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Cytoscape

  • Description

    a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

  • Usage

    To list all executables provided by Cytoscape, run: $ biogrids-list cytoscape Copy to clipboard

  • Usage Notes

    Cytoscape runs in a read-only directory (/programs). As such you may receive a warning message:

    Unable to update instance pid: Unable to create directory /nfs/programs/x86_64-linux/cytoscape/3.7.1/framework/instances

    This is harmless and can be ignored.

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install cytoscape Copy to clipboard Available operating systems: Linux 64, OS X INTEL

  • Primary Citation*

    P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research. Cold Spring Harbor Laboratory Press. 13(11): 2498-2504.


    • *Full citation information available through

  • Keywords

    Bioinformatics Infrastructure, Figure Creation, Visualization

  • Default Versions

    Linux 64:  3.9.1 (292.4 MB)
    OS X INTEL:  3.9.1 (426.0 MB)

  • Other Versions

      Linux 64:

      3.2.1 (124.6 MB) , 3.7.1 (178.0 MB)

    • OS X INTEL:

      3.2.1 (126.2 MB) , 3.7.1 (369.2 MB)

  • Developers

    Barry Demchak, Benno Schwikowski, Keiichiro Ono, Trey Ideker

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