Cytoscape 3.0 has a clearly defined, simplified API. API jars are strictly separate from the implementation jars. We 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 the API won't change throughout 3.x, so an app designed to work with an early version of 3.x will be guaranteed to work up to 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.

For a jumpstart to app development, see the Cytoscape App Ladder.

And the Javadocs are here: Javadocs