Scientific Annals of Computer Science

"Alexandru Ioan Cuza" University of Iaşi

Petri Nets for Biologically Motivated Computing

Published in Volume XXI, Issue 2, 2011, p. 199-225, doi:

Authors: J. Kleijn, M. Koutny, G. Rozenberg


Petri nets are a general and well-established model of concurrent and distributed computation and behaviour, including that taking place in biological systems. In this survey paper, we are concerned with intrinsic relationships between Petri nets and two formal models inspired by aspects of the functioning of the living cell: membrane systems and reaction systems. In particular, we are interested in the benefits that can result from establishing strong semantical links between Petri nets and membrane systems and reaction systems. We first discuss Petri nets with localities reflecting the compartmentalisation modelled in membrane systems. Then special attention is given to set-nets, a new Petri net model for reaction systems and their qualitative approach to the investigation of the processes carried out by biochemical reactions taking place in the living cell.

Keywords:Petri net, biomodelling, membrane system, reaction system, locality, GALS, qualitative modelling, set-net, set membrane system

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