Paper Info
Title
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 tau-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.
Year
DOI
Venue
2018
10.1093/bioinformatics/btx253
BIOINFORMATICS
DocType
Volume
Issue
Journal
33
14
ISSN
Citations 
PageRank 
1367-4803
1
0.41
References 
Authors
9
3
Name
Order
Citations
PageRank
Dennis Pischel110.75
Kai Sundmacher24912.51
Robert J Flassig3364.76