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In Simbiology, is it possible to run stochastic simulations with Gillespie’s algorithm?

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I haven't found an option for stochastic simulation in the simulation tab? What are other options to run such kind of simulation without using the line command?

Accepted Answer

Sietse Braakman
Sietse Braakman on 2 Jun 2020
Edited: Sietse Braakman on 2 Jun 2020
Hi Hassan,
You can do this by choosing a stochastic solver. In the user interface, this can be done by going to the 'Simulation settings' and under 'Solvertype' selecting 'stochastic', 'implicit tau', or 'explicit tau' instead of e.g. ode15s or sundials. See the screenshots below. More on the difference between stochastic/implicit tau/explicit tau solvers can be found here:
If you want to do this programmatically, you can use getconfigset to change the solver. E.g. if your model is called m1:
cs = getconfigset(m1);
cs.SolverType = 'ssa'; % use 'ssa' for stochastic, 'expltau' for explicit or 'impltau' for implicit tau
Let me know if that answers your question.

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