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InfraPhenoGrid: A scientific workflow infrastructure for plant phenomics on the Grid

Pradal Christophe, Artzet Simon, Chopard Jérôme, Dupuis Dimitri, Fournier Christian, Mielewczik Michael, Nègre Vincent, Neveu Pascal, Parigot Didier, Valduriez Patrick, Cohen-Boulakia Sarah. 2017. InfraPhenoGrid: A scientific workflow infrastructure for plant phenomics on the Grid. Future Generation Computer Systems, 67 : pp. 341-353.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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Quartile : Outlier, Sujet : COMPUTER SCIENCE, THEORY & METHODS

Abstract : Plant phenotyping consists in the observation of physical and biochemical traits of plant genotypes in response to environmental conditions. Challenges , in particular in context of climate change and food security, are numerous. High-throughput platforms have been introduced to observe the dynamic growth of a large number of plants in different environmental conditions. Instead of considering a few genotypes at a time (as it is the case when phenomic traits are measured manually), such platforms make it possible to use completely new kinds of approaches. However, the data sets produced by such widely instrumented platforms are huge, constantly augmenting and produced by increasingly complex experiments, reaching a point where distributed computation is mandatory to extract knowledge from data. In this paper, we introduce InfraPhenoGrid, the infrastructure we designed and deploy to efficiently manage data sets produced by the PhenoArch plant phenomics platform in the context of the French Phenome Project. Our solution consists in deploying scientific workflows on a Grid using a middle-ware to pilot workflow executions. Our approach is user-friendly in the sense that despite the intrinsic complexity of the infrastructure, running scientific workflows and understanding results obtained (using provenance information) is kept as simple as possible for end-users. (Résumé d'auteur)

Mots-clés libres : Phenomics, Scientific workflows, Provenance, Grid computing, OpenAlea

Classification Agris : F30 - Plant genetics and breeding
F60 - Plant physiology and biochemistry
C30 - Documentation and information
U10 - Computer science, mathematics and statistics

Champ stratégique Cirad : Hors axes (2014-2018)

Auteurs et affiliations

  • Pradal Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2555-761X
  • Artzet Simon, INRA (FRA)
  • Chopard Jérôme, INRA (FRA)
  • Dupuis Dimitri, INRIA (FRA)
  • Fournier Christian, INRA (FRA)
  • Mielewczik Michael, INRA (FRA)
  • Nègre Vincent, INRA (FRA)
  • Neveu Pascal, INRA (FRA)
  • Parigot Didier, INRIA (FRA)
  • Valduriez Patrick, INRIA (FRA)
  • Cohen-Boulakia Sarah, INRIA (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/580898/)

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