Combining experiments with multi-cell agent-based modeling to study biological tissue patterning

Abstract

Agent-based modeling (ABM), also termed 'Individual-based modeling (IBM)', is a computational approach that simulates the interactions of autonomous entities (agents, or individual cells) with each other and their local environment to predict higher level emergent patterns. A literature-derived rule set governs the actions of each individual agent. While this technique has been widely used in the ecological and social sciences, it has only recently been applied in biomedical research. The purpose of this review is to provide an introduction to ABM as it has been used to study complex multi-cell biological phenomena, underscore the importance of coupling models with experimental work, and outline future challenges for the ABM field and its application to biomedical research. We highlight a number of published examples of ABM, focusing on work that has combined experimental with ABM analyses and how this pairing produces new understanding. We conclude with suggestions for moving forward with this parallel approach.

Agent-Based Modeling in Systems Pharmacology

“…These notations can also be used to provide an argument that the ABM and resultant simulator are a fit‐for‐purpose representation of the underlying biological domain of interest. 69 Aside from formal mathematical notations,68 a number of well‐established notations exist and are addressed in Table S1 .…”

An in silico future for the engineering of functional tissues and organs

“…The background to ABM and some insights emerging from its application to a number of different cell types have been reviewed by Thorne et al 51 An effective methodology based on the close co-operation of experimental biologists and modellers has been adopted by Walker et al 52 Individual biological cells, are controlled by a number of rules governing behavior including intercellular bonding, juxtacrine signaling, migration and proliferation. This approach has been used to simulate the growth of a monolayer of urothelial (bladder epithelium) cells in low and physiological calcium environments and also wound healing in different environments, comparing the emergent behavior to experimental observations made on urothelial cell monolayers cultured in vitro.…”

Designing and encoding models for synthetic biology

“…In these methods, interactions between autonomous individuals are simulated. They have been successfully employed to simulate, for instance, bacterial chemo-taxis (Shimizu et al 2003), tissue formation and developmental processes (reviewed in Thorne et al 2007) and cancer growth (Wang et al 2007;Zhang et al 2009). A related approach is the use of rule-based models, where actual reactions are not described, but only the rules to generate them during simulations (e.g.…”