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ytoscape 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 6. Cytoscape functionality has not been verified yet with SE 7. Link to download SE 6: Java SE 6

Install Cytoscape

A quick note on upgrading

There should really be no issue in upgrading. If you have a previous installation you have two options: 1) Starting with a clean slate: For this you should delete your previous installation directory and the .cytoscape directory. 2) Just keep what you have and simply pick a distinct, new directory for installation. In the unlikely event that you should encounter any problem, delete the .props files in your .cytoscape directory. If that doesn't help try deleting the .cytoscape directory. This latter step will cause you to loose all your plugins that you have installed via the plugin manager, so only do that if you are having problems or if you don't mind reinstalling your plugins. The core plugins will not be affected by this step.

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 Subversion repository.

Cytoscape installations (regardless of platform) containing the following files and directories:

File

Description

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 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):

Cytoscape_3/UserManual/Launching_Cytoscape (last edited 2016-04-26 22:09:02 by server2)

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+Cytoscape installations (regardless of platform) containing the following files and directories:



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=== 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:Cy3_cytoscape_startup_mac.png}}