gillespie algorithm implemented in Search Results


direct gillespie stochastic simulation algorithm  (MathWorks Inc)
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matlab software  (MathWorks Inc)
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gillespie reduction  (MathWorks Inc)
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Gillespie Reduction, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gillespie algorithm  (MathWorks Inc)
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Gillespie Algorithm, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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slow scale stochastic simulation algorithm  (MathWorks Inc)
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cuda-sim implementations of the lsoda algorithm  (MathWorks Inc)
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MathWorks Inc cuda-sim implementations of the lsoda algorithm
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 <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.
Cuda Sim Implementations Of The Lsoda Algorithm, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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et al, 1996  (Rauscher GmbH)
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Rauscher GmbH et al, 1996
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 <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.
Et Al, 1996, supplied by Rauscher GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gillespie’s stochastic additive scale–concave fitness function (sas-cff) model  (SAS institute)
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SAS institute gillespie’s stochastic additive scale–concave fitness function (sas-cff) model
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 <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.
Gillespie’s Stochastic Additive Scale–Concave Fitness Function (Sas Cff) Model, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gillespie mj  (Zambon)
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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 <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.
Gillespie Mj, supplied by Zambon, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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gartner-schmidt  (Gartner Inc)
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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 <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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gillespie’s algorithm r2008a  (MathWorks Inc)
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MathWorks Inc gillespie’s algorithm r2008a
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 <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.
Gillespie’s Algorithm R2008a, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


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: