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Keiichiro Ono (University of California, San Diego, USA)Cytoscape is a standard software package for biological network visualization. The latest version, 2.8.1, has useful new features such as Custom Graphics and Attribute Functions that greatly enhance Cytoscape visualization and analysis capabilities. Today, there more than 100 third-party plugins for Cytoscape. As the Cytoscape ecosystem grows new problems are introduced including the ability for plugins to communicate and library conflicts between plugins. Although Cytoscape users can use multiple plugins at once, communication between plugins is challenging. Plugins can also become incompatible with new versions of Cytoscape because of library version conflicts and API changes. Cytoscape 3.0 was designed to solve these problems. By using a modular architecture based on Spring and OSGi we open the doors to plugin communication and isolate library version conflicts. This architecture also provides a clear separation of API and implementation, which coupled with semantic versioning practices go a long way towards eliminating backwards compatibility problems.