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CYTOSCAPE

NETWORK DATA INTEGRATION, ANALYSIS, AND VISUALIZATION IN A BOX

Introduction
Download 3.10.3


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.

cytoscapenot running




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
 * Automate Cytoscape with any scripting language, see automation docs.


FEATURED VIDEO DEMOS





PUBLICATIONS USING CYTOSCAPE

Browse published figures referencing Cytoscape at PubMed Central.




CYTOSCAPE CONSORTIUM



Cytoscape project is supported by:

National Resource for Network Biology

National Human Genome Research Institute

Funding for continued development and maintenance of Cytoscape is provided by
the U.S. National Human Genome Rearch Institute (NHGRI) under award number NIH
NHGRI U24 HG012107
(Previously: R01 HG009979; R01 GM070743)
Cytoscape user support, education and new initiatives are supported by the
National Resource for Network Biology (NRNB) under award number P41 GM103504.
The content is solely the responsibility of the authors and does not necessarily
represent the official views of the National Institutes of Health.

©2001-2024 Cytoscape Consortium

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