Cytoscape on Biowulf
Cytoscape Logo

Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. With Cytoscape, you can load molecular and genetic interaction data sets in many standards formats, project and integrate global datasets and functional annotations, establish powerful visual mappings across these data, perform advanced analysis and modeling and visualize and analyze human-curated pathway datasets.

Important Notes

This application requires a graphical connection using NX

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session from Biowulf using a graphical connection (we recommend NX) and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=6
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

To use Cytoscape, you must load the module. Type:

module load Cytoscape

Cytoscape GUI

Cytoscape Configuration Directory

Cytoscape will create a configuration directory inside the user's home directory. This is usually /home/$USER/CytoscapeConfiguration. We have observed two potential issues around this:

Cytoscape Apps

Cytoscape functionality can be extended using plugins, called Cytoscape Apps. There is an "app store" from where users can download, install, and manage these apps. However, to use the app store from a compute node on Biowulf (i.e. from an interactive session) Cytoscape must be configured to use the node's http proxy. Here are the steps on how to do this:

  1. Allocate an sinteractive session as usual and run the following before starting Cytoscape:

    echo $http_proxy

    An example of the output you should see after running the above command is: http://dtn05-e0:3128. Here the proxy server is dtn05-e0 and port is 3128. You will likely see different values. Note them down.

  2. Run Cytoscape and navigate to Edit --> Preferences> --> Proxy Settings. For "Type" select http. Enter the proxy server and port you obtained in the previous steps. Leave the User Name and Password fields blank. Click "OK".

  3. Then open Cytoscape's App Manager by navigating to Apps --> App Manager. You should see the app manager contact the default App Store, and refresh the cache of available apps for installation.

If you want to install and manage Cytoscape apps in a different sinteractive session, you will may need to redo step 1. This is because the proxy server may be different between different compute nodes.