Towards Probabilistic Model Checking on P Systems Using PRISM

This paper presents the use of P systems and π-calculus to model interacting molecular entities and how they are translated into a probabilistic and symbolic model checker called PRISM.Ministerio de Educación y Ciencia TIN2005-09345-C04-01Junta de Andalucía TIC-58

Modelling and Analysing Genetic Networks: From Boolean Networks to Petri Nets

Abstract. In order to understand complex genetic regulatory networks researchers require automated formal modelling techniques that provide appropriate analysis tools. In this paper we propose a new qualitative model for genetic regulatory networks based on Petri nets and detail a process for automatically constructing these models using logic mini-mization. We take as our starting point the Boolean network approach in which regulatory entities are viewed abstractly as binary switches. The idea is to extract terms representing a Boolean network using logic minimization and to then directly translate these terms into appropri-ate Petri net control structures. The resulting compact Petri net model addresses a number of shortcomings associated with Boolean networks and is particularly suited to analysis using the wide range of Petri net tools. We demonstrate our approach by presenting a detailed case study in which the genetic regulatory network underlying the nutritional stress response in Escherichia coli is modelled and analysed.