For convenience, Cytoscape shows Welcome Screen at startup timewhich provides easy way to access sample data sets and public databases.
Edge Bend is now a standard Visual Property. You can use it as a part of your Visual Style.
You can bundle edges by automatic Edge Bundling. This feature is useful for dense network views.
You can add notes and simple shapes to background or foreground of network view.
From this version, EnhancedSearch plugin is part of core. You can search networks using Lucene syntax.
By selecting Show All option in Data Table Browser, you can display all network objects in the table. Nodes and edges will be selected when you select associated rows in the table.
Cytoscape 3 manages networks based on Network Collection. When you load networks to Cytoscape, you can choose creating a new set of networks or adding them to existing collection.
User manual for Cytoscape 3 is available here.
You can run Cytoscape 3 on Java 6 or 7. However, there are several problems if you use OpenJDK. Please use Oracle JRE/JDK or Apple Java Virtual Machine.
If you run Cytoscape on Mac OS X 10.7.5+ and 10.8+, you need to disable Gatekeeper before running the installer.
This version of Cytoscape is still in beta status and your bug reports are very important to improve the quality of final version of Cytoscape 3. If you notice any problems, please report them from:
We need your feedback to improve Cytoscape 3! Please send your questions and comments to our mailing list.