Diff for "Cytoscape_User_Manual/Launching_Cytoscape"

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Cytoscape is a Java application verified to run on Linux, Windows, and Mac OS X. Although not officially supported, other UNIX platforms such as Solaris or FreeBSD may run Cytoscape if Java version 5 or later is available for the platform.

System requirements

The system requirements for Cytoscape depend on the size of the networks the user wants to load, view and manipulate.

	Small Network Visualization	Large Network Analysis/Visualization
Processor	1GHz	As fast as possible
Memory	512MB	2GB+
Graphics Card	On board Video	Highend Graphics Card
Monitor	XGA (1024X768)	Wide or Dual Monitor

Getting Started

Install Java

If not already installed on your computer, download and install Java SE 5 or 6. Cytoscape 2.5 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.

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:

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/ from "A merged human interactome" by Andrew Garrow, Yeyejide Adeleye and Guy Warner (Unilever, Safety and Environmental Assurance Center).

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 Mac OS 10.4):

attachment:cytoscape_startup_mac.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

Number of Objects (nodes + edges)	Suggested Memory Size
0 - 70,000	512M (default)
70,000 - 150,000	800M

Suggested Memory Size With View

Number of Objects (nodes + edges)	Suggested Memory Size
0 - 20,000	512M (default)
20,000 - 70,000	800M
70,000 - 150,000	1G

Overall Memory Size for Cytoscape

To increase the maximum memory size for Cytoscape, you can specify it from command line. For example, if you want to assign 1GB of memory, type:

java -Xmx1GB -jar cytoscape.jar -p plugins

from the command line.

Stack Size

There is one more option related to memory allocation. Some of the functions in Cytoscape use larger stack space (a temporary memory for sope oprations, such as Layout). Since this value is set independently from the Xmx value above, sometimes Layout algorithms fails due to the out of memory error. To avoid this, you can set larger heap size by -Xss option. If layout fails for large networks, please try the following:

java -Xmx1GB -Xss10M -jar cytoscape.jar -p plugins

The option -Xss10M means set the heap size to 10MB. In many cases, this solves out of memory error for Layouts.

Note: Some of the web service clients are multi-thread programs and each thread uses the memory size specified by -Xss option. If web service clients fails due to the out of memory error, please reduce the stack size and try again.

For more details, see [:How to increase memory for Cytoscape:How to increase memory for Cytoscape].

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.

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

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There is one more option related to memory allocation.  Some of the functions in Cytoscape use larger stack space (a temporary memory for sope oprations, such as Layout).  Since this value is set independently from the ''Xmx'' value above, sometimes Layout algorithms fails due to the ''out of memory'' error.  To avoid this, you can set larger heap size by '''''-Xss''''' option.  If layout fails for large networks, please try the following:



'''''java -Xmx1GB -Xss10M -jar cytoscape.jar -p plugins'''''



The option '''''-Xss10M''''' means set the heap size to 10MB.  In many cases, this solves ''out of memory'' error for Layouts. 



Note: Some of the web service clients are multi-thread programs and each thread uses the memory size specified by '''''-Xss''''' option.  If web service clients fails due to the ''out of memory'' error, please reduce the stack size and try again.