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Journal
2009 | 58 | 1-2 | 79-88
Article title

Zastosowanie sieci petriego do modelowania procesów biologicznych

Content
Title variants
EN
Applications of petri nets for modeling of biological processes
Languages of publication
PL EN
Abstracts
EN
Rapid growth of the amount of available biological data made it clear that an analysis of complex biological processes can be made only with the support of mathematics and computer sciences. It is especially important nowadays when the systems biology approach is becoming more and more widely used in biological science. This new way of investigation of biological phenomena allows, at least in principle, to observe complex relationships between different parts of the analyzed system. These interactions may be crucial for the system's nature and behavior, so observing them may lead to important biological discoveries. Probably the most important part of this process consists in building of a formal model of the biological process. One of the promising methods of such an analysis is based on the theory of Petri nets. Models expressed in the language of this theory are very precise on the one hand, and on the other, they are intuitive, which makes their analysis easier in comparison, for example, to models based on ordinary differential equations. In this paper, a brief introduction to the theory of Petri nets is given and its applications for modeling of some exemplary biological processes are shortly discussed. Moreover, some extensions of the classical Petri nets and their biological applications are also presented.
Keywords
Journal
Year
Volume
58
Issue
1-2
Pages
79-88
Physical description
Dates
published
2009
Contributors
  • Instytut Informatyki, Politechnika Poznańska, Piotrowo 2, 60-965 Poznań, Polska
  • Katedra Chemii i Biochemii Klinicznej, Uniwersytet Medyczny im. Karola Marcinkowskiego, Grunwaldzka 6, 60-780 Poznań, Polska
  • Instytut Informatyki, Politechnika Poznańska, Piotrowo 2, 60-965 Poznań, Polska
References
  • Ajmone M., Balbo G., Chiola G., Conte G., Donatelli S., Frances-chinis G., 1991. An introduction to generalized stochastic Petri nets. Microelectron. Reliab. 34, 699-725.
  • Alla H., David R.,1998. Continuous and hybrid Petri nets. J. Circuits Syst. Comput. 8, 159-188.
  • Blazewicz J., Formanowicz D., Formanowicz P., Sajkowski M., Sackmann A., 2009. Modeling the process of human body iron homeostasis using a variant of timed Petri nets. Discrete Applied Mathematics, doi: 10.1016/j.dam.2008.06.053
  • Chen M., Hofestädt R., 2003. Quantitative Petri net model of gene regulated metabolic networks in the cell. In Silico Biol. 3, 0030.
  • Chaouiya C., 2007. Petri net modelling of biological networks. Brief. Bioinform. 8, 210-219.
  • Fisher J., Henzinger T. A., 2007. Executable cell biology. Nature Biotechnol. 25, 1239-1249.
  • Formanowicz D., Sackmann A., Formanowicz P., Błażewicz J., 2007. Petri net based model of the body iron homeostasis. J. Biomed. Inform. 40, 476-485.
  • Formanowicz D., Formanowicz P., Nowak T., 2008. Modelowanie procesu powstawania i rozwoju miażdżycy za pomocą sieci Petriego. Raport RB-24/08 Instytutu Informatyki Politechniki Poznańskiej.
  • Goss P., Peccoud J., 1998. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. USA 95, 6750-6755.
  • Hardy S., Robillard P. N., 2004. Modeling and simulation of molecular biology systems using Petri nets: modeling goals of various approaches. J. Bioinform. Computat. Biol. 2, 619-637.
  • Heiner M., Koch I., Will J., 2004. Model validation of biological pathways using Petri nets-demonstrated for apoptosis. BioSystems 75, 15-28.
  • Jawień J., 2008. Nowe immunologiczne spojrzenie na patogenezę miażdżycy. Polskie Archiwum Medycyny Wewnętrznej 118, 127-131.
  • Jensen K., 1992. Coloured Petri nets: basic concepts, analysis methods an practical use. Monographs on Theoretical Computer Sciences, Springer Verlag.
  • Lautenbach K., 1973. Exact liveness conditions of a Petri net class. GMD Report, 82, Bonn.
  • Libby P., 2002. Inflammation in atherosclerosis. Nature 420, 868-874.
  • Libby P., Ridker P. M., Maseri A., 2002. Inflammation and atherosclerosis. Circulation 105, 1135-1143.
  • Matsuno H., Doi A., Hirata Y., Miyano S., 2001. XML documentation of biopathways and their simulations in Genomic Object Net. Genome Informat. 12, 54-62.
  • Matsuno H., Tanaka Y., Aoshima H., Doi A., Matsui M., Miyano S., 2003. Biopath-ways representation and simulation on hybrid functional Petri net. In Silico Biol. 3, 0032.
  • Murata T., 1989. Petri nets: properties, analysis and applications. Proc. IEE 77, 541-580.
  • Park C. H., Valore E. V., Waring A.J., Ganz T., 2001. Hepcidin, a urinary antimicrobial peptide synthesized in the liver. J. Biol. Chem. 276, 7806-7810.
  • Petri C. A., 1962. Communications with automata. Schriften des IIM Nr.3, Institut für Instrumentelle Mathematik, Bonn, 16-27.
  • Sackmann A., Formanowicz D., Formanowicz P., Koch I., Blazewicz J., 2007. An analysis of the Petri net based model of the human body homeostasis process. Computat. Biol. Chem. 31, 1-10.
  • Sackmann A., Formanowicz D., Formanowicz P., Blazewicz J., 2009. New insights into the human body iron metabolism analysed by a Petri net based approach. BioSystems 96, 104-113.
  • Shaw O., Steggles J., Wipat A., 2005. Automati-parameterisation of stochastic Petri net models of biological networks. Electronic Notes in Theoretical Computer Science 151, 111-129.
  • Skoczyńska A., 2006. Patogeneza miażdżycy. Elsevier Urban & Partner, Wrocław.
  • Szpyrka M., 2008. Sieci Petriego w modelowaniu i analizie systemów współbieżnych. Wydawnictwa Naukowo-Techniczne, Warszawa.
  • Valk R., 1978. Self-modifying nets, a natural extension of Petri nets. Lecture Notes in Computer Science 62, 464-476.
  • Voss K., Heiner M., Koch I., 2003. Steady state analysis of metabolic pathways using Petri nets. In Silico Biol. 3, 0031
  • Zevedei-Oancea I., Schuster S., 2003. Topological analysis of metabolic networks based on Petri net theory. In Silico Biol. 3, 0029.
Document Type
Publication order reference
Identifiers
YADDA identifier
bwmeta1.element.bwnjournal-article-ksv58p79kz
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