The Cytoscape Automation app article collection [version 1; peer review: not peer reviewed]

Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowe...

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Published inF1000 research Vol. 7; p. 800
Main Authors Demchak, Barry, Otasek, David, Pico, Alexander R, Bader, Gary D, Ono, Keiichiro, Settle, Brett, Sage, Eric, Morris, John H, Longabaugh, William, Lopes, Christian, Kucera, Michael, Treister, Adam, Schwikowski, Benno, Molenaar, Piet, Ideker, Trey
Format Journal Article
LanguageEnglish
Published England Faculty of 1000 Ltd 2018
Faculty of 1000
F1000 Research Limited
Subjects
Automation
Bioinformatics
Computer Science
La Jolla California
Canada
Netherlands
San Francisco California
United States > US
California
France
App
Network Biology
Cytoscape
Automation
Network Visualization
Network Analysis
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Summary:Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality. This article collection is a resource to assist readers in quickly and economically leveraging such apps in reproducible workflows that scale independently to large data sets and production runs.
Bibliography:SourceType-Other Sources-1
content type line 63
ObjectType-Editorial-2
ObjectType-Commentary-1
PMCID: PMC6013757
No competing interests were disclosed.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.15355.1