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Applications and Theory of Petri Nets 2004

Volume 3099 of the series Lecture Notes in Computer Science pp 216-237

Petri Net Based Model Validation in Systems Biology

  • Monika HeinerAffiliated withDepartment of Computer Science, Brandenburg University of Technology Cottbus
  • , Ina KochAffiliated withDepartment of Bioinformatics, Technical University of Applied Sciences Berlin

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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.