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.
Cytoscape 3 supports the following systems:
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.
On Linux, on the proxy configuration dialog box, fonts are clipped and messages are truncated.
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).
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.
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.
Your bug reports are very important to improve quality of future versions of Cytoscape 3. If you notice any problems, please report them from:
We need your feedback to improve Cytoscape 3! Please send your questions and comments to our mailing list.