Lac Operon

Consider the lac operon model presented in Section 7.5 of Stochastic Modelling for Systems Biology. Open the file examples/cain/WilkinsonSMfSB/ch07-lac-stoch.xml and generate a trajectory. Note that the method uses the a Python solver that is capable of simulating events. As this is not a high performance solver, generating a trajectory will take a couple of minutes. So launch the simulation now and then continue reading.

When the trajectory has been generated, open the plot configuration window by clicking the plot button   in the output panel. First unselect all of the species by right-clicking on the "Show" column header. Then select the Rna, Z, and Lactose species. Next left-click on the "Line Color" header to color these three species with different hues. Unselect the "Legend" toggle, we will enter the species names in the Y axis label. Select a custom figure size of 8 by 2 inches. Now we are prepared to plot each of the three species in a separate window by selecting each in turn. The resulting plot configuration window is shown below.

This model has a time event: at time t = 20,000, the amount of Lactose is increased by 10,000. The interesting feature of this model is how the system responds to the influx of Lactose. The plots below reproduce the results in the text.