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GillesPy: A Python Package for Stochastic Model Building and Simulation
John H Abel1, Brian Drawert2, Andreas Hellander3
1Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA and the Department of Chemical Engineering, University of California, Santa Barbara, CA 93106 USA.
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 (SSA). 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.
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