OpenAlea: scientific workflows combining data analysis and simulation

Pradal Christophe, Fournier Christian, Valduriez Patrick, Cohen-Boulakia Sarah. 2015. OpenAlea: scientific workflows combining data analysis and simulation. In : Proceedings of the 27th International Conference on Scientific and Statistical Database Management. Gupta Amarnath (ed.), Rathbun Susan (ed.). New York : ACM, 6 p. ISBN 978-1-4503-3709-0 International Conference on Scientific and Statistical Database Management. 27, San Diego, États-Unis, 29 Juin 2015/1 Juillet 2015.

Note générale : Article N°11

Résumé : Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve very complex and interlinked steps where several tools are combined together. Scientific workflow systems have reached a level of maturity that makes them able to support the design and execution of such in-silico experiments, and thus making them increasingly popular in the bioinformatics community. However, in some emerging application domains such as system biology, developmental biology or ecology, the need for data analysis is combined with the need to model complex multi-scale biological systems, possibly involving multiple simulation steps. This requires the scientific workflow to deal with retro-action to understand and predict the relationships between structure and function of these complex systems. OpenAlea (openalea.gforge.inria.fr) is the only scientific workflow system able to uniformly address the problem, which made it successful in the scientific community. One of its main originality is to introduce higher-order dataflows as a means to uniformly combine classical data analysis with modeling and simulation. In this demonstration paper, we provide for the first time the description of the OpenAlea system involving an original combination of features. We illustrate the demonstration on a high-throughput workflow in phenotyping, phenomics, and environmental control designed to study the interplay between plant architecture and climatic change.

Classification Agris : U10 - Informatique, mathématiques et statistiques
U30 - Méthodes de recherche
A50 - Recherche agronomique
F30 - Génétique et amélioration des plantes
P40 - Météorologie et climatologie
C30 - Documentation et information

Auteurs et affiliations

• Pradal Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2555-761X
• Fournier Christian, INRA (FRA)
• Valduriez Patrick, INRIA (FRA)
• Cohen-Boulakia Sarah, INRIA (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/576434/)

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