Reuse of process-based models: automatic transformation into many programming languages and simulation platforms

• Published in: in silico plants Vol. 2; no. 1
• Main Authors: Midingoyi, Cyrille Ahmed, Pradal, Christophe, Athanasiadis, Ioannis N, Donatelli, Marcello, Enders, Andreas, Fumagalli, Davide, Garcia, Frédérick, Holzworth, Dean, Hoogenboom, Gerrit, Porter, Cheryl, Raynal, Hélène, Thorburn, Peter, Martre, Pierre
• Format: Journal Article
• Language: English
• Published: UK Oxford University Press 01.01.2020; Oxford Academic
• Subjects: Agricultural sciences; Algorithms; Computer Science; Exchanging; Life Sciences; Mathematical models; Modeling and Simulation; Modelling; Plant diversity; Programming languages; Python; Reuse; Software reuse; Source code; Specifications; Transformations (mathematics); model reuse; transpiler; source transformation; software reuse; Crop model; crop model; Source transformation
• ISSN: 2517-5025; 2517-5025
• DOI: 10.1093/insilicoplants/diaa007

The diversity of plant and crop process-based modelling platforms in terms of implementation language, software design and architectural constraints limits the reusability of the model components outside the platform in which they were originally developed, making model reuse a persistent issue. To facilitate the intercomparison and improvement of process-based models and the exchange of model components, several groups in the field joined to create the Agricultural Model Exchange Initiative (AMEI). Agricultural Model Exchange Initiative proposes a centralized framework for exchanging and reusing model components. It provides a modular and declarative approach to describe the specification of unit models and their composition. A model algorithm is associated with each model specification, which implements its mathematical behaviour. This paper focuses on the expression of the model algorithm independently of the platform specificities, and how the model algorithm can be seamlessly integrated into different platforms. We define CyML, a Cython-derived language with minimum specifications to implement model component algorithms. We also propose CyMLT, an extensible source-to-source transformation system that transforms CyML source code into different target languages such as Fortran, C#, C++, Java and Python, and into different programming paradigms. CyMLT is also able to generate model components to target modelling platforms such as DSSAT, BioMA, Record, SIMPLACE and OpenAlea. We demonstrate our reuse approach with a simple unit model and the capacity to extend CyMLT with other languages and platforms. The approach we present here will help to improve the reproducibility, exchange and reuse of process-based models.