Stochastic models for the in silico simulation of synaptic processes

BMC Bioinformatics

Volumn 9, Issue SUPPL. 4, 2008, Pages

  Bracciali, Andrea ^a   Brunelli, Marcello ^a   Cataldo, Enrico ^a   Degano, Pierpaolo ^a  

^a UNIVERSITY OF PISA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PHENOMENA; COMPOSITIONAL PROPERTIES; ELEMENT CONCENTRATIONS; FORMAL DESCRIPTION TECHNIQUES; GLUTAMATERGIC SYNAPSE; SHORT TERM PLASTICITY; STOCHASTIC SEMANTICS; SYNAPTIC TRANSMISSION;

COMPUTER SCIENCE; MAMMALS; SEMANTICS; STOCHASTIC CONTROL SYSTEMS; STOCHASTIC MODELS; VIRTUAL REALITY;

EXPERIMENTS;

ARTICLE; AUDITORY NERVOUS SYSTEM; COMPUTER MODEL; COMPUTER SIMULATION; CONTROLLED STUDY; HELD CALYX; NERVE CELL PLASTICITY; NERVE CELL STIMULATION; NERVE CONDUCTION; NEUROTRANSMITTER RELEASE; POSTSYNAPTIC POTENTIAL; PRESYNAPTIC NERVE; PRESYNAPTIC POTENTIAL; SENSITIVITY ANALYSIS; STOCHASTIC MODEL; SYNAPSE; SYNAPTIC TRANSMISSION; VALIDATION STUDY; ACTION POTENTIAL; ANIMAL; BIOLOGICAL MODEL; HUMAN; METABOLISM; NERVE CELL; NERVE CELL NETWORK; PHYSIOLOGY;

MAMMALIA;

AGENTS INTERACTING WITH TRANSMITTER, HORMONE OR DRUG RECEPTORS;

ACTION POTENTIALS; ANIMALS; COMPUTER SIMULATION; HUMANS; MODELS, NEUROLOGICAL; NERVE NET; NEURONS; NEUROTRANSMITTER AGENTS; SYNAPSES; SYNAPTIC TRANSMISSION;

EID: 44649093360     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-S4-S7     Document Type: Article

References (36)

1. Methods in Neuronal Modeling Cambridge: The MIT Press Koch C, Segev I 1998.
2. Computational Cell Biology New York: Springer Fall CP, Marland ES, Wagner JM, Tyson JJ 2002.
3. Rediscovering Biology - Molecular to Global Perspectives - Neurobiology [http://www.learner.org/channel/courses/biology/support/10_neuro.pdf].
4. Frotscher M Gundelfinger E Jonas P Neher E Seeburg P The most important recent advances in synsapse research from my point of view - and what remains to be done Cell Tissue Res 2006, 326:203-204. 16998655
5. Zucker RS Kullmann DM Schwartz TL Release of Neurotransmitters From Molecules to Networks - An Introduction to Cellular and Molecular Neuroscience San Diego: Elsevier - Academic Press Byrne JH, Roberts JL 2004, 197-244.
6. Sudhof TC The synaptic vesicle cycle Annual Review of Neuroscience 2004, 27:509-547. 15217342
7. Schneggenburger R Neher E Intracellular calcium dependence of transmitter release rates at a fast central synapse Nature 2000, 46:889-893.
8. Schneggenburger R Neher E Presynaptic calcium and control of vesicle fusion Current Opinion in Neurobiology 2005, 15:266-274. 15919191
9. Meinrenken CJ Borst JGG Sakmann B The Hodgkin-Huxley-Katz Prize Lecture. Local routes revisited the space and time dependence of the Ca signal for phasic transmitter release at the rat calyx of Held The Journal of Physiology in press 12562955
10. Smolen PD Baxter DA Byrne JH Mathematical Modeling and Analysis of Intracellular Signaling Pathways From Molecules to Networks - An Introduction to Cellular and Molecular Neuroscience Elsevier - Academic Press Byrne JH, Roberts JL 2004, 391-429.
11. Wilkinson DJ Stochastic Modelling for System Biology London: Chapman and Hall - CRC Press 2006.
12. Gillespie DT Exact stochastic simulation of coupled chemical reactions The Journal of Physical Chemistry 1977, 81:2340-2361.
13. Savtchenko LP Rusakov DA The optimal height of the synaptic cleft PNAS 2007, 104:1823-1828. 1783902 17261811
14. Graham B Wong AYC Forsythe ID A computational model of synaptic transmission at the calyx of Held Neurocomputing 2001, 38-40:37-42.
15. Wong AY Graham BP Billups B Forsythe ID Distinguishing between presynaptic and postsynaptic mechanisms of short-term depression during action potentials trains J Neurosci 2003, 23:4868-4877. 12832509
16. Destexhe A Mainen ZF Sejnowski TJ Synthesis of models for Excitable membrane, synaptic transmission and neuromodulation using a common kinetic formulation The Journal of Computational Neuro science 1994, 1:195-231.
17. Holmes WR Calcium Signaling in Dendritic Spines Modeling in the Neuroscience - From Biological Systems to Neuromimetic Robotics NewYork: CRC Press Reeke GN, Poznanski RR, Lindsay KA, Rosenberg JR, Sporns O 2nd edition 2005, 25-60.
18. Hillston J A Compositional Approach to Performance Modelling Cambridge: Cambridge University Press 1996.
19. Regev A Shapiro E Cellular Abstractions: Cells as Computation Nature 2002, 419:343. 12353013
20. Kitano H Systems Biology: A brief overview Science 2002, 295(5560):1662-1664. 11872829
21. Cassman M Arkin A Doyle F Katagiri F Lauffenburger D Stokes C System Biology - International Research and Development The Netherlands: Springer 2007.
22. Nagasaki M Onami S Miyano S Kitano H Bio-calculus: Its concept and molecular interaction Genome Informatics 1999, 10:133-143. 11072350
23. Priami C Regev A Shapiro E Silvermann W Application of a stochastic name-passing calculus to representation and simulation of molecular processes Theoretical Computer Science 2004, 325:141-167.
24. Regev A Panina E Silverman W Cardelli L Shapiro E Bioambients: An abstraction for biological compartements Theoretical Computer Science 2004, 325:141-167.
25. Cardelli L Brane calculi-interactions of biological membranes Proceedings of Computational Methods in Systems Biology Paris: Springer Vincent V, Schachter V 2004, 257-280. LNCS 3082
26. Priami C Stochastic π-calculus The Computer Journal 1995, 36(6):578-589.
27. Lecca P Priami C Quaglia P Rossi B Laudanna C Costantin G A stochastic process algebra approach to simulation of autoreactive lymphocyte recruitment SIMULATION: Trans. of the society for modelling and simulation international 2004, 80(4):273-288.
28. Calder M Gilmore S Hillston J Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA Transactions on Computational System Biology VII 2006, 1-23. LNBI 4230
29. Milner R Communicating and Mobile Systems: The π-Calculus Cambridge University Press 1999.
30. Phillips A Cardelli L Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus Proceedings of Computational Methods in Systems Biology Edinburgh: Springer Calder M, Gilmore S 2007, 184-199. LNCS 4695
31. Kierzek AM Stocks: Stochastic kinetic simulations of biochemical system with Gillespie algorithm Bioinformatics 2002, 18:470-481. 11934747
32. Schneggenburger R Forsythe ID The calxy of Held Cell Tissue Res 2006, 326:311-337. 16896951
33. Bollmann JH Sakmann B Control of synaptic strength and timing by the release-site Ca2+ signal Nature Neuroscience 2005, 8:426-434. 15750590
34. Destexhe A Mainen ZF J ST Kinetic Models of Synaptic Transmission Methods in Neuronal Modeling Cambridge: The MIT Press Koch C, Segev I 1998, 1-25.
35. Clements JD Transmitter timecourse in the synaptic cleft: Its role in central synaptic function TINS 1996, 19:163-171. 8723198
36. Neher E A comparison between exocytic control mechanisms in adrenal chromaffin cells and a glutamatergic synapse Pflugers Arch - Eur J Physiol 2006, 453:261-268.