OpenAlea: Scientific Workflows Combining Data Analysis and Simulation

Christophe Pradal 1, 2, 3 Christian Fournier 4 Patrick Valduriez 5, 1 Sarah Cohen-Boulakia 1, 2, 5, 6
2 VIRTUAL PLANTS - Modeling plant morphogenesis at different scales, from genes to phenotype
CRISAM - Inria Sophia Antipolis - Méditerranée , INRA - Institut National de la Recherche Agronomique, UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
5 ZENITH - Scientific Data Management
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : Analyzing biological data (e.g., annotating genomes, assembling NGS data...) may involve very complex and inter-linked 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 work-flow 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.
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Christophe Pradal, Christian Fournier, Patrick Valduriez, Sarah Cohen-Boulakia. OpenAlea: Scientific Workflows Combining Data Analysis and Simulation. SSDBM: Scientific and Statistical Database Management, Jun 2015, San Diego, United States. ⟨10.1145/2791347.2791365⟩. ⟨hal-01166298⟩

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