Biowulf High Performance Computing at the NIH
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 ahd 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.

Because it is a GUI, you will be unable to submit batch or swarm jobs on biowulf. You can, however, request an interactive node.

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

Allocate an interactive session 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

To run Cytoscape, an X Windows connection is required. NoMachine's NX is the X-Windows client currently recommended by staff for Windows and Mac users.