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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2017
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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. |
format | Online Article Text |
id | pubmed-5662523 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
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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