Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.
Cytoscape 3 is the mainstream version of Cytoscape with modular architecture. It is designed for long-term maintainability and it replaced 2.x series. It is a Java desktop application designed for large-scale network analysis and visualization. New features, including new user interfaces, advanced visualization functions, headless (command-line) distribution, RESTful API, and multiple rendering engine support, will be released for this version. As of May 2016, transition from Cytoscape 2.x to 3.x is complete, and 2.x is no longer supported. If you really need to use Plugins only available for 2.x, you may use Cytoscape 2.8.3, but otherwise, please use the latest version of Cytoscape 3.x series.
Cytoscape 3.5 Desktop