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gillespie algorithm  (Pine Tree Inc)

 
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    Pine Tree Inc gillespie algorithm
    Gillespie Algorithm, supplied by Pine Tree Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/gillespie+algorithm+implemented+in/gillespie+algorithm/pmc06792109-83-10-3
    Average 90 stars, based on 1 article reviews
    gillespie algorithm - by Bioz Stars, 2026-10
    90/100 stars

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    Article Title: Pinetree: a step-wise gene expression simulator with codon-specific translation rates
    Article Snippet: Future versions of Pinetree could implement alternate versions of the Gillespie algorithm that make some approximations in order to decrease run times and increase efficiency ( Gillespie, 2001 ; Ramaswamy and Sbalzarini, 2010 ).



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    Timing comparisons. ( A – C ) Time taken to simulate a given number of realisations for a single core of an Intel Core i7-975 Extreme Edition Processor 3.33 GHz (solid line) and one Tesla C2050 GPU (dashed line) for (A) the <t>LSODA</t> (B) the Euler–Maruyama and (C) <t>the</t> <t>Gillespie</t> algorithm, respectively. The relative speed-ups for given numbers of simulations are indicated next to the GPU simulation results. ( D ) Summary of the relative speed-up of the three different algorithms.
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    Timing comparisons. ( A – C ) Time taken to simulate a given number of realisations for a single core of an Intel Core i7-975 Extreme Edition Processor 3.33 GHz (solid line) and one Tesla C2050 GPU (dashed line) for (A) the LSODA (B) the Euler–Maruyama and (C) the Gillespie algorithm, respectively. The relative speed-ups for given numbers of simulations are indicated next to the GPU simulation results. ( D ) Summary of the relative speed-up of the three different algorithms.

    Journal: Bioinformatics

    Article Title: GPU accelerated biochemical network simulation

    doi: 10.1093/bioinformatics/btr015

    Figure Lengend Snippet: Timing comparisons. ( A – C ) Time taken to simulate a given number of realisations for a single core of an Intel Core i7-975 Extreme Edition Processor 3.33 GHz (solid line) and one Tesla C2050 GPU (dashed line) for (A) the LSODA (B) the Euler–Maruyama and (C) the Gillespie algorithm, respectively. The relative speed-ups for given numbers of simulations are indicated next to the GPU simulation results. ( D ) Summary of the relative speed-up of the three different algorithms.

    Article Snippet: But since in most applications of these algorithms, either in order to explore the parameter space or to perform inference, at least thousands of simulations will be needed for which the GPU outperforms the CPU even for the rather simple p53-Mdm2 model. We also compared the cuda-sim implementations of the LSODA and Gillespie algorithms with implementations in the Matlab package SBTOOLBOX2 ( ) and our Euler–Maruyama implementation with the native sde function within Matlab.

    Techniques: