For an introduction to Cytoscape 3 and overview of App development, see the related wiki pages. Here you will find detailed tutorials for developing Cytoscape Apps.
Cytoscape 3 User Tutorials
Introduction to Cytoscape 3: User Interface
Introduction to Cytoscape 3: Welcome Screen
Introduction to Cytoscape 3: Networks, Data, VizMapper, Layouts and App Manager
Introduction to Cytoscape 3.1: Networks, Data, Styles, Layouts and App Manager
Filtering and Editing in Cytoscape 3
Cytoscape 3 App Developer Tutorials
These tutorials are for developers either a) porting 2.x plugins to 3.x apps, or b) writing a new 3.x app from scratch. We hope they give developers an easy way to get started, with information up to date and all in one place. We assume that app developers have a working knowledge of Java programming, ant, Maven, Git, and optionally Eclipse.
Setup App Development Environment
Two types of App -- Simple App and Bundle App
Debug: Work with OSGi Console
Debug: Remote Execution for Debugging
Start Your App from Template -- Sample Apps
Start Your App from App Developer Template Project
Find Code Snippet in the Cookbook
Checkout Cytoscape Source Code from GitHub Repositories
Porting 2.x plugin to 3.0 App???
Submit Your App to Cytoscape App Store
Cytoscape 3 App Tutorials
Extend Biological Process with regulatory interactions