L-Grass

L-Grass is a Functional Structural Plant Model (FSPM) of perennial rye grass morphogenesis and phenology.

L-Grass simulates:

• Above-ground 3D architecture and morphogenesis (leaf extension, growth and tillering) as a self-regulated system. See Verdenal et al. (2008).
• Morphogenesis of the root system in 3D. The model is inspired from ArchiSimple model and accounts for C partioning between shoot and roots. See [Migault thesis (2015)] (https://hal.inrae.fr/tel-02799991)
• Floral transition of individual apex and heading of the spike according to temperature, photoperiod and vegetative morphogenesis. See Rouet et al. (2022).

Table of Contents

• Installation
  • Prerequisites
  • Installing
    • Users
    • Developers
• Usage
• Credits
  • Authors
  • Contributors
  • Funding
• License

Installation

Lgrass has been tested on Windows 10 64 bit. Lgrass was iniatially implemented in Python 2.7 and is now under Python 3.

Prerequisites

Lgrass has the following dependencies (see documentation in the links provided, instructions for their installation are given in Installing):

• To run the model:
  • Python >= 3.7 (old releases in Python 2.7)
  • NumPy
  • SciPy
  • Pandas
  • Openalea.MTG
  • Openalea.Plantgl
  • Openalea.Lpy
  • Alinea.Caribu
  • ephem
  • geopy
  • xlrd

Installing

Lgrass has to be installed in a conda environment containing all dependencies.

• Install Miniconda 2 or 3 for Python 3.7: https://docs.conda.io/en/latest/miniconda.html
• Create a new environment in an Anaconda prompt: conda create -n Lgrass python=3.7 openalea.mtg openalea.plantgl openalea.lpy alinea.caribu ephem geopy xlrd -c conda-forge -c fredboudon

Users

• Download Lgrass package from https://github.com/openalea-incubator/lgrass/archive/master.zip
• Extract archive
• Open an Anaconda promt in your local copy of Lgrass,
• Activate the conda environment: conda activate Lgrass
• Run command: python setup.py install --user

Developers

• Fork Lgrass repository in your own account
• Clone your fork with git : git clone https://github.com/my_account/lgrass.git
• Open an Anaconda promt in your cloned copy of Lgrass,
• Activate the conda environment: conda activate Lgrass
• Run command: python setup.py develop --user

Updating submodules

If you want to update Lgrass:

git pull origin/master

Usage

• For a basic usage of Lgrass, go to lgrass/lgrass and open lgrass.lpy with the Lpy software which was installed in your conda environment. Then click on Run
• For external call of lgrass, examples are provided in lgrass/example

The version of lgrass integrating the flowering stages (Lgrass-F) is available in:

• lgrass/example/calibration_GEVES_2021

calibration_GEVES_2021

This example deals with the implementation of the reproductive development in the model and its calibration by Rouet et coll. This work led to the research article Rouet et al. (2022). Results were obtained from the tag paper_ISPLANTS_2022. To run the model used for the paper, please download the code archives at

Credits

Authors

• Alban VERDENAL - model designing, development and validation
• Vincent MIGAULT - model designing, development and validation
• Simon ROUET - model designing, development and validation - SimonRouet
• Abraham ESCOBAR-GUTIERREZ - model designing and validation, scientific project management
• Didier COMBES - model designing, development and validation, scientific project management - dicombes

Contributors

• Romain BARILLOT - rbarillot
• Thibault RAQUET - traquet
• Jean-Louis DURAND

Funding

• INRAE: salaries of permanent staff
• itk company and ANRT: funded the Cifre PhD thesis of V. Migault
• Région Nouvelle-Aquitaine: funding of PhD thesis of S. Rouet to be continued...

License

This project is licensed under the CeCILL-C License - see file LICENSE for details