SimBiology

Simulating Deterministic and Stochastic Systems

You can simulate models using deterministic or stochastic solvers. Simulations return time and state information of model components. You can also simulate systems that incorporate discontinuities, such as events and dose administration.

Drug concentration profile. SimBiology lets you treat doses as discontinuous events.

SimBiology provides several deterministic and stochastic solvers. You can perform a deterministic simulation using MATLAB ODE solvers or the CVODE solver from the SUNDIALS suite. SimBiology also provides three stochastic solvers: stochastic simulation algorithm (SSA), explicit tau-leaping, and implicit tau-leaping.

3D phase plot of cell-cycle regulation dynamics at steady state.

Prior to simulation, SimBiology verifies the validity of the model structure and expressions, and reports warnings if errors are detected. For dimensional analysis, you can configure SimBiology to automatically convert units for consistency.

Accelerating a Simulation

You can accelerate a simulation by converting models to compiled C code. Compiling a model can significantly improve performance speed and is particularly useful when performing Monte Carlo simulations, estimating parameters, fitting models to experimental data, or working with large models.