Introduction

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:

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.