Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation

BioSystems

Volumn 82, Issue 1, 2005, Pages 26-38

  Hardy, S ^a   Robillard, P N ^a  

^a ÉCOLE POLYTECHNIQUE DE MONTRÉAL   (Canada)

Author keywords

Hybrid functional Petri net; Modeling; Simulation; Synaptic plasticity; Systems biology

Indexed keywords

MODELING; SIMULATION;

ARTICLE; KINETICS; LONG TERM POTENTIATION; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; MOLECULAR MODEL; NERVE CELL PLASTICITY; PHENOMENOLOGY; SIMULATION; SYNAPSE;

EID: 24644473129     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.05.008     Document Type: Article

References (35)

1. H.D.I. Abarbanel, R. Huerta, and M.I. Rabinovich Dynamical model of long-term synaptic plasticity Proc. Natl. Acad. Sci. U.S.A. 99 15 2002 10132 10137
2. U.S. Bhalla Use of kinetikit and GENESIS for modeling signaling pathways Methods Enzymol. 345 2002 3 23
3. U.S. Bhalla, and R. Iyengar Emergent properties of networks of biological signaling pathways Science 283 1999 381 387
4. T. Bliss, and T. Lømo Long-lasting potentiation of synaptic transmission in the dentate area of the anaesthetized rabbit following stimulation of the perforant path J. Physiol. 232 2 1979 1979
5. H. de Jong Modeling and simulation of genetic regulatory systems: a literature review J. Comput. Biol. 9 1 2002 67 103
6. Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S., 2003. Constructing biological pathway models with hybrid functional Petri nets. Silico Biol., 4 (2), 271-291. http://www.bioinfo.de/isb/2004/04/0023/.
7. S. Hardy, and P.N. Robillard Modeling and simulation of molecular biology systems using petri nets: modeling goals of various approaches J. Bioinform. Comput. Biol. 2 4 2004 595 613
8. Hofestädt, R., 1994. A Petri net application of metabolic processes. J. Syst. Anal. Model. Simul. 16, 113-122.
9. Hofestädt, R., Thelen, S., 1998. Quantitative modeling of biochemical networks. Silico Biol. 1 (1), 39-53. http://www.bioinfo.de/isb/1998/ 01/0006/.
10. T. Ideker, T. Galitski, and L. Hood A new approach to decoding life: systems biology Annu. Rev. Genomics Hum. Genet. 2 2001 343 372
11. M. Ito, and M. Kano Long-lasting depression of parallel fiber-purkinje cell transmission induced by conjunctive stimulation of parallel fibers and climbing fibers in the cerebellar cortex Neurosci. Lett. 33 3 1982 253 258
12. S. Kikuchi, K. Fujimoto, M. Kitagawa, T. Fuchikawa, M. Abe, K. Oka, K. Takei, and M. Tomita Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A Neural Netw. 16 9 2003 1389 1398
13. Y. Kubota, and J.M. Bower Transient versus asymptotic dynamics of CaM kinase II: possible roles of phosphatase J. Comput. Neurosci. 11 3 2001 263 279
14. S. Kuroda, N. Schweighofer, and M. Kawato Exploration of signal transduction pathways in cerebellar long-term depression by kinetic simulation J. Neurosci. 21 15 2001 5693 5702
15. P.-M. Lledo, G.O. Hjelmstad, S. Mukherji, T.R. Soderling, R.C. Malenka, Nicoll, and A. Roger Calcium/calmodulin-dependent kinase II and long-term potentiation enhance synaptic transmission by the same mechanism Proc. Natl. Acad. Sci. U.S.A. 92 24 2002 11175 11179
16. H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano Hybrid Petri net representation of gene regulation network Proceedings of the Pacific Symposium on Biocomputing vol. 5 2000 338 349
17. H. Matsuno, R. Murakami, R. Yamane, N. Yamasaki, S. Fujita, Y. Haruka, and S. Miyano Boundary formation by notch signaling in drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net Proceedings of the Pacific Symposium on Biocomputing vol. 8 2003 152 163
18. Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S., 2003b. Biopathways representation and simulation on hybrid functional Petri net. Silico Biol. 3 (3), 389-404. http://www.bioinfo.de/isb/2003/03/0032/.
19. T. Meyer, P.I. Hanson, L. Stryer, and H. Schulman Calmodulin trapping by calcium-calmodulin-dependent protein kinase Science 256 5060 1992 1199 1202
20. L. Michaelis, and M.L. Menten Die kinetik der invertinwirkung Biochemische Zeitschrift 49 1913 333 369
21. M. Migliore, and P. Lansky Computational model of the effects of stochastic conditioning on the induction of long-term potentiation and depression Biol. Cybern. 81 4 1999 291 298
22. M. Migliore, and P. Lansky Long-term potentiation and depression induced by a stochastic conditioning of a model synapse Biophys. J. 77 3 1999 1234 1243
23. G.B. Murzina, and I.G. Sil'kis Studies of long-term potentiation and depression of inhibitory transmission by mathematical modeling of post-synaptic processes Neurosci. Behav. Physiol. 28 2 1998 121 129
24. M. Nagasaki, A. Doi, H. Matsuno, and S. Miyano Genomic Object Net: I. A platform for modeling and simulating biopathways Appl. Bioinform. 2 3 2003 181 184
25. P.V. Nguyen, T. Abel, and E.R. Kandel Requirement of a critical period of transcription or induction of a late phase of LTP Science 265 5175 1994 1104 1107
26. 2+/calmodulin-dependent protein kinase II Biol. Cybern. 82 1 2000 35 47
27. Reddy, V.N., 1994. Modeling biological pathways: a discrete event systems approach, Master's Thesis, University of Maryland, p. 82.
28. V.N. Reddy, M.N. Liebman, and M.L. Mavrovouniotis Qualitative analysis of biochemical reaction systems Comput. Biol. Med. 26 1 1996 9 24
29. V.N. Reddy, M.L. Mavrovouniotis, and M.N. Liebman Petri net representation in metabolic pathways L. Hunter D. Searls J. Shavlik Proceedings of the First International Conference on Intelligent Systems for Molecular Biology (ISMB) 1993 AIII Press 328 336
30. W. Reisig Petri nets: an introduction. Monographs on Theoretical Computer Science 1985 Springer-Verlag New York p. 161
31. A.R. Sargsyan, Melkonyan, A. Albert, C. Papatheodoropoulos, H.H. Mkrtchian, and G.K. Kostopoulos A model synapse that incorporates the properties of short- and long-term synaptic plasticity Neural Netw. 16 8 2003 1161 1177
32. S. Sivakuraman, S. Hariharaputran, J. Mishra, and U.S. Bhalla The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signaling networks Bioinformatics 19 3 2003 408 415
33. M. Tomita, K. Hashimoto, K. Takahashi, T.S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J.C. Venter, and C.A. Hutchison III E-CELL: software environment for whole-cell simulation Bioinformatics 15 1 1999 72 84
34. M. Tsodyks, K. Pawelzik, and H. Markram Neural networks with dynamic synapses Neural Comput. 10 4 1998 821 835
35. i elevation J. Neurophysiol. 81 2 1999 781 787