Cytoscape Developer's Documents
Introduction to Cytoscape 2.6 Architecture
CytoscapeRetreat2008/DeveloperTutorial - Introduction to Cytoscape graph model, view, vizMap and more.
How to Develop Plugins
Cytoscape_Plugin_Tutorial - General introduction to plugin development
Plugin Developer Cookbook - A list of sample plugins to show how to use various Cytoscape functionality.
Plugin_Download_Site_Tutorial - How to create your own plugin property file for Plugin manager