Cytoscape Advanced Tutorials

Some of the most interesting functionality available with Cytoscape comes from external plugins, which can be developed by anyone with a certain degree of Java programming skill.

This set of web pages contains a set of tutorials for advanced operation of Cytoscape, especially using selected plugins. Before starting these tutorials, we recommend that you first run through the introductory tutorials. While all of the introductory tutorials can be executed using Java Web Start, the advanced tutorials cannot, due to the redistribution terms of many of the plugin user agreements. Note that all plugins covered in these tutorials are freely available, as is Cytoscape.

To execute the advanced tutorials, you will first need to install Cytoscape (and any required plugins) on your local system. The Cytoscape manual includes instructions for installing Cytoscape. All plugins described are available through the Cytoscape plugins page. Most plugins can be installed by downloading the plugin JAR files and copying them to the plugins subdirectory of your Cytoscape directory. For some plugins, special download links are provided, detailing specific installation steps. Each tutorial lists the required plugins, and outlines the installation procedure in detail.

Note that for those interested in developing plugins, there is a tutorial on writing Cytoscape plugins.

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 and suggestions, please post to the cytoscape-discuss mailing list.

Advanced Tutorials

Tutorial 5: Literature Searching

Tutorial 6: Gene Ontology

Tutorial 7: Modules and Complexes

Tutorial 8: Public Web Services