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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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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. |
format | Online Article Text |
id | pubmed-4552468 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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