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Cytoscape MCP Server — Tutorial

Introduction

This tutorial walks through the complete workflow of connecting Claude Desktop to Cytoscape Desktop via the MCP server and using it to load a biological network from NDEx as the current view.

Prerequisites:

  • Cytoscape 3.10+ installed and running
  • Cytoscape MCP Server app installed (see User Manual)
  • MCP enabled Agent such as Claude or Codex installed.

Step 1: Verify the MCP Server is Running

After Cytoscape starts, look at the bottom-left corner of the Cytoscape window. You should see a bold MCP button:

  • Green label — the server started successfully and is ready.
  • Red label — the server is not responding. Check that CyREST is active and the mcp.http_port setting in Edit > Preferences > Properties > cytoscapemcp matches Cytoscape's actual CyREST port.

You can also confirm via curl:

curl http://localhost:{rest.port}/mcp/health

Replace {rest.port} with the CyREST port shown in the Agent Configuration dialog. A {"status":"ok"} response confirms the server is ready. A "connection refused" error means Cytoscape is not running.

Step 2: Connect Agent

Click the MCP button in the bottom-left corner of Cytoscape to open the Agent Configuration dialog. It shows the current MCP endpoint URL and step-by-step instructions for your most agents.

Step 3: Use the tools from Agent

Invoking the MCP tools requires some prompt engineering to provide key words or phrases which will activate the LLM to choose usage of a tool. Check out MCPManifest.md which contains 3 to 4 examples of Prompt snippets on each tool's description as reference of how to trigger LLM activation.

  • an example of a simple prompt which will lead the LLM to reason over the available tools as a whole and orchestrate their usage as building blocks into a sequence to reach the requested end result:
 > open a network in cytoscape desktop

Step 4: Verify in Cytoscape

Switch to Cytoscape Desktop. The loaded network should be visible in the Network panel and rendered in the main canvas.

Changing the NDEx Server (Optional)

If you are using a custom NDEx instance, update the base URL via Edit > Preferences > Properties > cytoscapemcp and set mcp.ndexbaseurl to your server's URL. Changes take effect immediately for subsequent tool calls.

What's Next?

Explore the other available tools — ask your agent to:

  • List all networks loaded in Cytoscape desktop
  • Change the active network view to a different network
  • Apply a different layout in Cytoscaep desktop