BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
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hdl:2117/186796
Tipus de documentArticle
Data publicació2019-09-10
EditorNature
Condicions d'accésAccés obert
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Reconeixement 4.0 Internacional
ProjecteCOMPUTACION DE ALTAS PRESTACIONES VII (MINECO-TIN2015-65316-P)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
BioExcel-2 - BioExcel Centre of Excellence for ComputationalBiomolecular Research (EC-H2020-823830)
ELIXIR-EXCELERATE - ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. (EC-H2020-676559)
BARCELONA SUPERCOMPUTING CENTER - CENTRO. NACIONAL DE SUPERCOMPUTACION (MINECO-SEV-2015-0493)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
BioExcel-2 - BioExcel Centre of Excellence for ComputationalBiomolecular Research (EC-H2020-823830)
ELIXIR-EXCELERATE - ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences. (EC-H2020-676559)
BARCELONA SUPERCOMPUTING CENTER - CENTRO. NACIONAL DE SUPERCOMPUTACION (MINECO-SEV-2015-0493)
Abstract
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.
CitacióAndrio, P. [et al.]. BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows. "Scientific data", 10 Setembre 2019, vol. 6, article 169, p. 1-8.
ISSN2052-4463
Versió de l'editorhttps://www.nature.com/articles/s41597-019-0177-4
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