New Features in Cytoscape 3

Updated Welcome Screen

For convenience, Cytoscape shows Welcome Screen at startup timewhich provides easy way to access sample data sets and public databases.

Edge Bend Visual Property

Edge Bend is now a standard Visual Property. You can use it as a part of your Visual Style.

Edge Bundling

You can bundle edges by automatic Edge Bundling. This feature is useful for dense network views.

Network Annotations

You can add notes and simple shapes to background or foreground of network view.

Advanced Search Function

From this version, EnhancedSearch plugin is part of core. You can search networks using Lucene syntax.

Show All feature in Data Table Browser

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.

Network Collection

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

System Requirments

Cytoscape 3 supports the following systems:


  • Windows XP and newer. 64 Bit version is recommended due to memory size problem
  • 64 bit version of Windows 7 or newer is recommended
  • Latest version of Java 6 or 7 from Oracle. OpenJDK and other implementations are not tested


  • Mac OS X 10.5 and later
  • Latest version of Apple Java 6 or Java 7 from Oracle
  • Latest version of Java is required. Please install all system/Java updates before installing Cytoscape 3. Cytoscape does not start on older versions of Apple Java 6


  • Tested on Ubuntu 11.x and 12.x, but may work on other distributions
  • Latest version of JDK 6 or 7 from Oracle is recommended. Not tested on OpenJDK.
  • 64 bit version distributions with latest version of Oracle JDK is recommended

Known Issues

Java Versions

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.

Windows XP Problems

For Windows XP systems running on PCs having more than 1GB RAM, attempting to start Cytoscape may fail (as shown in the picture below).

Windows XP Warning

To solve the problem, execute the gen_vmoptions.bat file to calibrate the memory allocation configured in the Cytoscape.vmoptions file so it does not exceed 800MB.

Installation Problem on Mac OS X Lion and Mountain Lion

From Mac OS X 10.7.5, default security option is set to allow applications only from Apple's App Store. If you try to install Cytoscape 3 with the default setting, you will see the following warning message:

Mac Security Warning

To avoid this problem, you need to change your system's security setting. From System Preferences, you need to change Allow applications downloaded from option to Anywhere.

Mac change security

How to Report Bugs

Your bug reports are very important to improve quality of future versions of Cytoscape 3. If you notice any problems, please report them from:

Help → Report a bug...

Need Help?

We need your feedback to improve Cytoscape 3! Please send your questions and comments to our mailing list.

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