SimBiology 3.1

Running a Simulation

Together, SimBiology and MATLAB provide a wide range of solvers for simulating stochastic and deterministic systems.

Solvers

SimBiology provides three types of stochastic solvers: a stochastic simulation algorithm (SSA), explicit tau-leaping, and implicit tau-leaping.

SimBiology also provides deterministic solvers for stiff and nonstiff systems. In addition to the traditional MATLAB solvers, SimBiology adds CVODE from the SUNDIALS suite of solvers.

Simulation Events

Simulation events let you define a sudden change in model behavior. You can specify that an event occurs at a specific simulation time or in response to a change within the system, such as the value of a species.

Ensemble Runs

Ensemble runs let you analyze model output over multiple simulations—helpful when you are dealing with stochastic simulations or need to perform parameter scans on your model. You specify the model and number of iterations as inputs. You can calculate the mean and variance of the ensemble data, and visualize your ensemble results with distribution and mountain plots.

Simulation Settings

You can specify the solver type, simulation stop time, and other simulation options. You can also specify whether dimensional analysis should be performed on the model as a verification step. Dimensional analysis checks that all mathematical expressions in the model are in consistent dimensions and then performs unit conversions automatically.