Release Notes for Cytoscape 3.9.1
About Version 3.9.1
Cytoscape 3.9.1 is a Cytoscape Desktop BugFix release, addressing the following issues:
- Updated log4j dependencies in core to 2.17.1 via pax-logging (1.11.13)
- Updated log4j dependencies to 2.17.1 in SBMLReader core app
- Automation: updates to annotation and app-related commands
- Minor fixes to table equations
Java 11 is Required -- Automatically Installed
For Windows and Mac users, the Cytoscape installer automatically downloads and installs Java 11 if it's not available on your workstation. For Linux, please use Java 11 as described below.
- Windows XP and newer (including Windows 7, 8 and 10). 64 bit version is recommended.
- Cytoscape installer automatically downloads a suitable Java 11 if none is available on your workstation. You can manually download and install latest version of
OpenJDK 11. Oracle Java and other implementations are not tested.
- Mac OS X 10.11 (El Capitan) and later
- Cytoscape installer automatically downloads a suitable Java 11 if none is available on your workstation. You can manually download and install latest version of OpenJDK 11.
- Tested on
Latest version of Java is required (minimum Java 11.0.6).
For Ubuntu, a simple way of installing the OpenJDK JVM is described
- Java 11 must be on the PATH (ahead of any other JVM) or referenced by JAVA_HOME environment variable.
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.
We need your feedback to improve Cytoscape 3! Please send your questions and comments to our