Cytoscape Plugins

Plugins are available for Cytoscape (version 2.3 and above) that duplicate some of FCModeler's most useful features. The plugins are under development.

Installation

To use a plugin, download the jar file and put it in Cytoscape's "plugins" folder (the default location in Windows is C:\Program Files\Cytoscape-v2.3\plugins). The plugin should be automatically loaded the next time Cytoscape is started, and will appear as a menu item (in the plugins menu and/or when right-clicking a node).

Download

• FCMPlugin
  • This plugin contains several functions/forms from FCModeler: the subgraph creator, identify node dialog, cycle finder, and path finder. It also has a function to select the p-neighborhood of a selected node or group of nodes. This plugin has been developed to work with Cytoscape 2.3. Many (but not all) of the functions also work with 2.3 (also 2.3.1 and 2.3.2). For Cycle finder, Filter function does not work completely yet. We are working on that. Please read the manual for more information.
• GEM Layout
  • This plugin works but is not tested extensively. It is more of a proof-of-concept in preparation for the Dot plugin.
• Dot
  • This plugin interfaces with the GraphViz package. The plugin now supports both simple and rank-cluster layout.
    For Window, you must have the dot executable file, and simply put dot.exe file in the Cytoscape plugins directory.
    • To run Dot Layout on window, you need to set up dot exe file on "Configure Dot Layout" option on the layout menu.
    For Macs and Linux, the dot path must be set manually. Download GraphViz package and install this package.
    • For Macs, the dot path should be "/opt/GraphViz/bin/dot" on "Configure Dot Layout" option on the layout menu.
    • In Linux, it is probably either "/usr/bin/dot" or "/usr/local/bin/dot".
• CytoScript
  • The plugin executes scripts in languages such as R, Scheme, Python, and Perl in Cytoscape. The goal of CytoScript is to extend Cytoscape through scripts, with the target application being the analysis of network or experimental data. The results of the analysis may then be represented in the Cytoscape network view. It is neccesary to have Script in Cytoscape Plugin directory to run Cytoscript. The installation is as follows.
    • Dependencies :
      • The javax.script-compliant R engine provided by edu.iastate.metnet.R (part of CytoScript) requires R (of course) and the JRI library.
    • Environment Variables :
      • Users of all operating systems need to set R_HOME to the root directory of your R installation (ie /usr/lib/R).
      • The JRI library needs to be on your java.library.path. To achieve this, set the following environment variable (depending on your operating system) to the location of JRI.
        • Linux: LD_LIBRARY_PATH
        • Windows: PATH
        • Mac: DYLD_LIBRARY_PATH
    • In detail, please follow this step to set up CytoScript.
      1. Download CytoScript.jar and Script.jar and put these files in Cytoscape Plugins directory
      2. Install rJava" package in R
      3. Copy JRI.jar and jri.dll (for Window) or libjri.so (for Linux) in rJava (for example : C:\Program Files\R\R-2.4.0\library\rJava\jri) to Cytoscape directory
    • If you want to run demo program,
      1. Install RBGL package in R from bioconductor.org
      2. Install rmetnet package in R
      3. Run Cytoscript with example1 file to find strongly connected components in a given network or example2 file to animate the result
    • For more detail, please look at CytoScript PDF file.
• Animator
  • The Animator plugin provides animation support to Cytoscape. One may use animations to show analysis results. Animations may be created and edited through a GUI. For more details, look at the Animator matual.
• Manual : MetNet tools