In: Proceedings of Applications and Theory of Petri Nets 2004: 25th International Conference, ICATPN 2004, Bologna, Italy, June 21-25, 2004, pages 216-237. Volume 3099 of Lecture Notes in Computer Science / Cortadella, Reisig (Eds.) --- Springer-Verlag, September 2004.
Abstract: This paper describes the thriving application of Petri net theory for model validation of different types of molecular biological systems. After a short introduction into systems biology we demonstrate how to develop and validate qualitative models of biological pathways in a systematic manner using the well-established Petri net analysis technique of place and transition invariants. We discuss special properties, which are characteristic ones for biological pathways, and give three representative case studies, which we model and analyse in more detail. The examples used in this paper cover signal transduction pathways as well as metabolic pathways.