SERVER

Cytoscape Desktop MCP

Rank #11,937

io.github.cytoscape/cytoscape-desktop-mcp-bridge

Drive a running Cytoscape Desktop to load, lay out, and style biological networks.

1 version

7 GitHub stars

by cytoscape (1 servers)View repository ↗Claim this server

First listed

Apr 30, 2026

Last publish date

Aug 11, 2026

OVERVIEW

Cytoscape Desktop MCP is a Model Context Protocol (MCP) server published by cytoscape. It ranks #11,937 of 132,046 servers tracked on MCP Toplist, and its repository has 7 GitHub stars. Cytoscape Desktop MCP is listed across 2 registries — Official MCP and Glama, with 1 tracked version. It was first listed on Apr 30, 2026 and most recently updated on Aug 11, 2026.

STANDING

#11,937of 132,046 tracked serversTop 10%

Ranks ahead of 120,109 of 132,046 servers on MCP Toplist.

CONNECT

Use Cytoscape Desktop MCP

No setupRuns out of the box

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

claude mcp add cytoscape-desktop-mcp-bridge -e "CYREST_PORT=<your CYREST_PORT>" -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge

Replace each placeholder with your own value before saving.

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

[mcp_servers.cytoscape-desktop-mcp-bridge]
command = "npx"
args = ["-y", "@cytoscape/cytoscape-desktop-mcp-bridge"]

[mcp_servers.cytoscape-desktop-mcp-bridge.env]
CYREST_PORT = "<your CYREST_PORT>"

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "<your CYREST_PORT>"
      }
    }
  }
}

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "<your CYREST_PORT>"
      }
    }
  }
}

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

{
  "servers": {
    "cytoscape-desktop-mcp-bridge": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "<your CYREST_PORT>"
      }
    }
  }
}

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "<your CYREST_PORT>"
      }
    }
  }
}

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

MCP bundle

Published as mcp bundle `https://github.com/cytoscape/cytoscape-desktop-mcp/releases/download/mcpb-v1.0.3/cytoscape-mcp.mcpb` — install it through your client’s extension manager.

npm package

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "<your CYREST_PORT>"
      }
    }
  }
}

Replace each placeholder with your own value before saving.

BADGE

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Markdown

[![MCP Toplist](https://mcptoplist.com/badge/io.github.cytoscape%2Fcytoscape-desktop-mcp-bridge.svg)](https://mcptoplist.com/server/io.github.cytoscape%2Fcytoscape-desktop-mcp-bridge)

HTML

<a href="https://mcptoplist.com/server/io.github.cytoscape%2Fcytoscape-desktop-mcp-bridge"><img src="https://mcptoplist.com/badge/io.github.cytoscape%2Fcytoscape-desktop-mcp-bridge.svg" alt="MCP Toplist: Top 10% of 132,046" /></a>

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

REGISTRIES

Listed on 2 registries

ORGANIZATION

cytoscape

Organization

Servers in org

1

Versions across org

1

VERSIONS

Available versions (1)

Version	Published
1.0.3	Aug 11, 2026

FAQ

Frequently asked questions

Who maintains Cytoscape Desktop MCP?: Cytoscape Desktop MCP is maintained by cytoscape, which publishes 1 MCP server (1 total version) tracked on MCP Toplist.
Is Cytoscape Desktop MCP listed on the Official MCP Registry?: Yes — Cytoscape Desktop MCP is listed on the Official MCP Registry, alongside Glama.
How many versions does Cytoscape Desktop MCP have?: MCP Toplist tracks 1 version of Cytoscape Desktop MCP, most recently published on Aug 11, 2026.
Where can I find the source code for Cytoscape Desktop MCP?: The source code for Cytoscape Desktop MCP is hosted at github.com/cytoscape/cytoscape-desktop-mcp.

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