HydroRoot

OpenAlea.HydroRoot is a hydraulic root architecture modelling and a root architecture system generator package.

Heat map representation of the incoming local radial flows on an arabidopsis root.

Description

The OpenAlea.HydroRoot package contains a root architecture simulation model coupled with a water and solute transport solver. It contains a pure hydraulic solver that is solved using resistance network analogy. It also contains a water and solute transport solver that is more complex and see the root as a continuous medium.

Authors

• Christophe Pradal
• Yann Boursiac
• Mikael Lucas
• Fabrice Bauget
• Christophe Godin
• Christophe Maurel

Institutes

CIRAD / INRAE / inria / CNRS

Status

Python package

License

CecILL-C

Installation

for user

mamba create -n myenv -c openalea3 -c conda-forge openalea.my_pkg openalea.plantgl

for developer

mamba env create -f ./conda/environment.yml

Requirements

• openalea.mtg
• openalea.plantgl
• openalea.rsml
• openalea.widgets (for the notebook examples)
• matplotlib-base
• yaml
• pandas
• numpy
• scipy

Usage

See notebooks in example directory, they are listed here and can be played following

Documentation

https://hydroroot.rtfd.io

Citations

If you use Hydroroot for your research, please cite:

1. Yann Boursiac, Christophe Pradal, Fabrice Bauget, Mikaël Lucas, Stathis Delivorias, Christophe Godin, Christophe Maurel, Phenotyping and modeling of root hydraulic architecture reveal critical determinants of axial water transport, Plant Physiology, Volume 190, Issue 2, October 2022, Pages 1289--1306, https://doi.org/10.1093/plphys/kiac281
2. Fabrice Bauget, Virginia Protto, Christophe Pradal, Yann Boursiac, Christophe Maurel, A root functional--structural model allows assessment of the effects of water deficit on water and solute transport parameters, Journal of Experimental Botany, Volume 74, Issue 5, 13 March 2023, Pages 1594--1608, https://doi.org/10.1093/jxb/erac471