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One of our long term research goals is to develop systems to answer realisticquestions (e.g., some mentioned in textbooks) about biological pathways that abiologist may ask. To answer such questions we need formalisms that can modelpathways, simulate their execution, model intervention to those pathways, andcompare simulations under different circumstances. We found Petri Nets to bethe starting point of a suitable formalism for the modeling and simulationneeds. However, we need to make extensions to the Petri Net model and alsoreason with multiple simulation runs and parallel state evolutions. Towardsthat end Answer Set Programming (ASP) implementation of Petri Nets would allowus to do both. In this paper we show how ASP can be used to encode basic PetriNets in an intuitive manner. We then show how we can modify this encoding tomodel several Petri Net extensions by making small changes. We then highlightsome of the reasoning capabilities that we will use to accomplish our ultimateresearch goal.

Encoding Petri Nets in Answer Set Programming for Simulation Based Reasoning