A Tutorial on Analysis and Simulation of Boolean Gene Regulatory Network Models

Driven by the desire to understand genomic functions through the interactions among genes and gene products, the research in gene regulatory networks has become a heated area in genomic signal processing. Among the most studied mathematical models are Boolean networks and probabilistic Boolean networks, which are rule-based dynamic systems. This tutorial provides an introduction to the essential concepts of these two Boolean models, and presents the up-to-date analysis and simulation methods developed for them. In the Analysis section, we will show that Boolean models are Markov chains, based on which we present a Markovian steady-state analysis on attractors, and also reveal the relationship between probabilistic Boolean networks and dynamic Bayesian networks (another popular genetic network model), again via Markov analysis; we dedicate the last subsection to structural analysis, which opens a door to other topics such as network control. The Simulation section will start from the basic tasks of creating state transition diagrams and finding attractors, proceed to the simulation of network dynamics and obtaining the steady-state distributions, and finally come to an algorithm of generating artificial Boolean networks with prescribed attractors. The contents are arranged in a roughly logical order, such that the Markov chain analysis lays the basis for the most part of Analysis section, and also prepares the readers to the topics in Simulation section.