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mcp/harbor
Zed

BioMapper for Zed

io.github.trentleslie/biomapper

Resolve metabolite, lipid, protein, gene and lab names to knowledge-graph IDs.

client:Zed transport:stdio runtime:pypi

Install BioMapper in Zed

~/.config/zed/settings.json · windows: %APPDATA%\Zed\settings.json

Held in this page only — never stored, logged, or sent anywhere but back to your screen. 

{
  "context_servers": {
    "biomapper": {
      "command": "uvx",
      "args": [
        "biomapper"
      ],
      "env": {
        "BIOMAPPER_MCP_ROOTS": "<BIOMAPPER_MCP_ROOTS>",
        "BIOMAPPER_API_KEY": "<BIOMAPPER_API_KEY>",
        "BIOMAPPER_BASE_URL": "<BIOMAPPER_BASE_URL>",
        "BIOMAPPER_MCP_HOME": "<BIOMAPPER_MCP_HOME>"
      }
    }
  }
}

Merge this into your existing settings object — do not replace the file. Zed docs

BioMapper in other clients

BioMapper MCP server