Release Notes for Cytoscape 3.1.1

About Version 3.1.1

Cytoscape 3.1.1 is a bug-fix release of Cytoscape 3.x series. This is a mainstream release of Cytoscape 3 and is recommended for all users.

Major Bug Fixes

The following major issues have been fixed in Cytoscape 3.1.1.

For complete list of fixed bugs, please visit our issue tracker web site. More details are available in the last section of Welcome Letter.

System Requirements

Important: Cytoscape 3.1.1 is not compatible with Java 8. Please use Java 6 or 7 instead.

Cytoscape 3.1.1 supports the following systems:


  • Windows XP and newer (including Windows 7 and 8). 64 bit version is recommended for larger networks.
  • Latest version of Java 6 or 7 from Oracle. OpenJDK and other implementations are not tested.
  • Note that the website installs a 32 bit JVM by default (to match Windows’ 32 bit browsers). To download a 64 bit JVM, use this page.


  • Mac OS X 10.7 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 CentOS 6, Fedora 19/20, and Ubuntu 12.x/13.x/14.x, but may work on other distributions
  • Latest version of Java 6 or 7 from Oracle, or latest version of OpenJDK 7. Earlier versions of OpenJDK are not tested.
  • For Ubuntu, a simple way of installing the Oracle JVM is described here.

User Manual

Known Issues

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.


The latest privacy policy is posted here.

Proxy Settings

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

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.

Deprecating Support for 32 bit OSs and Java 6

While v3.1 has both 32 bit OS and Java 6 support, we plan to remove support for these configurations in Cytoscape v3.2, which is under development and will likely be released in the later third of 2014. This matches current industry practice, and allows us to focus our resources on more advanced feature development. Once v3.2 is released, we will continue to make previous Cytoscape versions available, and they will continue to have 32 bit OS and Java 6 support.

Missing Edge Columns After Loading Multiple Networks

When loading multiple networks into the same network collection, it is important to import edge tables only after each of the networks is loaded. Interspersing edge table imports with network loads may cause edge columns to become inaccessible to some networks. Node columns are unaffected by this issue.

Java 6 used on Mac, even with Java 7 installed

On the Mac platform, Java 6 will be used by default (and automatically installed if necessary), even if Oracle Java 7 is installed. To use Oracle Java 7, you will have to set the JAVA_HOME environment variable to the Java 7 installation path.

To do this automatically on startup, add the following line to the .bashrc file in your home directory:

export JAVA_HOME=$(/usr/libexec/java_home)

And the following to the .profile file in your home directory:

if [ -f ~/.bashrc ]; then
  source ~/.bashrc

Note that this only applies to Cytoscape instances launched from the command line using the script - Java 7 is not supported when launching from the GUI. This issue will be resolved in a future release.

File Encoding

On all platforms, all Cytoscape session files recorded since v3.0.1 are 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).

Missing Organism Networks on Welcome Screen

Users upgrading from previous Cytoscape versions (e.g., 3.0.2) may notice that the Welcome Screen contains only six of the eight organism networks shown in the user manual. To add the two new networks, terminate Cytoscape, remove the biogrid directory in the CytoscapeConfiguration directory, and restart Cytoscape. For more information on the CytoscapeConfiguration directory, see Launching Cytoscape in manual.

Executing Scripts from Command Line

Executing Cytoscape command scripts using the -S (or —script) command line option may not work if an app does not start properly or no apps are installed. If you are experiencing this issue on a clean install of Cytoscape, installing a small app (such as Cy3PerformanceReporter) should resolve the problem. Additionally, relative file paths are not supported by -S/—script, nor are any paths with backslashes, spaces, or colons. As an alternative, command scripts can be executed using the Tools-Execute Command File menu item.

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...

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

Need Help?

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