Crop modeling frameworks interoperability through bidirectional source code transformation

Cyrille Ahmed Midingoyi; Christophe Pradal; Andreas Enders; Davide Fumagalli; Patrice Lecharpentier; Hélène Raynal; Marcello Donatelli; Davide Fanchini; Ioannis N. Athanasiadis; Cheryl Porter; Gerrit Hoogenboom; F.A.A. Oliveira; Dean Holzworth; Pierre Martre

doi:10.1016/j.envsoft.2023.105790

Crop modeling frameworks interoperability through bidirectional source code transformation

Cyrille Ahmed Midingoyi, Christophe Pradal^*, Andreas Enders, Davide Fumagalli, Patrice Lecharpentier, Hélène Raynal, Marcello Donatelli, Davide Fanchini, Ioannis N. Athanasiadis, Cheryl Porter, Gerrit Hoogenboom, F.A.A. Oliveira, Dean Holzworth, Pierre Martre^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

3 Citations (Scopus)

Abstract

Recently, we proposed Crop2ML, an open-source modeling framework for exchanging and reusing crop model components between modeling platforms. Here, we present an approach based on reverse engineering to automatically extract and transform meta-information and algorithms of existing crop biophysical models into a platform-independent model component. A search algorithm using Crop2ML concepts, and a many-to-one transformation system were used for producing high-level models. The system consists of parsing the codebase of model components written in different languages using the ANother Tool for Language Recognition (ANTLR) parser generator and processing the generated syntax trees to produce various model implementations. The system was evaluated for three crop model components provided by the BioMA, SIMPLACE, and DSSAT platforms. We demonstrated the extensibility of our approach with the STICS, OpenAlea, and SiriusQuality modeling platforms. CyMLTx is a significant contribution towards the interoperability of crop modeling platforms and the reuse of model components beyond programming languages.

Original language	English
Article number	105790
Journal	Environmental Modelling and Software
Volume	168
DOIs	https://doi.org/10.1016/j.envsoft.2023.105790
Publication status	Published - Oct 2023

Keywords

Crop model
Crop2ML
Model exchange and reuse
One-to-many transformation

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Midingoyi, C. A., Pradal, C., Enders, A., Fumagalli, D., Lecharpentier, P., Raynal, H., Donatelli, M., Fanchini, D., Athanasiadis, I. N., Porter, C., Hoogenboom, G., Oliveira, F. A. A., Holzworth, D., & Martre, P. (2023). Crop modeling frameworks interoperability through bidirectional source code transformation. Environmental Modelling and Software, 168, Article 105790. https://doi.org/10.1016/j.envsoft.2023.105790

@article{2ab0758ee6e741198dd2fcc26414785d,

title = "Crop modeling frameworks interoperability through bidirectional source code transformation",

abstract = "Recently, we proposed Crop2ML, an open-source modeling framework for exchanging and reusing crop model components between modeling platforms. Here, we present an approach based on reverse engineering to automatically extract and transform meta-information and algorithms of existing crop biophysical models into a platform-independent model component. A search algorithm using Crop2ML concepts, and a many-to-one transformation system were used for producing high-level models. The system consists of parsing the codebase of model components written in different languages using the ANother Tool for Language Recognition (ANTLR) parser generator and processing the generated syntax trees to produce various model implementations. The system was evaluated for three crop model components provided by the BioMA, SIMPLACE, and DSSAT platforms. We demonstrated the extensibility of our approach with the STICS, OpenAlea, and SiriusQuality modeling platforms. CyMLTx is a significant contribution towards the interoperability of crop modeling platforms and the reuse of model components beyond programming languages.",

keywords = "Crop model, Crop2ML, Model exchange and reuse, One-to-many transformation",

author = "Midingoyi, \{Cyrille Ahmed\} and Christophe Pradal and Andreas Enders and Davide Fumagalli and Patrice Lecharpentier and H{\'e}l{\`e}ne Raynal and Marcello Donatelli and Davide Fanchini and Athanasiadis, \{Ioannis N.\} and Cheryl Porter and Gerrit Hoogenboom and F.A.A. Oliveira and Dean Holzworth and Pierre Martre",

year = "2023",

month = oct,

doi = "10.1016/j.envsoft.2023.105790",

language = "English",

volume = "168",

journal = "Environmental Modelling and Software",

issn = "1364-8152",

publisher = "Elsevier",

}

Midingoyi, CA, Pradal, C, Enders, A, Fumagalli, D, Lecharpentier, P, Raynal, H, Donatelli, M, Fanchini, D, Athanasiadis, IN, Porter, C, Hoogenboom, G, Oliveira, FAA, Holzworth, D & Martre, P 2023, 'Crop modeling frameworks interoperability through bidirectional source code transformation', Environmental Modelling and Software, vol. 168, 105790. https://doi.org/10.1016/j.envsoft.2023.105790

TY - JOUR

T1 - Crop modeling frameworks interoperability through bidirectional source code transformation

AU - Midingoyi, Cyrille Ahmed

AU - Pradal, Christophe

AU - Enders, Andreas

AU - Fumagalli, Davide

AU - Lecharpentier, Patrice

AU - Raynal, Hélène

AU - Donatelli, Marcello

AU - Fanchini, Davide

AU - Athanasiadis, Ioannis N.

AU - Porter, Cheryl

AU - Hoogenboom, Gerrit

AU - Oliveira, F.A.A.

AU - Holzworth, Dean

AU - Martre, Pierre

PY - 2023/10

Y1 - 2023/10

N2 - Recently, we proposed Crop2ML, an open-source modeling framework for exchanging and reusing crop model components between modeling platforms. Here, we present an approach based on reverse engineering to automatically extract and transform meta-information and algorithms of existing crop biophysical models into a platform-independent model component. A search algorithm using Crop2ML concepts, and a many-to-one transformation system were used for producing high-level models. The system consists of parsing the codebase of model components written in different languages using the ANother Tool for Language Recognition (ANTLR) parser generator and processing the generated syntax trees to produce various model implementations. The system was evaluated for three crop model components provided by the BioMA, SIMPLACE, and DSSAT platforms. We demonstrated the extensibility of our approach with the STICS, OpenAlea, and SiriusQuality modeling platforms. CyMLTx is a significant contribution towards the interoperability of crop modeling platforms and the reuse of model components beyond programming languages.

AB - Recently, we proposed Crop2ML, an open-source modeling framework for exchanging and reusing crop model components between modeling platforms. Here, we present an approach based on reverse engineering to automatically extract and transform meta-information and algorithms of existing crop biophysical models into a platform-independent model component. A search algorithm using Crop2ML concepts, and a many-to-one transformation system were used for producing high-level models. The system consists of parsing the codebase of model components written in different languages using the ANother Tool for Language Recognition (ANTLR) parser generator and processing the generated syntax trees to produce various model implementations. The system was evaluated for three crop model components provided by the BioMA, SIMPLACE, and DSSAT platforms. We demonstrated the extensibility of our approach with the STICS, OpenAlea, and SiriusQuality modeling platforms. CyMLTx is a significant contribution towards the interoperability of crop modeling platforms and the reuse of model components beyond programming languages.

KW - Crop model

KW - Crop2ML

KW - Model exchange and reuse

KW - One-to-many transformation

U2 - 10.1016/j.envsoft.2023.105790

DO - 10.1016/j.envsoft.2023.105790

M3 - Article

AN - SCOPUS:85169019585

SN - 1364-8152

VL - 168

JO - Environmental Modelling and Software

JF - Environmental Modelling and Software

M1 - 105790

ER -

Crop modeling frameworks interoperability through bidirectional source code transformation

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Keywords

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