Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermedia...

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Authors: Bayarri, Genís, Andrio, Pau, Gelpi, Josep|||0000-0002-0566-7723, Hospital, Adam, Orozco, Modesto
Format: article
Publication Date:2024
Country:España
Institution:Universitat Politècnica de Catalunya (UPC)
Repository:UPCommons. Portal del coneixement obert de la UPC
Language:English
OAI Identifier:oai:upcommons.upc.edu:2117/413104
Online Access:https://hdl.handle.net/2117/413104
https://dx.doi.org/10.1371/journal.pcbi.1012173
Access Level:Open access
Keyword:Molecular dynamics
Biochemical simulations
Protein interactions
Protein structure databases
Protein structure
Molecular structure
Computer software
Protein extraction
Protein structure prediction
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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spelling Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflowsBayarri, GenísAndrio, PauGelpi, Josep|||0000-0002-0566-7723Hospital, AdamOrozco, ModestoMolecular dynamicsBiochemical simulationsProtein interactionsProtein structure databasesProtein structureMolecular structureComputer softwareProtein extractionProtein structure predictionSimulació per ordinadorÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaInteractive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein–ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.Authors acknowledge funding from the BioExcel Centre of Excellence for Computational Biomolecular Research (BioExcel-2 [823830]; BioExcel-3 [European Union: 101093290; Ministerio de Ciencia e Innovación: PCI2022-134976-2]) the Spanish Ministry of Science [RTI2018-096704-B-100, PID2021-122478NB-I00] the Instituto de Salud Carlos III–Instituto Nacional de Bioinformatica, Fondo Europeo de Desarrollo Regional [ISCIII PT 17/0009/0007], the European Regional Development Fund, ERFD Operative Programme for Catalunya, the Catalan Government AGAUR [SGR2021 00863] and the MDDB: Molecular Dynamics Data Bank European Repository for Biosimulation Data [101094651], all of them awarded to M.O. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer ReviewedPublic Library of Science20242024-01-0120242024-07-29journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/413104https://dx.doi.org/10.1371/journal.pcbi.1012173reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 823830 BioExcel Centre of Excellence for ComputationalBiomolecular ResearchEuropean Commission http://doi.org/10.13039/501100000780 HE 101093290 BioExcel Centre of Excellence for Computational Biomolecular ResearchAgencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PCI2022-134976-2 BIOEXCEL-3 CENTRE OF EXCELLENCE FOR COMPUTATIONAL BIOMOLECULAR RESEARCHAgencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-122478NB-I00 ESTUDIO MULTIESCALA DEL PLEGAMIENTO DE ACIDOS NUCLEICOSopen accesshttp://purl.org/coar/access_right/c_abf2Attribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/4131042026-05-27T15:37:01Z
dc.title.none.fl_str_mv Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
title Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
spellingShingle Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
Bayarri, Genís
Molecular dynamics
Biochemical simulations
Protein interactions
Protein structure databases
Protein structure
Molecular structure
Computer software
Protein extraction
Protein structure prediction
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
title_short Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
title_full Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
title_fullStr Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
title_full_unstemmed Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
title_sort Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows
dc.creator.none.fl_str_mv Bayarri, Genís
Andrio, Pau
Gelpi, Josep|||0000-0002-0566-7723
Hospital, Adam
Orozco, Modesto
author Bayarri, Genís
author_facet Bayarri, Genís
Andrio, Pau
Gelpi, Josep|||0000-0002-0566-7723
Hospital, Adam
Orozco, Modesto
author_role author
author2 Andrio, Pau
Gelpi, Josep|||0000-0002-0566-7723
Hospital, Adam
Orozco, Modesto
author2_role author
author
author
author
dc.subject.none.fl_str_mv Molecular dynamics
Biochemical simulations
Protein interactions
Protein structure databases
Protein structure
Molecular structure
Computer software
Protein extraction
Protein structure prediction
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Molecular dynamics
Biochemical simulations
Protein interactions
Protein structure databases
Protein structure
Molecular structure
Computer software
Protein extraction
Protein structure prediction
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
description Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein–ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024-01-01
2024
2024-07-29
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/413104
https://dx.doi.org/10.1371/journal.pcbi.1012173
url https://hdl.handle.net/2117/413104
https://dx.doi.org/10.1371/journal.pcbi.1012173
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 823830 BioExcel Centre of Excellence for ComputationalBiomolecular Research
European Commission http://doi.org/10.13039/501100000780 HE 101093290 BioExcel Centre of Excellence for Computational Biomolecular Research
Agencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PCI2022-134976-2 BIOEXCEL-3 CENTRE OF EXCELLENCE FOR COMPUTATIONAL BIOMOLECULAR RESEARCH
Agencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-122478NB-I00 ESTUDIO MULTIESCALA DEL PLEGAMIENTO DE ACIDOS NUCLEICOS
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,228081

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