Cytoscape WikiCytoscape is a Java application that runs on Linux, Windows, and Mac OS X.
System requirements: The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate. We recommend a recent computer (1GHz CPU or higher) with a high-end graphics card and at least 512MB of free physical RAM. Cytoscape expects a minimum screen resolution of 1024x768.
(1) If necessary, install Java
If not already installed on your computer, download and install Java SE 5 or 6. Cytoscape 2.4 will no longer run with Java version 1.4.x or lower. You must install Java SE 5 or 6!!!
These can be found at:
[http://java.sun.com/javase/downloads/index_jdk5.jsp Java SE 5]
[http://java.sun.com/javase/downloads/index.jsp Java SE 6]
(2) Install Cytoscape
There are a number of options for downloading and installing Cytoscape. All options can be downloaded from the [http://cytoscape.org] website.
- Automatic installation packages exist for Windows, Mac OS X, and Linux platforms.
- You can install cytoscape from a compressed archive distribution.
- You can build cytoscape from source.
You can check out the latest and greatest software from our [http://chianti.ucsd.edu/svn Subversion repository].
Cytoscape installations (regardless of platform) containing the following files and directories:
File |
Description |
cytoscape.jar |
Main Cytoscape application (Java archive) |
cytoscape.sh |
Script to run Cytoscape from command line (Linux, Mac OS X) |
cytoscape.bat |
Script to run Cytoscape (Windows) |
LICENSE.txt/html |
Cytoscape GNU LGPL License |
lib/ |
library jar files needed to run Cytoscape. |
docs/ |
Manuals in different formats. What you are reading now. |
licenses/ |
Licence files for the various libraries distributed with Cytoscape. |
plugins/ |
Directory containing cytoscape PlugIns, in .jar format. |
sampleData/ |
|
|
galFiltered.gml -- Sample molecular interaction network file * |
|
galFiltered.sif -- Identical network in Simple Interaction Format * |
|
galExpData.pvals -- Sample gene expression matrix file * |
|
galFiltered.nodeAttrTable.xls -- Sample node attribute file in Microsoft Excel format |
|
galFiltered.cys -- Sample session file created from datasets above plus GO Annotations * |
|
BINDyeast.sif -- Network of all yeast protein-protein interactions in the BIND database as of Dec, 2006 ** |
|
BINDhuman.sif -- Network of all human protein-protein interactions in the BIND database as of Dec, 2006 ** |
|
yeastHighQuality.sif -- Sample molecular interaction network file *** |
|
interactome_merged.networkTable.gz -- Human interactome network file in tab-delimited format **** |
* From Ideker et al., Science 292:929 (2001)
** Obtained from data hosted at http://www.blueprint.org/bind/bind_downloads.html
** From von Mering et al., Nature, 417:399 (2002) and Lee et al, Science 298:799 (2002)
**** Created from Cytoscape tutorial web page. Original data sets are available at: http://www.cytoscape.org/cgi-bin/moin.cgi/Data_Sets/ A merged human interactome by Andrew Garrow, Yeyejide Adeleye and Guy Warner Unilever, Safety and Environmental Assurance Center
(3) Launch the application
Double-click on the icon created by the installer or by running cytoscape.sh from the command line (Linux or Mac OS X) or double-clicking cytoscape.bat (Windows). Alternatively, you can pass the .jar file to Java directly using the command java -Xmx512M -jar cytoscape.jar -p plugins. The -Xmx512M flag tells java to allocate more memory for Cytoscape and the -p plugins option tells cytoscape to load all of the plugins in the plugins directory. Loading the plugins is important because many key features like layouts, filters and the attribute browser are included with Cytoscape as plugins in the plugins directory. See the Command Line chapter for more detail. In Windows, it is also possible to directly double-click the .jar file to launch it. However, this does not allow specification of command-line arguments (such as the location of the plugin directory).
Cytoscape Window When you succeed in launching Cytoscape, a window will appear that looks like this (captured on Linux):
attachment:cytoscape_startup.png
Note on Memory Consumption
For users interested in loading large networks, the amount of memory needed by Cytoscape will increase. Memory usage depends on both number of network objects (nodes+edges) and the number of attributes. Here are some rough suggestions for memory allocation:
Suggested Memory Size
Number of Objects (nodes + edges) |
Create View |
Suggested Memory Size |
~70,000 |
No |
512M (default) |
70,000-150,000 |
No |
800M |
~70,000 |
Yes |
800M |
70,000-150,000 |
Yes |
1G |
Note on Directory Location
For the application to work properly, all files should be left in the directory in which they were unpacked. The core Cytoscape application assumes this directory structure when looking for the various libraries needed to run the application. If you are adventurous, you can get creative with the $CLASSPATH and/or the cytoscape.jar manifest file and run Cytoscape from any location you want.