English: (a) A simple, standard Petri net. The circles denote places, whereas the boxes denote transitions. The distribution of tokens (black dots) in the places at a given time defines a marking. Transitions change the marking by removing a token from each incoming arrow and adding a token to each outgoing arrow. (b) Simplified logical regulatory graph for the biosynthesis of tryptophan in E. coli. Each node of the regulatory graph represents an active component: tryptophan (Trp), the active enzyme (TrpE) and the active repressor (TrpR). The node marked by a rectangle accounts for the import of Trp from external medium. All nodes are binary (that is, can take the value 0 or 1), except Trp, which is represented by a ternary variable (taking the values 0, 1, 2). Arrows represent activation and bars denote inhibition. (c) Petri net of the Trp regulatory network. Each of the four components of b is represented by two complementary places and all the different situations that lead to a change of the state of the system are modeled by one of the nine transitions (t1–t 9).