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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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000Research
2014
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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. |
format | Online Article Text |
id | pubmed-4133763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | F1000Research |
record_format | MEDLINE/PubMed |
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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