Simulation-Based Reasoning about Biological Pathways Using Petri Nets and ASP

It presents how Petri nets and answer set programming (ASP) can be used to answer simulation-based reasoning questions about biological systems. It shows how Petri nets can be encoded in ASP in an intuitive manner. The chapter discusses how additional Petri net extensions, such as firing semantics, reset arcs, inhibit arcs, read arcs, timed arcs, priority transitions and higher level extensions, such as colored tokens, can be easily encoded by making localized changes to the initial encoding and put these extensions in a biological perspective. The chapters approach is different from others in that it model questions to be answered as interventions and observations on the evolution trajectories of the pathway being modeled. ASP encoding enables easy filtering of Petri Net trajectories through observations. ASP syntax allows more general observations to be easily encoded as compared to encoding such observations directly in Petri Nets.