Cargando…

Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem

Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct...

Descripción completa

Detalles Bibliográficos
Autores principales: Honorato, Rodrigo V., Koukos, Panagiotis I., Jiménez-García, Brian, Tsaregorodtsev, Andrei, Verlato, Marco, Giachetti, Andrea, Rosato, Antonio, Bonvin, Alexandre M. J. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8356364/
https://www.ncbi.nlm.nih.gov/pubmed/34395534
http://dx.doi.org/10.3389/fmolb.2021.729513
_version_ 1783736931505405952
author Honorato, Rodrigo V.
Koukos, Panagiotis I.
Jiménez-García, Brian
Tsaregorodtsev, Andrei
Verlato, Marco
Giachetti, Andrea
Rosato, Antonio
Bonvin, Alexandre M. J. J.
author_facet Honorato, Rodrigo V.
Koukos, Panagiotis I.
Jiménez-García, Brian
Tsaregorodtsev, Andrei
Verlato, Marco
Giachetti, Andrea
Rosato, Antonio
Bonvin, Alexandre M. J. J.
author_sort Honorato, Rodrigo V.
collection PubMed
description Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently.
format Online
Article
Text
id pubmed-8356364
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-83563642021-08-12 Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem Honorato, Rodrigo V. Koukos, Panagiotis I. Jiménez-García, Brian Tsaregorodtsev, Andrei Verlato, Marco Giachetti, Andrea Rosato, Antonio Bonvin, Alexandre M. J. J. Front Mol Biosci Molecular Biosciences Structural biology aims at characterizing the structural and dynamic properties of biological macromolecules at atomic details. Gaining insight into three dimensional structures of biomolecules and their interactions is critical for understanding the vast majority of cellular processes, with direct applications in health and food sciences. Since 2010, the WeNMR project (www.wenmr.eu) has implemented numerous web-based services to facilitate the use of advanced computational tools by researchers in the field, using the high throughput computing infrastructure provided by EGI. These services have been further developed in subsequent initiatives under H2020 projects and are now operating as Thematic Services in the European Open Science Cloud portal (www.eosc-portal.eu), sending >12 millions of jobs and using around 4,000 CPU-years per year. Here we review 10 years of successful e-infrastructure solutions serving a large worldwide community of over 23,000 users to date, providing them with user-friendly, web-based solutions that run complex workflows in structural biology. The current set of active WeNMR portals are described, together with the complex backend machinery that allows distributed computing resources to be harvested efficiently. Frontiers Media S.A. 2021-07-28 /pmc/articles/PMC8356364/ /pubmed/34395534 http://dx.doi.org/10.3389/fmolb.2021.729513 Text en Copyright © 2021 Honorato, Koukos, Jiménez-García, Tsaregorodtsev, Verlato, Giachetti, Rosato and Bonvin. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Honorato, Rodrigo V.
Koukos, Panagiotis I.
Jiménez-García, Brian
Tsaregorodtsev, Andrei
Verlato, Marco
Giachetti, Andrea
Rosato, Antonio
Bonvin, Alexandre M. J. J.
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title_full Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title_fullStr Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title_full_unstemmed Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title_short Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem
title_sort structural biology in the clouds: the wenmr-eosc ecosystem
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8356364/
https://www.ncbi.nlm.nih.gov/pubmed/34395534
http://dx.doi.org/10.3389/fmolb.2021.729513
work_keys_str_mv AT honoratorodrigov structuralbiologyinthecloudsthewenmreoscecosystem
AT koukospanagiotisi structuralbiologyinthecloudsthewenmreoscecosystem
AT jimenezgarciabrian structuralbiologyinthecloudsthewenmreoscecosystem
AT tsaregorodtsevandrei structuralbiologyinthecloudsthewenmreoscecosystem
AT verlatomarco structuralbiologyinthecloudsthewenmreoscecosystem
AT giachettiandrea structuralbiologyinthecloudsthewenmreoscecosystem
AT rosatoantonio structuralbiologyinthecloudsthewenmreoscecosystem
AT bonvinalexandremjj structuralbiologyinthecloudsthewenmreoscecosystem