  Answering realistic questions about biological systems and pathways similar
to the ones used by text books to test understanding of students about
biological systems is one of our long term research goals. Often these
questions require simulation based reasoning. To answer such questions, we need
formalisms to build pathway models, add extensions, simulate, and reason with
them. We chose Petri Nets and Answer Set Programming (ASP) as suitable
formalisms, since Petri Net models are similar to biological pathway diagrams;
and ASP provides easy extension and strong reasoning abilities. We found that
certain aspects of biological pathways, such as locations and substance types,
cannot be represented succinctly using regular Petri Nets. As a result, we need
higher level constructs like colored tokens. In this paper, we show how Petri
Nets with colored tokens can be encoded in ASP in an intuitive manner, how
additional Petri Net extensions can be added by making small code changes, and
how this work furthers our long term research goals. Our approach can be
adapted to other domains with similar modeling needs.
