抄録
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
and urothelial tissue and the investigation of the role of calcium and juxtracrine
signalling in the development and differentiation of tissue. Again, the models
have been validated with ’in vitro’ tissue cultures under a number of important
laboratory conditions.
• Populations of Pharoah’s ants have been simulated and closely compared with
real populations within the laboratory. The role of pheromone signalling has
been studied and the modelling has led to a new understanding of the use of
pheromone trails in foraging behaviour. This has shown that the geometry of the
trails contains vital information that is used in the navigation of the trails by the
insects.
