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

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          Abstract

          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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          Most cited references 11

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          ABINIT: First-principles approach to material and nanosystem properties

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            cp2k:atomistic simulations of condensed matter systems

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              The Blue Obelisk—Interoperability in Chemical Informatics

              The Blue Obelisk Movement (http://www.blueobelisk.org/) is the name used by a diverse Internet group promoting reusable chemistry via open source software development, consistent and complimentary chemoinformatics research, open data, and open standards. We outline recent examples of cooperation in the Blue Obelisk group:  a shared dictionary of algorithms and implementations in chemoinformatics algorithms drawing from our various software projects; a shared repository of chemoinformatics data including elemental properties, atomic radii, isotopes, atom typing rules, and so forth; and Web services for the platform-independent use of chemoinformatics programs.
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                Author and article information

                Contributors
                marcus.hanwell@kitware.com
                WAdeJong@lbl.gov
                chris.harris@kitware.com
                Journal
                J Cheminform
                J Cheminform
                Journal of Cheminformatics
                Springer International Publishing (Cham )
                1758-2946
                30 October 2017
                30 October 2017
                2017
                : 9
                Affiliations
                [1 ]ISNI 0000 0001 1015 4706, GRID grid.32348.3e, Kitware, Inc., ; 28 Corporate Drive, Clifton Park, NY 12065 USA
                [2 ]ISNI 0000 0001 2231 4551, GRID grid.184769.5, LBNL, ; One Cyclotron Road, Berkeley, CA 94720 USA
                Article
                241
                10.1186/s13321-017-0241-z
                5662523
                29086154
                © 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.

                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100006151, Basic Energy Sciences;
                Award ID: DE-SC0013250
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Chemoinformatics

                json, chemistry, web, data, semantic, nwchem

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