# Modeling and simulation of intracellular dynamics: choosing an appropriate framework

@article{Wolkenhauer2004ModelingAS, title={Modeling and simulation of intracellular dynamics: choosing an appropriate framework}, author={Olaf Wolkenhauer and Mukhtar Ullah and Walter Kolch and Kwang-Hyun Cho}, journal={IEEE Transactions on NanoBioscience}, year={2004}, volume={3}, pages={200-207} }

Systems biology is a reemerging paradigm which, among other things, focuses on mathematical modeling and simulation of biochemical reaction networks in intracellular processes. For most simulation tools and publications, they are usually characterized by either preferring stochastic simulation or rate equation models. The use of stochastic simulation is occasionally accompanied with arguments against rate equations. Motivated by these arguments, we discuss in this paper the relationship between…

## 141 Citations

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The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed, by reporting the principal conceptualizations suggested by A. Langevin, A. Fokker, M. Planck, D. van Kampfen, and recently by D. Wilkinson.

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A novel derivation of the differential Chapman-Kolmogorov equation for a general multidimensional Markov process made up of both continuous and jump processes, is presented, and a 'family tree' for stochastic models in systems biology is sketched.

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Simulation and Verification for Computational Modelling of Signalling Pathways

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An overview of the simulation, verification and differential equation approaches to modelling biochemical reaction networks is given and the advantages and disadvantages are discussed, using as an illustration a fragment of the FGF signalling pathway.

Modelling the dynamics of signalling pathways.

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The discussion begins with the typical range of techniques for modelling that might be employed to go from the chemical kinetics to a mathematical model of biochemical pathways, and considers the decision-making processes involved in selecting the right mechanism and level of detail of representation of the biochemical interactions.

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- BiologyProceedings of the 2009 Winter Simulation Conference (WSC)
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This work presents a case study of reusing parameters and reactions of a deterministic model of a biochemical system in order to implement a stochastic one and reports on the approaches to solve two major challenges.

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