Release Notes for Cytoscape 3.0.2

Cytoscape 3.0.2 is the latest version of Cytoscape 3.x series with many bug fixes. This is a mainstream release of Cytoscape 3 and is recommended for all users.

User Manual

HTML (Wiki) version of Cytoscape 3 Manual

PDF version

System Requirements

Cytoscape 3 supports the following systems:


Windows 8

While Windows 8 is a 64 bit system, the web site installs a 32 bit JVM by default under the theory that it is important for the JVM to match Windows 8’s Internet Explorer browser (also 32 bit). For best results with Cytoscape, you should install the 64 bit JVM, available at this page.



For Linux, a simple way of installing the Oracle JVM is described here.

Known Issues

Mac and the Java Virtual Machine

There is a known issue with a recent Java update distributed by Apple -- it causes Cytoscape not to start up properly. This can occur even if you've installed the latest version of Oracle Java 7 as Cytoscape uses the Apple JVM. To find out if you have the problematic update, run the following command in a Terminal window:

/usr/libexec/java_home -v 1.6 -exec java -version

If the output contains “xM4508”, you have the broken version. In that case, you will need to install the latest update from Apple according to your OS version:

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.

Ubuntu and Java 7

Ubuntu 13.04 with Java 7 has known stability issues with Cytoscape 3.x - please use Java 6 or an earlier version of Ubuntu as a workaround.

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

Need Help?

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...

Or, you can directly report it from Report a bug link on the navigation bar.

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