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_2
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 biophys.hoc
 * @brief Biophysics
 * @author Etay Hay, Werner Van Geit @ BBP
 * @date 2015
*/
begintemplate cACint209_biophys
public biophys, distribute

proc distribute(){local x localobj sl
        strdef stmp,distfunc,mech
        sl = $o1
        mech = $s2
        distfunc = $s3
        sprint(distfunc,"%%s %s(%%f) = %s",mech, distfunc)
        forsec sl for(x) {
            sprint (stmp,distfunc,secname(),x,distance(x))
            execute(stmp)
        }
    }

proc biophys() {
	forsec $o1.basal {
		insert NaTs2_t
		insert SKv3_1
		insert Nap_Et2
		insert Ih
		insert Im
		insert K_Pst
		insert K_Tst
	}

	forsec $o1.all {
		insert pas
	}

	forsec $o1.somatic {
		insert NaTs2_t
		insert SKv3_1
		insert Ca
		insert SK_E2
		insert Ca_LVAst
		insert Nap_Et2
		insert Im
		insert K_Pst
		insert K_Tst
		insert CaDynamics_E2
	}

	forsec $o1.apical {
		insert NaTs2_t
		insert SKv3_1
		insert Nap_Et2
		insert Ih
		insert Im
		insert K_Pst
		insert K_Tst
	}

	forsec $o1.axonal {
		insert SKv3_1
		insert Ca
		insert SK_E2
		insert CaDynamics_E2
		insert Nap_Et2
		insert Im
		insert K_Pst
		insert K_Tst
		insert Ca_LVAst
		insert NaTa_t
	}

	forsec $o1.all {
		Ra = 100.0 
	}

	forsec $o1.all {
		cm = 1.0 
	}

	forsec $o1.all {
		e_pas = -75.300257 
	}

	forsec $o1.apical {
		ena = 50 
	}

	forsec $o1.apical {
		ek = -85 
	}

	forsec $o1.axonal {
		ena = 50 
	}

	forsec $o1.axonal {
		ek = -85 
	}

	forsec $o1.basal {
		ena = 50 
	}

	forsec $o1.basal {
		ek = -85 
	}

	forsec $o1.somatic {
		ena = 50 
	}

	forsec $o1.somatic {
		ek = -85 
	}

		distribute($o1.basal,"gK_Tstbar_K_Tst","(0.0 * %g + 1.0)*0.007375")
		distribute($o1.basal,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.000041")
		distribute($o1.basal,"gNap_Et2bar_Nap_Et2","(0.0 * %g + 1.0)*0.000000")
		distribute($o1.basal,"gNaTs2_tbar_NaTs2_t","(0.0 * %g + 1.0)*0.001373")
		distribute($o1.basal,"gIhbar_Ih","(-0.869600 + 2.087000*exp((%g-0.000000)*0.003000))*0.000023")
		distribute($o1.basal,"e_pas","(0.0 * %g + 1.0)*-63.118492")
		distribute($o1.basal,"g_pas","(0.0 * %g + 1.0)*0.000001")
		distribute($o1.basal,"gImbar_Im","(0.0 * %g + 1.0)*0.000014")
		distribute($o1.apical,"gK_Tstbar_K_Tst","(0.0 * %g + 1.0)*0.007375")
		distribute($o1.apical,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.000041")
		distribute($o1.apical,"gNap_Et2bar_Nap_Et2","(0.0 * %g + 1.0)*0.000000")
		distribute($o1.apical,"gNaTs2_tbar_NaTs2_t","(0.0 * %g + 1.0)*0.001373")
		distribute($o1.apical,"gIhbar_Ih","(-0.869600 + 2.087000*exp((%g-0.000000)*0.003000))*0.000023")
		distribute($o1.apical,"e_pas","(0.0 * %g + 1.0)*-63.118492")
		distribute($o1.apical,"g_pas","(0.0 * %g + 1.0)*0.000001")
		distribute($o1.apical,"gImbar_Im","(0.0 * %g + 1.0)*0.000014")
		distribute($o1.axonal,"gNaTa_tbar_NaTa_t","(0.0 * %g + 1.0)*3.993125")
		distribute($o1.axonal,"gK_Tstbar_K_Tst","(0.0 * %g + 1.0)*0.000000")
		distribute($o1.axonal,"gamma_CaDynamics_E2","(0.0 * %g + 1.0)*0.000503")
		distribute($o1.axonal,"gNap_Et2bar_Nap_Et2","(0.0 * %g + 1.0)*0.000000")
		distribute($o1.axonal,"gCa_LVAstbar_Ca_LVAst","(0.0 * %g + 1.0)*0.009986")
		distribute($o1.axonal,"gSK_E2bar_SK_E2","(0.0 * %g + 1.0)*0.005611")
		distribute($o1.axonal,"gK_Pstbar_K_Pst","(0.0 * %g + 1.0)*0.068460")
		distribute($o1.axonal,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.517764")
		distribute($o1.axonal,"decay_CaDynamics_E2","(0.0 * %g + 1.0)*573.007045")
		distribute($o1.axonal,"e_pas","(0.0 * %g + 1.0)*-64.601696")
		distribute($o1.axonal,"g_pas","(0.0 * %g + 1.0)*0.000063")
		distribute($o1.axonal,"gImbar_Im","(0.0 * %g + 1.0)*0.000345")
		distribute($o1.axonal,"gCabar_Ca","(0.0 * %g + 1.0)*0.000501")
		distribute($o1.somatic,"gK_Tstbar_K_Tst","(0.0 * %g + 1.0)*0.077616")
		distribute($o1.somatic,"gamma_CaDynamics_E2","(0.0 * %g + 1.0)*0.000814")
		distribute($o1.somatic,"gNap_Et2bar_Nap_Et2","(0.0 * %g + 1.0)*0.000001")
		distribute($o1.somatic,"gCa_LVAstbar_Ca_LVAst","(0.0 * %g + 1.0)*0.009728")
		distribute($o1.somatic,"gSK_E2bar_SK_E2","(0.0 * %g + 1.0)*0.002099")
		distribute($o1.somatic,"gK_Pstbar_K_Pst","(0.0 * %g + 1.0)*0.000114")
		distribute($o1.somatic,"gSKv3_1bar_SKv3_1","(0.0 * %g + 1.0)*0.260872")
		distribute($o1.somatic,"decay_CaDynamics_E2","(0.0 * %g + 1.0)*967.678789")
		distribute($o1.somatic,"e_pas","(0.0 * %g + 1.0)*-69.781406")
		distribute($o1.somatic,"g_pas","(0.0 * %g + 1.0)*0.000020")
		distribute($o1.somatic,"gImbar_Im","(0.0 * %g + 1.0)*0.000032")
		distribute($o1.somatic,"gNaTs2_tbar_NaTs2_t","(0.0 * %g + 1.0)*0.395881")
		distribute($o1.somatic,"gCabar_Ca","(0.0 * %g + 1.0)*0.000028")
}

endtemplate cACint209_biophys

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