BioCro II: a software package for modular crop growth simulations

Authors: LOCHOCKI, EDWARD - University Of Illinois; ROHDE, SCOTT - University Of Illinois; JAISWAL, DEEPAK - Indian Institute Of Technology; MATTHEWS, MEGAN - University Of Illinois; MIGUEZ, FERNANDO - Iowa State University; LONG, STEPHEN - University Of Illinois; McGrath, Justin

Submitted to: in silico Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/10/2022
Publication Date: 2/12/2022
Citation: Lochocki, E., Rohde, S., Jaiswal, D., Matthews, M., Miguez, F., Long, S., McGrath, J.M. 2022. BioCro II: a software package for modular crop growth simulations. in silico Plants. 4(1). Article diac002. https://doi.org/10.1093/insilicoplants/diac003.
DOI: https://doi.org/10.1093/insilicoplants/diac003

Interpretive Summary: Mathematical models are in their simplest form are a list of equations. However, using these models on computers requires a lot of in depth knowledge of computer and programming languages. Although most modelers have familiarity with these areas, it is difficult to get the details right. BioCro II attempts to minimize the amount of computer science knowledge required to write models. Moreover, it provides the ability to swap submodels within a larger model, a feature we do not think is present in any other software, but which is very valuable for comparing the performance of variations of submodels.

Technical Abstract: The central motivation for mechanistic crop growth simulation has remained the same for decades: to reliably predict changes in crop yields and water usage in response to previously unexperienced increases in air temperature and CO2 concentration across different environments, species and genotypes. Over the years, individual process-based model components have become more complex and specialized, increasing their fidelity but posing a challenge for integrating them into powerful multiscale models. Combining models is further complicated by the common strategy of hard-coding intertwined parameter values, equations, solution algorithms and user interfaces, rather than treating these each as separate components. It is clear that a more flexible approach is now required. Here we describe a modular crop growth simulator, BioCro II. At its core, BioCro II is a cross-platform representation of models as sets of equations. This facilitates modularity in model building and allows it to harness modern techniques for numerical integration and data visualization. Several crop models have been implemented using the BioCro II framework, but it is a general purpose tool and can be used to model a wide variety of processes.