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. [PubMed]
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];
/
AberraEtAl2018
cells
L4_LBC_cACint209_3
hoc_recordings
mechanisms
morphology
python_recordings
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.

THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJECT
BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/4.0/legalcode or send a letter to Creative Commons, 171
Second Street, Suite 300, San Francisco, California, 94105, USA.
*/


/*                                                                               
 * @file creategui.hoc                                                           
 * @brief Draw the GUI                                
 * @author Werner Van Geit @ BBP                                                 
 * @date 2015                                                                    
*/        

load_file("ringplot.hoc")

pwmcnt = PWManager[0].count  // the initial GUIs should not be dismissed

objref mainhbox
objref plotvbox
objref shapehbox
objref synapsevbox
objref synapsevbox_size
objref gV, sP, rP, synapse_plot                                                               


xres = 1200
yres = 800
xstart = 50
ystart = 0

proc make_mainwindow() {
    mainhbox = new HBox(3)
    mainhbox.intercept(1)

    mainhbox.adjuster(200)
    make_runcontrol()

    mainhbox.adjuster(700)
    make_plottingpanel()

    mainhbox.adjuster(250)
    make_synapsepanel($o1)

    mainhbox.adjuster(250)
    mainhbox.intercept(0)   
    mainhbox.full_request(1) 
    mainhbox.map("Main", xstart, ystart, xres, yres)
}

proc make_plottingpanel() {
    plotvbox = new VBox()
    plotvbox.intercept(1)

    plotvbox.adjuster(300)
    make_shapepanel()
    
    plotvbox.adjuster(500)
    rP = new RingPlot()                                                         

    plotvbox.intercept(0)    
    mainhbox.full_request(1) 
    plotvbox.map("Plotting", 0, 0, -1, -1)
}


proc make_runcontrol() {                                                   
    xpanel("RunControl", 0)                                                     
    xbutton("Init & Run","restart()")                                           
    xbutton("Stop","stoprun=1")                                                 
    xvalue("Total time", "tstop")                                                 
    xvalue("Sim Time","t", 0,"", 0, 1 )                                 
    xvalue("Real Time","realtime", 0,"", 0, 1 )                                 
    xbutton("Quit","quit()")
    
    xlabel("Step current")
    xradiobutton("No step","stepcurrent=\"none\"", 1)                                                                                
    xradiobutton("Step current 1","stepcurrent=\"stepcurrent1\"")            
    xradiobutton("Step current 2","stepcurrent=\"stepcurrent2\"")               
    xradiobutton("Step current 3","stepcurrent=\"stepcurrent3\"")               
    xpanel(1498, 0)
} 
                                                                                
proc make_shapepanel() {                                                                                                                                                                                                     
    shapehbox = new HBox()
    shapehbox.intercept(1)

    shapehbox.adjuster(350)
    sP = new PlotShape(0)                                                       
    sP.variable("soma", "v(0.5)")                                               
    sP.view(-594.956, -98.0373, 1260.25, 1188.42, 573, 0, 505.92, 592)         
    sP.exec_menu("Shape Plot")                                                  

    shapehbox.adjuster(350)                                    
    synapse_plot = new Shape(0)
    synapse_plot.view(-594.956, -98.0373, 1260.25, 1188.42, 49, 0, 500.16, 592)
 
    shapehbox.intercept(0)    
    shapehbox.full_request(1) 
    plotvbox.full_request(1) 
    mainhbox.full_request(1) 
    shapehbox.map("Shapes", 1104, 0, -1, -1)                                                          
}                  

proc make_synapsepanel() { local n_of_pre_mtypes, pre_mtype_id localobj active_pre_mtypes, pre_mtype_freqs
    strdef pre_mtype_name

    synapsevbox = new HBox()
    synapsevbox.intercept(1)
    xpanel("Synapses")
    xlabel("Presyn m-types")
    for i=0, $o1.synapses.pre_mtypes.size-1 {
         pre_mtype_id = $o1.synapses.pre_mtypes.x[i]
         pre_mtype_freqs = $o1.synapses.pre_mtype_freqs
         pre_mtype_name = $o1.synapses.id_mtype_map.o(pre_mtype_id).s
         active_pre_mtypes = $o1.synapses.active_pre_mtypes
         xstatebutton(pre_mtype_name, &active_pre_mtypes.x[pre_mtype_id], "cell.synapses.update_synapses(synapse_plot)")
    }
    xpanel(100, 0)

    xpanel("Freq")
    xlabel("Frequency (Hz)")
    for i=0, $o1.synapses.pre_mtypes.size-1 {
         pre_mtype_id = $o1.synapses.pre_mtypes.x[i]
         pre_mtype_freqs = $o1.synapses.pre_mtype_freqs
         pre_mtype_name = $o1.synapses.id_mtype_map.o(pre_mtype_id).s
         active_pre_mtypes = $o1.synapses.active_pre_mtypes
         xpvalue("", &pre_mtype_freqs.x[pre_mtype_id], 0, "cell.synapses.update_synapses(synapse_plot)", 1)
    }
    xpanel(100, 0)

    synapsevbox.intercept(0)

    show_synapsepanel()
}

proc show_synapsepanel() {
    if (synapses_enabled == 1) {
        synapsevbox.map("Presynaptic activity", 0, 0, -1, -1)
    } else {
        synapsevbox.unmap()
    }
}

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