Towards virtual modelling environments for functional–structural plant models based on Jupyter notebooks: application to the modelling of mango tree growth and development. Issue 1 (14th December 2021)

• Record Type: Journal Article
• Authors: Vaillant, Jan; Grechi, Isabelle; Normand, Frédéric; Boudon, Frédéric
• Editors: Long, Stephen P
• Is Part Of: In silico plants. Volume 4:Issue 1(2022)
• Publication Date: 2021-12-14
• Subjects: Distributed 3D visualization -- distributed environment -- FSPM -- Jupyter notebooks -- mango tree; Plant physiology -- Periodicals; Botany -- Periodicals; Botany -- Mathematical models -- Periodicals; Crop science -- Periodicals; 580
• DOI: 10.1093/insilicoplants/diab040
• Languages: English
• ISSNs: 2517-5025

Abstract

Abstract: 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.