# Table 3

• Initialize all species and rate constants
• Compute all reaction rates
• Loop:
* Set μ = sum of rates for the discrete reactions
* if (p t = μΔt > ε), use Gillespie algorithm:
* R = a uniform random number in (0,1)
* Set timeStep = -log(R)/μ
* Find which reaction occurred, update the species involved
* else, use small Δt approximation:
* R = a uniform random number in [0,1]
* timeStep = continuousTimeStep
* if (R <p t = μ × timeStep), discrete transition has occurred:
• Determine which discrete transition occurred:
• Find the first value of k for which • If , the forward reaction occurred, otherwise the backward reaction occurred
* else, no discrete transition:
• No discrete reaction occurs, update is entirely due to continuous reactions (below)
* end if (small Δt method, determination if discrete transition occurred)
* end if (selection of Gillespie or small Δt method for discrete reactions)
* 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
* Update any rates that have been changed by the continuous reactions and the single discrete reaction
* Break when user-defined total simulation time is reached
• end loop 