FROM MOLECULES TO INSECT COMMUNITIES - HOW FORMAL AGENT BASED COMPUTATIONAL MODELLING IS UNCOVERING NEW BIOLOGICAL FACTS
Simon Coakley, Rod H Smallwood, Mike Holcombe · 2006
Agent-based approaches to modelling biological phenomena are becoming popular and proving successful in a number of areas. However, the underlying basis of these techniques is sometimes rather ‘ad-hoc’ and the models are often only applied to specific systems. This paper describes a general approach that is based on the use of fully general computational models, using a formal model of an agent and a rigorous approach to building systems of communicating agents within virtual environments. A collection of tools has been built which allow for efficient simulation of such systems and their visualisation. Included in this work is the implementation of the simulations on parallel clusters of computers to enable large numbers of agents to be simulated. Application areas where the method has been successfully applied include: Signal transduction pathways, specifically the NF-κB pathway. This model has been validated using single cell data from GFP transvected cells. The model has enabled the prediction of the possible role of actin filaments in the sequestration and feedback control of IκB. The epitheliome project involves building models of the development of both skin