Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease

Constitutive elements of an FN and FN example. a Handlers provide a “flexible” layer between places and transitions. In the event net, places are connected to event handlers through arcs, and transitions are connected to event handlers through edges. In the intensity net, transitions are connected to intensity handlers through arcs, and places are connected to intensity handlers through edges. b FN modeling a system with two reactions, R1: A → B and R2: C → D？+？E, that are regulated by the molecules X (e.g., an enzyme) and Y (e.g., an activator). An FN consists of an event net (green elements) and an intensity net (blue elements) that share places and transitions. While the event net models how the reactions determine the changes in the state, the intensity net models how the state determines the rates of the reactions. The potential evolutions of the FN depend on the inequalities associated with handler