Journal of Computational Physics
Journal of Computational Physics
Computational Probability for Systems Biology
FMSB '08 Proceedings of the 1st international workshop on Formal Methods in Systems Biology
A numerical aggregation algorithm for the enzyme-catalyzed substrate conversion
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Exploring the performance of spatial stochastic simulation algorithms
Journal of Computational Physics
Proceedings of the Winter Simulation Conference
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The adaptive explicit-implicit tau-leaping method with automatic tau selection is a flexible algorithm for accelerated stochastic simulation of chemically reacting systems. It combines the advantages of different simulation schemes and is particularly useful when a system changes its dynamical behavior over time in the sense that it behaves well in some time periods but possesses stiffness in other time periods. However, the ingredients necessary to fully understand and implement the algorithm are spread over several papers, not always consistent in terminology and notation, which considerably hampers and possibly even prevents accessibility and widespread practical use. We present a streamlined description of the algorithm using a unified terminology and notation and introduce significantly simplified versions of two major ingredients, namely the step size selection and the switching mechanism between the sub-algorithms.