Dataset Information

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

ABSTRACT:

Motivation

Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution.

Results

In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples. The method relies on the combination of the sigma point approach to describe extrinsic and external variability and the ? -leaping algorithm to account for the stochasticity due to probabilistic reactions. The comparison of our method to extensive Monte Carlo calculations demonstrates an immense computational advantage while losing an acceptable amount of accuracy. Additionally, the application to parameter optimization problems in stochastic biochemical reaction networks is shown, which is rarely applied due to its huge computational burden. To give further insight, a MATLAB script is provided including the proposed method applied to a simple toy example of gene expression.

Availability and implementation

MATLAB code is available at Bioinformatics online.

Contact

flassig@mpi-magdeburg.mpg.de.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Pischel D

PROVIDER: S-EPMC5870780 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Publications

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

Pischel Dennis D Sundmacher Kai K Flassig Robert J RJ

Bioinformatics (Oxford, England) 20170701 14

<h4>Motivation</h4>Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution.<h4>Results</h4>In this ...[more]

PMID: 28881987

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Dataset Information

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

Motivation

Results

Availability and implementation

Contact

Supplementary information

Publications

Efficient simulation of intrinsic, extrinsic and external noise in biochemical systems.

Similar Datasets

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