Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization

Time 2021-11-22 08:10:27

Web Name: Cytoscape: An Open Source Platform for Complex Network Analysis and Visualization

WebSite: http://www.cytoscape.org

ID:245152

Keywords:

Source,Platform,Open,Cytoscape,An,for,and,Visualization,Cytoscape,visualization,

Description:

keywords:Cytoscape,visualization,interaction network, software,genetic,gene,expression,protein interaction,graph,bioinformatics, computational biology,UCSD,Whitehead Institute,Institute for Systems Biology, microarray analysis,clustering,pathways,integration,algorithm, statistical analysis,gene regulation,complex networks,social networks
description:Cytoscape Official Web Site
Cytoscape Network Data Integration, Analysis, and Visualization in a Box Introduction Download An Important Note for Mac Users

A recent update by Apple to Mac OS is causing Cytoscape to crash on startup

Click here for instructions on how to resolve this problem

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...

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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.

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The Cytoscape Consoritum, Tax ID: 20-4909879.


Tweets by @cytoscape 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

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Cytoscape Consortium

Cytoscape project is supported by:

National Resource for Network Biology

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

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