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Cytoscape: the network visualization tool for GenomeSpace workflows

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables anal...

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Detalles Bibliográficos
Autores principales: Demchak, Barry, Hull, Tim, Reich, Michael, Liefeld, Ted, Smoot, Michael, Ideker, Trey, Mesirov, Jill P.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000Research 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133763/
https://www.ncbi.nlm.nih.gov/pubmed/25165537
http://dx.doi.org/10.12688/f1000research.4492.2
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author Demchak, Barry
Hull, Tim
Reich, Michael
Liefeld, Ted
Smoot, Michael
Ideker, Trey
Mesirov, Jill P.
author_facet Demchak, Barry
Hull, Tim
Reich, Michael
Liefeld, Ted
Smoot, Michael
Ideker, Trey
Mesirov, Jill P.
author_sort Demchak, Barry
collection PubMed
description Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.
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spelling pubmed-41337632014-08-26 Cytoscape: the network visualization tool for GenomeSpace workflows Demchak, Barry Hull, Tim Reich, Michael Liefeld, Ted Smoot, Michael Ideker, Trey Mesirov, Jill P. F1000Res Software Tool Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013. F1000Research 2014-08-26 /pmc/articles/PMC4133763/ /pubmed/25165537 http://dx.doi.org/10.12688/f1000research.4492.2 Text en Copyright: © 2014 Demchak B et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/publicdomain/zero/1.0/ Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
spellingShingle Software Tool
Demchak, Barry
Hull, Tim
Reich, Michael
Liefeld, Ted
Smoot, Michael
Ideker, Trey
Mesirov, Jill P.
Cytoscape: the network visualization tool for GenomeSpace workflows
title Cytoscape: the network visualization tool for GenomeSpace workflows
title_full Cytoscape: the network visualization tool for GenomeSpace workflows
title_fullStr Cytoscape: the network visualization tool for GenomeSpace workflows
title_full_unstemmed Cytoscape: the network visualization tool for GenomeSpace workflows
title_short Cytoscape: the network visualization tool for GenomeSpace workflows
title_sort cytoscape: the network visualization tool for genomespace workflows
topic Software Tool
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133763/
https://www.ncbi.nlm.nih.gov/pubmed/25165537
http://dx.doi.org/10.12688/f1000research.4492.2
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