Dendrite

Dendrite is an open-source, agentic biomedical discovery workbench. It converts a natural-language research question into:

• a live, evidence-attributed graph (diseases, targets, pathways, compounds, exposures)
• a mechanism-focused synthesis with citations, caveats, and next-step suggestions

This project is for research synthesis and hypothesis generation only. It is not for clinical decision-making.

What Dendrite Does

• Resolves query entities and relations from free text.
• Runs multi-hop retrieval across OpenTargets, Reactome, STRING, ChEMBL, PubMed/BioMCP, and Medical MCP.
• Streams run progress, warnings, and graph updates in real time.
• Preserves uncertainty: partial/contested connections remain visible instead of being overstated.
• Supports replayable canned runs for demos without requiring a live OpenAI key.

System Overview

• apps/web: Next.js app (UI + API orchestration routes).
• services/*: MCP services used as biomedical data providers.
• docker-compose.yml: local orchestration for MCP services and the web app.
• scripts/bootstrap-services.sh: clones/builds missing service repos.
• scripts/check-services.sh: quick endpoint/health checks.

Requirements

• Node.js >=20
• npm >=10
• Docker + Docker Compose
• OpenAI API key for live agentic runs (optional for replay mode)

Quick Start

1) Configure environment

cp .env.example .env

2) Bootstrap service repos (first-time setup)

./scripts/bootstrap-services.sh

3) Start the full stack in Docker

docker compose up --build -d web

web depends on MCP services, so this brings up the full stack.

4) Open the app

• http://localhost:3000

Local Web Development (optional)

If you want hot reload in apps/web:

1. Start only MCP backends in Docker.
2. Run the Next.js app locally.

docker compose up --build -d mcp-opentargets mcp-reactome mcp-string mcp-chembl mcp-pubmed mcp-medical biomcp
npm --prefix apps/web ci
npm --prefix apps/web run dev

Configuration

Core variables (see .env.example for the full list):

OPENAI_API_KEY=
MCP_TRANSPORT_MODE=auto
OPENTARGETS_MCP_URL=http://localhost:7010/mcp
REACTOME_MCP_URL=http://localhost:7020/mcp
STRING_MCP_URL=http://localhost:7030/mcp
CHEMBL_MCP_URL=http://localhost:7040/mcp
PUBMED_MCP_URL=http://localhost:7050/mcp
MEDICAL_MCP_URL=http://localhost:7060/mcp
BIOMCP_URL=http://localhost:8000/mcp

MCP_TRANSPORT_MODE values:

• auto (default)
• prefer_mcp
• fallback_only

Deployment (Vercel)

Use apps/web as the Vercel project root:

1. Import repository in Vercel.
2. Set Root Directory to apps/web.
3. Keep default Next.js commands (npm ci, npm run build).
4. Set environment variables needed for your deployment.

Notes:

• Local MCP URLs (localhost) do not work on Vercel; configure externally reachable endpoints or use fallback transport.

Validation

npm --prefix apps/web run lint
npm --prefix apps/web run build
./scripts/check-services.sh

Contributing

1. Create a branch from main.
2. Keep changes focused and include tests/checks where relevant.
3. Open a pull request with a clear summary, risk notes, and validation steps.

License

The Dendrite application code in this repository is licensed under Apache 2.0 (LICENSE).

Some directories under services/ are upstream projects with their own licenses. Check each service directory for license details.