Release Notes for Cytoscape 3.0.1

Cytoscape 3.0.1 is the latest version of Cytoscape 3.x series with a lot of bug fixes. This is the first mainstream version of Cytoscape 3 recommended for all users. There is no major new features in this version, but we strongly recommend to upgrade if you use 3.0.0.

Learn more about new features introduced in 3.0

User Manual

System Requirments

Cytoscape 3 supports the following systems:


  • Windows XP and newer. 64 Bit version is recommended for larger networks
  • 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.

Proxy Settings

On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.

File Encoding

On all platforms, all Cytoscape session files are now encoded in UTF-8 instead of the native language encoding. This makes session files portable between workstations in all locales. Users in Japan, Korea, and China are most affected – existing v3.0.0 or v2.x session files must be translated to UTF-8 using a platform-dependent editor (which most users are already using for this purpose). Users in Europe and the Americas are affected, too, if they use characters beyond the standard ANSI 128 – they can translate to UTF-8 using a platform-dependent editor (e.g., Notepad for Windows).

Conflict with Older Versions

On all platforms, users installing Cytoscape directly from a ZIP or TAR file should manually clear the Cytoscape cache by deleting the CytoscapeConfiguration folder in the user’s home directory.

Internationalization (PDF Export)

For Japanese, Korean, and Chinese users, rendering a network to a PDF file can result in loss of labeling information in the PDF. As a workaround, users can generate any type of image file and use the image file instead.

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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