Plugin

*To begin using the CARLSBAD Plugin to Cytoscape, please see installation instructions below or in the manual. After proper installation, you will begin your network exploration with SNAKE. A link is provided towards the bottom of this page.

CARLSBAD Manual & Tutorial [HTML] [PDF]

CARLSBAD Work Flow

Installation Procedures for Cytoscape and the CARLSBAD Plugin

To begin using the CARLSBAD platform you will first need to install Cytoscape 2.8.2 (free) and a ChemAxon license (free for some categories such as academics and non-commercial usage). Once you have obtained a ChemAxon license, copy the retrieved file, “license.cxl,” to one of the following directories according to the operating system on your machine:

  • Windows 7
    • C:Usersyour_usernamechemaxon
  • UNIX
    • /home/your_username/.chemaxon/
  • Apple
    • $HOME/your_username/.chemaxon/
      • Substitute $HOME with the path to your home folder.

Note: You may have to create the directory yourself by simply creating a folder named “chemaxon” in the highlighted region above on Windows machines and for Apple and UNIX machines via terminal:

  1. mkdir .chemaxon
  2. cp ~/Downloads/license.cxl .chemaxon/

Next, load the CARLSBAD plugin to Cytoscape. The plugin can be installed via the provided link or through Cytoscape after launch.

In addition, we recommend that you ensure your computer is equipped as a Java Virtual Machine.

SNAKE – SubNet Application, Kit, and Extractor

Downloads

  • Alternate Visualization Style designed for CARLSBAD network visualization in Cytoscape
  • Right click on file and click “Save link as”
  • See manual for import into Cytoscape (File >Import >Vismap property file … )

Usage Examples 

Additional Documentation