To analyze a CRN, we perform a large number of kMC simulations in parallel (Figure ). The result of each simulation is a series of reactions defining a trajectory of the system state. If a molecule of interest is known, we can use these trajectories to identify potential formation pathways to that molecule. We trace each trajectory; if the molecule of interest is formed at any point, we then identify the shortest sequence of reactions leading to its first formation (Figure ). Performing this method of stochastic pathfinding over many trajectories, we identify a range of possible pathways to the molecule of interest. We then rank the identified paths in order to identify the "best" paths among those observed, as defined by some cost function (see Methods). The thermodynamic pathways obtained from network analysis can then be subjected to further analysis to identify complete mechanisms, including transition-states (TS) and energy barriers.