DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia

Abstract Summary DelaySSAToolkit.jl is a Julia package for modelling reaction systems with non-Markovian dynamics, specifically those with time delays. These delays implicitly capture multiple intermediate reaction steps and hence serve as an effective model reduction technique for complex systems i...

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Bibliographic Details
Published in:Bioinformatics Vol. 38; no. 17; pp. 4243 - 4245
Main Authors: Fu, Xiaoming, Zhou, Xinyi, Gu, Dongyang, Cao, Zhixing, Grima, Ramon
Format: Journal Article
Language:English
Published: England Oxford University Press 02.09.2022
Subjects:
Algorithms
Computer Simulation
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary:Abstract Summary DelaySSAToolkit.jl is a Julia package for modelling reaction systems with non-Markovian dynamics, specifically those with time delays. These delays implicitly capture multiple intermediate reaction steps and hence serve as an effective model reduction technique for complex systems in biology, chemistry, ecology and genetics. The package implements a variety of exact formulations of the delay stochastic simulation algorithm. Availability and implementation The source code and documentation of DelaySSAToolkit.jl are available at https://github.com/palmtree2013/DelaySSAToolkit.jl.
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btac472