STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
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منابع مشابه
STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm
MOTIVATION The availability of a huge amount of molecular data concerning various biochemical reactions provoked numerous attempts to study the dynamics of cellular processes by means of kinetic models and computer simulations. Biochemical processes frequently involve small numbers of molecules (e.g. a few molecules of a transcriptional regulator binding to one 'molecule' of a DNA regulatory re...
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Spatial stochastic simulation is a valuable method for studying processes of reaction and diffusion in biological systems. This technique requires significant computational efforts, but the availability of high-performance computing made it possible to develop coherent computational models of cells [1]. Several approaches were introduced in order to utilize parallel execution to speed up simula...
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ODE simulations of chemical systems perform poorly when some of the species have extremely low concentrations. Stochastic simulation methods, which can handle this case, have been impractical for large systems due to computational complexity. We observe, however, that when modeling complex biological systems: (1) a small number of reactions tend to occur a disproportionately large percentage of...
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Several discrete, as well as continuous, stochastic approaches have been developed for the time-series simulation of biochemical systems. Stochastic approaches, in general, are needed because chemical reactions involve discrete, random collisions between individual chemical species. One of the well-known discrete stochastic approaches is the computationally demanding Gillespie stochastic simula...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2002
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/18.3.470