Cytoscape Desktop MCP Server

by cytoscape Your server? Claim it

local only

Cytoscape Desktop MCP runs on your own machine — the client starts it, so there is no endpoint to ping. 38 installs a week from npm. Last commit 1 Sep 2026.

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

Installs per day peak 11 · avg 4 · -12% w/w

a month agotoday

Installs / week

npm · @cytoscape/cytoscape-desktop-mcp-bridge

Stars

3 open issues

1 Sep 2026

Last commit

no releases in 90 days

BSD-3-Clause

License

Java

Nothing serious here today

Today is the operative word: we check Cytoscape Desktop MCP every 15 minutes and re-read its code on every release. Watch it and you find out the day that stops being true.

Connect this server

This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.

Claude Code Claude Desktop Codex Cursor VS Code

run in your terminal

claude mcp add cytoscape-desktop-mcp-bridge -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge

~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ]
    }
  }
}

~/.codex/config.toml

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

.cursor/mcp.json

{
  "mcpServers": {
    "cytoscape-desktop-mcp-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ]
    }
  }
}

.vscode/mcp.json

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

Optional settings from the registry entry, left out of the block above: CYREST_PORT (Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)).

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Cytoscape Desktop MCP — questions

Answers built from our own checks of this server.

Why is there no uptime for Cytoscape Desktop MCP?

Cytoscape Desktop MCP runs on your own machine over stdio — there is no network address to reach, so uptime cannot be measured for it by anyone. What can be measured is adoption: the npm package @cytoscape/cytoscape-desktop-mcp-bridge was installed 38 times last week.

How do I connect Cytoscape Desktop MCP?

Copy the ready config from this page. We generate it for Claude Code, Claude Desktop, Codex, Cursor and VS Code, each in the form that client actually reads. It runs locally, so the command pulls @cytoscape/cytoscape-desktop-mcp-bridge straight from npm; nothing to host, nothing to sign up for.

How many people use Cytoscape Desktop MCP?

The npm package @cytoscape/cytoscape-desktop-mcp-bridge was installed 38 times in the last week. Week over week that is -12%. We show installs rather than GitHub stars on purpose: a star is a bookmark, an install is someone actually running it.

Is Cytoscape Desktop MCP open source?

Yes — it is published under the BSD-3-Clause licence, written in Java, 8 stars on GitHub and 3 open issues. The source link is on this page, so you can read exactly what it does with your data before you connect it.