Launching Cytoscape

Cytoscape 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 at least 512MB of free physical RAM, preferably 1GB if you are working with larger networks. Cytoscape expects a minimum screen resolution of 1024x768.

Installing Cytoscape

There are a number of options for downloading Cytoscape.

(1) Download and unpack the distribution.
Cytoscape is distributed as a compressed archive (tar.gz or zip) containing the following files and directories:

cytoscape.jar Main Cytoscape application (Java archive)

cytoscape.props User-configurable properties and preferences

vizmap.props User-configurable visual mapping preferences

cytoscape.sh Script to run Cytoscape from command line (Linux, Mac OS X)

cytoscape.bat Script to run Cytoscape (Windows)

LICENSE.txt Cytoscape GNU LGPL License

Cytoscape2_2Manual.pdf Cytoscape 2.2 Manual (the document you are reading now)

sampleData/

galFiltered.gml Sample molecular interaction network file *
galFiltered.sif Identical network in Simple Interaction Format *
galExpData.pvals Sample gene expression matrix file *
BINDyeast.sif Network of all yeast protein-protein interactions in the BIND database as of Nov, 2005 **
BINDhuman.sif Network of all human protein-protein interactions in the BIND database as of Nov, 2005 **
yeastHighQuality.sif Sample molecular interaction network file ***

annotation/ Directory containing Gene Ontology database entries (currently for yeast only). Info in this directory is used to associate gene names with synonyms as well as process, function, and cellular location data.


plugins/ Directory containing cytoscape PlugIns, in .jar 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)


(2) If necessary, install Java.
If not already installed on your computer, download and install the Java 2 Runtime Environment, version 1.4.2 or higher. It can be found at:
http://java.sun.com/j2se/1.4.2/download.html

(3) Launch the application.
Run "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 -jar cytoscape.jar". 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 annotation data directory, see the section 4. Command Line Arguments for details). On Mac OS X, users who downloaded the Mac OS X version of Cytoscape, can double-click on the Cytoscape icon to start Cytoscape. Either double-clicking or dragging onto the Cytoscape application icon any .sif or .gml file will load that file into Cytoscape.

Important Note:
For the application to work properly, ALL FILES MUST BE LEFT IN THE DIRECTORY IN WHICH THEY ARE UNPACKED. The core Cytoscape applications assumes this directory structure when looking for certain files, sucah as cytoscape.props, vizmap.props, and the annotation database.

Cytoscape Window

When you succeed in launching Cytoscape, a window will appear that looks like this:

Cytoscape Window