Johnson, C.G.M., Fletcher, A.G. orcid.org/0000-0003-0525-4336 and Soyer, O.S. (2022) ChemChaste : simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks. GigaScience, 11 (2022). ISSN 2047-217X
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.
Metadata
Item Type: | Article |
---|---|
Authors/Creators: |
|
Copyright, Publisher and Additional Information: | © 2022 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | Chaste; biofilms; microbial communities; Computational Biology; Computer Simulation; Databases, Factual; Feedback; Models, Biological; Software |
Dates: |
|
Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Mathematics and Statistics (Sheffield) |
Funding Information: | Funder Grant number Biotechnology and Biological Sciences Research Council BB/R016925/1 |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 27 Jul 2022 09:31 |
Last Modified: | 18 Nov 2024 13:01 |
Status: | Published |
Publisher: | Oxford University Press (OUP) |
Refereed: | Yes |
Identification Number: | 10.1093/gigascience/giac051 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:189394 |