CBNSimulator: a simulator tool for understanding the behaviour of complex biomolecular networks using discrete time simulation

Abstract

Because of the lack of satisfactory solutions to explain biological systems, biologists usually focus on modelling and simulation tools to understand the behaviour of these complex organisms. Indeed, computational modelling and simulation of cells plays a pivotal role in systems biology. In this paper, we tackle the problem of studying the behaviour of human cells by reproducing the behaviour of complex biomolecular networks. To this end, we present in this paper an approach for simulating complex biomolecular networks inspired by the discrete-event simulation model (DEVS), a formalism developed for supporting the modelling of complex systems. In this paper, we propose a simulation tool, named ”CBNSimulator”, based on a logical model of the biomolecular network and taking advantage of the performance of a discrete-time simulation model for understanding the evolution and the behaviour of complex biomolecular networks as a discrete sequence of events in time. The proposed tool has been applied to the case study of a ribosomal protein regulation network, named ”the bacteriophage T4 gene 32”, and results given by this simulation tool are in agreement with the expert’s judgement. Moreover, the graphical user interface of CBNSimulator allows biologists to easily reproduce, analyse and understand behaviour of complex biomolecular networks through discrete simulation.