, fills params, runs on BioMate cloud, and streams progress back. |
upload_file |
Get a presigned S3 URL to upload a local file before running a workflow. |
export_report |
Download the findings report (PDF / DOCX) after a run completes. |
Beyond the lite set, you get workflow primitives (search_workflow, get_workflow_spec, run_workflow, get_run, cancel_run, list_runs), output tools (preview_file, analyze_results, explain_error), database access (query_database), memory (recall_memory), and data connectors (resolve_accession, browse_data, fetch_public_data).
See connectors/README.md for the full tool reference.
The goal parameter in biomate_session is plain English — one to three sentences. Include:
- What — the analysis type (
ADMET screening,RNA-seq DE,variant calling,cryo-EM refinement) - Data — inline SMILES/sequences,
s3://paths, GEO/SRA accession numbers, or upload first withupload_file - Key parameters — organism, comparisons, thresholds, symmetry, strand orientation — anything that matters
You can omit anything BioMate can reasonably infer. It will ask if something is genuinely ambiguous.
Examples that work well:
Screen aspirin (CC(=O)Oc1ccccc1C(=O)O) and caffeine (Cn1cnc2c1c(=O)n(c(=O)n2C)C)
for hERG inhibition, CYP3A4 liability, and oral bioavailability.
RNA-seq differential expression on s3://lab-bucket/exp42/fastqs/ — human GRCh38,
dUTP strand-specific, treated (n=3) vs control (n=3), FDR threshold 0.05.
Whole-genome variant calling on the uploaded FASTQ pair, GRCh38,
GATK HaplotypeCaller, germline mode.
Fetch GSE183947 from GEO and run the same RNA-seq DE pipeline.
Run CryoSPARC homogeneous 3D refinement on s3://cryo/job042/, C2 symmetry, box 256.
BioMate connectors use an API key (or OAuth 2.1 + PKCE for browser-based surfaces).
Generate an API key:
- Go to biomate.ai → Settings → API Keys
- Click New key, give it a name, and copy the value — it's only shown once
- Set it in your environment:
export BIOMATE_API_KEY=bm_live_...
Test your key:
curl -H "X-API-Key: $BIOMATE_API_KEY" https://app.biomate.ai/api/tools/ping
# → {"status": "ok", "user": "you@example.com"}For Claude Desktop / Cursor / Codex (MCP config):
{
"mcpServers": {
"biomate": {
"command": "python3",
"args": ["-m", "mcp.biomate_mcp_server"],
"env": {
"BIOMATE_API_URL": "https://app.biomate.ai",
"BIOMATE_API_KEY": "bm_live_..."
}
}
}
}If you're integrating BioMate into your own infrastructure, the OAuth 2.1 + PKCE server in oauth_server/ is self-contained and runnable independently.
pip install -r requirements.txt
python -m oauth_serverSee oauth_server/oauth/server.py for configuration options.
- OAuth 2.1 + PKCE — no shared secrets, no passwords stored
- Per-surface scope grants, individually revocable at biomate.ai/account/connectors
- Refresh tokens hashed at rest (HMAC-SHA256) and rotated on every use
- 30-minute JWT access tokens
- Privacy policy: biomate.ai/legal/privacy — what the connector sends to BioMate, and how it is used, stored, shared, and retained. Source:
connectors/legal/privacy.md. - Terms of service: biomate.ai/terms
- Support: support@biomate.ai · biomate.ai/support
MIT — for the connector code in this repository. BioMate platform usage is governed by biomate.ai/terms.
Questions? support@biomate.ai