stochastic simulation output

Here, Tj is a time period that species X spent in state n, and Tsim is the total simulation time. For the species X1 shown in Figure 1 of the manuscript, as first sight, one might think that P (X1 = 0) << P (X1 = 1) because X1 = 1 during 19 of the 20 simulated time steps. In stochastic simulations, reaction events are irregular due to their stochastic nature. In this particular example, the first reaction event took 39.976 time units, while the next 19 reaction events together took only 1.002 time units. Therefore, the probabilities of being in state zero and one are P (X1 = 0) = 39.976/40.978 ≈ 0.975 and P (X1 = 1) = 1.002/40.978 ≈ 0.025 and therefore P (X1 = 0) >> P (X1 = 1). Subsequently, StochPy can determine the mean of this species by taking the sum of the product of species state probabilities and species state values,