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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:
Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors, Barcelona Supercomputing Center, Ejarque Artigas, Jorge, Andrio Balado, Pau, Hospital Gasch, Adam, Conejero Bañón, Francisco Javier, Lezzi, Daniele, Badia Sala, Rosa Maria, Gelpi Buchaca, Josep Lluís
Publisher Information:
Institute of Electrical and Electronics Engineers (IEEE) 2022
Document Type:
E-Ressource Electronic Resource
Index 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), Conference report
URL:
http://hdl.handle.net/2117/385365
https://ieeexplore.ieee.org/document/9973566
Availability:
Open access content. Open access content
Open Access
Note:
10 p.
application/pdf
English
Other Numbers:
HGF oai:upcommons.upc.edu:2117/385365
Ejarque, 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.
978-1-6654-6124-5
10.1109/eScience55777.2022.00049
1379092031
Contributing Source:
UNIV POLITECNICA DE CATALUNYA
From OAIster®, provided by the OCLC Cooperative.
Accession Number:
edsoai.on1379092031
Database:
OAIster

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)