COURSES

-> About this Resource
Scope *______
Map *____

-> Preliminary Courses
Contents & Objectives *__________________
Map *____
-> Botany
Contents & Objectives *__________________
Map *____
-> Axis Typology Patterns
Typology basis *___________
Pictograms *_________
Sexuality & development *___________________
Growth *______
Branching rhythms *______________
Branching delays *_____________
Branching positional *________________
Branching arrangement *__________________
Axis orientation *_____________
Architectural models *________________
-> Architectural Unit
About Arc. Models *______________
Models limitations *______________
Architectural Units *______________
Reiteration *_________
Sequence of development *___________________
Morphogenetic gradients *___________________
Physiological age *_____________
-> An Example
Wild Cherry (young) *_______________
Wild Cherry (adult) *______________
Wild Cherry (mature) *________________
Quiz *____
Case study Quiz *_____________
Supplementary resources *____________________

-> Eco-Physiology
Contents & Objectives *__________________
Map *____
-> Growth Factors
Factors affecting Growth *___________________
Endogenous Processes *_________________
Environmental Factors *_________________
Thermal Time *___________
-> Light interaction
P.A.R. *_____
Light absorption *_____________
Photosynthesis *___________
Respiration *_________
Maintenance respiration *__________________
L.U.E. Model *__________
Density effect *___________
Density effect on crop *__________________
-> Biomass
Biomass Pool *__________
Biomass Partitioning *_______________
Crop models *__________
A Crop model example *__________________
Quiz *____
Supplementary resources *___________________

-> Applied Mathematics
Contents & Objectives *__________________
Map *____
-> Probabilities
Section contents *____________
Discrete Random Variable *___________________
Expected value, Variance *___________________
Properties *________
-> Useful Laws
Bernoulli Trials *___________
Binomial Law *__________
Geometric Law *____________
Negative Binomial Law *_________________
-> Dynamic systems
Section contents *_____________
Useful functions *____________
Beta density *__________
Exercises *________
Negative Exponential *________________
Systems functions *______________
Discrete dynamic systems *___________________
Parameter Identification *__________________
Parameter estimation *________________
Supplementary Resources *____________________


-> GreenLab courses
GreenLab presentation *__________________
-> Overview
Presentation & Objectives *____________________
Map *____
Growth and components *___________________
Plant architecture *_______________
Biomass production *________________
Modelling - FSPM *______________
GreenLab principles *________________
Applications *__________
Supplementary resources *_____________________
-> Principles
Presentation & Objectives *____________________
Map *____
-> About modelling
Scientific disciplines *________________
Organs: tree components *___________________
Factors affecting growth *___________________
Model-simulation workflow *____________________
GreenLab inherits from *__________________
GreenLab positioning *_________________
The growth cycle *______________
Inside the growth cycle *___________________
Implementations *______________
Supplementary resources *____________________
-> Development
Presentation & Objectives *____________________
Map *____
Modelling Scheme *______________
Tree traversal modes *________________
-> Stochastic modelling
Principles *_______
-> Development
Growth Rhythm *____________
Damped growth *____________
Viability *______
Rhythmic axis *___________
Branching *________
Stochastic automaton *_________________
-> Organogenesis equations
Principles *_______
Organ cohorts *___________
Organ numbering *_____________
Substructure factorization *____________________
Stochastic case *____________
-> Structure construction
Construction modes *_______________
Construction basis *______________
Axis of development *________________
Stochastic reconstruction *___________________
Implicit construction *________________
Explicit construction *________________
3D construction *____________
Supplementary resources *____________________
-> Production-Expansion
Presentation & Objectives *____________________
Map *____
-> EcoPhysiology reminders
Relevant concepts *______________
Temperature *__________
Light interception *______________
Photosynthesis *___________
Biomass common pool *_________________
Density *______
-> Principals
Growth cycle *__________
Refining PbMs *___________
Organ cohorts *___________
GreenLab vs PbM & FSPM *___________________
-> GreenLab's equations
Summary *_______
Production equation *_______________
Plant demand *__________
Organ dimensions *______________
A dynamic system view *__________________
Equation terms *____________
Full Model *________
Model behaviour *______________
Supplementary resources *____________________
-> Applications
Presentation & Objectives *____________________
Map *____
-> Measurements
Agronomic traits *_____________
Mesurable/hidden param. *___________________
Fitting procedure *______________
-> Fitting structure
Principles *_______
-> Development
Simple development *_______________
Damped growth *____________
Rhythmic growth *_____________
Rhythmic growth samples *___________________
Mortality *_______
Branching *________
-> Crown analysis
Analysis principles *______________
Equations *________
Example / Exercise *_______________
-> Case study
Plant Architecture *______________
Development simulation *__________________
Introducing Biomass *_______________
Biomass partitioning *_______________
Equilibrium state *_____________
Supplementary resources *____________________

-> Tools (software)
Presentation & Objectives *_____________________
Map *____
Fitting, Stats *___________
Simulation *_________
Online tools *__________

GreenLab Course

Overview

History.


Authors share a long history in plant modelling, from late seventies to nowadays.

Computational models

    Started in the late seventies, the first developments of Ph. de Reffye on Coffea lead to the definition of a structural or geometrical plant growth model called AMAP.
    This model became popular for various applications included Computer Graphics.


      Structural 3D plant simulations
        Left : Benson plotter 4 colors drawing(1984)
        Middle: Tektronix 256 colors screen shot on a Coffee Tree branch (1988)
        Right: Silicon Graphics simulated Cypress (1990).


    In the late eighties, the structure was used as a transport path support to host functional aspects such as leaf evapotranspiration and secondary growth, building a Functional Structural Plant Model (FSPM).


      An FSPM implementation: tha Amap Para Software P. de Reffye, F. Blaise, 1993
        Plant structure, leaf evapotranspiration and secondary growth simulation


      Those approchaes were computational:
      the structure is simulated applying rules of development defined from field observations.

Mathematical models

    The next model generation, developped in cooperation with China, called GreenLab is a mathematical model.

    It differs from computational models from the fact that both development and functional process are described by equations and not strictely resulting from simulation.
    The model quantifies therefore the structure (the number of organs, their apparition time ...) without requesting a exhaustive structural implementation.
    This plant model is therefore seen as a classical mathematical dynamic model.
    Such an approach makes the model be reversable, making parameter identification and optimization more affordable.

    In its latest developments GreenLab can afford functional feedback on the structure under various environmental conditions.


      Plant structure plasticity due to density simulated by the GreenLab Model
        This example shows three tree growth stages under two different densities.
        The underlying concept is the Projection Area, that thresholds branching and axis lengthning in the structure development.
        (© Digiplante software, Ecole Centrale of Paris, 2007)



      Plant structure plasticity due to environmental conditions simulated by the GreenLab Model
        This example shows three Crysanthemium growth stages under two different light and temperature conditions.
        (© GreenScilab software, LIAMA-CASIA, 2007)

Definition

SPM (Structural Plant Model)
Modelling. (abrev.) Stands for "Structural Plant Model", or "Geometrical Plant Model". Qualifies a mathematical or computational model that expresses the plant architecture (the structure) dynamics thru the development. Such a model offers usually a 3D output.

Definition

FSPM (Functional Structural Plant Model)
Modelling. (abrev.) Stands for "Functional Structural Plant Model". Qualifies a mathematical or computational model that expresses both the plant architecture (the structure) dynamics thru the development and its production dynamics thru the organ geometrical development.

Definition

(Mathematical) Model
Mathematics. Set of equations, forming a simplified representation of a system.