NEURON DEMO FOR SIMULATING THALAMOCORTICAL CONVERGENCE CIRCUITS

                       Sebastien Behuret
                    behuret@unic.cnrs-gif.fr
					 
           CNRS, UNIC (Bat-33), Avenue de la Terrasse,
                 91198 Gif-sur-Yvette, France


PACKAGE DESCRIPTION
===================

This package is running with the NEURON (v7.x) simulation program
   written by Michael Hines and available on internet at:
   http://www.neuron.yale.edu/neuron/

The package contains programs needed to simulate the thalamocortical
convergence model circuits relative to the paper:

   Béhuret S, Deleuze C, Gomez L, Frégnac Y, Bal T (2013)
   Cortically-Controlled Population Stochastic Facilitation as a
   Plausible Substrate for Guiding Sensory Transfer across the
   Thalamic Gateway.  PLoS Comput Biol 9(12):
   e1003401. doi:10.1371/journal.pcbi.1003401

An electronic version of this paper is available at:
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003401
(alternate links)
http://www.behuret.net/sci/Behuret_et_al_Sensory_Transfer_Stochastic_Facilitation_PLoSCompBiol_2013.pdf
http://www.behuret.net/sci/Behuret_et_al_Supporting_Information_PLoSCompBiol_2013.zip

A demonstration of the circuit activity will be shown upon startup
along with a simple GUI intended at easily changing the model
parameters. A simulation mode is also provided (to activate this mode,
please refer to the instructions given in Run.hoc).

In the demo mode, activity traces for the cortical and the
thalamocortical cells in an optimal regime (uncorrelated synaptic
noise) will be simulated for 1s. After this period, correlation of the
synaptic noise across the TC cells will be switched from 0% to
99%. Simulated voltage traces will be displayed in a graph.


INCLUDED FILES
==============

Run.hoc                  Main program file
Demo.hoc                 Main file for the demo mode
Simulation.hoc           Main file for the simulation mode
Templates.hoc            Cortical and thalamocortical cellular models
Geometry.hoc             Retino-thalamo-cortical core circuit implementation
Recording.hoc            Activity recording functions
GUI.hoc                  Graphical user interface initialization
RetinalInput.mod         Retinal input spike train generator
ConductancePattern.mod   Synaptic conductance patterns
SynapticNoise.mod        Synaptic bombardment model
ConstantCurrent.mod      Basic current injection
SineWaveCurrent.mod      Sine-wave current injection
RandomGenerator.mod      Random number generator

cadecay.mod              Intracellular calcium dynamics                  (From Alain Destexhe)
hh2.mod                  Fast sodium spikes (Na and K currents)          (From Alain Destexhe)
IM.mod                   Slow voltage-dependent potassium current (IM)   (From Alain Destexhe)
ITGHK.mod                T-type calcium current of TC cells              (From Alain Destexhe)
IT.mod                   T-type calcium current                          (From Alain Destexhe)


HOW TO RUN THE DEMO
===================

To compile the program, NEURON and INTERVIEWS must be installed and
   working on the machine you are using with appropriately set
   environment variables. To compile the mechanisms given in the mod
   files, just type from the main directory: nrnivmodl

Then, execute the demo by typing:
   nrniv Run.hoc -

The simulation will be started automatically.  Here are zoomed in
displays of 100 ms before and after the time at 1s were the simulation
changes from optimal activity to 99% synaptic noise correlation.
screenshot

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


For further information, please contact:

Sebastien Behuret

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

email: behuret@unic.cnrs-gif.fr