Abstract
This chapter introduces the basic notions and notations, as employed in the rest of this book. This includes the distinct modeling of substances and reactions, together with their logical connection. We explain the graphical representation of Petri nets, as well as the “token flow mechanics”, representing dynamic behavior. We show how sequential, alternative and concurrent occurrences of reactions are modeled, including quantitative aspects of stoichiometric reactions. We present a number of specific analysis techniques for Petri nets, including place invariants and transition invariants, based on systems of linear equations. Further analysis techniques such as traps and siphons exploit the graph-based structure of nets. The use of Petri nets as a modeling- and analysis technique for biological process is illustrated by a fraction of the combined glucose and pentose phosphate pathway.
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© 2011 Springer-Verlag London Limited
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Reisig, W. (2011). Petri Nets. In: Koch, I., Reisig, W., Schreiber, F. (eds) Modeling in Systems Biology. Computational Biology, vol 16. Springer, London. https://doi.org/10.1007/978-1-84996-474-6_3
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DOI: https://doi.org/10.1007/978-1-84996-474-6_3
Publisher Name: Springer, London
Print ISBN: 978-1-84996-473-9
Online ISBN: 978-1-84996-474-6
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