# Cytoscape Desktop MCP

Connects an AI agent to a running Cytoscape Desktop to load, arrange, and style biological networks when network work needs agent control.

- MCP server · `type=mcp` · Claude Code, Codex, Cursor, GitHub Copilot, Windsurf (Devin Desktop), Cline, Zed, Gemini CLI · ★ 8
- Author: cytoscape
- License: BSD-3-Clause · policy=link-only · description only; the file stays with the author
- Source: https://github.com/cytoscape/cytoscape-desktop-mcp
- Updated: 2026-09-01
- HTML: https://affpapa.org/en/nevibecode/mcp/cytoscape-desktop-mcp

## What it does

Cytoscape Desktop MCP lets an AI client operate a running Cytoscape Desktop through HTTP. Its tools can load a network from NDEx or a file, inspect loaded views, select the active view, and create another view. The server also supports layout and styling work on biological networks.

The MCP server ships as a Cytoscape app and exposes an endpoint through the existing CyREST HTTP service. A status-bar MCP button shows whether the server is active, while Cytoscape’s Task History records each tool call. You can inspect health at `http://localhost:{rest.port}/mcp/health` and retrieve the tool catalog from `http://localhost:{rest.port}/mcp/manifest`.

Cytoscape Desktop 3.10 or newer is required, along with an MCP client that supports Streamable HTTP. Loading networks from NDEx needs an internet connection. If Cytoscape is stopped or `CYREST_PORT` points to the wrong port, the connection fails; the server interface is experimental and subject to change.

## Requirements
- Needs: Node.js (commands run via npx)
- Environment variables: `CYREST_PORT` — keys and tokens: ask the human for the values, never commit them or put them in shared files.

## Install

### Claude Code (native platform)

**Platform CLI**
```bash
claude mcp add --env CYREST_PORT=<CYREST_PORT> --transport stdio cytoscape-desktop-mcp -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge
```
Replace <…> with your own values

### Codex

**Platform CLI**
```bash
codex mcp add cytoscape-desktop-mcp --env CYREST_PORT=<CYREST_PORT> -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge
```
Replace <…> with your own values

### Cursor

**Config file**
File `.cursor/mcp.json`:
```json
{
    "mcpServers": {
        "cytoscape-desktop-mcp": {
            "command": "npx",
            "args": [
                "-y",
                "@cytoscape/cytoscape-desktop-mcp-bridge"
            ],
            "env": {
                "CYREST_PORT": "<CYREST_PORT>"
            }
        }
    }
}
```
Replace <…> with your own values

### GitHub Copilot

**Config file**
File `.vscode/mcp.json`:
```json
{
    "servers": {
        "cytoscape-desktop-mcp": {
            "type": "stdio",
            "command": "npx",
            "args": [
                "-y",
                "@cytoscape/cytoscape-desktop-mcp-bridge"
            ],
            "env": {
                "CYREST_PORT": "<CYREST_PORT>"
            }
        }
    }
}
```
Replace <…> with your own values

### Gemini CLI

**Platform CLI**
```bash
gemini mcp add -e CYREST_PORT=<CYREST_PORT> cytoscape-desktop-mcp npx -y @cytoscape/cytoscape-desktop-mcp-bridge
```
Replace <…> with your own values

## When to use it
- load a network from NDEx or a local file
- inspect the views available for a network
- switch Cytoscape to the requested network view
- create an additional network view
- review agent tool calls in Task History

## Example prompts
- Open a biological network in Cytoscape Desktop and prepare its current view.
- Load a network from NDEx, then switch to the view used for analysis.
- Create another view for the loaded network and arrange it for inspection.

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