P Systems, a New Computational Modelling Tool for Systems Biology

Abstract

In this paper we present P systems as a reliable computa- tional modelling tool for Systems Biology that takes into account the discrete character of the quantity of components of biological systems, the inherently randomness in biological phenomena and the key role played by membranes in the function of living cells. We will introduce two different strategies for the evolution of P systems, namely, Multi- compartmental Gillespie’s Algorithm based on the well known Gillespie’s Algorithm but running on more than one compartment; and Determin- istic Waiting Times Algorithm, an exact deterministic method. In order to illustrate these two strategies we have modelled two biological sys- tems: the EGFR Signalling Cascade and the Quorum Sensing System in the bacterium Vibrio Fischeri. Our simulations results show that for the former system a deterministic approach is valid whereas for the latter a stochastic approach like Multi-compartmental Gillespie’s Algorithm is necessary.