GillesPy: A Python Package for Stochastic Model Building and Simulation

Abstract

GillesPy is an open-source Python package for model construction and simulation of stochastic biochemical systems. GillesPy consists of a Python framework for model building and an interface to the StochKit2 suite of efficient simulation algorithms based on the Gillespie stochastic simulation algorithms. To enable intuitive model construction and seamless integration into the scientific Python stack, we present an easy-to-understand action-oriented programming interface. Here, we describe the components of this package and provide a detailed example relevant to the computational biology community.