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Exact stochastic simulation is an indispensable tool for a quantitative study of biochemical reaction networks. The simulation realizes the time evolution of the model by randomly choosing a reaction to fire and update the system state according to a probability that is proportional to the reaction propensity. Two computationally expensive tasks in simulating large biochemical networks are the selection...
We present a new model of anisotropic reaction-diffusion systems and the algorithmic framework of the software Redi (Reaction-Diffusion simulator) that implements this model. As illustrative application, we show the ability of Redi to reproduce the observed dynamics of the bicoid protein gradient in the Drosophila Melanogaster embryo.
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