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, for compliance with the
redistribution terms of many plugins' 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, to detailing specific
installation steps. Each tutorial lists the required plugins, and outlines
the installation procedure in detail.
Note that for those interested in writing 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, suggestions, or shouts of pure joy, please contact Melissa Cline
at cline (at) pasteur.fr, or post to the
cytoscape-discuss list.