Reviving the Two-State Markov Chain Approach

ASSA-PBN: A Toolbox for Probabilistic Boolean Networks

As a well-established computational framework, probabilistic Boolean networks (PBNs) are widely used for modelling, simulation, and analysis of biological systems. To analyze the steady-state dynamics of PBNs is of crucial importance to explore the characteristics of biological systems. However, the analysis of large PBNs, which often arise in systems biology, is prone to the infamous state-space explosion problem. Therefore, the employment of statistical methods often remains the only feasible solution. We present ${\mathsf{ASSA-PBN}}$ , a software toolbox for modelling, simulation, and analysis of PBNs. ${\mathsf{ASSA-PBN}}$ provides efficient statistical methods with three parallel techniques to speed up the computation of steady-state probabilities. Moreover, particle swarm optimisation (PSO) and differential evolution (DE) are implemented for the estimation of PBN parameters. Additionally, we implement in-depth analyses of PBNs, including long-run influence analysis, long-run sensitivity analysis, computation of one-parameter profile likelihoods, and the visualization of one-parameter profile likelihoods. A PBN model of apoptosis is used as a case study to illustrate the main functionalities of ${\mathsf{ASSA-PBN}}$ and to demonstrate the capabilities of ${\mathsf{ASSA-PBN}}$ to effectively analyse biological systems modelled as PBNs.