In this tutorial we will take our first steps visualizing and analyzing networks using Cytoscape. The Cytoscape user manual can be found here. References the the manual are made throughout the tutorial. Open Tutorials also has a series on Cytoscape 3 here.
Cytoscape was developed in 2002, with funding from the National Instute of General Med- ical Sciences and the National Resource for Network Biology. The primary user base is the biomedical research community, especially systems biologists who study gene or protein in- teraction networks and pathways. Cytoscape 3 provides a framework for developing “apps” or plug-ins that extend the program’s functionality; you can browse the Cytoscape App Store at http://apps.cytoscape.org/
You can download Cytoscape 3 from http://www.cytoscape.org. You’ll also need a spread- sheet application, such as Excel. OpenOffice or Numbers are perfectly acceptable alternatives, provided that you export your data to .xls, .xlsx, or .csv formats.