on verifying bio-pepa models
Verifying that a computational model implements the conceptual model of some dynamic biological phenomena is an important yet non-trivial task. In this paper, we discuss a variety of steps that contribute to this verification process, using the Bio-PEPA process algebra as a modelling language and describing the verification steps that are supported by the Bio-PEPA tool. In particular, we elaborate on both static analysis based on the structure of models and dynamic analysis of generated stochastic simulation traces performed using the Traviando trace analyser. We illustrate the approach with a model of a JAK/STAT signalling pathway.
verification bio-pepa static analysis stochastic simulation traviando trace analysis dynamic modelling gillespie algorithm