The Cytoscape Automation app article collection [version 1; peer review: not peer reviewed]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

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Abstract 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.
AbstractList 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.
Author Ono, Keiichiro
Sage, Eric
Bader, Gary D
Treister, Adam
Demchak, Barry
Settle, Brett
Otasek, David
Longabaugh, William
Schwikowski, Benno
Kucera, Michael
Morris, John H
Ideker, Trey
Pico, Alexander R
Lopes, Christian
Molenaar, Piet
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  surname: Morris
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  organization: University of California, San Francisco, San Francisco, CA, 94143, USA
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  surname: Longabaugh
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  organization: Institute for Systems Biology, Seattle, WA, 98109, USA
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  organization: Amsterdam Medical Centre, Ansterdam, 1105 AZ, The Netherlands
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  fullname: Ideker, Trey
  organization: Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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Cites_doi 10.12688/f1000research.4642.1
10.1093/bioinformatics/btp101
10.12688/f1000research.6767.1
ContentType Journal Article
Copyright Copyright: © 2018 Demchak B et al.
Copyright: © 2018 Demchak B et al. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Copyright: © 2018 Demchak B et al. 2018
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Network Biology
Cytoscape
Automation
Network Visualization
Network Analysis
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References K Ono (ref-3) 2015; 4
G Bindea (ref-2) 2009; 25
A Pico (ref-1) 2014; 3
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  start-page: 138
  year: 2014
  ident: ref-1
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    fullname: A Pico
– volume: 25
  start-page: 1091-1093
  year: 2009
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– volume: 4
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  year: 2015
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  publication-title: F1000Res.
  doi: 10.12688/f1000research.6767.1
  contributor:
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Snippet Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic...
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Title The Cytoscape Automation app article collection [version 1; peer review: not peer reviewed]
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