Equivalences for a biological process algebra

This paper investigates Bio-PEPA, the stochastic process algebra for biological modelling developed by Ciocchetta and Hillston. It focuses on Bio-PEPA with levels where molecular counts are grouped or concentrations are discretised into a finite number of levels. Basic properties of well-defined Bio-PEPA systems are established after which equivalences used for the stochastic process algebra PEPA are considered for Bio-PEPA, and are shown to be identical for well-defined Bio-PEPA systems. Two new semantic equivalences parameterised by functions, called g-bisimilarity and weak g-bisimilarity are introduced. Different functions lead to different equivalences for Bio-PEPA. Congruence is shown for both forms of g-bisimilarity under certain reasonable conditions on the function and the use of these equivalences are demonstrated with a biologically-motivated example where two similar species are treated as a single species, and modelling of alternative pathways in the MAPK kinase signalling cascade.