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In Silico Biology 6, 0010 (2006); ©2006, Bioinformation Systems e.V.  

Analyzing stationary states of gene regulatory network using Petri nets

Anna Gambin, Sławomir Lasota and Michał Rutkowski*

Institute of Informatics, Warsaw University, Banacha 2, 02-097 Warszawa, Poland

* Corresponding author

Edited by E. Wingender; received September 30, 2005; revised January 16, 2006; accepted February 01, 2006; published February 19, 2006


We introduce and formally define the notion of a stationary state for Petri nets. We also propose a fully automatic method for finding such states. The procedure makes use of the Presburger arithmetic to describe all the stationary states. Finally we apply this novel approach to find stationary states of a gene regulatory network describing the flower morphogenesis of A. thaliana. This shows that the proposed method can be successfully applied in the study of biological systems.

Keywords: Petri net, stationary state, gene regulatory network, Presburger arithmetic, flower morphogenesis, Arabidopsis thaliana