Cytoscape: A Community-Based Framework for Network Modeling View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2009-05-29

AUTHORS

Sarah Killcoyne , Gregory W. Carter , Jennifer Smith , John Boyle

ABSTRACT

Cytoscape is a general network visualization, data integration, and analysis software package. Its development and use has been focused on the modeling requirements of systems biology, though it has been used in other fields. Cytoscape’s flexibility has encouraged many users to adopt it and adapt it to their own research by using the plugin framework offered to specialize data analysis, data integration, or visualization. Plugins represent collections of community-contributed functionality and can be used to dynamically extend Cytoscape functionality. This community of users and developers has worked together since Cytoscape’s initial release to improve the basic project through contributions to the core code and public offerings of plugin modules.This chapter discusses what Cytoscape does, why it was developed, and the extensions numerous groups have made available to the public. It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape. More... »

PAGES

219-239

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-60761-175-2_12

DOI

http://dx.doi.org/10.1007/978-1-60761-175-2_12

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1006415364

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19597788


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