Selecting Simulation Output

RoadRunner supports a range of options for selecting what data a simulation should return. For more detailed information on selections, see the Selecting Values section.

The simulate method, by default returns an structured array, which are arrays that also contain column names. These can be plotted directly using the built in plot() function.

The output selections default to time and the set of floating species. It is possible to change the simulation result values by changing the selection list. For example assume that a model has three species, S1, S2, and S3 but we only want simulate() to return time in the first column and S2 in the second column. To specify this we would type:

rr.timeCourseSelections = ['time', 'S2']
result = rr.simulate (0, 10, 100)

In another example let say we wanted to plot a phase plot where S1 is plotted against S2. To do this we type the following:

rr.timeCourseSelections = ['S1', 'S2']
result = rr.simulate(0, 10, 100)

Some additional examples include:

# Select time and two rates of change (dS1/dt and dS2/dt)
rr.timeCourseSelections = ["time", "S1'", "S2'"]

# By default species names yield amounts, concentrations can be obtained
# using square brackets, e.g.
rr.timeCourseSelections = ['time', '[S1]', '[S2]']