  The vast majority of biochemical systems involve the exchange of information
between different compartments, either in the form of transportation or via the
intervention of membrane proteins which are able to transmit stimuli between
bordering compartments. The correct quantitative handling of compartments is,
therefore, extremely important when modelling real biochemical systems. The
Bio-PEPA process algebra is equipped with the capability of explicitly defining
quantitative information such as compartment volumes and membrane surface
areas. Furthermore, the recent development of the Bio-PEPA Eclipse Plug-in
allows us to perform a correct stochastic simulation of multi-compartmental
models.
  Here we present a Bio-PEPA compartmental model of the cAMP/PKA/MAPK pathway.
We analyse the system using the Bio-PEPA Eclipse Plug-in and we show the
correctness of our model by comparison with an existing ODE model. Furthermore,
we perform computational experiments in order to investigate certain properties
of the pathway. Specifically, we focus on the system response to the inhibition
and strengthening of feedback loops and to the variation in the activity of key
pathway reactions and we observe how these modifications affect the behaviour
of the pathway. These experiments are useful to understand the control and
regulatory mechanisms of the system.
