Abstract

GillesPy is an open-source Python language package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a pythonic framework for model building and an interface to the StochKit2 suite of efficient Gillespie stochastic simulation algorithms (SSAs). To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy to understand action-oriented programming interface. GillesPy also supports the import of legacy SBML models. Here, we describe the components of this package and provide a simple example relevant to the computational biology community.