Colouring fuzziness for systems biology

Abstract

Abstract Snoopy is a powerful modelling and simulation tool for various types of Petri nets, which have been applied to a wide range of biochemical reaction networks. We present an enhanced version of Snoopy, now supporting coloured and uncoloured stochastic, continuous and hybrid Petri Nets with fuzzy kinetic parameters. Colour helps to cope with modelling challenges imposed by larger and more complex networks. Fuzzy parameters are specifically useful when kinetic parameter values can not be precisely measured or estimated. By running fuzzy simulation we obtain output bands of the variables of interest induced by the effect of the fuzzy kinetic parameters. Simulation is always done on the uncoloured level. For this purpose, coloured fuzzy Petri nets are automatically unfolded to their corresponding uncoloured counterparts. Combining the power of fuzzy kinetic parameters with the modelling convenience of coloured Petri nets provides a new quality in user support with sophisticated modelling and analysis features.