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Cytoscape on Biowulf and Helix
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.

On Helix

To use Cytoscape on either system, you must load the module. There are a couple of Cytoscape modules available. To see a list of modules, type

module avail Cytoscape

To load the default version of Cytoscape, type

module load Cytoscape
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.

Running Cytoscape interactively

If you want to run your job interactively, you can allocate a node for interactive use. Once the node is allocated, you can type commands directly on the command-line. Example:

[user@biowulf ~]$ sinteractive
salloc.exe: Pending job allocation 15323416
salloc.exe: job 15323416 queued and waiting for resources
salloc.exe: job 15323416 has been allocated resources
salloc.exe: Granted job allocation 15323416salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn1640 are ready for job
[user@cn1640 ~]$ module load Cytoscape
[user@cn1640 dir]$ Cytoscape&

If you need more memory than the default 4 GB, use sinteractive --mem=#g

Documentation