Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows

Francois Moreews 1, 2 Dominique Lavenier 2
2 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
Abstract : To be easily constructed, shared and maintained, complex in silico bioinformatics analysis are structured as workflows. Furthermore, the growth of computational power and storage demand from this domain, requires workflows to be efficiently executed. However, workflow performances usually rely on the ability of the designer to extract potential parallelism. But atomic bioinformatics tasks do not often exhibit direct parallelism which may appears later in the workflow design process. In this paper, we propose a Model-Driven Architecture approach for capturing the complete design process of bioinformatics workflows. More precisely, two workflow models are specified: the first one, called design model, graphically captures a low throughput prototype. The second one, called execution model, specifies multiple levels of coarse grained parallelism. The execution model is automatically generated from the design model using annotation derived from the EDAM ontology. These annotations describe the data types connecting differents elementary tasks. The execution model can then be interpreted by a workflow engine and executed on hardware having intensive computation facility.
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Contributeur : Francois Moreews <>
Soumis le : mercredi 18 mai 2016 - 17:35:52
Dernière modification le : mercredi 16 mai 2018 - 11:23:35

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Francois Moreews, Dominique Lavenier. Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows. 2016. 〈hal-00908842〉

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