Table 3 |
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• Initialize all species and rate constants |
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• Compute all reaction rates |
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• Loop: |
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* Set μ = sum of rates for the discrete reactions |
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* if (pt = μΔt > ε), use Gillespie algorithm: |
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* R = a uniform random number in (0,1) |
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* Set timeStep = -log(R)/μ |
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* Find which reaction occurred, update the species involved |
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* else, use small Δt approximation: |
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* R = a uniform random number in [0,1] |
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* timeStep = continuousTimeStep |
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* if (R <pt = μ × timeStep), discrete transition has occurred: |
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• Determine which discrete transition occurred: |
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• Find the first value of k for which |
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• If |
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* else, no discrete transition: |
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• No discrete reaction occurs, update is entirely due to continuous reactions (below) |
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* end if (small Δt method, determination if discrete transition occurred) |
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* end if (selection of Gillespie or small Δt method for discrete reactions) |
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* Update the continuous species using the Langevin equation, with step size timeStep (where timeStep is either equal to continuousTimeStep or to the step size found by the Gillespie algorithm), using a semi-implicit numerical method |
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* Update any rates that have been changed by the continuous reactions and the single discrete reaction |
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* Break when user-defined total simulation time is reached |
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• end loop |
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Adalsteinsson et al. BMC Bioinformatics 2004 5:24 doi:10.1186/1471-2105-5-24 |
, the forward reaction occurred, otherwise the backward reaction occurred