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 *__________

Tools (software)

Simulators

GreenLab implementations.


Since 2003, various GreenLab have beed developped.

GreenLab implementations

    Various GreenLab implementations under different environments are available.
      They also differ in their specifications, allowing stochastic simulation or not, fitting or not, retroaction on structure or not.

      The following table summarises the implementations and their specifications

    Name Environment Stochastic Retroaction Diffusion Language Main developer Usage Url
    StemGL Windows/Linux - - Freeware Matlab/Octave CIRAD - Amap & BioAgresseur Education - Research StemGL
    GreenScilab Windows Os - - Freeware Scilab Chinese Academy of Sciences - CASIA Education GreenScilab
    Xplo with GreenLab Plug-in All Os - - Freeware Java CIRAD - Amap (Amapstudio) Research Xplo
    dgpSDK libraries Windows and Linux Os X X Free to partners C++ Ecole Centrale Paris Research digiplante's software
    GLOUPS Windows and Linux Os X X Free to partners Mathlab CIRAD- Amap Unit Research GLOUPS
    QingYuan Windows Os X X Contractual Qt / C++ Chinese Academy of Sciences - CASIA Research QingYuan

      Some GreenLab implementations and their specifications


      StemGL
        StemGL is a simple tool covering both calibration and simulation aspects of biomass production and allocation. The application limits to continuous growth single stem plants, involving a limited set of parameters. The tool implements stochastic simulation capabilities. It include physiological advanced processes with density effect, seed size effect, and biomass reallocation; it offers virtual insights in the plant's growth, including evolution in biomass demand and production, details of the biomass at each date and representation of sink functions. This tool is running under Matlab and GNU Octave environments. Its iterative form makes it possible to consider coupling this tool with other models, for example physiological ones. The tool operated with a simple dataset frame of 8 parameter item sets, whatever the species considered. Datasets with adjusted parameters are already available for various temperate and tropical agronomic plants (beetroot, maize, sunflower, tmato, coffee tree, banana tree ). Climatic variations that limit production can also be introduced.
        See StemGL page (http://greenlab.cirad.fr/StemGL/) for download and tutorial.


        StemGL fitting output example (© CIRAD)



      GreenScilab
        GreenScilab is a toolbox developed by Mengzhen Kang and Qi Riu (CASIA) in the Scilab environment to run the GreenLab model.
        GreenScilab can simulate many crop plants, such as tomato, cucumber, chrysanthemum and maize, and these crops have been calibrated with experimental data.
        See GreenScilab inline page for download and tutorial.


        GreenScilab interface (© LIAMA-CASIA)



      Gloups
        Gloups (GreenLab Universal Plant Simulator) is a toolbox developed by Philippe de Reffye (CIRAD Amap) in the Matlab environment to run the GreenLab model.
        Gloups is a research prototype. It is the most advanced GreenLab implementation, allowing both simulation and fitting.
        See Gloups inline page for more information.


        Gloups interface (Snap shot M. Jaeger, CIRAD)



      Qinyuan
        Qingyuan, written by Hua Jing (CASIA) under the Qt programing environment, in C++, offers an advanced GreenLab implementation with high performance.
        It can simulate trees, such as albizia, ginkgo, pine and orange tree....
        See http://www.cybernature.com.cn/cPlant/software.html for further information.


        Some QingYuan simulations (H. Jing, LIAMA-CASIA)



      PyGMAlion and dgpSDK
        Developed by Ecole Centrale Paris, in C++, these environments are dedicated to researchers.

        PyGMAlion (Plant Growth Modelling Analysis and identification) is a C++ framework embedding modelling, simulation, parameter estimation, and discrete system sensibility analysis tools.
        dgpSDK is a library set implementing the GreenLab model with basic applications.
        See http://digiplante.mas.ecp.fr/software for further information.