Cytoscape_3/AppDeveloper

Cytoscape 3.0 App Development

Introduction

Cytoscape 3.0 has a greatly simplified API that is clearly defined. API jars are strictly separate from the implementation jars. We believe that we’ve learned our lessons with 2.x and have greatly improved the usability of the API to benefit our active developer community. The API is versioned using the Semantic Versioning standard. This means that an app designed to work with an early version of 3.x will be guaranteed to work through at least version 4.0 of Cytoscape. Our commitment to supporting app developers is stated in an explicit backwards compatibility contract found in each class in the public API so that both core developers and app writers will understand how a class might change.

Architecture and Technologies

• Architecture

• We’ve introduced a few new technologies to 3.0 to help solve many of our existing problems. OSGi is a java based module system. We’ve introduced the use of OSGi as a way to create and enforce a modular code base. We’ve introduced Maven as a build system to help manage the many jar files created.

API and Javadocs

• API

• Javadocs

Porting a 2.x Plugin to a 3.0 App

• How to port a 2.x Plugin to a 3.0 App

• List of Plugins Being Ported

Tutorials

• Introduction to Cytoscape 3 App Development

• Creating a Simple Cytoscape 3 App

• Creating an OSGi Bundle Cytoscape 3 App

• Cytoscape 3 App Cookbook

• Cytoscape 3 Architecture

TEMP

Getting Started

• Using Eclipse

• Using Command Line tools