City Research Online

Abstract

Spatial agent-based models are frequently used to investigate the evolution of solid tumours subject to localised cell-cell interactions and microenvironmental heterogeneity. As spatial genomic, transcriptomic and proteomic technologies gain traction, spatial computational models are predicted to become ever more necessary for making sense of complex clinical and experimental data sets, for predicting clinical outcomes, and for optimising treatment strategies. Here we present a nontechnical step by step guide to developing such a model from first principles. Stressing the importance of tailoring the model structure to that of the biological system, we describe methods of increasing complexity, from the basic Eden growth model up to off-lattice simulations with diffusible factors. We examine choices that unavoidably arise in model design, such as implementation, parameterisation, visualisation, and reproducibility. Each topic is illustrated with examples drawn from recent research studies and state of the art modelling platforms. We emphasise the benefits of simpler models that aim to match the complexity of the phenomena of interest, rather than that of the entire biological system. Our guide is aimed at both aspiring modellers and other biologists and oncologists who wish to understand the assumptions and limitations of the models on which major cancer studies now so often depend.

Publication Type:	Article
Additional Information:	© 2024 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Publisher Keywords:	cancer, computational modelling, evolution, evolutionary medicine, population genetics
Subjects:	Q Science > QA Mathematics R Medicine > RC Internal medicine > RC0254 Neoplasms. Tumors. Oncology (including Cancer)
Departments:	School of Science & Technology School of Science & Technology > Mathematics
SWORD Depositor:	Symplectic Administrator

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