Cytoscape Desktop MCP

Name: Cytoscape Desktop MCP
Author: cytoscape

by cytoscapeversion 1.0.3i★ 8iRuns on your computer

Registry nameio.github.cytoscape/cytoscape-desktop-mcp-bridge

How to install

Overview

Description from the maker (original English)

Drive a running Cytoscape Desktop to load, lay out, and style biological networks.

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Other

Install

Pick the AI app you use, then copy the settings.

Passed 2/2 checks · Runs on your computer

First: which AI do you use?

ClaudeWeb · app · phoneChatGPTWebClaude CodeTerminalCursorCode editorVS CodeCode editorOtherOther apps

Pick your app and the steps appear below.

Works with Claude, with some setup first

No key, nothing to install · Only the Claude desktop app (Windows or Mac), not the web or phone

Download the maker’s installer
Download the maker’s .mcpb file
The .mcpb file comes straight from the maker; we do not change it
Done
Double-click the file, then click Install in the Claude desktop app
Done
Try it
Use Cytoscape Desktop MCP and tell me what you can do for me, then show me one thing
✓ If Claude says it is using Cytoscape Desktop MCP or shows a Cytoscape Desktop MCP tool in the answer, you are connected

Menu names checked against Anthropic’s help page on Nov 11, 2026 · your screen may differ slightly by app version

ChatGPT cannot connect Cytoscape Desktop MCP yet

Cytoscape Desktop MCP runs on your computer, but ChatGPT can only connect servers that run on the web

What you can do instead

A · Use an app that can connect Cytoscape Desktop MCP

Steps for Claude →No key, nothing to install · Only the Claude desktop app (Windows or Mac), not the web or phone
Steps for Claude Code →You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)
Steps for Cursor →You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)
Steps for VS Code →You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)

B · Others in Other that work with ChatGPT

Picked from the most used in the same category, only ones that connect by address with no key

Hostinger✓ ChatGPT
World Monitor✓ ChatGPT
Svelte MCP✓ ChatGPT

Works with Claude Code, with some setup first

You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)

Install Node.js
One time only; it works for every server that needs Node.js
Open the Node.js download page ↗
Done
Sign up and create a Cytoscape Desktop MCP key
Open the maker’s site, sign up and create an API key for the next step. It may cost money.
Open the Cytoscape Desktop MCP site ↗
Done
Open Terminal
Mac: press Command+Space and type Terminal · Windows: open PowerShell
Done
4
Paste this command and press Enter
```
claude mcp add cytoscape-desktop-bridge --env CYREST_PORT=your-value -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge
```
Replace “your-value” with your key before pressing Enter
Paste the key only into the app’s field, never into a chat or to anyone
Done
Type /mcp in Claude Code
You should see Cytoscape Desktop MCP listed as connected
Done
Try it
Use Cytoscape Desktop MCP and tell me what you can do for me, then show me one thing
✓ If Claude Code says it is using Cytoscape Desktop MCP or shows a Cytoscape Desktop MCP tool in the answer, you are connected

Menu names checked against Anthropic’s help page on Nov 11, 2026 · your screen may differ slightly by app version

Works with Cursor, with some setup first

You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)

Install Node.js
One time only; it works for every server that needs Node.js
Open the Node.js download page ↗
Done
Sign up and create a Cytoscape Desktop MCP key
Open the maker’s site, sign up and create an API key for the next step. It may cost money.
Open the Cytoscape Desktop MCP site ↗
Done
Click this button to open Cursor
Open in Cursor
Cursor asks you to confirm; click Install
Done
Fill in your key
In the Cytoscape Desktop MCP settings, CYREST_PORT is empty; add your key and save
Paste the key only into the app’s field, never into a chat or to anyone
Done
Open the AI chat in Cursor in Agent mode
Done
Try it
Use Cytoscape Desktop MCP and tell me what you can do for me, then show me one thing
✓ If Cursor says it is using Cytoscape Desktop MCP or shows a Cytoscape Desktop MCP tool in the answer, you are connected

Menu names checked against Cursor’s help page on Nov 11, 2026 · your screen may differ slightly by app version

Works with VS Code, with some setup first

You need a Cytoscape Desktop MCP key (sign up on the maker’s site, may cost money) · Install Node.js on your computer first (one time)

Install Node.js
One time only; it works for every server that needs Node.js
Open the Node.js download page ↗
Done
Sign up and create a Cytoscape Desktop MCP key
Open the maker’s site, sign up and create an API key for the next step. It may cost money.
Open the Cytoscape Desktop MCP site ↗
Done
Click this button to open VS Code
Open in VS Code
VS Code asks you to confirm; click Install
Done
Fill in your key
In the Cytoscape Desktop MCP settings, CYREST_PORT is empty; add your key and save
Paste the key only into the app’s field, never into a chat or to anyone
Done
Open the AI chat in VS Code in Agent mode
Done
Try it
Use Cytoscape Desktop MCP and tell me what you can do for me, then show me one thing
✓ If VS Code says it is using Cytoscape Desktop MCP or shows a Cytoscape Desktop MCP tool in the answer, you are connected

Menu names checked against VS Code’s help page on Nov 11, 2026 · your screen may differ slightly by app version

Other apps that use MCP, such as Windsurf, Zed or Gemini CLI, each add servers differently. See how in the app list.

See every app that uses MCP →

JSON settings are under “For developers” below

Stuck? Ask people who use Cytoscape Desktop MCP💬 Discussion →

For developers: Terminal commands and JSON settings

Installed on your computer

Claude Code

claude mcp add cytoscape-desktop-bridge --env CYREST_PORT=your-value -- npx -y @cytoscape/cytoscape-desktop-mcp-bridge

Claude Desktop (claude_desktop_config.json)

{
  "mcpServers": {
    "cytoscape-desktop-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "your-value"
      }
    }
  }
}

Cursor (~/.cursor/mcp.json)

{
  "mcpServers": {
    "cytoscape-desktop-bridge": {
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "your-value"
      }
    }
  }
}

VS Code (mcp.json)

{
  "servers": {
    "cytoscape-desktop-bridge": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cytoscape/cytoscape-desktop-mcp-bridge"
      ],
      "env": {
        "CYREST_PORT": "your-value"
      }
    }
  }
}

Values you fill in

CYREST_PORT env
Port Cytoscape Desktop's REST interface listens on (Edit > Preferences > REST API)

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

At a glance

GitHub stars i: 8
Downloads per weeki: 38/wk
Licence i: No licence stated
Connection: Runs on your computer
Transport: stdio
Latest versioni: 1.0.3
Categoryi: Other
Published to registryi: Aug 12, 2026
Code last changedi: Sep 1, 2026
Maker: cytoscape
Packages: mcpb: https://github.com/cytoscape/cytoscape-desktop-mcp/releases/
npm: @cytoscape/cytoscape-desktop-mcp-bridge
Repo: cytoscape/cytoscape-desktop-mcp
Website: github.com
Registry status: Active

Which apps can use it

Based on how this server connects and on each app’s own docs, checked Nov 10, 2026.

Run on your computer in

Claude Goose LM Studio Msty Studio Cherry Studio Cursor VS Code + GitHub Copilot Visual Studio Windsurf (Devin Desktop)Zed Kiro Cline Continue JetBrains AI Assistant Claude Code Codex CLI Gemini CLI OpenCode nodecode Warp LibreChat Raycast

All apps, with pros and cons →

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 11, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account cytoscape, which owns the repo
✓ Pass
Still maintained
Code last changed 2 months ago
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Discussion

Ask, share a tip or report that it does not work. Sorted by what people marked helpful.

No posts yet. Be the first to ask or share.

Posts here are written by users, not the PopNx team.

User reviews

No reviews yet

Compared with others in Otheri

More stars than 96% of the other 19193 servers in this category
Published to the registry more recently than 19% of the other 19193 servers in this category
Basic checks equal to or better than 100% of the other 19193 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is Cytoscape Desktop MCP safe?

It passed 2 of 2 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed 2 months ago, and the latest version (1.0.3) reached the registry 3 months ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need MCPB, Node.js on your computer.

What can I use instead?

In the same category: World Monitor, Claude Flow, Tldraw

Alternatives

Servers in the same category from other makers, sorted by stars.

Reading a card:↓ Downloads per weeki★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

World Monitor

Real-time global intelligence on conflict, markets, energy, trade, shipping and cyber. 102 tools.

by koala73Widely used★ 90.5KUpdated 6 days ago

Runs in the cloud✓ worldmonitor.app

Install

Claude Flow

AI orchestration with hive-mind swarms, neural networks, and 87 MCP tools for enterprise dev.

by ruvnetWidely used↓ 13.5K/wk★ 81.4KUpdated 14 months ago

Runs on your computer

Install

Tldraw

Draw and visually collaborate with your agents on tldraw's canvas.

by tldrawWidely used★ 51.4KUpdated 8 months ago

Runs in the cloud

Install

README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

Cytoscape MCP Server

An embedded Model Context Protocol (MCP) server for Cytoscape Desktop, 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 3.10 or above
Internet connection (for loading networks from 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:

https://apps.cytoscape.org/apps/cytoscapemcpserver

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:

Open Cytoscape Desktop.
Navigate to Apps > App Manager > Install from File.
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.

Cytoscape Desktop MCP Diagnostics

Most agents will have a /mcp command or UI settings panel which will show status of connection to the MCP server and a list of tools currently published by this server, check to see if it is denoted as 'connected'.
Check the MCP health endpoint

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

Replace {rest.port} with Cytoscape's CyREST port (shown in the Agent Configuration dialog). You should see {"status":"ok","transport":"mcp-streamable-http"}. A "connection refused" error means Cytoscape is not running or the port is wrong.

Use external MCP introspection tools against the Desktop MCP server running at http://localhost:{rest.port}/mcp to validate or view current tools catalog - modelcontextprotocol/inspector

Building from source

If you want to build the app jar directly from source instead of using release jars.

Requirements:

Java 17 with JDK
Git
Make

git clone https://github.com/cytoscape/cytoscape-desktop-mcp

cd cytoscape-desktop-mcp make install

The JAR is produced at build/libs/cytoscape-mcp- .jar.

For a full list of build targets:

make help

Release tags

Two components ship from this repo on separate tag namespaces:

Component	Tag	Produces
Cytoscape App (the MCP server)	`vX.Y.Z`	`cytoscape-mcp- .jar`, plus a convenience copy of the `.mcpb`
MCPB bridge (`claude-extension/`)	`mcpb-vX.Y.Z`	`cytoscape-mcp.mcpb`, and publishes to npm and the MCP Registry

The bridge is versioned independently of the app because the bridge is distinctly separate deliverable with separate source tree for it to provide a stdio-to-http transport bridge that some agents may use. See registry/README.md for the release runbook.

Cytoscape Desktop MCP Tool Catalog

The MCP server provides a human-readable catalog of every tool registered on the server formatted as Markdown with complete MCP Protocol JSON schema definitions for each tool's input and output. You can obtain the catalog through multiple options:

When the app is loaded in Desktop, at runtime the MCP server exposes /mcp/manifest endpoint which can be retrieved by browser or command line

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

After any build locally, make build will generate the MCP manifest based on current code into a static file at build/generated/manifest/MCPManifest.md for same review.
Static copy of the catalog is also stored in repo at MCPManifest.md

Activate Cytoscape Desktop MCP tools from Agent prompts:

Invoking the 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 using cytoscape desktop

Cytoscape Desktop MCP Configuration properties

Properties are editable at runtime via Edit > Preferences > Properties > cytoscapemcp:

Property	Default	Description
`mcp.ndexbaseurl`	`https://www.ndexbio.org`	NDEx base URL (takes effect immediately)

Documentation

Full documentation is in the docs/ directory:

Agent Configuration — connecting Claude Desktop, Claude Code, GitHub Copilot, Codex CLI, and others
User Manual — configuration reference and available tools
Tutorial — end-to-end walkthrough: install, connect, load a network
FAQ — common questions and troubleshooting

COPYRIGHT AND LICENSE

Click here

Acknowledgements

TODO: denote funding sources

Cytoscape Desktop MCP

Overview

What you can do with it

Install

Download the maker’s installer

Double-click the file, then click Install in the Claude desktop app

Try it

What you can do instead

Install Node.js

Sign up and create a Cytoscape Desktop MCP key

Open Terminal

Paste this command and press Enter

Type /mcp in Claude Code

Try it

Install Node.js

Sign up and create a Cytoscape Desktop MCP key

Click this button to open Cursor

Fill in your key

Open the AI chat in Cursor in Agent mode

Try it

Install Node.js

Sign up and create a Cytoscape Desktop MCP key

Click this button to open VS Code

Fill in your key

Open the AI chat in VS Code in Agent mode

Try it

Installed on your computer

Values you fill in

At a glance

Which apps can use it

Related guides

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Discussion

User reviews

Compared with others in Otheri

Common questions

Alternatives

World Monitor

Claude Flow

Tldraw

README from the maker

Cytoscape MCP Server

Architecture

How It Works

MCP toolbar button

Task History entries

Requirements

Try it!

Install from the Cytoscape App Store (recommended)

Install a JAR manually

Connecting an Agent to Cytoscape Desktop MCP

Cytoscape Desktop MCP Diagnostics

Building from source

Release tags

Cytoscape Desktop MCP Tool Catalog

Activate Cytoscape Desktop MCP tools from Agent prompts:

Cytoscape Desktop MCP Configuration properties

Documentation

COPYRIGHT AND LICENSE

Acknowledgements