NEURON DEMO FOR SIMULATING THALAMOCORTICAL CONVERGENCE CIRCUITS Sebastien Behuret email@example.com 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. 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: firstname.lastname@example.org CHANGELOG ========= 2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.