Cytoscape Wiki
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
Cytoscape 3.0 strives for a modular architecture where the application consists of a set of jar files where each jar contributes a well defined subset of functionality to the application. The design is oriented around the OSGi service model (i.e. micro service) with API and implementation separated into different jar files. We’ve introduced the use of OSGi as a way to create and enforce a modular, sustainable code base. We’ve introduced Maven as a build system to help manage the many jar files created.
API and Javadocs
Porting a 2.x Plugin to a 3.0 App
Tutorials
TEMP