A Framework for Modeling and Verifying Biological Systems Using Membrane Computing

Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 202)

Abstract

Membrane computing can abstract biological structures and behaviors, and formally represent them without disregarding their biological characteristics. However, there is the lack of a proper framework to model and verify biological systems with membrane computing that could act as a guideline for researchers in computational biology or systems biology in using and exploring the advantages of membrane computing. This paper presents a framework for modeling and verifying biological systems using membrane computing. The framework processes are made up of biological requirement and property specification, membrane computing model, membrane computing simulation strategy, and model checking approach. The evaluation of the framework with biological systems shows that the proposed framework can be used as the first step to further improve the modeling and verification approaches in membrane computing.

Keywords

Membrane computing Framework Simulation strategy Model checking Biological systems 

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Notes

Acknowledgments

This work supported by the Young Researcher Grant of the National University of Malaysia (Grant code: GGPM-2011-051).

References

  1. Paun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108-143 (1998)Google Scholar
  2. Ciobanu, G., Perez-Jimenez, M. J., Paun, G.: Application of Membrane Computing. Springer Verlag, Berlin (2006)Google Scholar
  3. Nishida, T.Y.: Simulations of photosynthesis by a K-subset transforming system with membranes. Fundam. Inform. 49, 249-259 (2002)Google Scholar
  4. Ardelean, I.I., Besozzi, D., Garzon, M.H., Mauri, G., Roy, S.: P-System Models for Mechanosensitive Channels. Springer Verlag, Berlin (2005)Google Scholar
  5. Besozzi, D., Ciobanu, G.: A P-system description of the sodium-potassium pump. Lecture Notes Comput. Sci. 3365, 210-223 (2004)Google Scholar
  6. Romero-Campero, F.J, Perez-Jimenez, M.J.: A Model of the Quorum Sensing System in Vibrio fischeri Using P Systems. Artificial Life 14(1), 99 – 109 (2008)Google Scholar
  7. Corne, D.W. Frisco, P. (2008). 2008. Dynamics of HIV infection studied with cellular automata and conformon-P systems. Biosystems 91(3), 531-544Google Scholar
  8. Esmaeili, A., Yazdanbod, I., Jacob, C.: A Model of the Quorum Sensing System in Genetically Engineered E.coli Using Membrane Computing. International Genetically Engineered Machine (iGEM) competition (2009)Google Scholar
  9. Pauling, L.: General chemistry. Courier Dover Publications, London (1998)Google Scholar
  10. Gillespie, D.T.: Stochastic Simulation of Chemical Kinetics. Annual Review of Physical Chemistry 58, 35-55 (2007)Google Scholar
  11. Beizer, B.: Black-Box Testing: Techniques for Functional Testing of Software and Systems. Wiley, London (1995)Google Scholar
  12. Kwiatkowska, M., Norman, G., Parker, D: Stochastic Model Checking. Lecture Notes in Computer Science 4486, 220-270 (2007)Google Scholar
  13. Romero-Campero, F.J, Gheorghe, M., Bianco, L., Pescini, D., Pérez-Jiménez, M.J., Ceterchi, R. Towards Probabilistic Model Checking on P Systems Using PRISM. Lecture Notes Comput. Sci. 4361, 477-495 (2006)Google Scholar
  14. Muniyandi, R.C., Abdullah, M.Z.: Evaluating Ligand-Receptor Networks of TGF-β with Membrane Computing. Pakistan Journal of Biological Sciences 14(24), 1100-1108 (2011)Google Scholar
  15. Muniyandi, R.C., Abdullah, M.Z.: Modeling Hormone-induced Calcium Oscillations in Liver Cell with Membrane Computing. Romanian Journal of Information Science and Technology 15(1), 63-76 (2012)Google Scholar

Copyright information

© Springer India 2013

Authors and Affiliations

  • Ravie Chandren Muniyandi
    • 1
  • Abdullah Mohd Zin
    • 1
  1. 1.Research Center for Software Technology and Management (SOFTAM), Faculty of Technology and Information ScienceUniversity Kebangsaan MalaysiaSelangorMalaysia

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