Parallel implementation of stochastic simulation for large scale cellular processes

Tian, Tianhai & Burrage, Kevin (2005) Parallel implementation of stochastic simulation for large scale cellular processes. In Li, Kai & Sekiguchi, Satoshi (Eds.) Proceedings. Eighth International Conference on High-Performance Computing in Asia-Pacific Region, IEEE, China, Beijing, pp. 621-626.

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Abstract

Experimental and theoretical studies have shown the importance of stochastic processes in genetic regulatory networks and cellular processes. Cellular networks and genetic circuits often involve small numbers of key proteins such as transcriptional factors and signaling proteins. In recent years stochastic models have been used successfully for studying noise in biological pathways, and stochastic modelling of biological systems has become a very important research field in computational biology. One of the challenge problems in this field is the reduction of the huge computing time in stochastic simulations. Based on the system of the mitogen-activated protein kinase cascade that is activated by epidermal growth factor, this work give a parallel implementation by using OpenMP and parallelism across the simulation. Special attention is paid to the independence of the generated random numbers in parallel computing, that is a key criterion for the success of stochastic simulations. Numerical results indicate that parallel computers can be used as an efficient tool for simulating the dynamics of large-scale genetic regulatory networks and cellular processes

Impact and interest:

11 citations in Scopus
3 citations in Web of Science®
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ID Code: 46168
Item Type: Conference Paper
Refereed: Yes
DOI: 10.1109/HPCASIA.2005.67
ISBN: 0-7695-2486-9
Divisions: Past > QUT Faculties & Divisions > Faculty of Science and Technology
Deposited On: 26 Sep 2011 23:55
Last Modified: 14 Jul 2017 11:01

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