Analysing Biochemical Oscillation through Probabilistic Model Checking

Paolo Ballarini, Radu Mardare, Ivan Mura
2009 Electronical Notes in Theoretical Computer Science  
There are two popular approaches to modelling and verification of biological systems. In the first one a system of ordinary differential equations (ODEs) is developed and solved through numerical integration techniques yielding a deterministic solution of the model. In the second one a stochastic (discrete-state) model is obtained and analysed through (stochastic) simulation techniques, yielding statistical estimates of the system behaviour. We propose an alternative approach based on
more » ... tic/stochastic model checking techniques. Relaying on temporal logic formalisms we investigate the possibility for a query language for stating biological properties of a system's model. Such queries are then automatically evaluated through existing model checking algorithms. To exemplify such approach we consider a biochemical oscillator taken from the literature. First we study such oscillator through the classical ODEs and stochastic simulation approaches. Then we develop a number of (probabilistic) queries that we verify against a Markov chain model of the oscillator, through the probabilistic model checler PRISM.
doi:10.1016/j.entcs.2009.02.002 fatcat:xvikdggc35etvclo4jld4t3nnu