ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks

• Published in: Gigascience Vol. 11
• Main Authors: Johnson, Connah G M, Fletcher, Alexander G, Soyer, Orkun S
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 17.06.2022
• Subjects: Availability; Biochemistry; C plus plus; C++ (programming language); Cell fate; Chemical diffusion; Chemical reactions; Computational Biology; Computer applications; Computer Simulation; Coupling; Databases, Factual; Environment models; Feedback; Intracellular; Libraries; Mathematical models; Microorganisms; Models, Biological; Simulation; Software; Chaste; biofilms; microbial communities
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giac051

Abstract Background Spatial organization plays an important role in the function of many biological systems, from cell fate specification in animal development to multistep metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow the in silico testing and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling. Conclusions Here, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables (i) simulation of an arbitrary number of spatially diffusing chemicals, (ii) spatially heterogeneous chemical diffusion coefficients, and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modeling bulk chemical reactions and their coupling with intracellular reactions. Availability and implementation ChemChaste version 1.0 is a free, open-source C++ library, available via GitHub at https://github.com/OSS-Lab/ChemChaste under the BSD license, on the Zenodo archive at zendodo doi, as well as on BioTools (biotools:chemchaste) and SciCrunch (RRID:SCR022208) databases.