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. 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.

There are a number of options for downloading and installing Cytoscape:

• For Windows and Linux platforms, one-step installation is available via InstallAnywhere. For one-step installation, go to http://www.cytoscape.org, click Download Cytoscape, and follow the on-screen instructions.

• For Mac OS X, we provide an alternative installation, available as a .dmg.zip file. When installed via this method, Cytoscape functions as a regular Mac application, and can be accessed via your Applications folder.
• Finally, you can download and install a compressed archive distribution. Instructions for this option are provided below.

(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_4Manual.pdf  Cytoscape 2.4 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 *
  galFiltered.cys       Sample session file created from datasets above *
  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 ***

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 SE 5 or 6. It 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)

Cytoscape 2.4 does not support Java 1.4.x series. You must install Java SE 5 or 6.

(3) Launch the application 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). 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.

Suggested Memory Size

Memory usage depends on both number of objects (nodes+edges) and number of attributes. If the data includes a lot of attributes, more memory may be required.

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

attachment:cytoscape_startup.png