Diff for "Cytoscape_User_Manual/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.

(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]

In general, Java SE 6 is faster than 5. If your machine is compatible with the 6 series, please try version 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 the source code.

• 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:

* 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/ from "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 [:Cytoscape_User_Manual/Command_Line_Arguments: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).

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 Without View

Suggested Memory Size With View

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.