A critical comparison of rejection-based algorithms for simulation of large biochemical reaction networks

DOI10.1007/s11538-018-0462-yzbMath1422.92050OpenAlexW2824474752WikidataQ89451205 ScholiaQ89451205MaRDI QIDQ2325572

Vo Hong Thanh

Publication date: 26 September 2019

Published in: Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL: https://aaltodoc.aalto.fi/handle/123456789/32899

zbMATH Keywords

computational biologystochastic simulationrejection-based simulation technique

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Computational methods for problems pertaining to biology (92-08) Systems biology, networks (92C42)

Related Items (2)

Efficient finite-difference method for computing sensitivities of biochemical reactions ⋮ Stochastic simulation of biochemical systems: in memory of Dan T. Gillespie's contributions

Uses Software

• STEPS
• HRSSA
• HSimulator

Cites Work

• Unnamed Item
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• Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches
• HSimulator: hybrid stochastic/deterministic simulation of biochemical reaction networks
• HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks
• Efficient kinetic Monte Carlo simulation
• The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

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