Architecture de Dataflow pour des systèmes modulaires et génériques de simulation de plante

Christophe Pradal 1, 2
1 ZENITH - Scientific Data Management
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier, CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : Biological modeling, particularly of plant growth and functioning, is a rapidly expanding field that is useful in addressing climate change and food security issues at the global level. Modeling and simulation are essential tools for understanding the complex relationships between plant architecture and the processes that influence their growth in a changing environment. For plant modeling, a large number of formalisms have been developed in many disciplines and at different scales of representation. The objective of this thesis is to define a modular architecture that allows to simulate structural-functional plant systems by reusing and assembling different existing models. We will first study the different approaches to software reuse proposed by Krueger, then blackboard systems, and scientific workflow systems. These different approaches are used to cooperate, reuse and assemble software artifacts in a modular manner. Based on the observation that these systems provide the abstractions necessary for the integration of various artifacts, our working hypothesis is that a hybrid architecture, based on blackboard systems with dataflow-driven procedural control, would both achieve modularity while allowing the modeler to maintain control over execution. In Chapter 2, we describe the OpenAlea platform, a platform with software components and a scientific workflow system, allowing the assembly and composition of models through a visual programming interface. In Chapter 3, we propose a data structure for the blackboard, combining a topological representation of plant architecture at different scales, the Multiscale Tree Graph, and its geometric spatialization using the 3D PlantGL library. In chapter 4, we present the $\lambda$-dataflows, an extension of dataflows allowing to couple simulation and analysis. Then, in Chapter 5, we present a first application, which illustrates the use of a generic gramineous leaf model in different plant models. Finally, in Chapter 6, we present all the architectural elements used to develop a generic framework for modelling the development of foliar diseases in an architectural canopy. The architecture presented in this thesis and its implementation in OpenAlea are a first step towards the realization of open integrative modeling platforms, allowing the cooperation of heterogeneous models in biology. The use of scientific workflow formalism in analysis and simulation makes it possible to consider in the short term the development of collaborative and distributed simulation platforms on a large scale.
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Christophe Pradal. Architecture de Dataflow pour des systèmes modulaires et génériques de simulation de plante. Modélisation et simulation. Université de Montpellier, 2019. Français. ⟨tel-02193606⟩

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