Cytoscape Tutorial Introduction

Cytoscape is an open-source package for the visualization and analysis of biological network data. Cytoscape's core functionality includes methods for automated graph layout, integrating network data with other data such as expression data and Gene Ontology annotations, and setting visual attributes according to node or edge attributes. In addition, Cytoscape offers an open plugin architecture, allowing anyone to add functionality by writing a plugin, and maintains a library of available third-party plugins. There are currently plugins available for topics such as literature searching and module detection.

These pages contain a set of tutorials to serve as an introduction to Cytoscape and its plugins. The first group describes Cytoscape's core functionality. Using Java Web Start, you may run these tutorials on your personal computer without any need to install Cytoscape. Be aware that there are security issues with Java Web Start, as we have described on a related page. Java Web Start should work by default after it is installed on Windows and Mac OSX. On Linux, some extra set-up steps may be required.

A second group of tutorials describes the advanced operation of Cytoscape, with an emphasis on selected plugins. While all the plugins described are freely available, many require a user agreement, some of which preclude redistribution. Thus, Java Web Start is not available for this group, although instructions are provided for installing Cytoscape and its plugins on your local computer.

You may want to glance at the Cytoscape manual while running these tutorials.

The following web browsers are supported for these tutorials:

Netscape 5.0 or later
Internet Explorer 5.0 or later
Mozilla 6.0 or later

For comments or suggestions, please post to the cytoscape-discuss mailing list.

Basic Cytoscape Tutorials

Tutorial 1: Getting Started

Tutorial 2: Filters & Editor

Tutorial 3: Fetching External Data

Tutorial 4: Expression Analysis