Figure 2:

Visualization of the Tau-Hybrid simulation of a coupled discrete-continuous system. The model features three reactions: $R_1:A+B\to \varnothing$, $R_2:\varnothing \to A$, $R_3:\varnothing \to B$. The values of the reaction indicator variables, $r_1$, $r_2$, and $r_3$ are shown along with the populations of species $A$, which is set to be continuous, and species $B$, which is set to be discrete. The population of $B$ changes discretely when $r_1$ or $r_3$ fire, which occurs when their value crosses the $y = 0$ axis and becomes positive. We then use (11) to determine the number of times the reaction is fired and then reset the reaction indicator value to $\text{log}\left(URN\right)$ (a negative value). The reaction $R_2$ is simulated as deterministic because it depends only on species marked as continuous. Therefore, the indicator variable $r_2$ is ignored and the population of $A$ changes continuously. The population of $A$ also changes discretely when $R_1$ fires. The simulation $\tau$ step size is calculated adaptively, and the state of the simulation is sampled for output every 0.1 time units. All other options use the defaults (e.g., LSODA integrator).