WheatFspm is a Functional Structural Plant Model (FSPM) of wheat based on an innovative modelling framework for a better understanding of grass morphogenesis and C-N economy in interaction with environmental conditions
WheatFspm consists in a set of sub-models (named submodules in git) which share inputs/outputs through an MTG object:
Adapted from Gauthier et al. (2020)
- Farquhar-Wheat: Farquhar-based model of photosynthesis, stomatal conductance, organ temperature and transpiration.
- Elong-Wheat: regulation of leaf and internode elongation by C and N metabolites, temperature and coordination rules.
- Growth-Wheat: growth in biomass of leaves, internodes and roots ; related consumption in C and N metabolites.
- CN-Wheat: synthesis and degradation of C and N metabolites at organ level and allocation between tillers' organs.
- Respi-Wheat: respiratory-costs related to the main biological processes.
- Senesc-Wheat: organ senescence and consequences in organ biomass, green area and remoblisation of C and N metabolites.
- Fspm-Wheat: interfaces (facades) for reading/updating information between each sub-model and the MTG. Also includes the scripts to be run for using all sub-models.
WheatFspm has been tested on Windows 10 64 bit and Linux Fedora 24 64 bit.
To install and use WheatFspm, you need first to install the following dependencies:
-
To run the model:
- Python >= 2.7 (not tested for Python 3)
- NumPy >= 1.7.2
- SciPy >= 0.12.1
- Pandas >= 0.14.0
- Openalea.MTG
- Openalea.Plantgl
- Openalea.Lpy
- Alinea.Caribu
- Alinea.Adel
- Alinea.Astk
-
To run the tools: Matplotlib >= 1.3.1
-
To build the documentation: Sphinx >= 1.1.3
-
To run the tests: Nose >= 1.3.0
- Download WheatFspm package from https://github.com/openalea-incubator/WheatFspm/archive/master.zip
- Extract archive
- Open a command line interpreter in your local copy of WheatFspm,
- Run command:
python setup.py install --user
This package contains Git submodules (in French).
Development is done in the different submodules.
To clone the project, please use:
git clone --recurse-submodules https://github.com/openalea-incubator/WheatFspm
If you want to update all submodules:
git submodule update --remote
Otherelse, update each one to a specific version, branch or tag, do:
cd mypackage
git fetch
git merge origin/master
- Open a command line interpreter into each copy of submodels
- Run command:
python setup.py develop --user
The scripts to run WheatFSPM are located in fspm-wheat\example
This example deals with the post-flowering stages of wheat developement under 3 nitrogen fertilisation regies (H0, H3 and H15). The main processes described are leaf senescence, C and N remobilisation, grain filling). During that stages, all vegetative organs have completed their growth. This work led to the research articles Barillot et al. (2016a) and Barillot et al. (2016b). This example has been maintained in the current version ; results of above papers were generated using the tag release-1.0 of CN-Wheat.
To run the example:
- Open a command line interpreter in
WheatFspm\fspm-wheat\example\NEMA - Run each script called main.py located in NEMA_H0, NEMA_H3, NEMA_H15:
python main.py
This example deals with the effects of leaf inclination, radiations regimes, plant density and sowing patterns on plant metabolism and grain filling during the post-flowering stages.
This work led to the research article Barillot et al. (2019).
The scripts have not been maintained in the current version but are available using tags paper_FSPMA16 or each submodule.
To run the example:
- Open a command line interpreter in
WheatFspm\fspm-wheat\example\Papier_FSPMA2016 - Run each script called main.py located in the different sub-directories:
python main.py
This example deals with the early vegetative stages of wheat development. It mainly covers the processes of leaf, internode and roots growth. Tillering is simplified: tiller emergence is a model input while tiller metabolism and growth is approximated from that of the main stem. This work led to the research article Gauthier et al. (2020). Results were obtained from the tag paper_JXBot_2020. Code archives and a Singularity container are also available here.
To run the example:
- Open a command line interpreter in
WheatFspm\fspm-wheat\example\Vegetative_stages - Run script main.py:
python main.py
Work in progress for simulating wheat plasticity to contrasted environments
- Romain BARILLOT - model designing, development and validation - rbarillot
- Marion GAUTHIER - model designing, development and validation - mngauthier
- Camille CHAMBON - software designing, development, deployment and optimization - cachambon
- Bruno ANDRIEU - model designing and validation, scientific project management - bandrieu
- Christian FOURNIER - christian34
- Christophe PRADAL - pradal
- INRAE: salaries of permanent staff
- French Research National Agency: projects Breedwheat (ANR-10-BTBR-03) and Wheatamix (ANR-13-AGRO0008): postdoctoral research of R.Barillot
- itk company: funded the PhD thesis of M.Gauthier
This project is licensed under the CeCILL-C License - see file LICENSE for details