Towards virtual modelling environments for functional–structural plant models based on Jupyter notebooks: Application to the modelling of mango tree growth and development

Vaillant Jan, Grechi Isabelle, Normand Frédéric, Boudon Frédéric. 2022. Towards virtual modelling environments for functional–structural plant models based on Jupyter notebooks: Application to the modelling of mango tree growth and development. In Silico Plants, 4 (1), n.spéc. Functional-structural plant models:diab040, 16 p.

Url - jeu de données - Entrepôt autre : https://github.com/fredboudon/plantgl-jupyter/ / Url - jeu de données - Entrepôt autre : https://github.com/fredboudon/plantgl-jupyter/tree/isp2022/examples / Url - jeu de données - Entrepôt autre : https://github.com/fredboudon/vmango-lab-demo/tree/isp2022

Résumé : Functional–structural plant models (FSPMs) are powerful tools to explore the complex interplays between plant growth, underlying physiological processes and the environment. Various modelling platforms dedicated to FSPMs have been developed with limited support for collaborative and distributed model design, reproducibility and dissemination. With the objective to alleviate these problems, we used the Jupyter project, an open-source computational notebook ecosystem, to create virtual modelling environments for plant models. These environments combined Python scientific modules, L-systems formalism, multidimensional arrays and 3D plant architecture visualization in Jupyter notebooks. As a case study, we present an application of such an environment by reimplementing V-Mango, a model of mango tree development and fruit production built on interrelated processes of architectural development and fruit growth that are affected by temporal, structural and environmental factors. This new implementation increased model modularity, with modules representing single processes and the workflows between them. The model modularity allowed us to run simulations for a subset of processes only, on simulated or empirical architectures. The exploration of carbohydrate source–sink relationships on a measured mango branch architecture illustrates this possibility. We also proposed solutions for visualization, distant distributed computation and parallel simulations of several independent mango trees during a growing season. The development of models on locations far from computational resources makes collaborative and distributed model design and implementation possible, and demonstrates the usefulness and efficiency of a customizable virtual modelling environment.

Mots-clés Agrovoc : modèle végétal, écosystème, croissance, développement biologique, environnement, application des ordinateurs, Mangifera indica

Mots-clés libres : Distributed 3D visualization, Distributed environment, FSPM, Jupyter Notebooks, Mango tree

Classification Agris : F60 - Physiologie et biochimie végétale
U30 - Méthodes de recherche

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement européennes : European Regional Development Fund

Auteurs et affiliations

• Vaillant Jan, CIRAD-PERSYST-UPR HortSys (REU)
• Grechi Isabelle, CIRAD-PERSYST-UPR HortSys (REU) ORCID: 0000-0002-3399-6102
• Normand Frédéric, CIRAD-PERSYST-UPR HortSys (REU) ORCID: 0000-0002-4322-8262
• Boudon Frédéric, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9636-3102 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/600176/)

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