Cytoscape Desktop MCP Server
by cytoscapeio.github.cytoscape/cytoscape-desktop-mcp-bridgev1.0.3
Drive a running Cytoscape Desktop to load, lay out, and style biological networks.
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Maintained39d ago
Install Cytoscape Desktop MCP server
Install in Claude Code
claude mcp add cytoscape-desktop-mcp-bridge -- npx -y @cytoscape/cytoscape-desktop-mcp-bridgeInstall in Cursor
{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"command": "npx",
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
]
}
}
}Add to ~/.cursor/mcp.json (global) or .cursor/mcp.json (project).
Install in Claude Desktop
{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"command": "npx",
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
]
}
}
}Settings → Developer → Edit Config (claude_desktop_config.json), then restart.
Install in VS Code
{
"servers": {
"cytoscape-desktop-mcp-bridge": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
]
}
}
}Add to .vscode/mcp.json in your workspace.
Install in Windsurf
{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"command": "npx",
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
]
}
}
}Add to ~/.codeium/windsurf/mcp_config.json.
Configuration
| Variable | Required | Secret | Description |
|---|---|---|---|
| CYREST_PORT | — | — | Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API) |
Freshness
Maintained — last maintenance signal 39d ago. The newest of the signals below sets the band.
Last commit (default branch)
2026-09-01 · 39d ago · GitHub
Latest release
2026-09-01 · 39d ago · GitHub · 1.0.3
Package published
no data · npm/PyPI
Registry entry updated
2026-08-11 · 59d ago · official registry · v1.0.3
FAQ
›How do I install the Cytoscape Desktop MCP server in Claude Code?
Run: claude mcp add cytoscape-desktop-mcp-bridge -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge. For Cursor, VS Code, Claude Desktop and Windsurf, use the install tabs above.
›Does Cytoscape Desktop require an API key?
No required environment variables are declared in its published metadata.
›Can I use Cytoscape Desktop as a remote (hosted) MCP server?
No hosted endpoint is published; it runs locally over stdio.
›Is Cytoscape Desktop in the official MCP registry?
Yes, as io.github.cytoscape/cytoscape-desktop-mcp-bridge.