Titlebook: Simulation Algorithms for Computational Systems Biology; Luca Marchetti,Corrado Priami,Vo Hong Thanh Textbook 2017 Springer International

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Stochastic Simulation of Biochemical Reaction Systems,and the randomness of reactions are treated as an intrinsic part. The dynamical behavior of the biochemical reactions, based on the fundamental premise of the stochastic chemical kinetics, is exactly described by the . (CME). A class of Monte Carlo simulation techniques originating from the . (SSA)

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Implementations of the Stochastic Simulation Algorithm,em state. It has the nice property of producing an exact realization (with respect to the chemical master equation) of the temporal dynamics of biochemical reactions. The heart of SSA is the Monte Carlo step for sampling the next reaction firing and its firing time from the joint reaction probabilit

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Approximate Simulation of Biochemical Reaction Systems,ational challenges motivate the development of approximate algorithms to improve the simulation efficiency by sacrificing their accuracy. Multiple firings of reactions are coalesced and performed together in one simulation step with a huge potential speed up.

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1862-4499 tary material: .This book explains the state-of-the-art algorithms used to simulate biological dynamics. Each technique is theoretically introduced and applied to a set of modeling cases. Starting from basic simulation algorithms, the book also introduces more advanced techniques that support delays

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ts. We aim to address the arising challenges by utilizing dependency graphs of the underlying formal entities. For the Isabelle Archive of Formal Proofs, the individual entry graphs consist of 1.8 million nodes and 2.8 million edges in total, and exhibit certain complex network characteristics: Node

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