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Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can...

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Detalles Bibliográficos
Autores principales: King, Zachary A., Dräger, Andreas, Ebrahim, Ali, Sonnenschein, Nikolaus, Lewis, Nathan E., Palsson, Bernhard O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552468/
https://www.ncbi.nlm.nih.gov/pubmed/26313928
http://dx.doi.org/10.1371/journal.pcbi.1004321
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author King, Zachary A.
Dräger, Andreas
Ebrahim, Ali
Sonnenschein, Nikolaus
Lewis, Nathan E.
Palsson, Bernhard O.
author_facet King, Zachary A.
Dräger, Andreas
Ebrahim, Ali
Sonnenschein, Nikolaus
Lewis, Nathan E.
Palsson, Bernhard O.
author_sort King, Zachary A.
collection PubMed
description Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.
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spelling pubmed-45524682015-09-01 Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways King, Zachary A. Dräger, Andreas Ebrahim, Ali Sonnenschein, Nikolaus Lewis, Nathan E. Palsson, Bernhard O. PLoS Comput Biol Research Article Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. Public Library of Science 2015-08-27 /pmc/articles/PMC4552468/ /pubmed/26313928 http://dx.doi.org/10.1371/journal.pcbi.1004321 Text en © 2015 King et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
King, Zachary A.
Dräger, Andreas
Ebrahim, Ali
Sonnenschein, Nikolaus
Lewis, Nathan E.
Palsson, Bernhard O.
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title_full Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title_fullStr Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title_full_unstemmed Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title_short Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
title_sort escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4552468/
https://www.ncbi.nlm.nih.gov/pubmed/26313928
http://dx.doi.org/10.1371/journal.pcbi.1004321
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