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

DOI10.1016/j.compbiolchem.2005.10.007zbMath1086.92018OpenAlexW2072077152WikidataQ39216009 ScholiaQ39216009MaRDI QIDQ2490517

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

Publication date: 16 May 2006

Published in: Computational Biology and Chemistry (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.compbiolchem.2005.10.007

zbMATH Keywords

Gillespie algorithmStochastic simulationSystems biologyGene networksModeling biochemical systems

Mathematics Subject Classification ID

Probabilistic models, generic numerical methods in probability and statistics (65C20) Monte Carlo methods (65C05) Biochemistry, molecular biology (92C40)

Related Items (19)

Hybrid stochastic simulations of intracellular reaction-diffusion systems ⋮ Computationally-efficient stochastic cluster dynamics method for modeling damage accumulation in irradiated materials ⋮ HRSSA - efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks ⋮ Developing Itô stochastic differential equation models for neuronal signal transduction path\-ways ⋮ Extending the multi-level method for the simulation of stochastic biological systems ⋮ Conditional Monte Carlo for Reaction Networks ⋮ Stochastic simulation of biochemical reactions with partial-propensity and rejection-based approaches ⋮ Computational methods for multiscale modelling of virus infection dynamics ⋮ The effect of bottleneck size on evolution in nested Darwinian populations ⋮ Frequency domain analysis of noise in simple gene circuits ⋮ Efficient finite-difference method for computing sensitivities of biochemical reactions ⋮ \(L\)-leap: Accelerating the stochastic simulation of chemically reacting systems ⋮ ``Final all possible steps approach for accelerating stochastic simulation of coupled chemical reactions ⋮ Sparse grids and hybrid methods for the chemical master equation ⋮ Diagnostics for assessing the linear noise and moment closure approximations ⋮ Discrete-time stochastic modeling and simulation of biochemical networks ⋮ Markovian dynamics on complex reaction networks ⋮ Slow-scale split-step tau-leap method for stiff stochastic chemical systems ⋮ A critical comparison of rejection-based algorithms for simulation of large biochemical reaction networks

Uses Software

• Matlab
• ode23
• ode45
• Ode15s
• ODEPACK
• ode113
• ode23s
• MATLAB ODE suite
• Bio-SPICE

Cites Work

• Two-stage stochastic Runge-Kutta methods for stochastic differential equations
• Model based conjectures on mammalian clock controversies
• Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation
• Stochastic approaches for modelling in vivo reactions
• The MATLAB ODE Suite

This page was built for publication: The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior