Work

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

Year: 2022

Type: article

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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btac472

Authors: Xiaoming Fu, Xinyi Zhou, Dongyang Gu, Zhixing Cao, Ramon Grima

Institutions: East China University of Science and Technology, University of Edinburgh

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funder: National Natural Science Foundation of China

Award: G4852710174