-> 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
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Map *____
-> Probabilities
Section contents *____________
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Expected value, Variance *___________________
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Binomial Law *__________
Geometric Law *____________
Negative Binomial Law *_________________
-> Dynamic systems
Section contents *_____________
Useful functions *____________
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Exercises *________
Negative Exponential *________________
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Discrete dynamic systems *___________________
Parameter Identification *__________________
Parameter estimation *________________
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-> GreenLab courses
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-> Overview
Presentation & Objectives *____________________
Map *____
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Plant architecture *_______________
Biomass production *________________
Modelling - FSPM *______________
GreenLab principles *________________
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-> Principles
Presentation & Objectives *____________________
Map *____
-> About modelling
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Organs: tree components *___________________
Factors affecting growth *___________________
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GreenLab inherits from *__________________
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The growth cycle *______________
Inside the growth cycle *___________________
Implementations *______________
Supplementary resources *____________________
-> Development
Presentation & Objectives *____________________
Map *____
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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. *___________________
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-> 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


Functional Structural Plant Models.

Modelling plant production

Plant production (biomass) modelling may be complex, especially if structural aspects are also considered.

Plant production modelling simplified

    Sound simplifications, demonstrated by agronomic experiments, are of major interest for defining efficient models.

    At crop level, taking into account the architecture of the plant is not always necessary.
    However, knowing the distribution of the various organs at respective occurrence times and physiological ages is a key point.
    In other words, geometrical aspects may be ignored, but not the quantitative composition of the structure.
    We postulate the existence of a common biomass pool.

    Similarly, we can consider only net photosynthesis, i.e. the proportion of sugars involved as construction materials in the dry matter of the organs.

Plant modelling principles

    In general,dry matter production is divided into compartments (leaves, stems, roots, fruits) whose proportions are sinks for storage of the biomass produced.
    In fact, some organs produce biomass, such as leabes and seeds, are sources, while others consume, and are sinks, such as internodes and fruits.

    In models predicting crops, equation (1) defines the basic framework.
    Indeed, it accumulates dry matter in the compartment of interest, day after day, processing the energy received by the canopy, and sharing the dry matter among sinks.

Functional Structural Plant models (FSPM)

    Functional structural plant models are designed to model and simulate both plant structure establishment and biomass production.
    They are therefore centered on individual plants.

    Development of the architecture is controlled by a grammar or automaton that pilot organogenesis vs. time (ideally vs thermal time).
    Branches consist of phytomers, the elementary axis entity, consisting of an internode, one or more axillary buds and its leaves.
    Axillary buds may give rise to branches or fruit.

    Most FSPM approaches use the (dynamically computed) plant structure as a biomass transportation pathway.
    Production is thus not acomputed at organ compartment level, but at each individual organ level.
    Depending on its nature, each source organ may diffuse matter within the structure pathway, and/or, conversely, may consume biomass.
    In such approaches, local pools of biomass are locally stored and managed.

    FSPM implementation is based on a mesh that allows a geometric representation of the plant with polygons (these leaves will intercept light), or other shapes.
    An underlying graph structure reflects the plant architecture in order to compute the propagation of sugar and water in the structure. Source organs send the biomass they produce into the network and the sink organs intercept it according to their sink strength.

    the FSPM approach mimics the morphogenesis process in its entirety.
    Such systems provide a better understanding of the plant, but cannot address simulations on the scale of agricultural production.
    Indeed, simulation time and memory costs usually become substantial, which, added to a large number of parameters to be identified, may usually not be lead to convenient model calibration under true field conditions.