Diff for "Cytoscape_User_Manual/Launching_Cytoscape"

Differences between revisions 10 and 11

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.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 ****

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)
**** 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

(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

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

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.

Important Note: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.

Cytoscape Window When you succeed in launching Cytoscape, a window will appear that looks like this (captured on Linux):

attachment:cytoscape_startup.png

Cytoscape_User_Manual/Launching_Cytoscape (last edited 2010-10-07 18:01:55 by malbec)