Networks: Introduction to Cytoscape, Part 1

Erick Peirson's picture


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

You can download Cytoscape 3 from 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. 

Week 6: Introduction to Networks

Erick Peirson's picture

Modeling historical, philosophical, or sociological phenomena as networks can bring a powerful array of quantitative analytic techniques to bear on humanistic problems. But interpreting the results of those analyses in ways that are intellectually meaningful is not always straightforward. Networks can reveal previously unrecognized patterns in large systems, but they can also obscure significant patterns and even mislead. Understanding how networks are composed, and how they can be analyzed and visualized is crucial for knowing when network models are appropriate, and how to interpret the results of network-based scholarship.


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