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CYTOSCAPE

NETWORK DATA INTEGRATION, ANALYSIS, AND VISUALIZATION IN A BOX

Introduction
Download 3.9.1


ANALYZE YOUR GENES WITH NDEX IQUERY




Cytoscape is an open source software platform for visualizing complex networks
and integrating these with any type of attribute data. A lot of Apps are
available for various kinds of problem domains, including bioinformatics, social
network analysis, and semantic web. Learn more...

Release Notes Sample Visualizations

Cytoscape Tutorials

App Developers Docs


NRNB AND CYTOSCAPE



Introduction to the National Resource for Network Biology


HOW TO CITE CYTOSCAPE



CYTOSCAPE PROJECT NEEDS YOUR SUPPORT!

Please cite the original Cytoscape paper when you use Cytoscape. This is
critical to sustaining our federal funding.



Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski
B, Ideker T.

CYTOSCAPE: A SOFTWARE ENVIRONMENT FOR INTEGRATED MODELS OF BIOMOLECULAR
INTERACTION NETWORKS

Genome Research 2003 Nov; 13(11):2498-504

[Abstract] [PDF] [PubMed entry]

For automation usage and implementation leveraging CyREST, Commands or our R and
Python libraries, please cite: Otasek, et al., Cytoscape Automation: empowering
workflow-based network analysis Genome Biology, 20:185 (2019)
[Abstract] [PDF] [PubMed entry]

Other articles and papers about Cytoscape are available here.


HOW TO DONATE TO CYTOSCAPE


This is a tax deductible donation to a 501(c)(3) nonprofit organization,
The Cytoscape Consoritum, Tax ID: 20-4909879.






WHAT CAN YOU DO WITH CYTOSCAPE?


BIOLOGY

Cytoscape supports many use cases in molecular and systems biology, genomics,
and proteomics:

 * Load molecular and genetic interaction data sets in many standards formats
 * Project and integrate global datasets and functional annotations
 * Establish powerful visual mappings across these data
 * Perform advanced analysis and modeling using Cytoscape Apps
 * Visualize and analyze human-curated pathway datasets such as WikiPathways,
   Reactome, and KEGG.




SOCIAL SCIENCE

Cytoscape is used by social scientists to:
 * Visualize and analyze large social networks of interpersonal relationships
 * Assemble social networks from tables and forms
 * Gather social interactions from the web by variety of web service APIs with
   scripting languages and save it in standard data file formats. Cytoscape
   supports most of the standard file formats .
 * Calculate network statistics using Apps
 * Use with other tools, such as R with sna/ igraph package or NetworkX, for
   more advanced analysis




GENERAL COMPLEX NETWORK ANALYSIS

Cytoscape is domain-independent and therefore is a powerful tool for complex
network analysis in general.
 * Calculate statistics for networks by Apps such as NetworkAnalyzer or
   CentiScaPe
 * Find shortest path
 * Find clusters by various kinds of algorithms
 * Use with other tools for more advanced analysis
 * Perform advanced network analysis in popular tools, including igraph, Pajek,
   or GraphViz and import it to Cytoscape as standard file formats like GraphML


APP DEVELOPMENT

Cytoscape is expandable and extensible. Cytoscape has a vibrant App developer
community and over a hundred Apps developed by third parties.
 * Source code is available on GitHub
 * Running on OSGi framework
 * Develop simple and complex Apps in Java
 * Clean, Rich Cytoscape Application Programming Interface ( API)
 * Active developer community
 * Write simple functions with scripting languages, including Ruby, Python,
   Groovy, and JavaScript


FEATURED VIDEO DEMOS





FEATURED PUBLICATIONS

Tweet about it if you've published using Cytoscape and we will feature your
publication here!




CYTOSCAPE CONSORTIUM



Cytoscape project is supported by:

National Resource for Network Biology

National Institute of General Medical Sciences of the National Institutes of
Health

Funding for continued development and maintenance of Cytoscape is provided by
the U.S. National Institute of General Medical Sciences (NIGMS) under award
number R01 GM070743. Cytoscape user support, education and new initiatives are
supported by the National Resource for Network Biology (NRNB) under award number
P41 GM103504.

©2001-2018 Cytoscape Consortium

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