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dc.contributor.authorEjarque Artigas, Jorge
dc.contributor.authorAndrio Balado, Pau
dc.contributor.authorHospital Gasch, Adam
dc.contributor.authorConejero Bañón, Francisco Javier
dc.contributor.authorLezzi, Daniele
dc.contributor.authorBadia Sala, Rosa Maria
dc.contributor.authorGelpi Buchaca, Josep Lluís
dc.contributor.otherUniversitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2023-03-23T10:37:51Z
dc.date.available2023-03-23T10:37:51Z
dc.date.issued2022
dc.identifier.citationEjarque, J. [et al.]. The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows. A: IEEE International Conference on e-Science. "2022 IEEE 18th International Conference on e-Science, eScience 2022: Salt Lake City, Utah, USA, 10-14 October 2022: proceedings". Institute of Electrical and Electronics Engineers (IEEE), 2022, p. 357-366. ISBN 978-1-6654-6124-5. DOI 10.1109/eScience55777.2022.00049.
dc.identifier.isbn978-1-6654-6124-5
dc.identifier.urihttp://hdl.handle.net/2117/385365
dc.description.abstractDeveloping complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the pipelines on distributed systems increases the complexity of these developments. To address these issues, we propose a methodology to simplify the implementation of these workflows on HPC infrastructures. It combines a library, the BioExcel Building Blocks (BioBBs), that allows scientists to implement biomolecular pipelines as Python scripts, and the PyCOMPSs programming framework which allows to easily convert Python scripts into task-based parallel workflows executed in distributed computing systems such as HPC clusters, clouds, containerized platforms, etc. Using this methodology, we have implemented a set of computational molecular workflows and we have performed several experiments to validate its portability, scalability, reliability and malleability.
dc.description.sponsorshipThis work has been supported by Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033 under contract PID2019-107255GB-C21, by the Generalitat de Catalunya under contracts 2017-SGR-01414 and 2017-SGR1110, by the European Commission through the BioExcel Center of Excellence (Horizon 2020 Framework program) under contracts 823830, and 675728. This work is also partially supported by the CECH project which has been co-funded with 50% by the European Regional Development Fund under the framework of the ERFD Operative Programme for Catalunya 2014-2020, with a grant of 1.527.637,88€.
dc.format.extent10 p.
dc.language.isoeng
dc.publisherInstitute of Electrical and Electronics Engineers (IEEE)
dc.subjectÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica
dc.subjectÀrees temàtiques de la UPC::Informàtica::Arquitectura de computadors
dc.subject.lcshBioinformatics
dc.subject.lcshElectronic data processing -- Distributed processing
dc.subject.lcshParallel processing (Electronic computers)
dc.subject.otherParallel workflows
dc.subject.otherProgramming models
dc.subject.otherDistributed computing
dc.titleThe BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows
dc.typeConference report
dc.subject.lemacBioinformàtica
dc.subject.lemacProcessament distribuït de dades
dc.subject.lemacProcessament en paral·lel (Ordinadors)
dc.identifier.doi10.1109/eScience55777.2022.00049
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttps://ieeexplore.ieee.org/document/9973566
dc.rights.accessOpen Access
local.identifier.drac35612450
dc.description.versionPostprint (author's final draft)
dc.relation.projectidinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-107255GB-C21/ES/BSC - COMPUTACION DE ALTAS PRESTACIONES VIII/
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/823830/EU/BioExcel Centre of Excellence for ComputationalBiomolecular Research/BioExcel-2
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel
local.citation.authorEjarque, J.; Andrio, P.; Hospital, A.; Conejero, J.; Lezzi, D.; Badia, R.M.; Gelpi, J.L.
local.citation.contributorIEEE International Conference on e-Science
local.citation.publicationName2022 IEEE 18th International Conference on e-Science, eScience 2022: Salt Lake City, Utah, USA, 10-14 October 2022: proceedings
local.citation.startingPage357
local.citation.endingPage366


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