Cytoscape 3.0 is a cleaner and modular new generation of Cytoscape for future expansions. It benefits both users and developers.

Cytoscape 3 Desktop

New Features

Cytoscape 3 has new features including: Edge Bundling, Network Collections, Visual Annotations, Advanced Search, and Improved Data Table Browser.

Learn more about new features ›

App Store

You can install Apps directly from Cytoscape App Store.

Visit Cytoscape App Store ›

What is Cytoscape 3.0?

Cytoscape 3.0 is the latest version of Cytoscape, which introduces a whole new architecture, developer API and set of user controls. Cytoscape 3.0 represents a major redesign from the ground up, toward the goal of provide a stable, extensible, high-performance platform for network visualization and analysis. The initial Beta Release will introduce users to the new interfaces and features we've been working on:
  • New welcome screen and toolbar for quick access to common actions
  • New Data Table controls to interface with your data
  • Integrated support for graphical annotations in networks
  • Support for independent sets of networks within a single session
  • Advanced network and table import controls
  • Improved architecture and API for a more stable experience
  • Cut/Copy/Paste of nodes and edges
  • Metanode support in the core
  • Context menus for improved usability

Apps for Cytoscape 3.0

You can install Cytoscape 3 Apps directly from new Cytoscape App Store. Please visit apps.cytoscape.org.

Report Bugs

We need your help to improve quality of Cytoscape 3. You can report a bug from Help → Report a Bug.... Or, click this button:

Developer Documents

Cytoscape 3 is an open-source platform and source code is hosted on Github.