NeuReal: An interactive simulation system for implementing artificial dendrites and large hybrid networks

Journal of Neuroscience Methods

Volumn 169, Issue 2, 2008, Pages 290-301

  Hughes, Stuart W ^a   Lorincz, Magor ^a   Cope, David W ^a   Crunelli, Vincenzo ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Computer simulation; Dynamic clamp; Gap junctions; Oscillations; Thalamus

Indexed keywords

ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; DENDRITE; NERVE FUNCTION; PRIORITY JOURNAL;

ALGORITHMS; ANIMALS; CATS; COMPUTER GRAPHICS; COMPUTER SIMULATION; DENDRITES; ELECTRICAL SYNAPSES; ELECTROPHYSIOLOGY; MEMBRANE POTENTIALS; MODELS, NEUROLOGICAL; NEURAL CONDUCTION; NEURAL NETWORKS (COMPUTER); PATCH-CLAMP TECHNIQUES; SOFTWARE; THALAMUS;

EID: 41049110048     PISSN: 01650270     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2007.10.014     Document Type: Article

References (42)

1. Bloomfield S.A., Hamos J.E., and Sherman S.M. Passive cable properties and morphological correlates of neurones in the lateral geniculate nucleus of the cat. J Physiol (Lond) 383 (1987) 653-692
2. Bower J.M., and Beeman D. The book of genesis: exploring realistic neural models with the general neureal simulation system (1997), Springer, New York
3. Butera Jr. R.J., Wilson C.G., Delnegro C.A., and Smith J.C. A methodology for achieving high-speed rates for artificial conductance injection in electrically excitable biological cells. IEEE Trans Biomed Eng 48 (2001) 1460-1470
4. Davie J.T., Kole M.H., Letzkus J.J., Rancz E.A., Spruston N., Stuart G.J., et al. Dendritic patch-clamp recording. Nat Protoc 1 (2006) 1235-1247
5. De Schutter E., and Bower J.M. An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. J Neurophysiol 71 (1994) 375-400
6. Debay D., Wolfart J., Le Franc Y., Le Masson G., and Bal T. Exploring spike transfer through the thalamus using hybrid artificial-biological neuronal networks. J Physiol (Paris) 98 (2004) 540-558
7. Derjean D., Bertrand S., Le Masson G., Landry M., Morisset V., and Nagy F. Dynamic balance of metabotropic inputs causes dorsal horn neurons to switch functional states. Nat Neurosci 6 (2003) 274-281
8. Destexhe A., Mainen Z.F., and Sejnowsksi T.J. Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. J Comput Neurosci 1 (1994) 195-230
9. Dorval A.D., Christini D.J., and White J.A. Real-time linux dynamic clamp: a fast and flexible way to construct virtual ion channels in living cells. Ann Biomed Eng 29 (2001) 897-907
10. Emri Z., Antal K., Tóth T.I., Cope D.W., and Crunelli V. Backpropagation of the delta oscillation and the retinal excitatory postsynaptic potential in a multi-compartment model of thalamocortical neurons. Neuroscience 98 (2000) 111-127
11. Gleeson P., Steuber V., and Silver R.A. neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54 (2007) 219-235
12. Hausser M., Spruston N., and Stuart G.J. Diversity and dynamics of dendritic signaling. Science 290 (2000) 739-744
13. Hines M.L., and Carnevale N.T. The NEURON simulation environment. Neural Comput 9 (1997) 1179-1209
14. Hodgkin A.L., and Huxley A.F. A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol (Lond) 117 (1952) 500-544
15. Hughes S.W., and Crunelli V. Thalamic mechanisms of EEG alpha rhythms and their pathological implications. Neuroscientist 11 (2005) 357-372
16. Hughes S.W., and Crunelli V. Just a phase they're going through: the complex interaction of intrinsic high-threshold bursting and gap junctions in the generation of thalamic alpha and theta rhythms. Int J Psychophysiol 64 (2007) 3-7
17. Hughes S.W., Cope D.W., and Crunelli V. Dynamic clamp study of Ih modulation of burst firing and delta oscillations in thalamocortical neurons in vitro. Neuroscience 87 (1998) 541-550
18. Hughes S.W., Tóth T.I., Cope D.W., Parri H.R., and Crunelli V. Neureal: a real-time computer modelling system for integrating biological and simulated neurons and networks. Soc Neurosci Abstracts 24 (1998) 644.11
19. Hughes S.W., Cope D.W., Parri H.R., Tóth T.I., and Crunelli V. NEUREAL: real-time modelling software for integrating biological and simulated neurons and networks. J Physiol (London) (1999) 506P
20. Hughes S.W., Cope D.W., Tóth T.I., Williams S.R., and Crunelli V. All thalamocortical neurones possess a T-type Ca2+ 'window' current that enables the expression of bistability-mediated activities. J Physiol (Lond) 517 (1999) 805-815
21. Hughes S.W., Blethyn K.L., Cope D.W., and Crunelli V. Properties and origin of spikelets in thalamocortical neurones in vitro. Neuroscience 110 (2002) 395-401
22. Hughes S.W., Cope D.W., Blethyn K.L., and Crunelli V. Cellular mechanisms of the slow (<1 Hz) oscillation in thalamocortical neurons in vitro. Neuron 33 (2002) 947-958
23. Hughes S.W., Lorincz M., Cope D.W., Blethyn K.L., Kekesi K.A., Parri H.R., et al. Synchronized oscillations at alpha and theta frequencies in the lateral geniculate nucleus. Neuron 42 (2004) 253-268
24. Kullmann P.H., Wheeler D.W., Beacom J., and Horn J.P. Implementation of a fast 16-bit dynamic clamp using LabVIEW-RT. J Neurophysiol 91 (2004) 542-554
25. Leresche N., Lightowler S., Soltesz I., Jassik-Gerschenfeld D., and Crunelli V. Low-frequency oscillatory activities intrinsic to rat and cat thalamocortical cells. J Physiol (Lond) 441 (1991) 155-174
26. Mainen Z.F., and Sejnowski T.J. Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382 (1996) 363-366
27. McCormick D.A., and Pape H.C. Properties of a hyperpolarization-activated cation current and its role in rhythmic oscillation in thalamic relay neurones. J Physiol (Lond) 431 (1990) 291-318
28. Mũniz C., Arganda S., de Borja F., de Polavieja G., and Varona P. Realistic stimulation through advanced dynamic-clamp protocols. Mechanisms, symbols and models underlying cognition 3561 (2005), Springer, Berlin/Heidelberg pp. 95-105
29. Nevian T., Larkum M.E., Polsky A., and Schiller J. Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study. Nat Neurosci 10 (2007) 206-214
30. Nowotny T., Szucs A., Pinto R.D., and Selverston A.I. StdpC: a modern dynamic clamp. J Neurosci Methods 158 (2006) 287-299
31. Pinto R.D., Elson R.C., Szucs A., Rabinovich M.I., Selverston A.I., and Abarbanel H.D. Extended dynamic clamp: controlling up to four neurons using a single desktop computer and interface. J Neurosci Methods 108 (2001) 39-48
32. Pospischil M., Piwkowska Z., Rudolph M., Bal T., and Destexhe A. Calculating event-triggered average synaptic conductances from the membrane potential. J Neurophysiol 97 (2007) 2544-2552
33. Prinz A.A., Abbott L.F., and Marder E. The dynamic clamp comes of age. Trends Neurosci 27 (2004) 218-224
34. Raikov I., Preyer A., and Butera R.J. MRCI: a flexible real-time dynamic clamp system for electrophysiology experiments. J Neurosci Methods 132 (2004) 109-123
35. Robinson H.P., and Kawai N. Injection of digitally synthesized synaptic conductance transients to measure the integrative properties of neurons. J Neurosci Methods 49 (1993) 157-165
36. Rudolph M., Piwkowska Z., Badoual M., Bal T., and Destexhe A. A method to estimate synaptic conductances from membrane potential fluctuations. J Neurophysiol 91 (2004) 2884-2896
37. Sharp A.A., O'Neil M.B., Abbott L.F., and Marder E. Dynamic clamp: computer-generated conductances in real neurons. J Neurophysiol 69 (1993) 992-995
38. Sharp A.A., O'Neil M.B., Abbott L.F., and Marder E. The dynamic clamp: artificial conductances in biological neurons. Trends Neurosci 16 (1993) 389-394
39. Toth T.I., and Crunelli V. Computer simulation of the pacemaker oscillations of thalamocortical cells. Neuroreport 3 (1992) 65-68
40. Traub R.D., Jefferys J.G., Miles R., Whittington M.A., and Toth K. A branching dendritic model of a rodent CA3 pyramidal neurone. J Physiol (Lond) 481 (1994) 79-95
41. Williams S.R., and Stuart G.J. Action potential backpropagation and somato-dendritic distribution of ion channels in thalamocortical neurons. J Neurosci 20 (2000) 1307-1317
42. Wolfart J., Debay D., Le Masson G., Destexhe A., and Bal T. Synaptic background activity controls spike transfer from thalamus to cortex. Nat Neurosci 8 (2005) 1760-1767