Download User Manual

Cytoscape_3/UserManual
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
If you are installing Cytoscape for the first time on your workstation, skip to the Download section below.
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
CytoscapeConfiguration directory (see below for the location of this 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 CytoscapeConfiguration
directory. If that doesn't help try deleting the CytoscapeConfiguration directory. This latter step
will cause you to lose all of the apps that you have installed via the App Store, so only do that if you
are having problems or if you don't mind reinstalling your apps. The core apps will not be affected by
this step.
Download
There are a number of options for downloading and installing Cytoscape. See the download page at the
http://cytoscape.org website for all options.
• 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/Directory
Description
p/Cytoscape_v3.0.0
Cytoscape program files, startup scripts, and default
location for session files
p / C y t o s c a p e _ v 3 . 0 . 0 / C y t o - Cytoscape memory configuration settings
scape.vmoptions
p/Cytoscape_v3.0.0/sampleData
Preset networks as described in the embedded
README.txt file
p/Cytoscape_v3.0.0/framework
Cytoscape program files
u/CytoscapeConfiguration
Cytoscape properties and program cache files
u/CytoscapeConfiguration/cyto- Cytoscape configuration settings
scape3.props
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