Cytoscape Desktop MCP — Claude Code MCP server: install
Connects an AI agent to a running Cytoscape Desktop to load, arrange, and style biological networks when network work needs agent control.
claude mcp add --env CYREST_PORT=<CYREST_PORT> --transport stdio cytoscape-desktop-mcp -- npx -y @cytoscape/cytoscape-desktop-mcp-bridgeWhat Cytoscape Desktop MCP 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.
What it helps with
- 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 for the agent
- 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.
How to install Cytoscape Desktop MCP
Platform CLI
claude mcp add --env CYREST_PORT=<CYREST_PORT> --transport stdio cytoscape-desktop-mcp -- npx -y @cytoscape/cytoscape-desktop-mcp-bridgeReplace <…> with your own values
Platform CLI
codex mcp add cytoscape-desktop-mcp --env CYREST_PORT=<CYREST_PORT> -- npx -y @cytoscape/cytoscape-desktop-mcp-bridgeReplace <…> with your own values
Config file
{
"mcpServers": {
"cytoscape-desktop-mcp": {
"command": "npx",
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
],
"env": {
"CYREST_PORT": "<CYREST_PORT>"
}
}
}
}Replace <…> with your own values
Config file
{
"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
Platform CLI
gemini mcp add -e CYREST_PORT=<CYREST_PORT> cytoscape-desktop-mcp npx -y @cytoscape/cytoscape-desktop-mcp-bridgeReplace <…> with your own values
Step by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about Cytoscape Desktop MCP
How do I install Cytoscape Desktop MCP in Claude Code?
Run these commands in order: claude mcp add cytoscape-desktop-mcp-bridge -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge, then claude mcp add --env CYREST_PORT=<CYREST_PORT> --transport stdio cytoscape-desktop-mcp -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge.
What does Cytoscape Desktop MCP do?
It connects an MCP client with a running Cytoscape Desktop. The agent can then load networks, control their views, and inspect recorded tool calls.
What does Cytoscape Desktop MCP require?
Use Cytoscape Desktop 3.10 or newer and an MCP client with Streamable HTTP support. NDEx loading needs internet access, and the agent configuration needs the correct CYREST_PORT.
