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.
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References
Paun, G.: Computing with Membranes. Journal of Computer and System Sciences 61(1), 108-143 (1998)
Ciobanu, G., Perez-Jimenez, M. J., Paun, G.: Application of Membrane Computing. Springer Verlag, Berlin (2006)
Nishida, T.Y.: Simulations of photosynthesis by a K-subset transforming system with membranes. Fundam. Inform. 49, 249-259 (2002)
Ardelean, I.I., Besozzi, D., Garzon, M.H., Mauri, G., Roy, S.: P-System Models for Mechanosensitive Channels. Springer Verlag, Berlin (2005)
Besozzi, D., Ciobanu, G.: A P-system description of the sodium-potassium pump. Lecture Notes Comput. Sci. 3365, 210-223 (2004)
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)
Corne, D.W. Frisco, P. (2008). 2008. Dynamics of HIV infection studied with cellular automata and conformon-P systems. Biosystems 91(3), 531-544
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)
Pauling, L.: General chemistry. Courier Dover Publications, London (1998)
Gillespie, D.T.: Stochastic Simulation of Chemical Kinetics. Annual Review of Physical Chemistry 58, 35-55 (2007)
Beizer, B.: Black-Box Testing: Techniques for Functional Testing of Software and Systems. Wiley, London (1995)
Kwiatkowska, M., Norman, G., Parker, D: Stochastic Model Checking. Lecture Notes in Computer Science 4486, 220-270 (2007)
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)
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)
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)
Acknowledgments
This work supported by the Young Researcher Grant of the National University of Malaysia (Grant code: GGPM-2011-051).
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Muniyandi, R.C., Zin, .M. (2013). A Framework for Modeling and Verifying Biological Systems Using Membrane Computing. In: Bansal, J., Singh, P., Deep, K., Pant, M., Nagar, A. (eds) Proceedings of Seventh International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA 2012). Advances in Intelligent Systems and Computing, vol 202. Springer, India. https://doi.org/10.1007/978-81-322-1041-2_29
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DOI: https://doi.org/10.1007/978-81-322-1041-2_29
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