Human-L2-3-Cortical-Microcircuit/NeuroML2/HL23SST.cell.nml

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    <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.2.2 release/8.2 (93d41fafd) 2022-12-15
          Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
          Yale University and UCL 
  </notes>
    <include href="CaDynamics_E2_NML2.nml"/>
    <include href="channels/pas.channel.nml"/>
    <include href="channels/NaTg/NaTg.channel.nml"/>
    <include href="channels/Ih.channel.nml"/>
    <include href="channels/K_P.channel.nml"/>
    <include href="channels/K_T.channel.nml"/>
    <include href="channels/Kv3_1.channel.nml"/>
    <include href="channels/Im.channel.nml"/>
    <include href="channels/SK.channel.nml"/>
    <include href="channels/Ca_HVA.channel.nml"/>
    <include href="channels/Ca_LVA.channel.nml"/>
    <include href="channels/Nap.channel.nml"/>
    <cell id="HL23SST">
        <notes>Cell: HL23SST 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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                <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
             neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
             These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
                <member segment="1929"/>
                <member segment="1930"/>
                <member segment="1931"/>
                <member segment="1932"/>
                <member segment="1933"/>
                <member segment="1934"/>
                <member segment="1935"/>
            </segmentGroup>
            <segmentGroup id="dend_28" neuroLexId="sao864921383">
                <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
             neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
             These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
                <member segment="1900"/>
                <member segment="1901"/>
                <member segment="1902"/>
                <member segment="1903"/>
                <member segment="1904"/>
                <member segment="1905"/>
                <member segment="1906"/>
                <member segment="1907"/>
                <member segment="1908"/>
                <member segment="1909"/>
                <member segment="1910"/>
                <member segment="1911"/>
                <member segment="1912"/>
                <member segment="1913"/>
                <member segment="1914"/>
                <member segment="1915"/>
                <member segment="1916"/>
                <member segment="1917"/>
                <member segment="1918"/>
                <member segment="1919"/>
                <member segment="1920"/>
                <member segment="1921"/>
                <member segment="1922"/>
                <member segment="1923"/>
                <member segment="1924"/>
                <member segment="1925"/>
                <member segment="1926"/>
                <member segment="1927"/>
                <member segment="1928"/>
            </segmentGroup>
            <segmentGroup id="dend_53" neuroLexId="sao864921383">
                <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
             neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
             These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
                <member segment="3146"/>
                <member segment="3147"/>
                <member segment="3148"/>
                <member segment="3149"/>
                <member segment="3150"/>
                <member segment="3151"/>
                <member segment="3152"/>
                <member segment="3153"/>
                <member segment="3154"/>
                <member segment="3155"/>
                <member segment="3156"/>
                <member segment="3157"/>
                <member segment="3158"/>
                <member segment="3159"/>
                <member segment="3160"/>
                <member segment="3161"/>
                <member segment="3162"/>
                <member segment="3163"/>
                <member segment="3164"/>
            </segmentGroup>
            <segmentGroup id="dend_52" neuroLexId="sao864921383">
                <notes>This group contains an unbranched set of segments, and all of the segmentGroups marked with
             neuroLexId = sao864921383 form a non-overlapping set of all of the segments.
             These segmentGroups correspond to the 'cables' of NeuroML v1.8.1, and map to/from NEURON sections.</notes>
                <property tag="numberInternalDivisions" value="5"/>
                <annotation>
                    <property xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" tag="numberInternalDivisions" value="5"/> 
        
                </annotation>
                <member segment="3044"/>
                <member segment="3045"/>
                <member segment="3046"/>
                <member segment="3047"/>
                <member segment="3048"/>
                <member segment="3049"/>
                <member segment="3050"/>
                <member segment="3051"/>
                <member segment="3052"/>
                <member segment="3053"/>
                <member segment="3054"/>
                <member segment="3055"/>
                <member segment="3056"/>
                <member segment="3057"/>
                <member segment="3058"/>
                <member segment="3059"/>
                <member segment="3060"/>
                <member segment="3061"/>
                <member segment="3062"/>
                <member segment="3063"/>
                <member segment="3064"/>
                <member segment="3065"/>
                <member segment="3066"/>
                <member segment="3067"/>
                <member segment="3068"/>
                <member segment="3069"/>
                <member segment="3070"/>
                <member segment="3071"/>
                <member segment="3072"/>
                <member segment="3073"/>
                <member segment="3074"/>
                <member segment="3075"/>
                <member segment="3076"/>
                <member segment="3077"/>
                <member segment="3078"/>
                <member segment="3079"/>
                <member segment="3080"/>
                <member segment="3081"/>
                <member segment="3082"/>
                <member segment="3083"/>
                <member segment="3084"/>
                <member segment="3085"/>
                <member segment="3086"/>
                <member segment="3087"/>
                <member segment="3088"/>
                <member segment="3089"/>
                <member segment="3090"/>
                <member segment="3091"/>
                <member segment="3092"/>
                <member segment="3093"/>
                <member segment="3094"/>
                <member segment="3095"/>
                <member segment="3096"/>
                <member segment="3097"/>
                <member segment="3098"/>
                <member segment="3099"/>
                <member segment="3100"/>
                <member segment="3101"/>
                <member segment="3102"/>
                <member segment="3103"/>
                <member segment="3104"/>
                <member segment="3105"/>
                <member segment="3106"/>
                <member segment="3107"/>
                <member segment="3108"/>
                <member segment="3109"/>
                <member segment="3110"/>
                <member segment="3111"/>
                <member segment="3112"/>
                <member segment="3113"/>
                <member segment="3114"/>
                <member segment="3115"/>
                <member segment="3116"/>
                <member segment="3117"/>
                <member segment="3118"/>
                <member segment="3119"/>
                <member segment="3120"/>
                <member segment="3121"/>
                <member segment="3122"/>
                <member segment="3123"/>
                <member segment="3124"/>
                <member segment="3125"/>
                <member segment="3126"/>
                <member segment="3127"/>
                <member segment="3128"/>
                <member segment="3129"/>
                <member segment="3130"/>
                <member segment="3131"/>
                <member segment="3132"/>
                <member segment="3133"/>
                <member segment="3134"/>
                <member segment="3135"/>
                <member segment="3136"/>
                <member segment="3137"/>
                <member segment="3138"/>
                <member segment="3139"/>
                <member segment="3140"/>
                <member segment="3141"/>
                <member segment="3142"/>
                <member segment="3143"/>
                <member segment="3144"/>
                <member segment="3145"/>
            </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"/>
                <include segmentGroup="dend_30"/>
                <include segmentGroup="dend_31"/>
                <include segmentGroup="dend_32"/>
                <include segmentGroup="dend_33"/>
                <include segmentGroup="dend_34"/>
                <include segmentGroup="dend_35"/>
                <include segmentGroup="dend_36"/>
                <include segmentGroup="dend_37"/>
                <include segmentGroup="dend_38"/>
                <include segmentGroup="dend_39"/>
                <include segmentGroup="dend_40"/>
                <include segmentGroup="dend_41"/>
                <include segmentGroup="dend_42"/>
                <include segmentGroup="dend_43"/>
                <include segmentGroup="dend_44"/>
                <include segmentGroup="dend_45"/>
                <include segmentGroup="dend_46"/>
                <include segmentGroup="dend_47"/>
                <include segmentGroup="dend_48"/>
                <include segmentGroup="dend_49"/>
                <include segmentGroup="dend_50"/>
                <include segmentGroup="dend_51"/>
                <include segmentGroup="dend_52"/>
                <include segmentGroup="dend_53"/>
                <include segmentGroup="dend_54"/>
            </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="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="dend_30"/>
                <include segmentGroup="dend_31"/>
                <include segmentGroup="dend_32"/>
                <include segmentGroup="dend_33"/>
                <include segmentGroup="dend_34"/>
                <include segmentGroup="dend_35"/>
                <include segmentGroup="dend_36"/>
                <include segmentGroup="dend_37"/>
                <include segmentGroup="dend_38"/>
                <include segmentGroup="dend_39"/>
                <include segmentGroup="dend_40"/>
                <include segmentGroup="dend_41"/>
                <include segmentGroup="dend_42"/>
                <include segmentGroup="dend_43"/>
                <include segmentGroup="dend_44"/>
                <include segmentGroup="dend_45"/>
                <include segmentGroup="dend_46"/>
                <include segmentGroup="dend_47"/>
                <include segmentGroup="dend_48"/>
                <include segmentGroup="dend_49"/>
                <include segmentGroup="dend_50"/>
                <include segmentGroup="dend_51"/>
                <include segmentGroup="dend_52"/>
                <include segmentGroup="dend_53"/>
                <include segmentGroup="dend_54"/>
                <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="basal_dendrite_group"/>
            </segmentGroup>
            <segmentGroup id="all">
                <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="dend_30"/>
                <include segmentGroup="dend_31"/>
                <include segmentGroup="dend_32"/>
                <include segmentGroup="dend_33"/>
                <include segmentGroup="dend_34"/>
                <include segmentGroup="dend_35"/>
                <include segmentGroup="dend_36"/>
                <include segmentGroup="dend_37"/>
                <include segmentGroup="dend_38"/>
                <include segmentGroup="dend_39"/>
                <include segmentGroup="dend_40"/>
                <include segmentGroup="dend_41"/>
                <include segmentGroup="dend_42"/>
                <include segmentGroup="dend_43"/>
                <include segmentGroup="dend_44"/>
                <include segmentGroup="dend_45"/>
                <include segmentGroup="dend_46"/>
                <include segmentGroup="dend_47"/>
                <include segmentGroup="dend_48"/>
                <include segmentGroup="dend_49"/>
                <include segmentGroup="dend_50"/>
                <include segmentGroup="dend_51"/>
                <include segmentGroup="dend_52"/>
                <include segmentGroup="dend_53"/>
                <include segmentGroup="dend_54"/>
                <include segmentGroup="myelin_0"/>
                <include segmentGroup="soma_0"/>
            </segmentGroup>
        </morphology>
        <biophysicalProperties id="biophys">
            <membraneProperties>
                <channelDensity id="pas" ionChannel="pas" condDensity="0.0000232 S_per_cm2" erev="-81.5 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
                <channelDensity id="NaTg_somatic" ionChannel="NaTg_SST_somatic" condDensity="0.127 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
                <channelDensity id="Ih_somatic" ionChannel="Ih" condDensity="0.0000431 S_per_cm2" erev="-45 mV" segmentGroup="soma_group" ion="hcn"/>
                <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.0111 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="K_T_somatic" ionChannel="K_T" condDensity="0.00000 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="Kv3_1_somatic" ionChannel="Kv3_1" condDensity="0.871 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="Im_somatic" ionChannel="Im" condDensity="0.000158 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="SK_somatic" ionChannel="SK" condDensity="0.00 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                <channelDensity id="Ih_basal" ionChannel="Ih" condDensity="0.0000949 S_per_cm2" erev="-45 mV" segmentGroup="basal_dendrite_group" ion="hcn"/>
                <channelDensity id="NaTg_axonal" ionChannel="NaTg_SST_axonal" condDensity="0.343 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
                <channelDensity id="Nap_axonal" ionChannel="Nap" condDensity="0.000444 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
                <channelDensity id="K_P_axonal" ionChannel="K_P" condDensity="0.0295 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="K_T_axonal" ionChannel="K_T" condDensity="0.023 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.984 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="Im_axonal" ionChannel="Im" condDensity="0.000317 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="SK_axonal" ionChannel="SK" condDensity="0.00113 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                <channelDensity id="Ih_axonal" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="axon_group" ion="hcn"/>
                <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="0.00355 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.00314 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="0.00145 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
                <channelDensityNernst id="Ca_LVA_axonal" ionChannel="Ca_LVA" condDensity="0.0627 S_per_cm2" segmentGroup="axon_group" ion="ca"/>
                <spikeThresh value="10mV"/>
                <specificCapacitance value="1 uF_per_cm2" segmentGroup="all_minus_myelin"/>
                <specificCapacitance value="0.02 uF_per_cm2" segmentGroup="myelin_group"/>
                <specificCapacitance value="1 uF_per_cm2" segmentGroup="basal_dendrite_group"/>
                <initMembPotential value="-80mV"/>
            </membraneProperties>
            <intracellularProperties>
                <species id="ca" concentrationModel="CaDynamics_E2_NML2_SST_somatic" ion="ca" initialConcentration="1e-4 mM" initialExtConcentration="2.0E-6 mol_per_cm3" segmentGroup="soma_group"/>
                <species id="ca" concentrationModel="CaDynamics_E2_NML2_SST_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>