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.

• Cytoscape Home
• Cytoscape User Manual

This application requires a graphical connection. You can either use NoMachine or the browser-based Graphical Session on HPC OnDemand

• Module Name: Cytoscape (see the modules page for more information)
• Environment variables set: CYTOSCAPE_HOME
• Example files in $CYTOSCAPE_HOME/sampleData/
• Refrain from manually loading java modules as these may cause problems with Cytoscape
• We recommend allocated at least 8GB memory for Cytoscape jobs and sessions
• To use the cyREST API with client applications like the RCy3 library, make sure to set the following before running Cytoscape: export no_proxy=localhost

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&

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:

• Several batch jobs that automate task(s) in Cytoscape, usually running via an API, can write many files to the configuration directory. In some cases this can exceed the 16GB quota on the user's home directory causing many problems to the user and running jobs. A possible solution is to reset JAVA_OPTIONS and change the configuration directory location. For example, run the following before starting Cytoscape:

  export JAVA_OPTIONS="-Duser.home=/data/$USER/CytoscapeConfiguration"

• If user's switch between different versions of the Cytoscape module, they may encounter some incompatibilities since the same configuration directory is used regardless of which Cytoscape version is started. This could be especially true for Cytoscape plugins (apps) that are incompatible with certain versions of Cytoscape. Use the same solution as listed above or rename the previous configuration directory.

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, https://apps.cytoscape.org 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.