Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Modelling and Refinement in CODA

This paper provides an overview of the CODA framework for modelling and refinement of component-based embedded systems. CODA is an extension of Event-B and UML-B and is supported by a plug-in for the Rodin toolset. CODA augments Event-B with constructs for component-based modelling including components, communications ports, port connectors, timed communications and timing triggers. Component behaviour is specified through a combination of UML-B state machines and Event-B. CODA communications and timing are given an Event-B semantics through translation rules. Refinement is based on Event-B refinement and allows layered construction of CODA models in a consistent way.Comment: In Proceedings Refine 2013, arXiv:1305.563

Quantitative Analysis of Probabilistic Models of Software Product Lines with Statistical Model Checking

We investigate the suitability of statistical model checking techniques for analysing quantitative properties of software product line models with probabilistic aspects. For this purpose, we enrich the feature-oriented language FLan with action rates, which specify the likelihood of exhibiting particular behaviour or of installing features at a specific moment or in a specific order. The enriched language (called PFLan) allows us to specify models of software product lines with probabilistic configurations and behaviour, e.g. by considering a PFLan semantics based on discrete-time Markov chains. The Maude implementation of PFLan is combined with the distributed statistical model checker MultiVeStA to perform quantitative analyses of a simple product line case study. The presented analyses include the likelihood of certain behaviour of interest (e.g. product malfunctioning) and the expected average cost of products.Comment: In Proceedings FMSPLE 2015, arXiv:1504.0301