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Resource:Cytoscape

Name: Resource:Cytoscape
Description: An open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Additional features are available as plugins.

Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java technology and plugin community development is encouraged. Most of the plugins are freely available.

Cytoscape works as a web service client. This means Cytoscape can directly connect to the external public databases and imports network and annotation data. Currently, Pathway Commons, IntAct, BioMart, NCBI Entrez Gene, and PICR are supported. And they continue to develop new service clients for popular databases.
Other Name(s): Cytoscape: An Open Source Platform for Complex Network Analysis Visualization
Abbreviation: Cytoscape
Parent Organization: Institute for Systems Biology; Washington; USA, University of California at San Diego; California; USA
Supporting Agency: NCRR, Resource:National Resource for Network Biology, NIGMS
Grant: RR031228, GM070743
Resource Type(s): Software resource, Software repository
Resource: Resource
URL: http://cytoscape.org
Id: nif-0000-30404
PMID: PMID 21149340, 14597658
Availability: GNU Lesser General Public License, The community can contribute to this resource
Keywords: biological network visualization, systems biology, visualization, network, interaction, pathway, annotation, gene expression profile, gene expression
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to Resource:Cytoscape

Resource:AltAnalyze - Alternative Splicing Analysis Tool, Resource:BiNGO: A Biological Networks Gene Ontology tool, Resource:BioGRID, Resource:ClueGO, Resource:CoryneRegNet, Resource:DaTo, Resource:DisGeNET, Resource:DroID - Drosophila Interactions Database, Resource:EGAN: Exploratory Gene Association Networks, Resource:GeneMANIA, Resource:MiMI Plugin for Cytoscape, Resource:Network-based Prediction of Human Tissue-specific Metabolism, Resource:PhosphoSitePlus: Protein Modification Site, Resource:PiNGO, Resource:RamiGO, Resource:TRIP Database, Resource:cPath, Resource:categoryCompare, Resource:iBIOFind

Parts of Resource:Cytoscape

Curation status: Curated

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Notes

This page uses this default form:Resource

Contributors

Aarnaud, Ccdbuser, Memartone, Msmoot



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Facts about Resource:CytoscapeRDF feed
AbbrevCytoscape  +
AvailabilityGNU Lesser General Public License  +, and The community can contribute to this resource  +
CurationStatuscurated  +
DefiningCitationhttp://cytoscape.org  +
DefinitionAn open source bioinformatics software pla An open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Additional features are available as plugins.

Plugins are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. Plugins may be developed by anyone using the Cytoscape open API based on Java technology and plugin community development is encouraged. Most of the plugins are freely available.

Cytoscape works as a web service client. This means Cytoscape can directly connect to the external public databases and imports network and annotation data. Currently, Pathway Commons, IntAct, BioMart, NCBI Entrez Gene, and PICR are supported. And they continue to develop new service clients for popular databases.
new service clients for popular databases.
GrantCategory:RR031228   +, and Category:GM070743   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleSoftware resource  +, and Software repository  +
Idnif-0000-30404  +
Is part ofInstitute for Systems Biology; Washington; USA  +, and University of California at San Diego; California; USA  +
KeywordsBiological network visualization  +, Systems biology  +, Visualization  +, Network  +, Interaction  +, Pathway  +, Annotation  +, Gene expression profile  +, and Gene expression  +
LabelResource:Cytoscape  +
ModifiedDate30 May 2014  +
PMID21149340, 14597658  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyNational Center for Research Resources  +, Resource:National Resource for Network Biology  +, and National Institute of General Medical Sciences  +
SynonymCytoscape: An Open Source Platform for Complex Network Analysis Visualization  +