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Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling

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Modeling in Systems Biology

Part of the book series: Computational Biology ((COBO,volume 16))

Abstract

Using elementary Petri nets, it is difficult to mixturely model the discrete, continuous and other complicated events, for example, DNA, RNA and amino acid sequence events. Therefore, Hybrid Functional Petri Net with extension (HFPNe) was introduced to overcome this difficulty and also to allow representation of pathway models without loss of biological details. First, this book chapter explains how modeling with Petri net is done. After which, a full definition of HFPNe is given, along with its relation to hybrid Petri net and other related Petri net extension. Finally, to demonstrate the elegance of HFPNe architecture in handling complex pathway modeling, we chose a biological pathway that involves discrete, continuous and sequence events (gene regulatory network of the cell fate determination in C. elegans). We provide the biological mechanisms of this network and show how intuitively it could be modeled on HFPNe architecture using a software tool, Cell Illustrator.

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References

  1. Alla, H., David, R.: Continuous and hybrid Petri nets. JCSC 8, 159–188 (1998)

    MathSciNet  Google Scholar 

  2. Cell Illustrator Online 4.0: http://cionline.hgc.jp/

  3. Cell System Markup Language: http://www.csml.org/

  4. Chang, S., Johnston, R.J.Jr., Frokjaer-Jensen, C., Lockery, S., Hobert, O.: MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785–789 (2004)

    Article  Google Scholar 

  5. Doi, A., Nagasaki, M., Fujita, S., Matsuno, H., Miyano, S.: Abstract Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl. Bioinform. 2(3), 185–188 (2003)

    Google Scholar 

  6. Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.: Constructing biological pathway models with hybrid functional Petri nets. In Silico Biol. 4(3), 271–291 (2004)

    Google Scholar 

  7. Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.: Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biol. 6(1–2), 1–13 (2006)

    Google Scholar 

  8. Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S.: A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Inform. 17(1), 112–123 (2006)

    Google Scholar 

  9. Drath, R.: Hybrid object nets: an object oriented concept for modeling complex hybrid systems. In: Proc. 3rd International Conference on Automation of Mixed Processes: Hybrid Dynamical Systems (ADPM), pp. 437–442. Shaker Verlag, Aachen (1998)

    Google Scholar 

  10. Goss, P.J.E., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. USA. 95(12), 6750–6755 (1998)

    Article  Google Scholar 

  11. Grunwald, S., Speer, A., Ackermann, J., Koch, I.: Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosystems 92(2), 189–205 (2008)

    Article  Google Scholar 

  12. Hofestädt, R.: A petri net application to model metabolic processes. Syst. Anal. Mod. Simul. 16(2), 113–122 (1994)

    MATH  Google Scholar 

  13. Hofestädt, R., Thelen, S.: Quantitative modeling of biochemical networks. In Silico Biol. 1, 39–53 (1998)

    Google Scholar 

  14. Jeong, E., Nagasaki, M., Saito, A., Miyano, S.: Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol. 7(6), 623–638 (2007)

    Google Scholar 

  15. Johnston, R.J.Jr., Hobert, O.: A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845–849 (2003)

    Article  Google Scholar 

  16. Johnston, R.J.Jr., Hobert, O.: A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA. Development 132(24), 5451–5460 (2005)

    Article  Google Scholar 

  17. Johnston, R.J.Jr., Chang, S., Etchberger, J.F., Ortiz, C.O., Hobert, O.: MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl. Acad. Sci. USA 102(35), 12449–12454 (2005)

    Article  Google Scholar 

  18. Koch, I., Schüler, M., Heiner, M.: STEPP—search tool for exploration of Petri net paths: a new tool for Petri net-based path analysis in biochemical networks. In Silico Biol. 5(2), 129–137 (2005)

    Google Scholar 

  19. Koch, I., Junker, B.H., Heiner, M.: Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7), 1219–1226 (2005)

    Article  Google Scholar 

  20. Krull, M., Pistor, S., Voss, N., Kel, A., Reuter, I., Kronenberg, D., Michael, H., Schwarzer, K., Potapov, A., Choi, C., Kel-Margoulis, O., Wingender, E.: TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34, D546–D551 (2006)

    Article  Google Scholar 

  21. Li, C., Suzuki, S., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S.: Structural modeling and analysis of signaling pathways based on Petri nets. J. Bioinf. Comput. Biol. 4(5), 1119–1140 (2006)

    Article  Google Scholar 

  22. Li, C., Nagasaki, M., Ueno, K., Miyano, S.: Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst. Biol. 3, 42 (2009)

    Article  Google Scholar 

  23. Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid Petri net representation of gene regulatory network. Proc. Pac. Symp. Biocomput. 5, 341–352 (2000)

    Google Scholar 

  24. Matsuno, H., Murakami, R., Yamane, R., Yamasaki, N., Fujita, S., Yoshimori, H., Miyano, S.: Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net. Pac. Symp. Biocomput. 8, 152–163 (2003)

    Google Scholar 

  25. Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.: Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol. 3(3), 389–404 (2003)

    Google Scholar 

  26. Matsuno, H., Inouye, S.-I.T., Okitsu, Y., Fujii, Y., Miyano, S.: A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. J. Bioinf. Comput. Biol. 4(1), 139–153 (2006)

    Article  Google Scholar 

  27. Mito, N., Ikegami, Y., Matsuno, H., Miyano, S., Inouye, S.: Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm. Genome Inform. 21, 212–223 (2008)

    Article  Google Scholar 

  28. Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Genomic object net: I, a platform for modeling and simulating biopathways. Appl. Bioinform. 2(3), 181–184 (2003)

    Google Scholar 

  29. Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Inform. 15(1), 180–197 (2004)

    Google Scholar 

  30. Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Computational modeling of biological processes with Petri net based architecture. In: Chen, Y.P. (ed.) Bioinformatics Technologies, pp. 179–243. Springer, Berlin (2005)

    Chapter  Google Scholar 

  31. Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T.: Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform. 17(1), 46–61 (2006)

    Google Scholar 

  32. Nagasaki, M., Saito, A., Li, C., Jeong, E., Miyano, S.: Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2, 53 (2008)

    Article  Google Scholar 

  33. Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.: Foundations of Systems Biology—Using Cell Illustrator and Pathway Databases. Springer, Berlin (2009)

    Book  MATH  Google Scholar 

  34. Nakamura, K., Yoshida, R., Nagasaki, M., Miyano, S., Higuchi, T.: Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac. Symp. Biocomput. 14, 227–238 (2009)

    Google Scholar 

  35. Reddy, V.N., Mavrovouniotis, M.L., Liebman, M.N.: Petri net representation in metabolic pathways. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., vol. 1, pp. 328–336. MIT Press, Cambridge (1993)

    Google Scholar 

  36. Reisig, W., Rozenberg, G. (eds.): Lectures on Petri Nets I: Basic Models. LNCS, vol. 1491. Springer, Berlin (1998)

    MATH  Google Scholar 

  37. Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.: Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension. Genome Inform. 17(1), 100–111 (2006)

    Google Scholar 

  38. Sato, Y., Hashiguchi, Y., Nishida, M.: Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Syst. Biol. 3, 23 (2009)

    Article  Google Scholar 

  39. Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano, S., Miyano, S.: Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform. 17(2), 226–238 (2006)

    Google Scholar 

  40. Troncale, S., Tahi, F., Campard, D., Vannier, J.-P., Guespin, J.: Modeling and simulation with hybrid functional Petri nets of the role of interleukin-6 in human early haematopoiesis. Pac. Symp. Biocomput. 11, 427–438 (2006)

    Google Scholar 

  41. Voss, K., Heiner, M., Koch, I.: Steady state analysis of metabolic pathways using Petri nets. In Silico Biol. 3, 367–387 (2003)

    Google Scholar 

  42. WormBase: http://www.wormbase.org/db/gene/variation?name=pas40332;class=Variation

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Acknowledgement

We would like to thank André Fujita and Koh Chuan Hock for their helpful comments and critiques.

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Authors and Affiliations

    Authors
    1. Ayumu Saito
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    2. Masao Nagasaki
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    3. Hiroshi Matsuno
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    4. Satoru Miyano
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    Corresponding author

    Correspondence to Ayumu Saito .

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    Editors and Affiliations

    1. Institute for Computer Science, J.W. Goethe University Frankfurt, Robert-Mayer-Straße 11-15, Frankfurt am Main, 60325, Germany

      Ina Koch

    2. Department of Computer Science, Humboldt-Universität zu Berlin, Unter den Linden 6, Berlin, 10099, Germany

      Wolfgang Reisig

    3. Institute of Computer Science, Martin Luther Univ. Halle-Wittenberg, Von Seckendorff Platz 1, Halle, 06120, Germany

      Falk Schreiber

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    © 2011 Springer-Verlag London Limited

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    Saito, A., Nagasaki, M., Matsuno, H., Miyano, S. (2011). Hybrid Functional Petri Net with Extension for Dynamic Pathway Modeling. In: Koch, I., Reisig, W., Schreiber, F. (eds) Modeling in Systems Biology. Computational Biology, vol 16. Springer, London. https://doi.org/10.1007/978-1-84996-474-6_6

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    • DOI: https://doi.org/10.1007/978-1-84996-474-6_6

    • Publisher Name: Springer, London

    • Print ISBN: 978-1-84996-473-9

    • Online ISBN: 978-1-84996-474-6

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