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Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake

Research output: Journal contributions › Journal articles › Research › peer-review

Standard

Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake. / Schnepf, Andrea; Black, Christopher K.; Couvreur, Valentin et al.
In: In Silico Plants, Vol. 5, No. 1, diad005, 10.08.2023.

Research output: Journal contributions › Journal articles › Research › peer-review

Harvard

Schnepf, A, Black, CK, Couvreur, V, Delory, BM, Doussan, C, Heymans, A, Javaux, M, Khare, D, Koch, A, Koch, T, Kuppe, CW, Landl, M, Leitner, D, Lobet, G, Meunier, F, Postma, JA, Schäfer, ED, Selzner, T, Vanderborght, J & Vereecken, H 2023, 'Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake', In Silico Plants, vol. 5, no. 1, diad005. https://doi.org/10.1093/insilicoplants/diad005

APA

Schnepf, A., Black, C. K., Couvreur, V., Delory, B. M., Doussan, C., Heymans, A., Javaux, M., Khare, D., Koch, A., Koch, T., Kuppe, C. W., Landl, M., Leitner, D., Lobet, G., Meunier, F., Postma, J. A., Schäfer, E. D., Selzner, T., Vanderborght, J., & Vereecken, H. (2023). Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake. In Silico Plants, 5(1), Article diad005. https://doi.org/10.1093/insilicoplants/diad005

Vancouver

Schnepf A, Black CK, Couvreur V, Delory BM, Doussan C, Heymans A et al. Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake. In Silico Plants. 2023 Aug 10;5(1):diad005. doi: 10.1093/insilicoplants/diad005

Bibtex

@article{78856eedaefa4763a1e6f763a93ec42c,
title = "Collaborative benchmarking of functional-structural root architecture models: Quantitative comparison of simulated root water uptake",
abstract = "Functional-structural root architecture models have evolved as tools for the design of improved agricultural management practices and for the selection of optimal root traits. In order to test their accuracy and reliability, we present the first benchmarking of root water uptake from soil using five well-established functional-structural root architecture models: DuMux, CPlantBox, R-SWMS, OpenSimRoot and SRI. The benchmark scenarios include basic tests for water flow in soil and roots as well as advanced tests for the coupled soil-root system. The reference solutions and the solutions of the different simulators are available through Jupyter Notebooks on a GitHub repository. All of the simulators were able to pass the basic tests and continued to perform well in the benchmarks for the coupled soil-plant system. For the advanced tests, we created an overview of the different ways of coupling the soil and the root domains as well as the different methods used to account for rhizosphere resistance to water flow. Although the methods used for coupling and modelling rhizosphere resistance were quite different, all simulators were in reasonably good agreement with the reference solution. During this benchmarking effort, individual simulators were able to learn about their strengths and challenges, while some were even able to improve their code. Some now include the benchmarks as standard tests within their codes. Additional model results may be added to the GitHub repository at any point in the future and will be automatically included in the comparison.",
keywords = "benchmark, Functional-structural root architecture models, model comparison, quantitative comparison, root water uptake, Biology",
author = "Andrea Schnepf and Black, {Christopher K.} and Valentin Couvreur and Delory, {Benjamin M.} and Claude Doussan and Adrien Heymans and Mathieu Javaux and Deepanshu Khare and Axelle Koch and Timo Koch and Kuppe, {Christian W.} and Magdalena Landl and Daniel Leitner and Guillaume Lobet and Felicien Meunier and Postma, {Johannes A.} and Sch{\"a}fer, {Ernst D.} and Tobias Selzner and Jan Vanderborght and Harry Vereecken",
note = "Publisher Copyright: {\textcopyright} 2023 Authors",
year = "2023",
month = aug,
day = "10",
doi = "10.1093/insilicoplants/diad005",
language = "English",
volume = "5",
journal = "In Silico Plants",
issn = "2517-5025",
publisher = "Oxford University Press",
number = "1",

}

RIS

TY - JOUR

T1 - Collaborative benchmarking of functional-structural root architecture models

T2 - Quantitative comparison of simulated root water uptake

AU - Schnepf, Andrea

AU - Black, Christopher K.

AU - Couvreur, Valentin

AU - Delory, Benjamin M.

AU - Doussan, Claude

AU - Heymans, Adrien

AU - Javaux, Mathieu

AU - Khare, Deepanshu

AU - Koch, Axelle

AU - Koch, Timo

AU - Kuppe, Christian W.

AU - Landl, Magdalena

AU - Leitner, Daniel

AU - Lobet, Guillaume

AU - Meunier, Felicien

AU - Postma, Johannes A.

AU - Schäfer, Ernst D.

AU - Selzner, Tobias

AU - Vanderborght, Jan

AU - Vereecken, Harry

N1 - Publisher Copyright: © 2023 Authors

PY - 2023/8/10

Y1 - 2023/8/10

N2 - Functional-structural root architecture models have evolved as tools for the design of improved agricultural management practices and for the selection of optimal root traits. In order to test their accuracy and reliability, we present the first benchmarking of root water uptake from soil using five well-established functional-structural root architecture models: DuMux, CPlantBox, R-SWMS, OpenSimRoot and SRI. The benchmark scenarios include basic tests for water flow in soil and roots as well as advanced tests for the coupled soil-root system. The reference solutions and the solutions of the different simulators are available through Jupyter Notebooks on a GitHub repository. All of the simulators were able to pass the basic tests and continued to perform well in the benchmarks for the coupled soil-plant system. For the advanced tests, we created an overview of the different ways of coupling the soil and the root domains as well as the different methods used to account for rhizosphere resistance to water flow. Although the methods used for coupling and modelling rhizosphere resistance were quite different, all simulators were in reasonably good agreement with the reference solution. During this benchmarking effort, individual simulators were able to learn about their strengths and challenges, while some were even able to improve their code. Some now include the benchmarks as standard tests within their codes. Additional model results may be added to the GitHub repository at any point in the future and will be automatically included in the comparison.

AB - Functional-structural root architecture models have evolved as tools for the design of improved agricultural management practices and for the selection of optimal root traits. In order to test their accuracy and reliability, we present the first benchmarking of root water uptake from soil using five well-established functional-structural root architecture models: DuMux, CPlantBox, R-SWMS, OpenSimRoot and SRI. The benchmark scenarios include basic tests for water flow in soil and roots as well as advanced tests for the coupled soil-root system. The reference solutions and the solutions of the different simulators are available through Jupyter Notebooks on a GitHub repository. All of the simulators were able to pass the basic tests and continued to perform well in the benchmarks for the coupled soil-plant system. For the advanced tests, we created an overview of the different ways of coupling the soil and the root domains as well as the different methods used to account for rhizosphere resistance to water flow. Although the methods used for coupling and modelling rhizosphere resistance were quite different, all simulators were in reasonably good agreement with the reference solution. During this benchmarking effort, individual simulators were able to learn about their strengths and challenges, while some were even able to improve their code. Some now include the benchmarks as standard tests within their codes. Additional model results may be added to the GitHub repository at any point in the future and will be automatically included in the comparison.

KW - benchmark

KW - Functional-structural root architecture models

KW - model comparison

KW - quantitative comparison

KW - root water uptake

KW - Biology

UR - http://www.scopus.com/inward/record.url?scp=85168987380&partnerID=8YFLogxK

U2 - 10.1093/insilicoplants/diad005

DO - 10.1093/insilicoplants/diad005

M3 - Journal articles

AN - SCOPUS:85168987380

VL - 5

JO - In Silico Plants

JF - In Silico Plants

SN - 2517-5025

IS - 1

M1 - diad005

ER -

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DOI