The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

McCollum, James M.; Peterson, Gregory D.; Cox, Chris D.; Simpson, Michael L.; Samatova, Nagiza F.

doi:10.1016/j.compbiolchem.2005.10.007

Cited by 182Gene Regulatory Network AnalysisSimulation Techniques and Applicationsstochastic dynamics and bifurcation

The DOI matches its Crossref record; 35 of the 37 references it cites were found in a registry or an index.

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

McCollum, James M., Peterson, Gregory D., Cox, Chris D., Simpson, Michael L., Samatova, Nagiza F.·2006·Computational Biology and Chemistry

DOI 10.1016/j.compbiolchem.2005.10.007

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Abstract

A key to advancing the understanding of molecular biology in the post-genomic age is the development of accurate predictive models for genetic regulation, protein interaction, metabolism, and other biochemical processes. To facilitate model development, simulation algorithms must provide an accurate representation of the system, while performing the simulation in a reasonable amount of time. Gillespie's stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous models with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity. In this work, we examine the performance of different versions of the SSA when applied to several biochemical models. Through our analysis, we discover that transient changes in reaction execution frequencies, which are typical of biochemical models with gene induction and repression, can dramatically affect simulator performance. To account for these shifts, we propose a new algorithm called the sorting direct method that maintains a loosely sorted order of the reactions as the simulation executes. Our measurements show that the sorting direct method performs favorably when compared to other well-known exact stochastic simulation algorithms.

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The wide range of methods provided by JumpProcesses.jl enables Catalyst to outperform other packages.
“Here, the wide range of methods provided by the JumpProcesses.jl package [44], a component of DifferentialEquations, enables Catalyst to outperform the other packages (most of which only provide Gillespie’s direct method or its sorting direct variant [45]).”
From Catalyst: Fast and flexible modeling of reaction networks (2023) · cites this paper as [45]

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Authors: McCollum, J. M., Peterson, G. D., Cox, C. D., Simpson, M. L., & Samatova, N. F.
Affiliations: Oak Ridge National Laboratory (US)
University of Tennessee at Knoxville (US)
Corresponding author: Samatova, Nagiza F.
ORCID: Peterson, Gregory D.
Cox, Chris D.
Simpson, Michael L.
Venue: Computational Biology and Chemistry
Publisher: Elsevier BV
Published: 2006-02
Volume: 30
Issue: 1
Pages: 39-49
ISSN: 1476-9271 (ISSN-L)
DOI: 10.1016/j.compbiolchem.2005.10.007
OpenAlex: W2072077152
Cited by: 182
References: 37
Citations by year: 2026: 4 · 2025: 2 · 2024: 3 · 2023: 3 · 2022: 3 · 2021: 4 · 2020: 8 · 2019: 11 · 2018: 12 · 2017: 6 · 2016: 9 · 2015: 13 · 2014: 15 · 2013: 14 · 2012: 12
FWCI: 2.99
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Computational Biology and Chemistry (publishedVersion)
PubMed (publishedVersion)
Funders: U.S. Department of Energy
Defense Advanced Research Projects Agency
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: stochastic simulation, Gillespie algorithm, computational efficiency, biochemical systems, gene regulatory networks
MeSH terms: Algorithms, Escherichia coli, Models, Chemical, Stochastic Processes, Aliivibrio fischeri, Systems Biology

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The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

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