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Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and deskt...

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Detalles Bibliográficos
Autores principales: Hanwell, Marcus D., de Jong, Wibe A., Harris, Christopher J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662523/
https://www.ncbi.nlm.nih.gov/pubmed/29086154
http://dx.doi.org/10.1186/s13321-017-0241-z
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author Hanwell, Marcus D.
de Jong, Wibe A.
Harris, Christopher J.
author_facet Hanwell, Marcus D.
de Jong, Wibe A.
Harris, Christopher J.
author_sort Hanwell, Marcus D.
collection PubMed
description An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction—connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web—going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.
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spelling pubmed-56625232017-11-15 Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application Hanwell, Marcus D. de Jong, Wibe A. Harris, Christopher J. J Cheminform Research Article An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction—connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web—going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client. Springer International Publishing 2017-10-30 /pmc/articles/PMC5662523/ /pubmed/29086154 http://dx.doi.org/10.1186/s13321-017-0241-z Text en © The Author(s) 2017 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
Hanwell, Marcus D.
de Jong, Wibe A.
Harris, Christopher J.
Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title_full Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title_fullStr Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title_full_unstemmed Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title_short Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application
title_sort open chemistry: restful web apis, json, nwchem and the modern web application
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662523/
https://www.ncbi.nlm.nih.gov/pubmed/29086154
http://dx.doi.org/10.1186/s13321-017-0241-z
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