Application of a common kinetic formalism for synaptic models (Destexhe et al 1994)

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Accession:18198
Application to AMPA, NMDA, GABAA, and GABAB receptors is given in a book chapter. The reference paper synthesizes a comprehensive general description of synaptic transmission with Markov kinetic models. This framework is applicable to modeling ion channels, synaptic release, and all receptors. Please see the references for more details. A simple introduction to this method is given in a seperate paper Destexhe et al Neural Comput 6:14-18 , 1994). More information and papers at http://cns.iaf.cnrs-gif.fr/Main.html and through email: Destexhe@iaf.cnrs-gif.fr
References:
1 . Destexhe A, Mainen ZF, Sejnowski TJ (1994) Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. J Comput Neurosci 1:195-230 [PubMed]
2 . Destexhe A, Mainen Z, Sejnowski TJ (1994) An efficient method for computing synaptic conductances based on a kinetic model of receptor binding Neural Comput 6:14-18
3 . Destexhe A, Mainen Z, Sejnowski T (1995) Fast Kinetic Models for Simulating AMPA, NMDA, GABAA and GABAB Receptors The Neurobiology of Computation, Bower J, ed. pp.9
Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Electrogenic pump;
Brain Region(s)/Organism:
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s): Nicotinic; M1; M3; M4; M5; M2; mGluR1; mGluR2; mGluR3; mGluR4; mGluR5; mGluR6; mGluR7; mGluR8; Alpha; Alpha1; Alpha2; Beta; D1; D2; 5-HT1; 5-HT2; 5-HT4; H2; GabaA; GabaB; Muscarinic; AMPA; NMDA; mGluR; 5-HT3; Kainate; Monoamine Receptors; Glutamate; Gaba; Adrenergic; Serotonin; Histamine; Cholinergic Receptors; Amino Acid Receptors; Sensory Receptors; Olfactory Receptors; Opsins; Dopaminergic Receptor; Glycine; Gaseous Receptors; NO; Peptide Receptors; Dynorphin; H1; Ion Receptors; Zn2+; CO;
Gene(s):
Transmitter(s): Acetylcholine; Glycine; Dopamine; Zn2+; NO; CO; Dynorphin; Ephinephrine; Norephinephrine; Amino Acids; Gaba; Glutamate; Monoamines; Peptides; Ions; Gases; Histamine; Serotonin;
Simulation Environment: NEURON;
Model Concept(s): Ion Channel Kinetics;
Implementer(s): Destexhe, Alain [Destexhe at iaf.cnrs-gif.fr]; Mainen, Zach [Mainen at cshl.edu];
Search NeuronDB for information about:  Nicotinic; M1; M3; M4; M5; M2; mGluR1; mGluR2; mGluR3; mGluR4; mGluR5; mGluR6; mGluR7; mGluR8; Alpha; Alpha1; Alpha2; Beta; D1; D2; 5-HT1; 5-HT2; 5-HT4; H2; GabaA; GabaB; Muscarinic; AMPA; NMDA; mGluR; 5-HT3; Kainate; Monoamine Receptors; Glutamate; Gaba; Adrenergic; Serotonin; Histamine; Cholinergic Receptors; Amino Acid Receptors; Sensory Receptors; Olfactory Receptors; Opsins; Dopaminergic Receptor; Glycine; Gaseous Receptors; NO; Peptide Receptors; Dynorphin; H1; Ion Receptors; Zn2+; CO; Acetylcholine; Glycine; Dopamine; Zn2+; NO; CO; Dynorphin; Ephinephrine; Norephinephrine; Amino Acids; Gaba; Glutamate; Monoamines; Peptides; Ions; Gases; Histamine; Serotonin;
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SYN_NEW
README
ampa.mod *
ampa5.mod *
caL3d.mod *
gabaa.mod *
gabaa5.mod *
gabab.mod *
gabab3.mod
HH2.mod *
nmda.mod *
nmda5.mod *
release.mod
ampa.hoc
ampa5.hoc
gabaa.hoc
gabaa5.hoc
gabab.hoc
gabab3.hoc
mosinit.hoc *
nmda.hoc
nmda5.hoc
release.hoc
rundemo.hoc
                            
    NEURON TUTORIAL FOR IMPLEMENTING SIMULATIONS OF SYNAPTIC CURRENTS 
           AND SYNAPTIC INTERACTIONS IN NETWORK SIMULATIONS

                          Alain Destexhe

            Department of Physiology, Laval University,
                      Quebec G1K 7P4, Canada

Present address: CNRS, UNIC (Bat-33), Avenue de la Terrasse,
                 91198 Gif-sur-Yvette, France

                      Destexhe@iaf.cnrs-gif.fr
                     http://cns.iaf.cnrs-gif.fr


This package is running with the NEURON simulation program written by Michael
Hines and available on internet at:
  http://www.neuro.duke.edu/neuron/home.html

The package contains mechanisms (.mod files) and programs (.oc files) needed
to simulate excitatory and inhibitory synaptic currents corresponding to the
most common types of postsynaptic receptors (glutamate AMPA and NMDA, GABA-A
and GABA-B).  The "detailed" simulations include multistate kinetic models and
a model for the release of transmitter.  The "minimal" models use the simplest
kinetic schemes but are computationally much faster while still capturing the
most salient features of synaptic interactions.  The latter are well suited
for being implemented in network simulations.

The models given here are described in detail in the following paper:

  Destexhe, A., Mainen, Z.F. and Sejnowski, T.J.  Biophysical models of 
  synaptic transmission.  In: Methods in Neuronal Modeling (2nd edition; 
  edited by Koch, C. and Segev, I.), MIT press, Cambridge, 1998, pp. 1-25.

An electronic version of this paper is available at  http://cns.iaf.cnrs-gif.fr



  PROGRAMS
  ========

release.hoc : detailed kinetic model for the release of transmitter
                  (reproduces Fig. 1 of the paper)

ampa5.hoc   : detailed kinetic model for glutamate AMPA receptors
                  (shown in Fig. 2A)
nmda5.hoc   : detailed kinetic model for glutamate NMDA receptors
                  (shown in Fig. 2B)
gabaa5.hoc  : detailed kinetic model for GABA-A receptors
                  (shown in Fig. 2C)
gabab3.hoc  : detailed kinetic model for GABA-B receptors
                  (shown in Fig. 2D)

ampa.hoc    : minimal kinetic model for glutamate AMPA receptors
                  (shown in Fig. 3A and Fig. 4A)
nmda.hoc    : minimal kinetic model for glutamate NMDA receptors
                  (shown in Fig. 3B and Fig. 4B)
gabaa.hoc   : minimal kinetic model for GABA-A receptors
                  (shown in Fig. 3C and Fig. 4C)
gabab.hoc   : minimal kinetic model for GABA-B receptors
                  (shown in Fig. 3D and Fig. 4D)


  MECHANISMS
  ==========

release.mod     : kinetic model for the release of transmitter
HH.mod          : Hodgkin-Huxley kinetics for action potentials
caL3d.mod       : high-threshold calcium current in the presynaptic terminal
capump.mod      : calcium clearance mechanisms

ampa5.mod       : detailed kinetic model for glutamate AMPA receptors
nmda5.mod       : detailed kinetic model for glutamate NMDA receptors
gabaa5.mod      : detailed kinetic model for GABA-A receptors
gabab3.mod      : detailed kinetic model for GABA-B receptors

ampa.mod        : minimal kinetic model for glutamate AMPA receptors
nmda.mod        : minimal kinetic model for glutamate NMDA receptors
gabaa.mod       : minimal kinetic model for GABA-A receptors
gabab.mod       : minimal kinetic model for GABA-B receptors

Note from ModelDB admin Tom Morse: capump.mod (cad mechanism) was 
incorporated into release.mod (rel mechanism) to take care of problem
where each mechanism was writting cai. 9/16/2002

  HOW TO RUN
  ==========

To compile the demo, NEURON and INTERVIEWS must be installed and working on
the machine you are using.  Just type "nrnivmodl" to compile the mechanisms
given in the mod files.

Then, execute the main demo program by typing:

nrngui rundemo.hoc

Once the menu and graphics interface has appeared, click on "Init and Run"
button to start the simulation...

For more information about how to get NEURON and how to install it, please
refer to the following sites:
  http://neuron.duke.edu/
  http://www.neuron.yale.edu/

For further information, please contact:

Alain Destexhe

CNRS, UNIC (Bat-33), 
Avenue de la Terrasse,
91198 Gif-sur-Yvette, 
France

email: Destexhe@iaf.cnrs-gif.fr
http://cns.iaf.cnrs-gif.fr

10-2007: AD, better synaptic mechanisms using counters
20120111: removed some .old files and updated gabab3.mod (GABAb3)
gabab.mod (GABAb) release.mod (rel) mechanisms from euler method to
cnexp, and derivimplicit for rel as per
http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592
20150608 GABAb.mod was fixed from cnexp to derivimplicit

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