MP Systems and Hybrid Petri Nets

  • Alberto Castellini
  • Vincenzo Manca
  • Luca Marchetti
Part of the Studies in Computational Intelligence book series (SCI, volume 129)


Metabolic P systems are a special class of P systems developed to model dynamics of biological phenomena related to metabolism and signaling transduction in the living cell. The main target of this model is to give an intuitive representation of biochemical pathways in order to facilitate the understanding of biological mechanisms. A new notation of MP graphs [16] will be defined as a graphical representation of MP systems and the graphical user interface we devised to draw MP graphs while working with our MP simulator Psim [4] will be described. We will propose also a comparison between MP systems and Hybrid Functional Petri Nets (HFPN) [19], which are an extension of Petri nets for biopathways simulation, to highlight several similarities between the two formalisms. Finally, a definition of equivalence between MP systems and HFPN will conclude the paper.


Reaction Node Intuitive Representation Membrane Computing Substance Node Continuous Place 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Biology of the Cell. Garland Science, New York, 4th editionGoogle Scholar
  2. 2.
    Alla H, David R (1998) Journal of Circuits, Systems, and Computers 8(1):159–188MathSciNetGoogle Scholar
  3. 3.
    Bianco L (2007) PhD thesis, Verona UniversityGoogle Scholar
  4. 4.
    Bianco L, Manca V, Marchetti L, Petterlini M (2007) Psim: a simulator for biomolecular dynamics based on P systems. IEEE Congress on Evolutionary ComputationGoogle Scholar
  5. 5.
    David R, Alla H (1998) Discrete Event Dynamic Systems 11(1–2):9–40MathSciNetGoogle Scholar
  6. 6.
    Doi A, Fujita S, Matsuno H, Nagasaki M, Miyano S (2004) In Silico Biology 4:23Google Scholar
  7. 7.
    Fontana F, Bianco L, Manca V (2005) In: Freund R, Paun G, Rozenberg G, Salomaa A (eds) Workshop on Membrane Computing, 199–208. SpringerGoogle Scholar
  8. 8.
    Fontana F, Manca V (2007) Predator-prey Dynamics in P Systems Ruled by Metabolic Algorithm. Biosystems. To appearGoogle Scholar
  9. 9.
    Fontana F, Manca V (2007) Theoretical Computer Science 372:165–182zbMATHCrossRefMathSciNetGoogle Scholar
  10. 10.
    Hofestädt R (1994) Journal of System Analysis, Modeling and Simulation 16:113–122zbMATHGoogle Scholar
  11. 11.
    Manca V (2007) Discrete Simulations of Biochemical Dynamics. In: Garzon M, Yan H (eds) Preliminary proceedings of the 13th International Meeting on DNA Computing. University of Memphis, June 4-8, Memphis, TNGoogle Scholar
  12. 12.
    Manca V (2007) Metabolic Dynamics by MP Systems. In: InterLink ERCIM Workshop, Eze, FranceGoogle Scholar
  13. 13.
    Manca V (2007) Progress in Natural Sciences 17(4):384–391zbMATHCrossRefMathSciNetGoogle Scholar
  14. 14.
    Manca V. The Metabolic Algorithm for P systems Principles and Applications. Theoretical Computer Science. To appearGoogle Scholar
  15. 15.
    Manca V (2006) Topics and problems in metabolic P systems. In: Proceedings of the Fourth Brainstorming Week on Membrane Computing, BWMC4Google Scholar
  16. 16.
    Manca V, Bianco L. Biological Networks in Metabolic P Systems. BioSystems. To appearGoogle Scholar
  17. 17.
    Manca V, Bianco L, Fontana F (2005) Lecture Notes in Computer Science 3365:63–84. Springer-Verlag, BerlinGoogle Scholar
  18. 18.
    Martin-Vide C, Păun G, Rozenberg G (2002) Theoretical Computer Science 270:779–796zbMATHCrossRefMathSciNetGoogle Scholar
  19. 19.
    Matsuno H, Tanaka Y, Aoshima H, Doi A, Matsui M, Miyano S (2003) In Silico Biology, 3:32Google Scholar
  20. 20.
    Nagasaki M, Doi A, Matsuno H, Miyano S (2004) Applied Bioinformatics 2:181–184Google Scholar
  21. 21.
    Păun A, Păun G (2002) New Generation Computing 20(3):295–306zbMATHCrossRefGoogle Scholar
  22. 22.
    Păun G (2000) Journal of Computer and System Sciences, 61(1):108–143zbMATHCrossRefMathSciNetGoogle Scholar
  23. 23.
    Păun G (2002) Membrane Computing. An Introduction. Springer, Berlin, GermanyzbMATHGoogle Scholar
  24. 24.
    Păun G, Suzuki Y, Tanaka H (2001) International Journal of Computer Mathematics 78(3):343–364zbMATHCrossRefMathSciNetGoogle Scholar
  25. 25.
    Petri C A (1962) Kommunikation mit Automaten. Bonn: Institut fr Instrumentelle Mathematik, Schriften des IIM Nr. 2Google Scholar
  26. 26.
    Reddy V N, Mavrovouniotis M L, Liebman M N (1993) Petri Net representations in metabolic pathways. In: Hunter L et al (eds) Proc. of the 1st International Conference on Intelligent Systems for Molecular Biology. AAAI PressGoogle Scholar
  27. 27.
    Reisig W (1985) Petri Nets: An Introduction. EATCS, Monographs on Theoretical Computer Science, Springer-Verlag, Berlin/HeidelbergzbMATHGoogle Scholar
  28. 28.
    Valk R (1978) Lecture Notes in Computer Science 62:464–453MathSciNetGoogle Scholar
  29. 29.
    Cell Illustrator Project web site. Url:
  30. 30.
    The P Systems Web Site. Url:

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Alberto Castellini
    • 1
  • Vincenzo Manca
    • 1
  • Luca Marchetti
    • 1
  1. 1.Computer Science Dept.Verona UniversityVeronaItaly

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