RSSALib: a library for stochastic simulation of complex biochemical reactions

Abstract

Motivation: Stochastic chemical kinetics is an essential mathematical framework for investigating the dynamics of biological processes, especially when stochasticity plays a vital role in their development. Simulation is often the only option for the analysis of many practical models due to their analytical intractability. Results: We present in this article, the simulation library RSSALib, implementing our recently developed rejection-based stochastic simulation algorithm (RSSA) and a wide range of its improvements, to accelerate the simulation and analysis of biochemical reactions. RSSALib supports reactions with complex kinetics and time delays, necessary to model complexities of reaction mechanisms. Our library provides both an application program interface and a graphic user interface to ease the set-up and visualization of the simulation results.