ILRI Research Computing

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====== cytoscape ======

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

===== Information =====

  * Version: 3.10.2
  * Added: July, 2013
  * Updated: October, 2024
  * Link: https://cytoscape.org

===== Usage =====

See which versions are available:
<code>$ module avail cytoscape</code>

Load one version into your environment and run it:
<code>$ module load cytoscape/3.10.2
$ cytoscape</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://github.com/cytoscape/cytoscape/releases/download/3.10.2/Cytoscape_3_10_2_unix.sh
$ chmod +x Cytoscape_3_10_2_unix.sh
$ module load java/17
$ sudo mkdir -p /export/apps/cytoscape/3.10.2
$ sudo chown aorth:aorth /export/apps/cytoscape/3.10.2
$ ./Cytoscape_3_10_2_unix.sh -q -dir /export/apps/cytoscape/3.10.2
$ sudo chown -R root:root /export/apps/cytoscape/3.10.2</code>