Abstract
Herein is provided a brief overview of agent-based modeling (ABM), with a particular slant toward its potential as a tool for the theoretical biologist. Of course, its use for experimentalists is obvious; they are, as a group, already using agent-based models (ABMs) to examine contemporary biological questions ranging from molecular processes (e.g., stem cell and totipotency) to evolving ecological landscapes (Grimm and Railsback 2005). For the modeler-theoretician, ABMs offer a new tool for thinking about the structure of biological processes, thus creating a conduit for integrative perspective taking between the experimentalist and the theoretician.
To maintain brevity and because of the various types and range of work being done with ABMs in labs throughout the world, I will generally ignore scale: whether referring to molecular processes or social organization, or events that occur in milliseconds or decades; such features are details specific to the research question. Time, size, and distance are merely parameter values determined by the modeler. Instead I focus on critical features unique to ABMs: agent construction and heterogeneity, rule implementation, and scientific inference.
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Griffin, W.A. Agent-Based Modeling for the Theoretical Biologist. Biol Theory 1, 404–409 (2006). https://doi.org/10.1162/biot.2006.1.4.404
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DOI: https://doi.org/10.1162/biot.2006.1.4.404