1. Introduction

This version of Cytoscape builds upon the new 3.x architecture, developer API and set of user controls established. If you’re familiar with former versions of Cytoscape, this version will feel completely familiar and you’ll be all set to go. 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.

If you would prefer to learn by doing, consider starting with the Basic Expression Analysis Tutorial.

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:// website.