Agent-based modelling in synthetic biology

Biological systems exhibit complex behaviors that merge at many different levels of organization; from the regulation of gene expression within single cells, to the use of quorum sensing to coordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviors. However, in many cases it is not understood how individual cells should be programmed to ensure the emergence of a required collective behavior. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. Here, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions.