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Towards Biopathway Modeling and Simulation.

Matsuno, Hiroshi; Fujita, Sachie; Doi, Atsushi; Nagasaki, Masao; Miyano, Satoru

In: Proceedings of the 24th International Conference on Applications and Theory of Petri Nets (ICATPN 2003), Eindhoven, The Netherlands, June 23-27, 2003, pages 3-22. Volume 2679 of Lecture Notes in Computer Science / Wil M. P. van der Aalst and Eike Best (Eds.) --- Springer-Verlag, June 2003.

Abstract: Petri net has been employed for modeling metabolic pathways as well as signal transduction pathways and gene regulatory networks. The purpose of this paper is to introduce an extension of Petri net called hybrid functional Petri net (HFPN) which allows us to model biopathways naturally and effectively. The method for creating biopathways with HFPN is demonstrated through a well-known biopathway example " lac operon gene regulatory mechanism and glycolytic pathway." In order to evaluate this biopathway model, simulations of five mutants of the lac operon are carried out by Genomic Object Net which is a biopathway simulator based on the HFPN architecture. The software Genomic Object Net and the HFPN files presented in this paper can be downloaded from http://www.GenomicObject.Net/.

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