Figure 3

An example signaling Petri net simulation. (a) is the signaling network being simulated. (b) is the signaling Petri net that models that signaling Petri net. The table in (c) provides the markings for the Petri net over the course of a simulation run whose duration is two time blocks. The proteins are given the initial marking shown in the Initial column. Each subsequent column corresponds to a single time step during which one transition fired, producing a new marking of the network. The bold number in each column indicates which protein's marking was affected by the transition that fired in that time step. The red columns – always the last time step in the block – highlight the markings whose values would be averaged and used as part of the final result. These red columns are the sources of the markings that PathwayOracle reports.