eISSN: 2353-9461
ISSN: 0860-7796
BioTechnologia
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3/2011
vol. 92
 
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REVIEW PAPER
Deterministic models and stochastic simulations in multiple reaction models in systems biology

Paweł Lachor
,
Krzysztof Puszyński
,
Andrzej Polański

BioTechnologia vol. 92(3) C pp. 265-280 C 2011
Online publish date: 2014/10/28
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In this paper, we have overviewed deterministic and stochastic approaches for the modeling of bio-molecular

reactions in systems biology. We have described and compared different versions of stochastic simulation

approaches towards the modeling of bio-molecular reaction systems, the direct approach and the family of the tauleap

methods. We also have illustrated differences between different approaches by providing numerical examples

of computational analyses for selected models. Computational examples of application of stochastic simulation

algorithms involved two systems of different interacting bio-molecular species and one model from the area of

ecology, describing interactions between two animal populations. Apart from the direct approach and tau-leap

family of methods, we have also overviewed the so called hybrid algorithm of stochastic simulations, proven to

be very efficient when there are huge differences between reaction rates in the system.
keywords:

stochastic simulation algorithms, direct algorithm, Tau-Leap approximated stochastic simulation algorithms, hybrid algorithm



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