Hydraulic ViPeR

Virtual Phenotyping pipeline for Hydraulic Root traits





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What is Hydraulic ViPeR?

Hydraulic Viper is a virtual phenotyping pipeline for root hydraulic traits.

It is a collection of models working at different scales and able to simulate root water uptake

1. CPantBox creates of root system architecture.

2. GRANAR-MECHA estimate the specific radial and axial hydraulic conductivities for various types of roots, taking into account root anatomy, sub-cellular hydraulic properties, and maturation rates.

3. Hydrus-1D generates the initial soil water profile.

4. MARSHAL solve the root system hydraulic architecture and link the rhizosphere hydraulic conductivity with the root system using equation from Van Lier, et al. 2006 and Schroder, et al., 2009

5. Convergence between the water demand and the estimated root water uptake.

6. Hydrus-1D resolve water movement in the soil domain following Couvreur, et al. 2012 macro-hydraulic properties for root water uptake.

7. The atmospheric boundary condition are set following the Penman-Monteith equations coupled with weather data from NASA POWER

Installing Hydrualic Viper

Hydraulic Viper is a multi models pipeline which run on linux OS

1. Load the modules

CMake 3.9.6 ; GCC 7.3.0 ; Python 3.7.4 ; R 3.6.1

2. Download source code

git clone https://github.com/HydraulicViper/HydraulicViper/tree/MaizeB73.git

3. compile CPlantBox

cd ./CPlantBox
rm -f CMakeCache.txt
srun cmake . && make

4. compile Hydrus

cd Hydrus
cmake . [-G "MSYS Makefiles"] && make

5. Run Hydraulic Viper

Rscript Rscript B73_lite.R

Feeling adventurous? Check out the source code.

View source code

Using Hydraulic Viper

Input files

  • B73.xml : CplantBox input parameter file
  • Weather.csv : Weather time series associated with ET0, LAI, Transpiration data
  • Soil_type.xlsx : Lookup table for Soil hydraulic parameter
  • Zea_mays_CT.xml : General parameters for GRANAR anatomies

Ouput

Hydraulic Viper output are stored... 

 # R script example 
 
library(tidyverse)

About us

Hydraulic Viper was developed at the Université catholique de Louvain, in the Earth and Life Insititute, in the lab of Guillaume Lobet.

The primary developpers of the model are Adrien Heymans and Valentin Couvreur.

Hydraulic viper is in prep:

Quantitative multi-scale analysis of water flow determinants in the soil-root system of maize plant
Adrien Heymans, Valentin Couvreur, Clément Saint Cast, Guillaume Lobet
..., 2023

Hydraulic Viper is released under a GNU General Public Licence v3.0, which means that distribution and use and binary forms, with or without modification, are permitted under the GNU General Public License v3 and provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
Source code on GitHub