GreenLab structural functional plant growth model
Presentation.
GreenLab presentation
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Functional-structural plant models (FSPM) simulate plant development and growth,
usually accompanied with visualization of the plant 3D architecture.
Aside the classic process-based crop models and individual structural Plant models,
GreenLab model (De Reffye and Hu., 2003) displays an original positioning.
- An overview of GreenLab is presented first
- Principles of GreenLab are then presented
- Structural aspects of the GreenLab model follow
- Functional aspects of the GreenLab model are then explicited
- Lastly, appications section presents GreenLab model parameter fitting and a case study
GreenLab is a generic and mechanistic FSPM: various botanical architectures, as defined by (F. Hallé, 1978) can be produced by its organogenesis model, and the plant growth is governed by the competition on biomass among growing organs.
GreenLab is a mathematical dynamic model aiming to model and simulate plant structure establishment and production. It differs from computational models by the fact that both development and functional processes are described by equations.
The model therefore quantifies structure (the number of organs, etc.) without requiring exhaustive structural implementation.
It also differs from classic functional structural plant models by the fact that organ production is quantified by compartments, competing for a common biomass pool.
It also differs from biomass production based on the Beer Lambert Law, conventionally used in PBM. In a growth cycle, the model sequences organogenesis, biomass production and its partitioning in a dynamic loop.
A distinguished feature of GreenLab model is that, its organogenesis (in terms of the number of organs) and growth (in terms of organ biomass) are formulated with recurrent equations. It facilitates analytical study of model behaviour, bug-proof of simulation software, and application of efficient optimization algorithm for parameter identification or optimal control problems.
As a summary, the interest of the GreenLab model relies on its mathematical formulation as a dynamic system (Cournède et al., 2006) which allows efficient simulations, proper statistical identification and evaluation, but also an easy integration of the concepts classically used in crop models to describe plant-environment interactions (Feng et al, 2014). The latest developments also renew flexible structural representations and reconstructions (De Reffye, Jaeger, 2013).
Currently several levels of GreenLab model exist: (1) the deterministic one (GL1): plants have a fixed pattern for development without feedback from the plant growth; (2) the stochastic level (GL2): pant organogenesis parameters are probabilistic; (3) the feedback model (GL3, still on development): the plant development is dependent on the dynamic relationship between biomass demand and supply (and in turn the environment). It makes it possible to cover the different kinds of behaviour observed in real plants.
This pedagogic resource describes the deterministic and the stochastic levels (GL1 and GL2 levels).
The pedagogic resource splits as follows:
Bibliography
Cournède P.-H., Kang, M. Z., Mathieu, A., Barczi, J. F., Yan, H. P., Hu, B. G., and De Reffye, P. 2006. Structural factorization of plants to compute their functional and architectural growth. Simulation, 82(7), pp. 427-438 (access to paper and pdf)
Feng, L. , Mailhol, J. C. , Rey, H., Griffon, S., Auclair, D., de Reffye, P. 2014. Comparing an empirical crop model with a functional structural plant model to account for individual variability. European Journal of Agronomy, 53 (1) : pp. 16-27
Hallé, F., Oldemann, R.A.A., Tomlinson, P.B. 1978. Tropical trees and forests. Berlin: Springer-Verlag.
De Reffye P., Hu BG, 2003. Relevant qualitative and quantitative choices for building an efficient dynamic plant growth model: GreenLab case. In Hu BG, Jaeger M (Eds), Plant growth modelling and applications (PMA03), Proceedings of the 2003' International Symposium on Plant Growth Modeling, Simulation, Visualization and Their ApplicationsTsinghua University Press, Springer; pp. 87-107. (pdf)
De Reffye, P., Jaeger, M. 2013. Modèles mathématiques du développement et de la croissance de l'architecture des plantes. Le cas du modèle GreenLab. In Varenne, F., Silberstein, M. (Eds) Modéliser et simuler. Epistémologies et pratiques de la modélisation et de la simulation. Tome 1. Paris : Editions Matériologiques (Sciences et Philosophie, vol. Sciences et Philosophie). pp. 625-658
Requested background
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Students are supposed to master premiliminary notions:
- in Architectural Botany : ../P1_Prelim/Bota/Bota_intro.html
- in Eco-Physiology : ../P1_Prelim/EPhysio/Physio_intro.html
- on some element in Applied Mathematics : ../P1_Prelim/Math/Math_intro.html
- Introduction to plant an crop models: ../P1_Prelim/Model/Model_intro.html
Course Objectives
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The aim of this course is to enable students to:
- Learn about the GreenLab model assumptions and basis
- Understand the principles of structural modelling, derived from architectural botany
- Understand the principles of stochastic structural modelling, derived from statistical analysis
- Learn about structural parameter estimation from field measurements
- Understand the principles of fonctional modelling, derived from eco-physiology
- Understand the principles of fonctional parameter estimation