A Distributed-Based Stochastic Simulation Algorithm for Large Biochemical Reaction Networks

2007 1st International Conference on Bioinformatics and Biomedical Engineering ◽

10.1109/icbbe.2007.132 ◽

2007 ◽

Cited By ~ 1

Author(s):

Jun-qing Niu ◽

Hao-ran Zheng ◽

Jiu-sheng Chen ◽

Meng Ma ◽

Xu-fa Wang

Keyword(s):

Stochastic Simulation ◽

Stochastic Simulation Algorithm ◽

Biochemical Reaction ◽

Reaction Networks ◽

Simulation Algorithm ◽

Biochemical Reaction Networks

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An equation-free probabilistic steady-state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks

The Journal of Chemical Physics ◽

10.1063/1.2131050 ◽

2005 ◽

Vol 123 (21) ◽

pp. 214106 ◽

Cited By ~ 52

Author(s):

Howard Salis ◽

Yiannis N. Kaznessis

Keyword(s):

Steady State ◽

Stochastic Simulation ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

State Approximation ◽

Steady State Approximation

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HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

Journal of Computational Physics ◽

10.1016/j.jcp.2016.04.056 ◽

2016 ◽

Vol 317 ◽

pp. 301-317 ◽

Cited By ~ 20

Author(s):

Luca Marchetti ◽

Corrado Priami ◽

Vo Hong Thanh

Keyword(s):

Stochastic Simulation ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks ◽

Spatially Homogeneous

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Stochastic Simulation for Biochemical Reaction Networks in Infectious Disease

Medicinal Chemistry and Drug Design ◽

10.5772/38245 ◽

2012 ◽

Author(s):

Shailza Singh ◽

Sonali Shinde

Keyword(s):

Infectious Disease ◽

Stochastic Simulation ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays

The Journal of Chemical Physics ◽

10.1063/1.3521496 ◽

2011 ◽

Vol 134 (1) ◽

pp. 014106 ◽

Cited By ~ 9

Author(s):

Rajesh Ramaswamy ◽

Ivo F. Sbalzarini

Keyword(s):

Stochastic Simulation ◽

Chemical Reaction ◽

Stochastic Simulation Algorithm ◽

Chemical Reaction Networks ◽

Reaction Networks ◽

Simulation Algorithm

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A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks

The Journal of Chemical Physics ◽

10.1063/1.3297948 ◽

2010 ◽

Vol 132 (4) ◽

pp. 044102 ◽

Cited By ~ 25

Author(s):

Rajesh Ramaswamy ◽

Ivo F. Sbalzarini

Keyword(s):

Stochastic Simulation ◽

Chemical Reaction ◽

Stochastic Simulation Algorithm ◽

Chemical Reaction Networks ◽

Reaction Networks ◽

Simulation Algorithm

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Deterministic and Stochastic Simulation and Analysis of Biochemical Reaction Networks

Computer Methods, Part C - Methods in Enzymology ◽

10.1016/b978-0-12-381270-4.00012-3 ◽

2011 ◽

pp. 371-395 ◽

Cited By ~ 4

Author(s):

Necmettin Yildirim ◽

Caner Kazanci

Keyword(s):

Stochastic Simulation ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks

2015 Euromicro Conference on Digital System Design ◽

10.1109/dsd.2015.53 ◽

2015 ◽

Cited By ~ 1

Author(s):

Evangelos Koutsouradis ◽

George Provelengios ◽

Elias Kouskoumvekakis ◽

Elias S. Manolakos

Keyword(s):

Stochastic Simulation ◽

Large Scale ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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Toward a fast stochastic simulation processor for biochemical reaction networks

2013 IEEE 24th International Conference on Application-Specific Systems, Architectures and Processors ◽

10.1109/asap.2013.6567550 ◽

2013 ◽

Author(s):

Hyungman Park ◽

Andreas Gerstlauer

Keyword(s):

Stochastic Simulation ◽

Biochemical Reaction ◽

Reaction Networks ◽

Biochemical Reaction Networks

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Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space

The Journal of Chemical Physics ◽

10.1063/1.4937937 ◽

2015 ◽

Vol 143 (24) ◽

pp. 244103 ◽

Cited By ~ 3

Author(s):

Jakob Ruess

Keyword(s):

State Space ◽

Stochastic Models ◽

Biochemical Reaction ◽

Reaction Networks ◽

Moment Equations ◽

Biochemical Reaction Networks ◽

Finite State ◽

Finite State Space

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Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites

Journal of Computational Biology ◽

10.1089/cmb.2014.0064 ◽

2015 ◽

Vol 22 (3) ◽

pp. 218-226 ◽

Cited By ~ 1

Author(s):

Mattia Petroni ◽

Nikolaj Zimic ◽

Miha Mraz ◽

Miha Moškon

Keyword(s):

Stochastic Simulation ◽

Gene Regulatory Networks ◽

Binding Sites ◽

Regulatory Networks ◽

Stochastic Simulation Algorithm ◽

Simulation Algorithm ◽

Multiple Binding Sites ◽

Multiple Binding ◽

Gene Regulatory

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