On P systems as a modelling tool for biological systems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3850 LNCS, Issue , 2006, Pages 114-133

  Bernardini, Francesco ^a   Gheorghe, Marian ^a   Krasnogor, Natalio ^b   Muniyandi, Ravie C ^a   Pérez Jímenez, Mario J ^c   Romero Campero, Francisco José ^c  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c UNIVERSITY OF SEVILLE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CELLS; COMPUTER SIMULATION; PROBABILITY DISTRIBUTIONS;

KINETIC COEFFICIENT; MOLECULAR REACTION; P SYSTEMS; REAL NUMBERS;

COMPUTATION THEORY;

EID: 33745645876     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11603047_8     Document Type: Conference Paper

References (19)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P., (2002). The Molecular Biology of The Cell. Fourth Edition. Garland Publ. Inc., London.
2. Andrei, O., Ciobanu, G., Lucanu, D., (2005). Executable Specifications of P Systems. In [10], 126-145
3. Bernardini, F., Gheorghe, M., (2004). Population P systems. Journal of Universal Computer Science, 10, 509-539.
4. Besozzi, D., (2004). Computational and Modelling Power of P systems. PhD Thesis, Università degli Studi di Milano, Milan, Italy.
5. Bianco, L., Fontana, F., Franco, G., Manca, V. (2005). P Systems for Biological Dynamics. In: Applications of Membrane Computing (Ciobanu, G., Pǎun, Gh., Pérez-Jiménez, M.J., eds.), Springer-Verlag, Berlin, Heidelberg, New York, 81-126.
6. Fargerstron, T., James, G., James, S., Kjelleberg, S., Nilsson, P., (2000). Luminescence Control in the Marine Bacterium Vibrio Fischeri: An Analysis of the Dynamics of lux Regulation. Journal of Molecular Biology, 296, 1127-1137.
7. Gibson, M.A., Bruck, J., (2000). Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. Journal of Physical Chemistry, 104, 25, 1876-1889.
8. Gillespie, D.T., (1977). Exact Stochastic Simulation of Coupled Chemical Reactions. The Journal of Physical Chemistry, 81, 25, 2340-2361.
9. Martin-Vide, C., Mauri, G., Pǎun, Gh., Rozenberg, G., Salomaa, A., eds., (2004). Membrane Computing. International Workshop, WMC 2003, Tarragona, Spain, July 2003. Revised Papers. Lecture Notes in Computer Science, 2933, Springer-Verlag, Berlin, Heidelberg, New York.
10. Mauri, G., Pǎun, Gh., Pérez-Jiménez, M., J., Rozenberg, G., Salomaa, A., eds., (2005). Membrane Computing. International Workshop, WMC 2004, Milan, Italy, June 2004. Revised and Invited Papers. Lecture Notes in Computer Science, 3365, Springer-Verlag, Berlin, Heidelberg, New York.
11. Meng, T.C., Somani S., Dhar, P., (2004). Modelling and Simulation of Biological Systems with Stochasticity. In Silico Biology, 4, 0024.
12. Nepomuceno, I, Nepomuceno, J.,A, Romero-Campero, F., (2005). A Tool for Using the SBML Format to Represent P System which Model Biological Reaction Networks. In: Proceeding of the Third Brainstorming Week in Membrane Computing, Seville, Spain, January 31st-February 4th, 2005, University of Seville, Seville, Spain.
13. Pǎun, Gh., (2000). Computing with Membranes. Journal of Computer and System Sciences, 61, 1, 108-143.
14. Pǎun, Gh. (2002). Membrane Computing. An Introduction. Springer-Verlag, Berlin, Heidelberg, New York.
15. Pǎun, Gh., Rozenberg, G., Salomaa, A., Zandron, C., eds., (2003). Membrane Computing. International Workshop, WMC-CdeA 02, Curtea de Arges, Romania, August 19-23, 2002. Revised Papers. Lecture Notes in Computer Science, 2597, Springer-Verlag, Berlin, Heidelberg, New York.
16. Pérez-Jiménez, M.J.; Romero-Campero, F.J.,(2005). Modelling EGFR Signalling Cascade Using Continuous Membrane Systems. In: Proceedings of the Third International Workshop on Computational Methods in Systems Biology 2005 (CMSB 2005) (Plotkin, G., ed.), University of Edinburgh, Edinburgh, United Kingdom.
17. Philips, A., Cardelli, L., (2004). A Correct Abstract Machine for the Stochastic Pi-calculus. Electronical Notes in Theoretical Computer Science, to appear.
18. Priami, C., Regev, A., Shapiro, E., Silverman, W., (2001). Application of a Stochastic Name-Passing Calculus to Representation and Simulation of Molecular Processes. Information Processing Letters, 80, 25-31.
19. Taga, M., E., Bassler, B., L., (2003). Chemical Communication among Bacteria. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 100, 2, 14549-14554.