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HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard

Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open...

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Autor principal: Wist, Julien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896291/
https://www.ncbi.nlm.nih.gov/pubmed/33430999
http://dx.doi.org/10.1186/s13321-019-0399-7
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author Wist, Julien
author_facet Wist, Julien
author_sort Wist, Julien
collection PubMed
description Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open software may increase the fraction of shared data by decreasing the amount of effort required to publish them in a manner that is useful to others. However, a weakness of open software, when compared to commercial ones, is the lack of user-friendly graphical interface that may discourage inexperienced researchers. Here, a web-browser-oriented solution is presented and demonstrated for metabolic profiling analysis that combines the power of R for back-end statistical analyses and of JavaScript for front-end visualisations and user interactivity. This unique combination of statistical programming and web-browser visualisation brings enhanced data interoperability and interactivity into the open source realm. It is exemplified by characterizing the extent to which bariatric surgery perturbs the metabolisms of rats, showing the value of the approach in iterative analysis by the end-user to establish a deeper understanding of the system perturbation. HastaLaVista is available at: (https://github.com/jwist/hastaLaVista, 10.5281/zenodo.3544800) under MIT license. The approach described in this manuscript can be extended to connect the interface to other scripting languages such as Python, and to create interfaces for other types of data analysis.
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spelling pubmed-68962912019-12-16 HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard Wist, Julien J Cheminform Research Article Metabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open software may increase the fraction of shared data by decreasing the amount of effort required to publish them in a manner that is useful to others. However, a weakness of open software, when compared to commercial ones, is the lack of user-friendly graphical interface that may discourage inexperienced researchers. Here, a web-browser-oriented solution is presented and demonstrated for metabolic profiling analysis that combines the power of R for back-end statistical analyses and of JavaScript for front-end visualisations and user interactivity. This unique combination of statistical programming and web-browser visualisation brings enhanced data interoperability and interactivity into the open source realm. It is exemplified by characterizing the extent to which bariatric surgery perturbs the metabolisms of rats, showing the value of the approach in iterative analysis by the end-user to establish a deeper understanding of the system perturbation. HastaLaVista is available at: (https://github.com/jwist/hastaLaVista, 10.5281/zenodo.3544800) under MIT license. The approach described in this manuscript can be extended to connect the interface to other scripting languages such as Python, and to create interfaces for other types of data analysis. Springer International Publishing 2019-12-05 /pmc/articles/PMC6896291/ /pubmed/33430999 http://dx.doi.org/10.1186/s13321-019-0399-7 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Wist, Julien
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title_full HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title_fullStr HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title_full_unstemmed HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title_short HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
title_sort hastalavista, a web-based user interface for nmr-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896291/
https://www.ncbi.nlm.nih.gov/pubmed/33430999
http://dx.doi.org/10.1186/s13321-019-0399-7
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