Introduction to plant modelling:the Functional Structural Plant Models.

Dates: 30 Nov. - 3 Dec. 2020

Live Tutorials on Binder:

Monday 30/11 : Prerequisite

• 9h - 12h00 :

  • 15min : Class presentation - Frédéric Boudon (FB)
  • 15min : The modelling approach - Video - Christophe Pradal (CP)
  • 1h : Introduction to programming - Video - CP
    • The Python modelling language
      • types, control statements, functions, modules
      • numeric computation (numpy, scipy), data analysis (dataframe, pandas)
      • visualization (matplotlib)
  • 15mn: Modeling environment (conda, notebooks) and installation
  • 1h15 : Exercises (CP, FB, CF)
    • see the corresponding notebook
    • To launch the notebooks, launch in a conda console
      • jupyter notebook "python/PythonLecture.ipynb"

• 14h00 - 17h00 :

  • 45min : Plant Architecture - Video - Evelyne Costes (EC)
    • Plant organisation (meristems, phytomers, growth units, axis, crown, ...)
    • Ramification, Growth, Reiteration
    • Architectural Models
  • 15min : Questions - EC
  • 50min : Architecture phenotyping - Video - FB
    • Part 1 - Part 2 - Part 3 - Part 4 - Part 5
  • 15min : Questions - FB
  • 1h : Practical work and exercises : Analysis of LIDAR data - FB & Benoît Pallas (BP)
    • see the notebook 1 and notebook 2
    • To launch the notebooks, launch in a conda console
      • jupyter notebook "laserreconstruction/Reconstruction from laser scans.ipynb"
      • jupyter notebook "laserreconstruction/Analysis of laser scans.ipynb"

Tuesday 01/12 : Architecture modelling

• 9h - 12h :

  • 1h30 : The L-System formalism - Video - FB
    • Part 1 - Part 2 - Part 3 - Part 4
    • Topological representations of plants with strings.
    • Turtle geometric interpretation.
    • Rules of production, decomposition, sensitive to contexts, to the environment ...
    • Fractals
  • 15min - Questions - FB
  • 1h15 : Practical work and exercises - FB & CP
    • see the notebook 1
    • To launch the notebooks, launch in a conda console
      • jupyter notebook lsystem/L-systems.ipynb

• 14h00 - 17h00 :

  • 45min : Simulating fruit tree with L-systems - Video - FB

    • Part 1 - Part 2
    • Rules of organ development using a thermal time model
    • Stochastic modelling of budburst
    • Branch geometry (empirical model, mechanistic model)

  • 15min : Questions - FB

  • 1H : Practical work and exercises - FB & BP

    • see the notebook 1, notebook 2 and notebook 3
    • To launch the notebooks, launch in a conda console
      • jupyter notebook "archimodelling/ArchiModelling.ipynb"
      • jupyter notebook "archimodelling/Apple Tree Simulation - Organs.ipynb"
      • jupyter notebook "archimodelling/Apple Tree Simulation - Architecture.ipynb"

  • 1h : Modelling project - FB, CP, RP, BP, CF

Wednesday 02/12 : Modelling functioning

• 9h - 12h :

  • 45min : Ecophysiological processes. From crop model to FSPM - Video - BP
    • Part 1 - Part 2
    • Light interception, photosynthesis, Carbon Balance, Water Balance
    • Crop vs FSPM approaches
  • 15min : Questions - BP
  • 45min : Modelling Light and photosynthesis: Christian Fournier (CF)
    • Introduction - Video - CF
    • Light - Video - CF
    • Photosynthesis - Video - CF
  • 15min : Questions - CF
  • 1h : Practical work and exercises on light interception and photosynthesis - CF & RP
    • To launch the notebooks, launch in a conda console
      • jupyter notebook "light/light_interception.ipynb"

• 14h00 - 17h00 :

  • 45min : Recent work on carbon allocation model / signaling in apple tree - Video - Benoit Pallas
    • Part 1 - Part 2 - Part 3
  • 15min : Questions - BP
  • 1h : Practical work on carbon allocation model - BP & FB
  • 1h : Modelling project - FB, CP, RP, BP, CF

Thursday 03/12 : Sensitivity analysis and project

• 9h - 12h :

  • 45min : Sensitivity analysis - Video - Raphael Perez (RP)
    • Concepts and methods
  • 15min : Questions
  • 1H : Practical work and exercises. - RP & CF - see the notebook 1 and notebook 2 - To launch the notebooks, launch in a conda console - jupyter notebook "sensitivityanalysis/TD_SensitivityAnalysis_Part1.ipynb" - jupyter notebook "sensitivityanalysis/TD_SensitivityAnalysis_Part2.ipynb"
  • 1h : Modelling project - FB, CP, RP, BP, CF

• 14h - 17h :

  • 2H : Modelling project
  • 1H : Presentation of models first draft.

Wednesday 16/12 Afternoon : Presentation of the modelling projects

• 13h30 - 17h30 :
  • Each group will have to present its work for 15 minutes. It will be followed by 10 minutes of questions and 5 minutes of deliberation.

Modelling project

During this training, some time is devoted to the realization of an architectural and functional model (called FSPM) of a fruiting tree. Some hypothesis on the model should be set and addressed using a sensitivity analysis on the model. A presentation of the model, its hypothesis, the related bibliography, the analysis of the model and the biological conclusion should be prepared for the examination day. The presentation should follow a modelling approach as presented in the first day. A critical point will be to present clearly the research question that the model will address, and its hypotheses. The list of proposed fruiting trees to model with related information are given here

Groups of two should be constituted and each group will work on a different tree specie. To determine assignment, you need to fill the following form. If two people are already assigned to a tree specie, the specie is no more selectable.

Modelling environment

Conda Installation

Conda is a package manager that can be installed on Linux, Windows, and Mac. If you have not yet installed conda on your computer, follow these instructions:

Conda Installation. Follow instructions for Miniconda.

Conda Download. Use the Python 3.8 based installation.

Modules installation

Create an environment named training

Launch a console (See Anaconda Prompt in Start menu on windows)

conda create -n training -c fredboudon -c conda-forge python=3.8 openalea.pgljupyter openalea.plantscan3d alinea.caribu alinea.astk matplotlib pandas scipy git 

Install sensitivity analysis packages:

conda install -n training -c conda-forge r-irkernel R rpy2 r-rmarkdown r-car r-lme4 r-performanceanalytics r-agricolae r-lhs r-planor

Activate the training environment:

conda activate training

Under R, you can install everything using:

install.packages('sensitivity' ) # TOCHECK is still necessary

Installation of the training material

In a convenient directory, you will now download the training material using the following commands.

cd /path/to/your/documents
git clone https://github.com/openalea-training/hbma312_training.git
cd hbma312_training
python setup.py develop

To update the training material during the training

cd /path/to/your/documents/hbma312_training
git pull