Human-L2-3-Cortical-Microcircuit/NeuroML2/rotated_cells/HL23PYR_sim.cell.nml

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    <cell id="HL23PYR_sim">
        <notes>Cell: HL23PYR exported from NEURON ModelView. Reference: Yao, H. K.; Guet-McCreight, A.; Mazza, F.; Moradi Chameh, H.; Prevot, T. D.; Griffiths, J. D.; Tripathy, S. J.; Valiante, T. A.; Sibille, E. &amp; Hay, E.  Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits Cell Reports, Elsevier, 2022, 38</notes>
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                <member segment="2834"/>
            </segmentGroup>
            <segmentGroup id="basal_dendrite_group" neuroLexId="GO:0030425">
                <notes>Basal dendrites</notes>
                <include segmentGroup="dend_0"/>
                <include segmentGroup="dend_1"/>
                <include segmentGroup="dend_2"/>
                <include segmentGroup="dend_3"/>
                <include segmentGroup="dend_4"/>
                <include segmentGroup="dend_5"/>
                <include segmentGroup="dend_6"/>
                <include segmentGroup="dend_7"/>
                <include segmentGroup="dend_8"/>
                <include segmentGroup="dend_9"/>
                <include segmentGroup="dend_10"/>
                <include segmentGroup="dend_11"/>
                <include segmentGroup="dend_12"/>
                <include segmentGroup="dend_13"/>
                <include segmentGroup="dend_14"/>
                <include segmentGroup="dend_15"/>
                <include segmentGroup="dend_16"/>
                <include segmentGroup="dend_17"/>
                <include segmentGroup="dend_18"/>
                <include segmentGroup="dend_19"/>
                <include segmentGroup="dend_20"/>
                <include segmentGroup="dend_21"/>
                <include segmentGroup="dend_22"/>
                <include segmentGroup="dend_23"/>
                <include segmentGroup="dend_24"/>
                <include segmentGroup="dend_25"/>
                <include segmentGroup="dend_26"/>
                <include segmentGroup="dend_27"/>
                <include segmentGroup="dend_28"/>
                <include segmentGroup="dend_29"/>
            </segmentGroup>
            <segmentGroup id="apical_dendrite_group" neuroLexId="GO:0030425">
                <notes>Apical dendrite_group</notes>
                <include segmentGroup="apic_0"/>
                <include segmentGroup="apic_1"/>
                <include segmentGroup="apic_2"/>
                <include segmentGroup="apic_3"/>
                <include segmentGroup="apic_4"/>
                <include segmentGroup="apic_5"/>
                <include segmentGroup="apic_6"/>
                <include segmentGroup="apic_7"/>
                <include segmentGroup="apic_8"/>
                <include segmentGroup="apic_9"/>
                <include segmentGroup="apic_10"/>
                <include segmentGroup="apic_11"/>
                <include segmentGroup="apic_12"/>
                <include segmentGroup="apic_13"/>
                <include segmentGroup="apic_14"/>
                <include segmentGroup="apic_15"/>
                <include segmentGroup="apic_16"/>
                <include segmentGroup="apic_17"/>
                <include segmentGroup="apic_18"/>
                <include segmentGroup="apic_19"/>
                <include segmentGroup="apic_20"/>
                <include segmentGroup="apic_21"/>
                <include segmentGroup="apic_22"/>
                <include segmentGroup="apic_23"/>
                <include segmentGroup="apic_24"/>
                <include segmentGroup="apic_25"/>
                <include segmentGroup="apic_26"/>
                <include segmentGroup="apic_27"/>
                <include segmentGroup="apic_28"/>
                <include segmentGroup="apic_29"/>
                <include segmentGroup="apic_30"/>
                <include segmentGroup="apic_31"/>
                <include segmentGroup="apic_32"/>
                <include segmentGroup="apic_33"/>
                <include segmentGroup="apic_34"/>
                <include segmentGroup="apic_35"/>
                <include segmentGroup="apic_36"/>
                <include segmentGroup="apic_37"/>
                <include segmentGroup="apic_38"/>
                <include segmentGroup="apic_39"/>
                <include segmentGroup="apic_40"/>
                <include segmentGroup="apic_41"/>
                <include segmentGroup="apic_42"/>
                <include segmentGroup="apic_43"/>
                <include segmentGroup="apic_44"/>
                <include segmentGroup="apic_45"/>
                <include segmentGroup="apic_46"/>
                <include segmentGroup="apic_47"/>
                <include segmentGroup="apic_48"/>
                <include segmentGroup="apic_49"/>
                <include segmentGroup="apic_50"/>
                <include segmentGroup="apic_51"/>
                <include segmentGroup="apic_52"/>
                <include segmentGroup="apic_53"/>
                <include segmentGroup="apic_54"/>
                <include segmentGroup="apic_55"/>
                <include segmentGroup="apic_56"/>
                <include segmentGroup="apic_57"/>
                <inhomogeneousParameter id="PathLengthOverApicDends" variable="p" metric="Path Length from root">
                    <proximal translationStart="0.0"/>
                </inhomogeneousParameter>
            </segmentGroup>
            <segmentGroup id="myelin_group">
                <notes>Myelin group</notes>
                <include segmentGroup="myelin_0"/>
            </segmentGroup>
            <segmentGroup id="all_minus_myelin">
                <notes>All without myelin</notes>
                <include segmentGroup="apic_0"/>
                <include segmentGroup="apic_1"/>
                <include segmentGroup="apic_2"/>
                <include segmentGroup="apic_3"/>
                <include segmentGroup="apic_4"/>
                <include segmentGroup="apic_5"/>
                <include segmentGroup="apic_6"/>
                <include segmentGroup="apic_7"/>
                <include segmentGroup="apic_8"/>
                <include segmentGroup="apic_9"/>
                <include segmentGroup="apic_10"/>
                <include segmentGroup="apic_11"/>
                <include segmentGroup="apic_12"/>
                <include segmentGroup="apic_13"/>
                <include segmentGroup="apic_14"/>
                <include segmentGroup="apic_15"/>
                <include segmentGroup="apic_16"/>
                <include segmentGroup="apic_17"/>
                <include segmentGroup="apic_18"/>
                <include segmentGroup="apic_19"/>
                <include segmentGroup="apic_20"/>
                <include segmentGroup="apic_21"/>
                <include segmentGroup="apic_22"/>
                <include segmentGroup="apic_23"/>
                <include segmentGroup="apic_24"/>
                <include segmentGroup="apic_25"/>
                <include segmentGroup="apic_26"/>
                <include segmentGroup="apic_27"/>
                <include segmentGroup="apic_28"/>
                <include segmentGroup="apic_29"/>
                <include segmentGroup="apic_30"/>
                <include segmentGroup="apic_31"/>
                <include segmentGroup="apic_32"/>
                <include segmentGroup="apic_33"/>
                <include segmentGroup="apic_34"/>
                <include segmentGroup="apic_35"/>
                <include segmentGroup="apic_36"/>
                <include segmentGroup="apic_37"/>
                <include segmentGroup="apic_38"/>
                <include segmentGroup="apic_39"/>
                <include segmentGroup="apic_40"/>
                <include segmentGroup="apic_41"/>
                <include segmentGroup="apic_42"/>
                <include segmentGroup="apic_43"/>
                <include segmentGroup="apic_44"/>
                <include segmentGroup="apic_45"/>
                <include segmentGroup="apic_46"/>
                <include segmentGroup="apic_47"/>
                <include segmentGroup="apic_48"/>
                <include segmentGroup="apic_49"/>
                <include segmentGroup="apic_50"/>
                <include segmentGroup="apic_51"/>
                <include segmentGroup="apic_52"/>
                <include segmentGroup="apic_53"/>
                <include segmentGroup="apic_54"/>
                <include segmentGroup="apic_55"/>
                <include segmentGroup="apic_56"/>
                <include segmentGroup="apic_57"/>
                <include segmentGroup="axon_0"/>
                <include segmentGroup="axon_1"/>
                <include segmentGroup="dend_0"/>
                <include segmentGroup="dend_1"/>
                <include segmentGroup="dend_2"/>
                <include segmentGroup="dend_3"/>
                <include segmentGroup="dend_4"/>
                <include segmentGroup="dend_5"/>
                <include segmentGroup="dend_6"/>
                <include segmentGroup="dend_7"/>
                <include segmentGroup="dend_8"/>
                <include segmentGroup="dend_9"/>
                <include segmentGroup="dend_10"/>
                <include segmentGroup="dend_11"/>
                <include segmentGroup="dend_12"/>
                <include segmentGroup="dend_13"/>
                <include segmentGroup="dend_14"/>
                <include segmentGroup="dend_15"/>
                <include segmentGroup="dend_16"/>
                <include segmentGroup="dend_17"/>
                <include segmentGroup="dend_18"/>
                <include segmentGroup="dend_19"/>
                <include segmentGroup="dend_20"/>
                <include segmentGroup="dend_21"/>
                <include segmentGroup="dend_22"/>
                <include segmentGroup="dend_23"/>
                <include segmentGroup="dend_24"/>
                <include segmentGroup="dend_25"/>
                <include segmentGroup="dend_26"/>
                <include segmentGroup="dend_27"/>
                <include segmentGroup="dend_28"/>
                <include segmentGroup="dend_29"/>
                <include segmentGroup="soma_0"/>
            </segmentGroup>
            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
                <notes>Default soma segment group for the cell</notes>
                <include segmentGroup="soma_0"/>
            </segmentGroup>
            <segmentGroup id="axon_group" neuroLexId="GO:0030424">
                <notes>Default axon segment group for the cell</notes>
                <include segmentGroup="axon_0"/>
                <include segmentGroup="axon_1"/>
            </segmentGroup>
            <segmentGroup id="dendrite_group" neuroLexId="GO:0030425">
                <notes>Default dendrite segment group for the cell</notes>
                <include segmentGroup="apical_dendrite_group"/>
                <include segmentGroup="basal_dendrite_group"/>
            </segmentGroup>
            <segmentGroup id="all">
                <include segmentGroup="apic_0"/>
                <include segmentGroup="apic_1"/>
                <include segmentGroup="apic_2"/>
                <include segmentGroup="apic_3"/>
                <include segmentGroup="apic_4"/>
                <include segmentGroup="apic_5"/>
                <include segmentGroup="apic_6"/>
                <include segmentGroup="apic_7"/>
                <include segmentGroup="apic_8"/>
                <include segmentGroup="apic_9"/>
                <include segmentGroup="apic_10"/>
                <include segmentGroup="apic_11"/>
                <include segmentGroup="apic_12"/>
                <include segmentGroup="apic_13"/>
                <include segmentGroup="apic_14"/>
                <include segmentGroup="apic_15"/>
                <include segmentGroup="apic_16"/>
                <include segmentGroup="apic_17"/>
                <include segmentGroup="apic_18"/>
                <include segmentGroup="apic_19"/>
                <include segmentGroup="apic_20"/>
                <include segmentGroup="apic_21"/>
                <include segmentGroup="apic_22"/>
                <include segmentGroup="apic_23"/>
                <include segmentGroup="apic_24"/>
                <include segmentGroup="apic_25"/>
                <include segmentGroup="apic_26"/>
                <include segmentGroup="apic_27"/>
                <include segmentGroup="apic_28"/>
                <include segmentGroup="apic_29"/>
                <include segmentGroup="apic_30"/>
                <include segmentGroup="apic_31"/>
                <include segmentGroup="apic_32"/>
                <include segmentGroup="apic_33"/>
                <include segmentGroup="apic_34"/>
                <include segmentGroup="apic_35"/>
                <include segmentGroup="apic_36"/>
                <include segmentGroup="apic_37"/>
                <include segmentGroup="apic_38"/>
                <include segmentGroup="apic_39"/>
                <include segmentGroup="apic_40"/>
                <include segmentGroup="apic_41"/>
                <include segmentGroup="apic_42"/>
                <include segmentGroup="apic_43"/>
                <include segmentGroup="apic_44"/>
                <include segmentGroup="apic_45"/>
                <include segmentGroup="apic_46"/>
                <include segmentGroup="apic_47"/>
                <include segmentGroup="apic_48"/>
                <include segmentGroup="apic_49"/>
                <include segmentGroup="apic_50"/>
                <include segmentGroup="apic_51"/>
                <include segmentGroup="apic_52"/>
                <include segmentGroup="apic_53"/>
                <include segmentGroup="apic_54"/>
                <include segmentGroup="apic_55"/>
                <include segmentGroup="apic_56"/>
                <include segmentGroup="apic_57"/>
                <include segmentGroup="axon_0"/>
                <include segmentGroup="axon_1"/>
                <include segmentGroup="dend_0"/>
                <include segmentGroup="dend_1"/>
                <include segmentGroup="dend_2"/>
                <include segmentGroup="dend_3"/>
                <include segmentGroup="dend_4"/>
                <include segmentGroup="dend_5"/>
                <include segmentGroup="dend_6"/>
                <include segmentGroup="dend_7"/>
                <include segmentGroup="dend_8"/>
                <include segmentGroup="dend_9"/>
                <include segmentGroup="dend_10"/>
                <include segmentGroup="dend_11"/>
                <include segmentGroup="dend_12"/>
                <include segmentGroup="dend_13"/>
                <include segmentGroup="dend_14"/>
                <include segmentGroup="dend_15"/>
                <include segmentGroup="dend_16"/>
                <include segmentGroup="dend_17"/>
                <include segmentGroup="dend_18"/>
                <include segmentGroup="dend_19"/>
                <include segmentGroup="dend_20"/>
                <include segmentGroup="dend_21"/>
                <include segmentGroup="dend_22"/>
                <include segmentGroup="dend_23"/>
                <include segmentGroup="dend_24"/>
                <include segmentGroup="dend_25"/>
                <include segmentGroup="dend_26"/>
                <include segmentGroup="dend_27"/>
                <include segmentGroup="dend_28"/>
                <include segmentGroup="dend_29"/>
                <include segmentGroup="myelin_0"/>
                <include segmentGroup="soma_0"/>
            </segmentGroup>
        </morphology>
        <biophysicalProperties id="biophys">
            <membraneProperties>
                <channelDensity id="pas" ionChannel="pas" condDensity="0.0000954 S_per_cm2" erev="-80 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
                <channelDensity id="SK_somatic" ionChannel="SK" condDensity="0.000853 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="K_T_somatic" ionChannel="K_T" condDensity="0.0605 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.000208 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="Kv3_1_somatic" ionChannel="Kv3_1" condDensity="0.0424 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="Ih_somatic" ionChannel="Ih" condDensity="0.000148 S_per_cm2" erev="-45 mV" segmentGroup="soma_group" ion="hcn"/>
                <channelDensity id="Im_somatic" ionChannel="Im" condDensity="0.000306 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="NaTg_somatic" ionChannel="NaTg_PYR_somatic" condDensity="0.272 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
                <channelDensity id="Ih_basal" ionChannel="Ih" condDensity="0.000000709 S_per_cm2" erev="-45 mV" segmentGroup="basal_dendrite_group" ion="hcn"/>
                <channelDensity id="SK_axonal" ionChannel="SK" condDensity="0.0145 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="K_T_axonal" ionChannel="K_T" condDensity="0.0424 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="K_P_axonal" ionChannel="K_P" condDensity="0.338 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="Im_axonal" ionChannel="Im" condDensity="0.000 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.941 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="NaTg_axonal" ionChannel="NaTg_PYR_axonal" condDensity="1.38 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
                <channelDensity id="Nap_axonal" ionChannel="Nap" condDensity="0.00842 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
                <channelDensity id="Ih_axonal" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="axon_group" ion="hcn"/>
                <channelDensity id="TonicInhibition" ionChannel="TonicPavlov2009" condDensity="0.000938 S_per_cm2" erev="-75 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
                <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="0.00155 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.00296 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="0.0003060000 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
                <channelDensityNernst id="Ca_LVA_axonal" ionChannel="Ca_LVA" condDensity="0.0439000000 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
                <channelDensityNonUniform id="Ih_apical" ionChannel="Ih" erev="-45 mV" ion="hcn">
                    <variableParameter parameter="condDensity" segmentGroup="apical_dendrite_group">
                        <inhomogeneousValue inhomogeneousParameter="PathLengthOverApicDends" value="1E9 * (0.148 * 1E-8) * ((2.087 * exp( 3.6161 * (p/606.3464))) - 0.8696)"/>
                    </variableParameter>
                </channelDensityNonUniform>
                <specificCapacitance value="1 uF_per_cm2" segmentGroup="all_minus_myelin"/>
                <specificCapacitance value="0.02 uF_per_cm2" segmentGroup="myelin_group"/>
                <specificCapacitance value="2 uF_per_cm2" segmentGroup="apical_dendrite_group"/>
                <specificCapacitance value="2 uF_per_cm2" segmentGroup="basal_dendrite_group"/>
                <initMembPotential value="-80mV"/>
            </membraneProperties>
            <intracellularProperties>
                <species id="ca" concentrationModel="CaDynamics_E2_NML2_PYR_somatic" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="soma_group"/>
                <species id="ca" concentrationModel="CaDynamics_E2_NML2_PYR_axonal" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="axon_group"/>
                <resistivity value="0.1 kohm_cm" segmentGroup="all_minus_myelin"/>
                <resistivity value="0.1 kohm_cm" segmentGroup="myelin_group"/>
            </intracellularProperties>
        </biophysicalProperties>
    </cell>
</neuroml>