New Features in Cytoscape 3
Updated Welcome Screen
For convenience, Cytoscape shows Welcome Screen at
startup timewhich provides easy way to access sample data sets and public databases.
Edge Bend Visual Property
Edge Bend is now a standard Visual Property.
You can use it as a part of your Visual Style.
You can bundle edges by automatic Edge Bundling.
This feature is useful for dense network views.
You can add notes and simple shapes to background or foreground of network view.
Advanced Search Function
From this version, EnhancedSearch plugin is part of core.
You can search networks using Lucene syntax.
Show All feature in Data Table Browser
By selecting Show All option in Data Table Browser,
you can display all network objects in the
table. Nodes and edges will be selected when you select
associated rows in the table.
Cytoscape 3 manages networks based on Network Collection.
When you load networks to Cytoscape, you can choose
creating a new set of networks or adding them to existing collection.
Cytoscape 3 supports the following systems:
- Windows XP and newer. 64 Bit version is recommended due to memory size problem
- 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
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.
Windows XP Problems
For Windows XP systems running on PCs having more than 1GB RAM,
attempting to start Cytoscape may fail (as shown in the picture below).
To solve the problem, execute the gen_vmoptions.bat
file to calibrate the memory allocation configured in the
Cytoscape.vmoptions file so it does not exceed 800MB.
Installation Problem on Mac OS X Lion and Mountain Lion
From Mac OS X 10.7.5, default security option is set to
allow applications only from Apple's App Store. If you try to install
Cytoscape 3 with the default setting, you will see the following warning
To avoid this problem, you need to change your system's security setting.
From System Preferences, you need to change Allow applications
downloaded from option to Anywhere.
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...
We need your feedback to improve Cytoscape 3! Please send your questions and comments