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

Journal of Cheminformatics
Marcus D HanwellChristopher J Harris

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 computa...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
May 23, 2006·Journal of Chemical Information and Modeling·Rajarshi GuhaEgon L Willighagen
Oct 26, 1984·Science·S Pierson
Oct 11, 2011·Journal of Cheminformatics·Noel M O'BoyleGeoffrey R Hutchison
Oct 18, 2011·Journal of Cheminformatics·Noel M O'BoylePeter Murray-Rust
Oct 29, 2011·IEEE Transactions on Visualization and Computer Graphics·Michael BostockJeffrey Heer
Aug 15, 2012·Journal of Cheminformatics·Marcus D HanwellGeoffrey R Hutchison
May 28, 2013·Journal of Cheminformatics·Wibe A de JongMarcus D Hanwell
Dec 17, 2014·Bioinformatics·Nicholas Rego, David Koes
Dec 13, 2016·The Journal of Physical Chemistry. a·Bing WangNeil S Ostlund

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Citations

Dec 12, 2018·GigaScience·Kristian PetersChristoph Steinbeck
Nov 2, 2018·Neuroinformatics·Robert A McDougalGordon M Shepherd
May 22, 2019·Sensors·Vinicius Facco RodriguesAndreas Maier
Jul 26, 2019·Database : the Journal of Biological Databases and Curation·Jian LiuWeijun Zhou
Apr 1, 2021·Chemical Reviews·Karol KowalskiTheresa L Windus
Jun 1, 2019·Journal of Chemical Information and Modeling·Nenad KrdzavacMarkus Kraft

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Software Mentioned

Chrome
Gravatars
LD
mongochemserver
Python
HTML5
WebGL
Avogadro
CherryPy
Github

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