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DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia
Open accessPublished version of a preprint
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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Existing open-source biological modeling projects have extended Catalyst's intermediate representation.
“Finally, we demonstrate Catalyst’s broad extensibility and composability by highlighting how it can compose with a variety of Julia libraries, and how existing open-source biological modeling projects have extended its intermediate representation.”
From Catalyst: Fast and flexible modeling of reaction networks (2023) · cites this paper as [56]
Independent package developers already utilise Catalyst's extensibility.
“Indeed, this is already being utilised by independent package developers.”
From Catalyst: Fast and flexible modeling of reaction networks (2023) · cites this paper as [56]
DelaySSAToolkit.jl can accept Catalyst models as input to its SSAs that handle stochastic chemical kinetics models with delays.
“while DelaySSAToolkit.jl [56] can accept Catalyst models as input to its SSAs that handle stochastic chemical kinetics models with delays.”
From Catalyst: Fast and flexible modeling of reaction networks (2023) · cites this paper as [56]
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Research works printed but not linked: 14
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Cited by
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Catalyst: Fast and flexible modeling of reaction networks
Loman, T. E., Ma, Y., Ilin, V., Gowda, S., Korsbo, N., Yewale, N., Rackauckas, C., & Isaacson, S. A. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011530 · Cited by 47
Metadata
- Authors
- Fu, X., Zhou, X., Gu, D., Cao, Z., & Grima, R.
- Affiliations
- East China University of Science and Technology (CN)
- University of Edinburgh (GB)
- Corresponding author
- Fu, Xiaoming
- Cao, Zhixing
- Grima, Ramon
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-07-07
- Volume
- 38
- Issue
- 17
- Pages
- 4243-4245
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W4284896622
- Cited by
- 16
- References
- 0
- Citations by year
- 2026: 8 · 2025: 1 · 2024: 1 · 2023: 5 · 2022: 1
- FWCI
- 0.65
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- National Natural Science Foundation of China (62073137)
- CPSF (2021M071202)
- Shanghai Sailing Program (22YF1410700)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Social Sciences › Decision Sciences › Management Science and Operations Research › Simulation Techniques and Applications
- Physical Sciences › Physics and Astronomy › Statistical and Nonlinear Physics › stochastic dynamics and bifurcation
- Keywords
- time delay, reaction systems, non-Markovian dynamics, Julia package, model reduction, chemical reaction networks, stochastic simulation
- MeSH terms
- Algorithms, Computer Simulation, Software
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