Encoding Petri Nets in Answer Set Programming for Simulation Based
  Reasoning
  One of our long term research goals is to develop systems to answer realistic
questions (e.g., some mentioned in textbooks) about biological pathways that a
biologist may ask. To answer such questions we need formalisms that can model
pathways, simulate their execution, model intervention to those pathways, and
compare simulations under different circumstances. We found Petri Nets to be
the starting point of a suitable formalism for the modeling and simulation
needs. However, we need to make extensions to the Petri Net model and also
reason with multiple simulation runs and parallel state evolutions. Towards
that end Answer Set Programming (ASP) implementation of Petri Nets would allow
us to do both. In this paper we show how ASP can be used to encode basic Petri
Nets in an intuitive manner. We then show how we can modify this encoding to
model several Petri Net extensions by making small changes. We then highlight
some of the reasoning capabilities that we will use to accomplish our ultimate
research goal.
