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CNCSIS B+ (code 820) since 2007

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Journal Info

Title: Studia Universitatis Vasile Goldis, Seria Stiintele Vietii (Life Sciences Series)
Abbreviated title: Studia Univ. VG, SSV
Publisher: "Vasile Goldis" University Press
Owner: Western University "Vasile Goldis" Arad, Romania
ISSN: 1584-2363
e-ISSN: 1842-7863
ISSN-L: 1584-2363

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NWA a discrete stochastic simulation technique: a review Print E-mail
Written by Tusa I., Roata G., Paun P. A.   
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Article Title: NWA a discrete stochastic simulation technique: a review
Authors: Tusa I., Roata G., Paun P. A.
Affiliation: Department of Bioinformatics, National Institute for Research and Development for Biological Sciences, Bucharest, Romania
Abstract: We give the description for the Nondeterministic Waiting Time (NWT) algorithm, a biochemical modeling approach based on the Membrane Systems paradigm of computation. This simulation technique provides a unique perspective on the biochemical evolution of the cell different from Gillespie’s algorithm and different from ODE-based simulations. That is, depending on the reactions and molecular multiplicities of a given model, our simulator is capable of producing results comparable to the alternative techniques - continuous and deterministic or discrete and stochastic. Some results for a few models are given, illustrating the differences between the NWT algorithm, the Gillespie algorithm, and the solutions to systems of ordinary differential equations. We are able to show that in some cases the NWT technique yields results closer to Gillespie, while for other models the results of the NWT simulator are much closer to the results of the ODE simulator.
Keywords: Discrete simulation, Gillespie's algorithm, cellular pathways, deterministic simulation, nondeterministic waiting time simulation with memory
References:
*Correspondence: Paun Andrei, National Institute for Research and Development for Biological Sciences, Department of Bioinformatics, No. 296, Splaiul Independentei, Sector 6, postal code: 060031, Bucharest, Romania, Tel. +40-(21)-2207780, Fax. +40-(21)-2207695, email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it