Cytoscape
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.'
Topic
Bioinformatics;Molecular interactions, pathways and networks;Data visualisation
Detail
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 agri.huji.ac.il
Collection: -
Maturity: Mature
Publications
- 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.
- https://doi.org/10.1093/bioinformatics/btn208
- PMID: 18445605
- PMC: PMC2427162
- Cytoscape app store
- Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Cytoscape app store. Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16. PMID: 23595664; PMCID: PMC3654709.
- https://doi.org/10.1093/bioinformatics/btt138
- PMID: 23595664
- PMC: PMC3654709
Download and documentation
Documentation: https://cytoscape.org/what_is_cytoscape.html
Home page: http://www.cytoscape.org/
Links: https://apps.cytoscape.org/
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