Cytoscape is a tool to visualize molecular interaction networks and biological pathways that can include diverse data, such as various annotations gene expression profiles. Cytoscape works well with large networks and allows many additional operations vi plugin apps, such as import, calculation of over-represented GO terms, Wikipathways, and drug repurposing candidates, to mention a few. See the 'links.'


Bioinformatics;Molecular interactions, pathways and networks;Data visualisation


  • Operation: Network simulation;Pathway or network visualisation

  • Software interface: Graphical user interface;command-line user interface;library

  • Language: Java

  • License: GNU Lesser General Public License v2.1

  • Cost: Free

  • Version name: 3.9.0

  • Credit: Google Summer of Code program, NIH, Israel Science Foundation, Genome Canada via the Ontario Genomics Institute, National Resource fo Network Biology

  • Input: -

  • Output: -

  • Contact: ashkenaz at

  • Collection: -

  • Maturity: Mature


  • Cytoscape ESP: simple search of complex biological networks.
  • Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ. Cytoscape ESP: simple search of complex biological networks. Bioinformatics. 2008 Jun 15;24(12):1465-6. doi: 10.1093/bioinformatics/btn208. Epub 2008 Apr 28. PMID: 18445605; PMCID: PMC2427162.
  • PMID: 18445605
  • PMC: PMC2427162

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