Cytoscape Desktop MCP runs on your own machine — the client starts it, so there is no endpoint to ping. 31 installs a week from npm. Last commit 1 Sep 2026.
Drive a running Cytoscape Desktop to load, lay out, and style biological networks.
What the code does
We read the source, 1 h ago · rules 3dff92dd89df
What this server is able to do. For an MCP server this is often the job itself — a terminal server runs commands because that is what it is for. Listed so you know what you are plugging in, not as an accusation.
этот файл ставится пользователю, но в репозитории его нет
Is this your server and something here is wrong? Tell us — corrections are free and do not require a plan.
This code can reach further than it looks
We found places where it runs commands, builds paths or queries from values it is given. None of that is a flaw by itself — it becomes one when the code changes, and code changes quietly between releases. We re-read it on every one.
Connect this server
This server runs on your own machine — install it with the package manager and the client starts it for you. Package name taken from the official registry entry.
claude mcp add cytoscape-desktop-mcp-bridge -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
],
"command": "npx"
}
}
}[mcp_servers.cytoscape-desktop-mcp-bridge]
command = "npx"
args = ["-y", "@cytoscape/cytoscape-desktop-mcp-bridge"]{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
],
"command": "npx"
}
}
}{
"mcpServers": {
"cytoscape-desktop-mcp-bridge": {
"args": [
"-y",
"@cytoscape/cytoscape-desktop-mcp-bridge"
],
"command": "npx"
}
}
}This one needs environment variables set before it will start:
CYREST_PORT (Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)).
The author declared them in the registry entry; get the values from the project itself.
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Cytoscape Desktop MCP — questions
Answers built from our own checks of this server.