Ensembl Mcp Server

MCP server · by cyanheads

Databases npmStreamable HTTP v0.7.1

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

View source ↗ Generate config for multiple servers More servers

Install

Pin version registry version 0.7.1

npm
npx -y @cyanheads/ensembl-mcp-server

npm
npx -y @cyanheads/ensembl-mcp-server@0.7.1

npm
npx -y @cyanheads/ensembl-mcp-server

npm
npx -y @cyanheads/ensembl-mcp-server@0.7.1

Streamable HTTP
https://ensembl.caseyjhand.com/mcp

Setup by client

Pick your client — the config below is generated for this server (both local and hosted-endpoint forms). Copy respects the “Pin version” switch above.

claude_desktop_config.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ]
    }
  }
}

Remote (hosted) endpoint

https://ensembl.caseyjhand.com/mcp

Claude Desktop: Settings → Connectors → Add custom connector, paste this URL.

Format verified against the official Claude Desktop docs ↗.

terminal

claude mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server

claude mcp add ensembl-mcp-server -- npx -y @cyanheads/ensembl-mcp-server@0.7.1

terminal

claude mcp add --transport http ensembl-mcp-server https://ensembl.caseyjhand.com/mcp

Format verified against the official Claude Code docs ↗.

.cursor/mcp.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ]
    }
  }
}

.cursor/mcp.json (hosted endpoint)

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Format verified against the official Cursor docs ↗.

.vscode/mcp.json

{
  "servers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

{
  "servers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ]
    }
  }
}

.vscode/mcp.json (hosted endpoint)

{
  "servers": {
    "ensembl-mcp-server": {
      "type": "http",
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Format verified against the official VS Code docs ↗.

mcp_config.json

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ]
    }
  }
}

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server@0.7.1"
      ]
    }
  }
}

mcp_config.json (hosted endpoint)

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "serverUrl": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Format verified against the official Windsurf docs ↗.

Environment variables

Defined in the server's official registry manifest. Required secrets are shown as <YOUR_…> placeholders in the configs above.

ENSEMBL_BASE_URL — Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_LOG_LEVEL — Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').
MCP_TRANSPORT_TYPE — Selects the HTTP transport.
MCP_HTTP_HOST — The hostname for the HTTP server.
MCP_HTTP_PORT — The port to run the HTTP server on.
MCP_HTTP_ENDPOINT_PATH — The endpoint path for the MCP server.
MCP_AUTH_MODE — Authentication mode to use: 'none', 'jwt', or 'oauth'.

GitHub

⭐ 3 stars · 最近更新于 29 天前 · Apache-2.0 license

About this server

@cyanheads/ensembl mcp server Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP. 7 Tools • 4 Resources • 1 Prompt…

Summary from the project README — github.com/cyanheads/ensembl-mcp-server

Distributed as npm, Streamable HTTP, listed under Databases. Review our MCP security guide before granting access to real data.

Frequently asked questions

What does the Ensembl Mcp Server MCP server do?

How do I install Ensembl Mcp Server?

Run the install command shown above, then paste the config for your client (Claude Desktop, Claude Code, Cursor, VS Code or Windsurf) into its MCP settings and restart the client.

Is Ensembl Mcp Server free to use?

The MCP server itself is free to install. The source is public on https://github.com/cyanheads/ensembl-mcp-server. Any third-party service it calls may require its own API key and account.

Which clients support Ensembl Mcp Server?

Any MCP-compatible client can use it, including Claude Desktop, Claude Code, Cursor, VS Code, Windsurf and custom agents.

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