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MODELING AND SIMULATION OF MOLECULAR BIOLOGY SYSTEMS USING PETRI NETS: MODELING GOALS OF VARIOUS APPROACHES

Computer Engineering Department, École Polytechnique de Montréal, P.B. 6079, succ. Centre-Ville, Montréal, Québec H3C 3A7, Canada

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PIERRE N. ROBILLARD

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https://doi.org/10.1142/S0219720004000764Cited by:86 (Source: Crossref)

Abstract

Petri nets are a discrete event simulation approach developed for system representation, in particular for their concurrency and synchronization properties. Various extensions to the original theory of Petri nets have been used for modeling molecular biology systems and metabolic networks. These extensions are stochastic, colored, hybrid and functional. This paper carries out an initial review of the various modeling approaches based on Petri net found in the literature, and of the biological systems that have been successfully modeled with these approaches. Moreover, the modeling goals and possibilities of qualitative analysis and system simulation of each approach are discussed.

Keywords:

References

H. Kitano, Nature 420, 206 (2002). Crossref, Medline, Google Scholar
R. Heinrich and S. Schuster, Biosystems 47, 61 (1998). Crossref, Medline, Google Scholar
P. Mendes, Comput. Appl. Biosci. 9(5), 563 (1993). Medline, Google Scholar
M. Tomitaet al., Bioinformatics 15, 72 (1999). Crossref, Medline, Google Scholar
S. A. Kauffman , The Origins of Order: Self-Organization and Selection in Evolution ( Oxford University Press , New York , 1993 ) . Crossref, Google Scholar
C. H. Yuh, H. Bolouri and E. H. Davidson, Development 128, 617 (2001). Crossref, Medline, Google Scholar
P. J. E. Goss and J. Peccoud, Proc. Natl. Acad. Sci. USA 95, 6750 (1998). Crossref, Medline, Google Scholar
A. Arkin, J. Ross and H. H. McAdams, Genetics 149, 1633 (1998). Crossref, Medline, Google Scholar
H. de Jong, J. Comput. Biol. 9(1), 67 (2002). Crossref, Medline, Google Scholar
D. Endy and R. Brent, Nature 409, 391 (2001). Crossref, Medline, Google Scholar
J. M. Bower and H. Bolouri , Computational Modeling of Genetic and Biochemical Networks ( MIT Press , Cambridge, MA , 2001 ) . Google Scholar
J. Collado-Vides and R. Hofestädt , Gene Regulation and Metabolism ( MIT Press , Cambridge, MA , 2002 ) . Crossref, Google Scholar
V. N. Reddy, M. L. Mavrovouniotis and M. N. Liebman, Petri net representation in metabolic pathways, Proc First ISMB (1993) pp. 328–336. Google Scholar
N. Bahi-Jaber and D. Pontier, Math. Biosci. 185, 1 (2003). Crossref, Medline, Google Scholar
A. Gronewold and M. Sonnenschein, Ecol. Modelling 108, 37 (1998). Crossref, Google Scholar
A. Sharov, Biosystems 25(4), 237 (1991). Crossref, Medline, Google Scholar
M. Peleg, I. Yeh and R. B. Altman, Bioinformatics 18(6), 825 (2002). Crossref, Medline, Google Scholar
M. Chen and R. Hofestädt, In Silico Biol. 3, (2003), http://www.bioinfo.de/isb/2003/03/0030/. Medline, Google Scholar
H. Matsunoet al., In Silico Biol. 3, (2003), http://www.bioinfo.de/isb/2003/03/0032/. Medline, Google Scholar
H. Matsunoet al., Lect. Notes Comput. Sci. 2679 (2003) pp. 3–22. Google Scholar
J. S. Oliveiraet al., J. Comput. Biol. 10(1), 57 (2003). Crossref, Medline, Google Scholar
K. Voss, M. Heiner and I. Koch, In Silico Biol. 3, (2003), http://www.bioinfo.de/isb/2003/03/0031/. Medline, Google Scholar
I. Zevedei-Oancea and S. Schuster, In Silico Biol. 3, (2003), http://www.bioinfo.de/isb/2003/03/0029/. Medline, Google Scholar
H. Matsunoet al., Genome Inform. 12, 54 (2001). Medline, Google Scholar
M. Nagasakiet al., App. Bioinform. 2(3), 181 (2003). Medline, Google Scholar
A. Doiet al., App. Bioinform. 2(3), 185 (2003). Medline, Google Scholar
M. Chenet al., The biology Petri net markup language, Proc. Promise 2002 (2002) pp. 150–161. Google Scholar
R. Küffner, R. Zimmer and T. Lengauer, Bioinformatics 16, 825 (9). Crossref, Medline, Google Scholar
W. Reisig , Petri Nets: An Introduction , Monographs on Theoretical Computer Science ( Springer-Verlag , 1985 ) . Crossref, Google Scholar
V. N. Reddy, M. N. Liebman and M. L. Mavrovouniotis, Comput. Biol. Med. 26(1), 9 (1996). Crossref, Medline, Google Scholar
R. Hofestädt, J. System Analysis, Modeling and Simulation 16, 113 (1994). Google Scholar
R. Hofestädt and S. Thelen, In Silico Biol. 1, (1998), http://www.bioinfo.de/isb/1998/01/0006/. Medline, Google Scholar
R. Valk, Self-modifying nets, a natural extension of Petri nets, ICALP, Lect. Notes Comput. Sci. 62 (1978) pp. 464–476. Google Scholar
M. Ajmone Marsanet al., Microelectron. Reliab. 31(4), 699 (1991). Crossref, Google Scholar
P. J. E. Goss and J. Peccoud, Analysis of the stabilizing effect of Rom on the genetic network controllin ColE1 plasmid replication, Pac. Symp. Biocomput.4 (1999) pp. 65–76. Google Scholar
R. Srivastava, M. S. Peterson and W. E. Bentley, Biotechnol. Bioeng. 75(1), 120 (2001). Crossref, Medline, Google Scholar
R. Srivastavaet al., J. Theor. Biol. 218, 309 (2002). Crossref, Medline, Google Scholar
Möbius and UltraSAN, http://www.crhc.uiuc.edu/PER.FORM/ . Google Scholar
K. Jensen , Coloured Petri Nets: Basic Concepts, Analysis Methods and Practical Use , Monographs on Theoritical Computer Science ( Springer-Verlag , 1992 ) . Crossref, Google Scholar
Design/CPN, http://daimi.au.uk/designCPN/ . Google Scholar
H. Genrich, R. Küffner and K. Voss, Int. J. STTT 3(4), 394 (2001). Crossref, Google Scholar
BRENDA, http://www.brenda.uni-koeln.de:80/ . Google Scholar
M. Heiner, I. Koch and K. Voss, Analysis and simulation of steady states in metabolic pathways with Petri nets, Third Workshop and Tutorial on Practical Use of Colored Petri Nets and CPN Tools (Univ. of Aarhus, 2001) pp. 15–34. Google Scholar
H. Alla and R. David, J. Circuits Syst. Comp. 8(1), 159 (1998). Link, Google Scholar
H. Matsunoet al., Hybrid Petri net representation of generegulatory network, Pac. Symp. Biocomput.5 (2000) pp. 338–349. Google Scholar
Visual Object Net++, http://www.systemtechnik.tu-ilmenau.de/~drath/visual.htm . Google Scholar
Genomic Object Net, http://genomicobject.net . Google Scholar
H. Matsunoet al., Boundary formation by Notch signaling in Drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net, Pac. Symp. Biocomput.8 (2003) pp. 152–163. Google Scholar
M. Matsuiet al., Genome Inform. 12, 290 (2001). Google Scholar
J. S. Oliveiraet al., Bull. Math. Biol. 63, 1163 (2001). Crossref, Medline, Google Scholar
M. Chen, Modelling and simulation of metabolic networks: Petri net approach and perspective, Proc. ESM 2002 (2002) pp. 441–444. Google Scholar