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:
\begin{itemize}
\item Signal transduction pathways, specifically the NF-$\kappa$B 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 I$\kappa$B. 
\item 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. 
\item 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.
\end{itemize}