Building modular FSPM under OpenAlea: concepts and applications

Christian Fournier (1, 2) , Christophe Pradal (1, 3) , Gaëtan Louarn (4) , Didier Combes (5) , Jean-Christophe Soulié (6) , Delphine Luquet (6) , Frédéric Boudon (1, 3) , Michaël Chelle (7)

1 VIRTUAL PLANTS - Modeling plant morphogenesis at different scales, from genes to phenotype
2 LEPSE - Écophysiologie des Plantes sous Stress environnementaux
3 UMR DAP - Développement et amélioration des plantes
4 P3F - Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères
5 UEPF - Unité de recherche d'Écophysiologie des Plantes Fourragères
6 UPR AIVA - Adaptation agroécologique et innovation variétale
7 EGC - Environnement et Grandes Cultures

The OpenAlea platform (Pradal et al., 2008) was designed to facilitate the integration and inter-operability of heterogeneous models to get comprehensive FSPMs. It relies on Python gluing capabilities, that allow non intrusive integration of programs written in various languages (Fortran, C, C++, R, L-system); and on the dataflow computing paradigm, that promotes decomposition of applications into independent components that can be recombined dynamically into customized workflows. Still, a plugable collection of components is not by itself a solution to the modularity problem in FSPM modeling. First, heterogeneities between components inputs and outputs can lead to exponential needs for specific adaptors and converters to get functional assemblies. Second, several ways exist to decompose models into independent components. This can lead to incompatibilities or difficulties for re-assembly into comprehensive models. Last, users of the platform may find difficult to build applications, without some knowledge on how a simulation has to be reasoned within the data-flow computing paradigm. Here, we propose a modeling strategy to help for building coherent, yet modular FSPM under OpenAlea. We first define the key concepts of this strategy, illustrate how they can be used under Visualea and how it lead to a first set of reusable components resulting from various ecophysiological studies.

Mots clés: FSPM; MODULARITY; WHEAT; MAIZE; VINE; PHYLLOCLIMATE; RIZ

Mots clés: RICE; SIMULATION; PLANT ARCHITECTURE; ECOPHYSIOLOGIE

Domaines: Modélisation et simulation

Christian Fournier, Christophe Pradal, Gaëtan Louarn, Didier Combes, Jean-Christophe Soulié, et al.. Building modular FSPM under OpenAlea: concepts and applications. 6th International Workshop on Functional-Structural Plant Models, 2010, Davis, CA, United States. pp.109-112. ⟨hal-01192232v2⟩