Stochastic Differential Equations for Practical Simulation of Gene Circuits.
Chemical Langevin equation
Gene circuits
Stochastic Modeling
Synthetic biology
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
6
1
2021
pubmed:
7
1
2021
medline:
2
4
2021
Statut:
ppublish
Résumé
The Chemical Langevin Equation approach allows simple stochastic simulation of gene circuits under many practical situations where the number of molecules of the species involved is not extremely low. Here, we describe methods and a computational framework to simulate a population of cells containing gene circuits of interest. These methods account for both intrinsic and extrinsic noise sources, and allow us to have both individual cell-related species and population-related ones. The protocol covers aspects related to proper description of the system and setting the software tools. It also helps to deal with the optimization of data storage and the simulation precision versus computational time issue. Finally, it also gives practical tests to assess the validity of the underlying technical assumptions.
Identifiants
pubmed: 33405216
doi: 10.1007/978-1-0716-1032-9_2
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
41-90Références
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