Cytoscape Desktop MCP server

[gradle]: https://gradle.org/ [java]: https://www.oracle.com/java/index.html [git]: https://git-scm.com/ [make]: https://www.gnu.org/software/make [cytoscape]: https://cytoscape.org/ [mcp]: https://modelcontextprotocol.io/ [ndex]: https://www.ndexbio.org/

Cytoscape MCP Server

An embedded [Model Context Protocol (MCP)][mcp] server for [Cytoscape Desktop][cytoscape], packaged as a Cytoscape App. AI clients such as Claude Desktop connect to Cytoscape over HTTP and invoke tools that control the desktop application directly — loading networks, setting active views, and more.

NOTE: This app is experimental. The interface and available tools are subject to change.

Architecture

How It Works

Once installed, the app publishes an MCP endpoint inside Cytoscape's existing CyREST HTTP server — AI clients connect to the MCP endpoint with Streamable HTTP transport and call MCP tools which drive activity on the Cytoscape desktop display.

The app also adds two visual indicators to the Cytoscape Desktop UI:

MCP toolbar button

a bold MCP button in the bottom-left status bar. The label is green when the MCP server is running and red when it is not. Clicking it opens the Agent Configuration dialog which displays the full MCP url and connection instructions for all supported agents.

Task History entries

every MCP tool invocation is recorded in Cytoscape's Task History panel (View > Show Task History), so you can see exactly which tools an agent called and when.

AI Agent──► HTTP──► http://localhost:{rest.port}/mcp ──► Cytoscape Desktop
                                                               └── load network from NDEx or file
                                                               └── get loaded network views
                                                               └── set current network view
                                                               └── create network view

Requirements

• [Cytoscape][cytoscape] 3.10 or above
• Internet connection (for loading networks from [NDEx][ndex])
• An MCP-compatible AI client that also supports the Streamable HTTP transport(not SSE which is deprecated as of 02/2025) (e.g. Claude Desktop)

Try it!

Install from the Cytoscape App Store (recommended)

Install Cytoscape MCP Server from the App Store — this is the MCP server itself, and everything else on this page depends on it being installed and running:

Or from inside Cytoscape: Apps > App Manager, search for Cytoscape MCP Server, and install.

Install a JAR manually

Alternatively, get the app jar:

• Download the latest cytoscape-mcp-.jar from the Releases page.
• or Build the jar

Then:

1. Open Cytoscape Desktop.
2. Navigate to Apps > App Manager > Install from File.
3. Select the file path to the MCP App JAR and restart Cytoscape if prompted.

After startup, the MCP status can be viewed via the MCP button in the status bar.

Connecting an Agent to Cytoscape Desktop MCP

See docs/AgentConfiguration.md for step-by-step setup instructions for Claude Desktop, Claude Code, GitHub Copilot (VS Code), GitHub Copilot CLI, and OpenAI Codex CLI.

Shortened. The full README is on GitHub.