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Data-dependent visualization of biological networks in the web-browser with NDExEdit

Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging a...

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Detalles Bibliográficos
Autores principales: Auer, Florian, Mayer, Simone, Kramer, Frank
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9212158/
https://www.ncbi.nlm.nih.gov/pubmed/35675360
http://dx.doi.org/10.1371/journal.pcbi.1010205
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author Auer, Florian
Mayer, Simone
Kramer, Frank
author_facet Auer, Florian
Mayer, Simone
Kramer, Frank
author_sort Auer, Florian
collection PubMed
description Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis. A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available. NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG.
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spelling pubmed-92121582022-06-22 Data-dependent visualization of biological networks in the web-browser with NDExEdit Auer, Florian Mayer, Simone Kramer, Frank PLoS Comput Biol Research Article Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis. A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available. NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG. Public Library of Science 2022-06-08 /pmc/articles/PMC9212158/ /pubmed/35675360 http://dx.doi.org/10.1371/journal.pcbi.1010205 Text en © 2022 Auer et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Auer, Florian
Mayer, Simone
Kramer, Frank
Data-dependent visualization of biological networks in the web-browser with NDExEdit
title Data-dependent visualization of biological networks in the web-browser with NDExEdit
title_full Data-dependent visualization of biological networks in the web-browser with NDExEdit
title_fullStr Data-dependent visualization of biological networks in the web-browser with NDExEdit
title_full_unstemmed Data-dependent visualization of biological networks in the web-browser with NDExEdit
title_short Data-dependent visualization of biological networks in the web-browser with NDExEdit
title_sort data-dependent visualization of biological networks in the web-browser with ndexedit
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9212158/
https://www.ncbi.nlm.nih.gov/pubmed/35675360
http://dx.doi.org/10.1371/journal.pcbi.1010205
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