13 Simulation Trace

The Simulation Trace option allows the user to set up the parameters for a simulation run (or a number of independent simulation runs) and export the simulation trace to three different types of files, namely:

Traviando export file (.xml file)— export file for Traviando, a trace analyzer and visualizer for simulation traces of discrete event dynamic systems (see [8, 18, 16, 17, 24, 12, 26, 13, 9] for more information on Traviando)
BioNessie export file (.bn file)— export file for BioNessie, a free, state-of-the-art platform-independent biochemical networks simulation and analysis software environment (see [2, 25] for more information on BioNessie)
SBRML results export file (.sbrml file)— results export file for Systems Biology Markup Language (SBML) (see [6, 15] for more information on SBML)

In order to set up the simulation the user is allowed to set several parameters (see Figure 56):

Number of firings limit — A limit to the number of reactions that can occur (optional)
Time limit for the trace — The stop time of the simulation (optional)
Output comments - Enter a comment — If the user checks the output comments checkbox they are allowed to add a comment to the export file concerning the function of the model
Show results graph - Set the increment in data point size for the graph — If the user checks the appropriate checkbox the results of the simulation are plotted in a graph. In this case the user can set the time difference between consecutive data points in the graph (default value 1.0)
Number of independent runs — The number of simulation traces to be produced (default value 1)

The simulation set up for the a-b-c.biopepa model, as shown in Figure 56, produces three export files, the .bn BioNessie export file, the .sbrml SBML results export file and the .xml Traviando export file. The simulation trace data are also plotted in a graph, as shown in Figure 58.

$\includegraphics[scale=0.5]{screenshots/screenshots/simulation_trace1}$

Figure 72: Setting up a simulation for the a-b-c.biopepa model

$\includegraphics[scale=0.5]{screenshots/screenshots/simulation_trace2}$

Figure 73: Graph results of the simulation for the a-b-c.biopepa model