Allen Brain MCP Server: Install & Setup

Install Allen Brain in Claude Code

Remote URL

Claude Code

claude mcp add --transport http allen-brain https://gateway.pipeworx.io/allen-brain/mcp

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

{
  "mcpServers": {
    "allen-brain": {
      "url": "https://gateway.pipeworx.io/allen-brain/mcp"
    }
  }
}

npm

Claude Code

claude mcp add allen-brain -- npx -y @pipeworx/mcp-allen-brain

mcp.json (Claude Desktop, Cursor, VS Code, Windsurf)

{
  "mcpServers": {
    "allen-brain": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-allen-brain"
      ]
    }
  }
}

Frequently asked questions

What does the Allen Brain MCP server do?

Gene expression experiments and the brain structure ontology from the Allen Institute's Brain…

Is the Allen Brain MCP server free?

Yes, most likely. Open source and no paid account or API key is mentioned in the listing. Check the provider for current pricing.

Does Allen Brain run locally or remotely?

Local + Remote. Can run locally or be used as a hosted remote server.

How do I add Allen Brain to Claude Code?

Run: claude mcp add --transport http allen-brain https://gateway.pipeworx.io/allen-brain/mcp

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