• The BioExcel methodology for d...

Treffer: The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows

Title:
The BioExcel methodology for developing dynamic, scalable, reliable and portable computational biomolecular workflows
Authors:
Ejarque Artigas, Jorge, Andrio Balado, Pau, Hospital Gasch, Adam, Conejero Bañón, Francisco Javier, Lezzi, Daniele, Badia Sala, Rosa Maria, Gelpi Buchaca, Josep Lluís
Contributors:
Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors, Barcelona Supercomputing Center
Publisher Information:
Institute of Electrical and Electronics Engineers (IEEE)
Publication Year:
2022
Collection:
Universitat Politècnica de Catalunya, BarcelonaTech: UPCommons - Global access to UPC knowledge
Subject Terms:
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica, Àrees temàtiques de la UPC::Informàtica::Arquitectura de computadors, Bioinformatics, Electronic data processing -- Distributed processing, Parallel processing (Electronic computers), Parallel workflows, Programming models, Distributed computing, Bioinformàtica, Processament distribuït de dades, Processament en paral·lel (Ordinadors)
Document Type:
Konferenz conference object
File Description:
10 p.; application/pdf
Language:
English
Relation:
https://ieeexplore.ieee.org/document/9973566; info: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/; info:eu-repo/grantAgreement/EC/H2020/823830/EU/BioExcel Centre of Excellence for ComputationalBiomolecular Research/BioExcel-2; info:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel; http://hdl.handle.net/2117/385365
DOI:
10.1109/eScience55777.2022.00049
Availability:
http://hdl.handle.net/2117/385365
https://doi.org/10.1109/eScience55777.2022.00049
Rights:
Open Access
Accession Number:
edsbas.F70EA7ED
Database:
BASE

Weitere Informationen

Developing 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. ; This 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€. ; Peer Reviewed ; Postprint (author's final draft)