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BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinfo...

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Autores principales: Andrio, Pau, Hospital, Adam, Conejero, Javier, Jordá, Luis, Del Pino, Marc, Codo, Laia, Soiland-Reyes, Stian, Goble, Carole, Lezzi, Daniele, Badia, Rosa M., Orozco, Modesto, Gelpi, Josep Ll.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736963/
https://www.ncbi.nlm.nih.gov/pubmed/31506435
http://dx.doi.org/10.1038/s41597-019-0177-4
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author Andrio, Pau
Hospital, Adam
Conejero, Javier
Jordá, Luis
Del Pino, Marc
Codo, Laia
Soiland-Reyes, Stian
Goble, Carole
Lezzi, Daniele
Badia, Rosa M.
Orozco, Modesto
Gelpi, Josep Ll.
author_facet Andrio, Pau
Hospital, Adam
Conejero, Javier
Jordá, Luis
Del Pino, Marc
Codo, Laia
Soiland-Reyes, Stian
Goble, Carole
Lezzi, Daniele
Badia, Rosa M.
Orozco, Modesto
Gelpi, Josep Ll.
author_sort Andrio, Pau
collection PubMed
description In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.
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spelling pubmed-67369632019-09-17 BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows Andrio, Pau Hospital, Adam Conejero, Javier Jordá, Luis Del Pino, Marc Codo, Laia Soiland-Reyes, Stian Goble, Carole Lezzi, Daniele Badia, Rosa M. Orozco, Modesto Gelpi, Josep Ll. Sci Data Article In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments. Nature Publishing Group UK 2019-09-10 /pmc/articles/PMC6736963/ /pubmed/31506435 http://dx.doi.org/10.1038/s41597-019-0177-4 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Andrio, Pau
Hospital, Adam
Conejero, Javier
Jordá, Luis
Del Pino, Marc
Codo, Laia
Soiland-Reyes, Stian
Goble, Carole
Lezzi, Daniele
Badia, Rosa M.
Orozco, Modesto
Gelpi, Josep Ll.
BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title_full BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title_fullStr BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title_full_unstemmed BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title_short BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
title_sort bioexcel building blocks, a software library for interoperable biomolecular simulation workflows
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736963/
https://www.ncbi.nlm.nih.gov/pubmed/31506435
http://dx.doi.org/10.1038/s41597-019-0177-4
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