Once installed, the app publishes an MCP endpoint inside Cytoscape's existing CyREST HTTP server — Agents connect to the MCP url on CyREST as remote HTTP transport and then call MCP tools which will drive activity on the Cytoscape desktop display.
[User Manual](https://github.com/cytoscape/cytoscape-desktop-mcp/blob/main/docs/UserManual.md)
[MCP Tool Manifest](https://github.com/cytoscape/cytoscape-desktop-mcp/blob/1.0.0/MCPManifest.md)
**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.
**Agent MCP Configuration**:
See [Tutorial](https://github.com/cytoscape/cytoscape-desktop-mcp/blob/main/docs/AgentConfiguration.md) for step-by-step instructions on how to configure various Agents like Claude Desktop, Claude Code, GitHub Copilot CLI, and OpenAI Codex CLI to connect to the Cytoscape Desktop as an MCP server.
