BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations

We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein...

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Autores: Bayarri, Genís, Andrio, Pau, Hospital, Adam, Orozco, Modesto, Gelpi, Josep|||0000-0002-0566-7723
Formato: artículo
Fecha de publicación:2022
País:España
Recursos:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/370057
Acesso em linha:https://hdl.handle.net/2117/370057
https://dx.doi.org/10.1093/nar/gkac380
Access Level:acceso abierto
Palavra-chave:Molecular dynamics
Biomolecular simulations
BioExcel Building Blocks
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
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spelling BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulationsBayarri, GenísAndrio, PauHospital, AdamOrozco, ModestoGelpi, Josep|||0000-0002-0566-7723Molecular dynamicsBiomolecular simulationsBioExcel Building BlocksMolecular dynamicsSimulació per ordinadorÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaWe present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.Spanish Ministry of Science [RTI2018-096704-B-100]; Catalan SGR [2017SGR1110]; European Union's Horizon 2020 research and innovation program [BioExcel-2 project, 823830]; SIFECAT Ris3Cat Clúster Emergente del Cerebro Humano (CECH) [001-P-001682]; Fondo Europeo de Desarrollo Regional (FEDER); Instituto Nacional de Bioinformática, ISCIII, Biomolecular and Bioinformatics Resources Platform [ISCIII PT17/0009/0007 and PT17/0008/0001]; Fondo Europeo de Desarrollo Regional (FEDER); MINECO Severo Ochoa Award of Excellence (Government of Spain) (to IRB Barcelona). Funding for open access charge: BioExcel Centre of Excellence for ComputationalBiomolecular Research, EU-funded project [823830].Peer ReviewedOxford University Press20222022-07-0120222022-07-12journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/370057https://dx.doi.org/10.1093/nar/gkac380reponame: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 Researchopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial 4.0 Internationalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3700572026-05-27T15:37:01Z
dc.title.none.fl_str_mv BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
title BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
spellingShingle BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
Bayarri, Genís
Molecular dynamics
Biomolecular simulations
BioExcel Building Blocks
Molecular dynamics
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
title_short BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
title_full BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
title_fullStr BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
title_full_unstemmed BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
title_sort BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
dc.creator.none.fl_str_mv Bayarri, Genís
Andrio, Pau
Hospital, Adam
Orozco, Modesto
Gelpi, Josep|||0000-0002-0566-7723
author Bayarri, Genís
author_facet Bayarri, Genís
Andrio, Pau
Hospital, Adam
Orozco, Modesto
Gelpi, Josep|||0000-0002-0566-7723
author_role author
author2 Andrio, Pau
Hospital, Adam
Orozco, Modesto
Gelpi, Josep|||0000-0002-0566-7723
author2_role author
author
author
author
dc.subject.none.fl_str_mv Molecular dynamics
Biomolecular simulations
BioExcel Building Blocks
Molecular dynamics
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
topic Molecular dynamics
Biomolecular simulations
BioExcel Building Blocks
Molecular dynamics
Simulació per ordinador
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
description We present BioExcel Building Blocks Workflows, a web-based graphical user interface (GUI) offering access to a collection of transversal pre-configured biomolecular simulation workflows assembled with the BioExcel Building Blocks library. Available workflows include Molecular Dynamics setup, protein-ligand docking, trajectory analyses and small molecule parameterization. Workflows can be launched in the platform or downloaded to be run in the users’ own premises. Remote launching of long executions to user's available High-Performance computers is possible, only requiring configuration of the appropriate access credentials. The web-based graphical user interface offers a high level of interactivity, with integration with the NGL viewer to visualize and check 3D structures, MDsrv to visualize trajectories, and Plotly to explore 2D plots. The server requires no login but is recommended to store the users’ projects and manage sensitive information such as remote credentials. Private projects can be made public and shared with colleagues with a simple URL. The tool will help biomolecular simulation users with the most common and repetitive processes by means of a very intuitive and interactive graphical user interface. The server is accessible at https://mmb.irbbarcelona.org/biobb-wfs.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022-07-01
2022
2022-07-12
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/2117/370057
https://dx.doi.org/10.1093/nar/gkac380
url https://hdl.handle.net/2117/370057
https://dx.doi.org/10.1093/nar/gkac380
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
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/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-NonCommercial 4.0 International
http://creativecommons.org/licenses/by-nc/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
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 15,300719

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