Simulating gene regulatory networks using reaction systems

Gene Regulatory Networks represent the interactions among genes regulating the activation of specific cell functionalities and they have been successfully modeled using threshold Boolean networks. In this paper we propose a systematic translation of threshold Boolean networks into Reaction Systems. Our translation produces a non redundant set of rules with the minimal number of objects. This translation allows us to simulate the behavior of a Boolean network simply by executing the (closed) Reaction System we obtain. Moreover, it allows us to investigate the role of different genes simply by "playing" with the rules related to different genes. Starting from a well-known Boolean network model of the Yeast-Cell Cycle, we construct the corresponding Reaction System and start an investigation on causal dependencies among genes