WHONDRS-GUI: a web application for global survey of surface water metabolites

BACKGROUND: The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts....

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Autores principales: Lin, Xinming, Ren, Huiying, Goldman, Amy E., Stegen, James C., Scheibe, Timothy D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382364/
https://www.ncbi.nlm.nih.gov/pubmed/32765964
http://dx.doi.org/10.7717/peerj.9277
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author Lin, Xinming
Ren, Huiying
Goldman, Amy E.
Stegen, James C.
Scheibe, Timothy D.
author_facet Lin, Xinming
Ren, Huiying
Goldman, Amy E.
Stegen, James C.
Scheibe, Timothy D.
author_sort Lin, Xinming
collection PubMed
description BACKGROUND: The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. RESULTS: The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/).
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spelling pubmed-73823642020-08-05 WHONDRS-GUI: a web application for global survey of surface water metabolites Lin, Xinming Ren, Huiying Goldman, Amy E. Stegen, James C. Scheibe, Timothy D. PeerJ Bioinformatics BACKGROUND: The Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) is a consortium that aims to understand complex hydrologic, biogeochemical, and microbial connections within river corridors experiencing perturbations such as dam operations, floods, and droughts. For one ongoing WHONDRS sampling campaign, surface water metabolite and microbiome samples are collected through a global survey to generate knowledge across diverse river corridors. Metabolomics analysis and a suite of geochemical analyses have been performed for collected samples through the Environmental Molecular Sciences Laboratory (EMSL). The obtained knowledge and data package inform mechanistic and data-driven models to enhance predictions of outcomes of hydrologic perturbations and watershed function, one of the most critical components in model-data integration. To support efforts of the multi-domain integration and make the ever-growing data package more accessible for researchers across the world, a Shiny/R Graphical User Interface (GUI) called WHONDRS-GUI was created. RESULTS: The web application can be run on any modern web browser without any programming or operational system requirements, thus providing an open, well-structured, discoverable dataset for WHONDRS. Together with a context-aware dynamic user interface, the WHONDRS-GUI has functionality for searching, compiling, integrating, visualizing and exporting different data types that can easily be used by the community. The web application and data package are available at https://data.ess-dive.lbl.gov/view/doi:10.15485/1484811, which enables users to simultaneously obtain access to the data and code and to subsequently run the web app locally. The WHONDRS-GUI is also available for online use at Shiny Server (https://xmlin.shinyapps.io/whondrs/). PeerJ Inc. 2020-07-22 /pmc/articles/PMC7382364/ /pubmed/32765964 http://dx.doi.org/10.7717/peerj.9277 Text en ©2020 Battelle Memorial Institute 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, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Lin, Xinming
Ren, Huiying
Goldman, Amy E.
Stegen, James C.
Scheibe, Timothy D.
WHONDRS-GUI: a web application for global survey of surface water metabolites
title WHONDRS-GUI: a web application for global survey of surface water metabolites
title_full WHONDRS-GUI: a web application for global survey of surface water metabolites
title_fullStr WHONDRS-GUI: a web application for global survey of surface water metabolites
title_full_unstemmed WHONDRS-GUI: a web application for global survey of surface water metabolites
title_short WHONDRS-GUI: a web application for global survey of surface water metabolites
title_sort whondrs-gui: a web application for global survey of surface water metabolites
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382364/
https://www.ncbi.nlm.nih.gov/pubmed/32765964
http://dx.doi.org/10.7717/peerj.9277
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