Cytoscape 3.0.0 is the latest version of Cytoscape, which introduces a whole new architecture, developer API and set of user controls when compared with the 2.X series. Cytoscape 3.0.0 represents a major redesign from the ground up, toward the goal of providing a stable, extensible, high-performance platform for network visualization and analysis. That being said; if you're familiar with former versions of Cytoscape, this version will feel completely familiar and you'll be set to go directly
This manual describes the installation and use of Cytoscape. For a more thorough understanding of Cytoscape and its ecosystem, we highly recommend reading the Welcome Letter accessible on the http://cytoscape.org website.
This release introduces users to new interfaces and features:
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
In future releases, we will continue to tweak and improve both the software and the documentation. This manual will be updated to reflect all the latest changes.