SERVER

ensembl-mcp-server

Rank #4,804

io.github.cyanheads/ensembl-mcp-server

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

12 versions

3 GitHub stars

by cyanheads (135 servers)View repository ↗Claim this server

First listed

Jun 5, 2026

Last publish date

Sep 19, 2026

OVERVIEW

ensembl-mcp-server is a Model Context Protocol (MCP) server published by cyanheads. It ranks #4,804 of 132,046 servers tracked on MCP Toplist, and its repository has 3 GitHub stars. ensembl-mcp-server is listed across 3 registries — Official MCP, PulseMCP and Glama, with 12 tracked versions. It was first listed on Jun 5, 2026 and most recently updated on Sep 19, 2026.

STANDING

#4,804of 132,046 tracked serversTop 5%

Ranks ahead of 127,242 of 132,046 servers on MCP Toplist.

CONNECT

Use ensembl-mcp-server

No setupRuns out of the box

No credentials or required configuration declared — add it to your MCP client and go.

Remote · HTTP

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

npm package

claude mcp add ensembl-mcp-server -e "ENSEMBL_BASE_URL=<your ENSEMBL_BASE_URL>" -e "MCP_LOG_LEVEL=<your MCP_LOG_LEVEL>" -- npx -y @cyanheads/ensembl-mcp-server run start:stdio

Replace each placeholder with your own value before saving.

npm package

claude mcp add ensembl-mcp-server -e "ENSEMBL_BASE_URL=<your ENSEMBL_BASE_URL>" -e "MCP_HTTP_HOST=<your MCP_HTTP_HOST>" -e "MCP_HTTP_PORT=<your MCP_HTTP_PORT>" -e "MCP_HTTP_ENDPOINT_PATH=<your MCP_HTTP_ENDPOINT_PATH>" -e "MCP_AUTH_MODE=<your MCP_AUTH_MODE>" -e "MCP_LOG_LEVEL=<your MCP_LOG_LEVEL>" -- npx -y @cyanheads/ensembl-mcp-server run start:http

Replace each placeholder with your own value before saving.

Remote · HTTP

[mcp_servers.ensembl-mcp-server]
url = "https://ensembl.caseyjhand.com/mcp"

Add to ~/.codex/config.toml.

npm package

[mcp_servers.ensembl-mcp-server]
command = "npx"
args = ["-y", "@cyanheads/ensembl-mcp-server", "run", "start:stdio"]

[mcp_servers.ensembl-mcp-server.env]
ENSEMBL_BASE_URL = "<your ENSEMBL_BASE_URL>"
MCP_LOG_LEVEL = "<your MCP_LOG_LEVEL>"

Add to ~/.codex/config.toml. Replace each placeholder with your own value before saving.

npm package

[mcp_servers.ensembl-mcp-server]
command = "npx"
args = ["-y", "@cyanheads/ensembl-mcp-server", "run", "start:http"]

[mcp_servers.ensembl-mcp-server.env]
ENSEMBL_BASE_URL = "<your ENSEMBL_BASE_URL>"
MCP_HTTP_HOST = "<your MCP_HTTP_HOST>"
MCP_HTTP_PORT = "<your MCP_HTTP_PORT>"
MCP_HTTP_ENDPOINT_PATH = "<your MCP_HTTP_ENDPOINT_PATH>"
MCP_AUTH_MODE = "<your MCP_AUTH_MODE>"
MCP_LOG_LEVEL = "<your MCP_LOG_LEVEL>"

Add to ~/.codex/config.toml. Replace each placeholder with your own value before saving.

Remote · HTTP

https://ensembl.caseyjhand.com/mcp

Settings → Connectors → “Add custom connector”, then paste this URL.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to claude_desktop_config.json (Settings → Developer → Edit Config). Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:http"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to claude_desktop_config.json (Settings → Developer → Edit Config). Replace each placeholder with your own value before saving.

Remote · HTTP

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

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project).

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project). Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:http"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (per project). Replace each placeholder with your own value before saving.

Remote · HTTP

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

Save as .vscode/mcp.json in your workspace.

npm package

{
  "servers": {
    "ensembl-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Save as .vscode/mcp.json in your workspace. Replace each placeholder with your own value before saving.

npm package

{
  "servers": {
    "ensembl-mcp-server": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:http"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Save as .vscode/mcp.json in your workspace. Replace each placeholder with your own value before saving.

Remote · HTTP

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

Add to ~/.codeium/windsurf/mcp_config.json.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json. Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:http"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Add to ~/.codeium/windsurf/mcp_config.json. Replace each placeholder with your own value before saving.

Remote · HTTP

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

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:stdio"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Replace each placeholder with your own value before saving.

npm package

{
  "mcpServers": {
    "ensembl-mcp-server": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server",
        "run",
        "start:http"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "<your ENSEMBL_BASE_URL>",
        "MCP_HTTP_HOST": "<your MCP_HTTP_HOST>",
        "MCP_HTTP_PORT": "<your MCP_HTTP_PORT>",
        "MCP_HTTP_ENDPOINT_PATH": "<your MCP_HTTP_ENDPOINT_PATH>",
        "MCP_AUTH_MODE": "<your MCP_AUTH_MODE>",
        "MCP_LOG_LEVEL": "<your MCP_LOG_LEVEL>"
      }
    }
  }
}

Replace each placeholder with your own value before saving.

BADGE

Show your rank

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Markdown

[![MCP Toplist](https://mcptoplist.com/badge/io.github.cyanheads%2Fensembl-mcp-server.svg)](https://mcptoplist.com/server/io.github.cyanheads%2Fensembl-mcp-server)

HTML

<a href="https://mcptoplist.com/server/io.github.cyanheads%2Fensembl-mcp-server"><img src="https://mcptoplist.com/badge/io.github.cyanheads%2Fensembl-mcp-server.svg" alt="MCP Toplist: Top 5% of 132,046" /></a>

Variants: append ?metric=score or ?metric=stars to the image URL.

REGISTRIES

Listed on 3 registries

Official MCP

PulseMCP

Glama

ORGANIZATION

cyanheads

Organization

cyanheads

Servers in org

135

Versions across org

2337

Other servers by cyanheads

View all cyanheads servers →

VERSIONS

Available versions (12)

Version	Published
0.4.4	Sep 19, 2026
0.4.3	Aug 22, 2026
0.4.2	Jul 9, 2026
0.4.1	Jul 9, 2026
0.4.0	Jul 3, 2026
0.3.0	Jul 3, 2026
0.2.0	Jun 22, 2026
0.1.5	Jun 20, 2026
0.1.4	Jun 12, 2026
0.1.3	Jun 7, 2026
0.1.2	Jun 6, 2026
0.1.1	Jun 5, 2026

FAQ

Frequently asked questions

Who maintains ensembl-mcp-server?: ensembl-mcp-server is maintained by cyanheads, which publishes 135 MCP servers (2337 total versions) tracked on MCP Toplist.
Is ensembl-mcp-server listed on the Official MCP Registry?: Yes — ensembl-mcp-server is listed on the Official MCP Registry, alongside PulseMCP and Glama.
How many versions does ensembl-mcp-server have?: MCP Toplist tracks 12 versions of ensembl-mcp-server, most recently published on Sep 19, 2026.
Where can I find the source code for ensembl-mcp-server?: The source code for ensembl-mcp-server is hosted at github.com/cyanheads/ensembl-mcp-server.

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