# Setting Simulation Parameters

Simulation parameters must be set prior to requesting execution. The Simulation Settings button on the tool bar brings up the parameters and their options within the Simulation Settings Window.

#### Simulation Parameters:

- Sample Times, specifies time instances to output species and observables concentration values within a comma separated list. The list 0,1,10,100 would cause concentrations to be output at times of 0, 1, 10 and 100 seconds.
- Number of Steps,
- Step Length,

#### Iterative Network Generation:

- Maximum Rule Applications,
- Maximum Number of Multi-State Species in an Aggregate,

#### ODE Simulation:

- Absolute Integration Error Tolerance, specifies error tolerance for species concentrations, default value is 1e-8.
- Relative Integration Error Tolerance,

#### SSA and On-the-fly Simulation

- Update Interval,
- Number of Runs,
- Fly Interations Init,

#### Engine Arguments

- Default Method (ODEs),
- ODEs,
- Stochastic simulation algorithm (Gillespie direct),
- Generate SBML code,
- Generate input for ODE simulation in Matlab,
- Display plots for observables,
- SBML file, compute and display timecourses,
- Debugging output,
- Generate Network,
- Overwrite Previous Net Files,