Biophysically realistic neuron models for simulation of cortical stimulation (Aberra et al. 2018)

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Accession:241165
This archive instantiates the single-cell cortical models used in (Aberra et al. 2018) and sets up extracellular stimulation with either a point-current source, to simulate intracortical microstimulation (ICMS), or a uniform E-field distribution, with a monophasic, rectangular pulse waveform in both cases.
Reference:
1 . Aberra AS, Peterchev AV, Grill WM (2018) Biophysically realistic neuron models for simulation of cortical stimulation. J Neural Eng 15:066023 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Neuron or other electrically excitable cell; Axon;
Brain Region(s)/Organism: Neocortex; Barrel cortex;
Cell Type(s): Myelinated neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Action Potential Initiation; Detailed Neuronal Models;
Implementer(s): Aberra, Aman [aman.aberra at duke.edu];
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AberraEtAl2018
cells
L5_TTPC2_cADpyr232_1
mechanisms
morphology
synapses
README *
.provenance.json
biophysics.hoc *
cellinfo.json
CHANGELOG *
constants.hoc *
creategui.hoc *
createsimulation.hoc
current_amps.dat
init.hoc *
LICENSE *
morphology.hoc
mosinit.hoc *
ringplot.hoc *
run.py
run_hoc.sh *
run_py.sh *
run_RmpRiTau.py
run_RmpRiTau_py.sh *
template.hoc
VERSION *
                            
/*                                                                               
Copyright (c) 2015 EPFL-BBP, All rights reserved.                                
                                                                                 
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*/           

/*                                                                               
 * @file init.hoc                                                           
 * @brief Initialisation                                
 * @author Werner Van Geit @ BBP                                                 
 * @date 2015                                                                    
*/        

//----------------------------------------------------------------------------
//  define a panel to run the different demos
//----------------------------------------------------------------------------

load_file("nrngui.hoc")
load_file("constants.hoc")
load_file("creategui.hoc")
load_file("createsimulation.hoc")

// By default, disable the step currents
strdef stepcurrent
stepcurrent = "none"

// By default, enable synapses
synapses_enabled = 1

// Set up simulation
create_cell(synapses_enabled)
create_recording()


// Start the GUI
make_mainwindow(cell)

// Save the windows that already exist before this initialisation
pwmcnt = PWManager[0].count

/** Procedure linked to the Init & Run button */ 
proc restart() {
    cleanup()	

    // make_plottingpanel()
    create_stimulus(stepcurrent)

    cell.synapses.update_synapses(synapse_plot)
    simulate()

    save_recording()
}

/** Cleanup previous windows / simulations */
proc cleanup() { local i
	for i=0, n_graph_lists-1 {
		graphList[i].remove_all()
	}
	flush_list.remove_all()
	fast_flush_list.remove_all()

    rP.cleanup()
    fast_flush_list.append(rP)                                                  
    fast_flush_list.append(sP)                                                   

	doNotify()
	for (i = PWManager[0].count-1; i >= pwmcnt; i -= 1) {
		PWManager[0].close(i)
		doNotify()
	}
	stoprun = 0
    cell.synapses.reset_synapses()
}