# genefoundry

Routes 22 biomedical MCP servers through one HTTP endpoint and lets an agent discover tools by search. Use it for sources such as gnomAD, ClinVar, HPO, and VEP.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 6
- Author: berntpopp
- License: MIT · policy=link-only · description only; the file stays with the author
- Source: https://github.com/berntpopp/genefoundry-router
- Updated: 2026-10-24
- HTML: https://affpapa.org/en/nevibecode/mcp/genefoundry

## What it does

genefoundry puts 22 biomedical backends behind a single MCP connection. The agent does not receive a flat catalog of 285 tools: it searches with `search_tools`, then runs a selected namespaced tool through `call_tool`. Each backend can also expose a pinned entry point, which keeps its main operation reachable without relying on search ranking.

The router acts as a client for the backends and leaves their data unchanged. A hosted Streamable HTTP endpoint is available, so Claude Code can connect with `claude mcp add --transport http genefoundry https://genefoundry.org/mcp`. Running a private instance requires Python 3.14+, `uv`, backend URLs in `.env`, and `GF_AUTH_MODE`. This is for research use only, not clinical decision support, diagnosis, treatment, triage, or patient management.

## Requirements
- Remote server: `https://genefoundry.org/mcp`

## Install

### Claude Code (native platform)

**Platform CLI: remote server**
```bash
claude mcp add --transport http genefoundry https://genefoundry.org/mcp
```

### Codex

**Platform CLI: remote server**
```bash
codex mcp add genefoundry --url https://genefoundry.org/mcp
```

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "genefoundry": {
            "url": "https://genefoundry.org/mcp"
        }
    }
}
```

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "genefoundry": {
            "type": "http",
            "url": "https://genefoundry.org/mcp"
        }
    }
}
```

### Gemini CLI

**Platform CLI: remote server**
```bash
gemini mcp add -t http genefoundry https://genefoundry.org/mcp
```

## When to use it
- search the gnomAD backend for variant frequencies
- retrieve a variant’s clinical significance from ClinVar
- look up phenotype associations through HPO
- find variant consequence tools in VEP
- connect multiple biomedical MCP backends through one endpoint

## Example prompts
- Use `search_tools` to find a ClinVar tool for a variant, then call the matching result.
- Search with `search_tools` for population frequency data in gnomAD and run the returned tool.
- Use `search_tools` to locate an HPO tool for phenotype associations.

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NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md