The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems

Abstract

Rule-based models, which are typically formulated to represent cell signaling systems, can now be simulated via various network-free simulation methods. In a network-free method, reaction rates are calculated for rules that characterize molecular interactions, and these rule rates, which each correspond to the cumulative rate of all reactions implied by a rule, are used to perform a stochastic simulation of reaction kinetics. Network-free methods, which can be viewed as generalizations of Gillespie's method, are so named because these methods do not require that a list of individual reactions implied by a set of rules be explicitly generated, which is a requirement of other methods for simulating rule-based models. This requirement is impractical for rule sets that imply large reaction networks (i.e. long lists of individual reactions), as reaction network generation is expensive. Here, we compare the network-free simulation methods implemented in RuleMonkey and NFsim, general-purpose software tools for simulating rule-based models encoded in the BioNetGen language. The method implemented in NFsim uses rejection sampling to correct overestimates of rule rates, which introduces null events (i.e. time steps that do not change the state of the system being simulated). The method implemented in RuleMonkey uses iterative updates to track rule rates exactly, which avoids null events. To ensure a fair comparison of the two methods, we developed implementations of the rejection and rejection-free methods specific to a particular class of kinetic models for multivalent ligand–receptor interactions. These implementations were written with the intention of making them as much alike as possible, minimizing the contribution of irrelevant coding differences to efficiency differences. Simulation results show that performance of the rejection method is equal to or better than that of the rejection-free method over wide parameter ranges. However, when parameter values are such that ligand-induced aggregation of receptors yields a large connected receptor cluster, the rejection-free method is more efficient.