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pyr_model8.cell.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd" id="cell">
<notes>Layer 5 Pyramidal cell</notes>
<include href="kca.channel.nml"/>
<include href="sca.channel.nml"/>
<include href="cad.nml"/>
<include href="nat.channel.nml"/>
<include href="pas.channel.nml"/>
<include href="kfast.channel.nml"/>
<include href="kslow.channel.nml"/>
<include href="nap.channel.nml"/>
<include href="IKM.channel.nml"/>
<include href="ih.channel.nml"/>
<cell id="pyr_model8">
<morphology id="morphology">
<segment id="0" name="Seg0_soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="23.1453"/>
<distal x="11.5726" y="0.0" z="0.0" diameter="23.1453"/>
</segment>
<segment id="1" name="Seg1_soma">
<parent segment="0"/>
<distal x="23.1453" y="0.0" z="0.0" diameter="23.1453"/>
</segment>
<segment id="2" name="Seg0_hillock">
<parent segment="0"/>
<proximal x="0.0" y="0.0" z="0.0" diameter="3.35"/>
<distal x="-2.0" y="1.74846e-07" z="0.0" diameter="3.35"/>
</segment>
<segment id="3" name="Seg1_hillock">
<parent segment="2"/>
<distal x="-6.0" y="5.24537e-07" z="0.0" diameter="3.05"/>
</segment>
<segment id="4" name="Seg2_hillock">
<parent segment="3"/>
<distal x="-10.0" y="8.74228e-07" z="0.0" diameter="2.75"/>
</segment>
<segment id="5" name="Seg3_hillock">
<parent segment="4"/>
<distal x="-14.0" y="1.22392e-06" z="0.0" diameter="2.45"/>
</segment>
<segment id="6" name="Seg4_hillock">
<parent segment="5"/>
<distal x="-18.0" y="1.57361e-06" z="0.0" diameter="2.15"/>
</segment>
<segment id="7" name="Seg5_hillock">
<parent segment="6"/>
<distal x="-20.0" y="1.7486e-06" z="0.0" diameter="2.15"/>
</segment>
<segment id="8" name="Seg0_basal">
<parent segment="0"/>
<proximal x="11.5726" y="0.0" z="0.0" diameter="8.74536"/>
<distal x="11.5726" y="128.5" z="0.0" diameter="8.74536"/>
</segment>
<segment id="9" name="Seg1_basal">
<parent segment="8"/>
<distal x="11.5726" y="257.0" z="0.0" diameter="8.74536"/>
</segment>
<segment id="10" name="Seg0_apical">
<parent segment="1"/>
<proximal x="23.1453" y="0.0" z="0.0" diameter="5.92845"/>
<distal x="73.1453" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="11" name="Seg1_apical">
<parent segment="10"/>
<distal x="173.145" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="12" name="Seg2_apical">
<parent segment="11"/>
<distal x="273.145" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="13" name="Seg3_apical">
<parent segment="12"/>
<distal x="373.145" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="14" name="Seg4_apical">
<parent segment="13"/>
<distal x="473.145" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="15" name="Seg5_apical">
<parent segment="14"/>
<distal x="523.145" y="0.0" z="0.0" diameter="5.92845"/>
</segment>
<segment id="16" name="Seg0_iseg">
<parent segment="7"/>
<proximal x="-20.0" y="1.74846e-06" z="0.0" diameter="1.95"/>
<distal x="-22.5" y="2.12595e-06" z="0.0" diameter="1.95"/>
</segment>
<segment id="17" name="Seg1_iseg">
<parent segment="16"/>
<distal x="-27.5" y="2.88092e-06" z="0.0" diameter="1.85"/>
</segment>
<segment id="18" name="Seg2_iseg">
<parent segment="17"/>
<distal x="-32.5" y="3.6359e-06" z="0.0" diameter="1.75"/>
</segment>
<segment id="19" name="Seg3_iseg">
<parent segment="18"/>
<distal x="-37.5" y="4.39088e-06" z="0.0" diameter="1.65"/>
</segment>
<segment id="20" name="Seg4_iseg">
<parent segment="19"/>
<distal x="-42.5" y="5.14586e-06" z="0.0" diameter="1.55"/>
</segment>
<segment id="21" name="Seg5_iseg">
<parent segment="20"/>
<distal x="-45.0" y="5.52335e-06" z="0.0" diameter="1.55"/>
</segment>
<segment id="22" name="Seg0_tuft">
<parent segment="15"/>
<proximal x="523.145" y="0.0" z="0.0" diameter="6.01807"/>
<distal x="647.895" y="0.0" z="0.0" diameter="6.01807"/>
</segment>
<segment id="23" name="Seg1_tuft">
<parent segment="22"/>
<distal x="897.395" y="0.0" z="0.0" diameter="6.01807"/>
</segment>
<segment id="24" name="Seg2_tuft">
<parent segment="23"/>
<distal x="1022.15" y="0.0" z="0.0" diameter="6.01807"/>
</segment>
<segment id="25" name="Seg0_axon">
<parent segment="21"/>
<proximal x="-45.0" y="5.52335e-06" z="0.0" diameter="1.5"/>
<distal x="-295.0" y="4.32723e-05" z="0.0" diameter="1.5"/>
</segment>
<segment id="26" name="Seg1_axon">
<parent segment="25"/>
<distal x="-545.0" y="8.10213e-05" z="0.0" diameter="1.5"/>
</segment>
<segmentGroup id="all">
<member segment="0"/>
<member segment="1"/>
<member segment="2"/>
<member segment="3"/>
<member segment="4"/>
<member segment="5"/>
<member segment="6"/>
<member segment="7"/>
<member segment="8"/>
<member segment="9"/>
<member segment="10"/>
<member segment="11"/>
<member segment="12"/>
<member segment="13"/>
<member segment="14"/>
<member segment="15"/>
<member segment="16"/>
<member segment="17"/>
<member segment="18"/>
<member segment="19"/>
<member segment="20"/>
<member segment="21"/>
<member segment="22"/>
<member segment="23"/>
<member segment="24"/>
<member segment="25"/>
<member segment="26"/>
</segmentGroup>
<segmentGroup neuroLexId="GO:0043025" id="soma_group">
<notes>Default soma segment group for the cell</notes>
<property tag="color" value="0 0 0.8"/>
<member segment="0"/>
<member segment="1"/>
<include segmentGroup="soma_0"/>
</segmentGroup>
<segmentGroup neuroLexId="GO:0030424" id="axon_group">
<notes>Default axon segment group for the cell</notes>
<property tag="color" value="0 0.8 0"/>
<member segment="25"/>
<member segment="26"/>
<include segmentGroup="axon_0"/>
<include segmentGroup="hillock_0"/>
<include segmentGroup="iseg_0"/>
</segmentGroup>
<segmentGroup neuroLexId="GO:0030425" id="dendrite_group">
<notes>Default dendrite segment group for the cell</notes>
<property tag="color" value="0.8 0 0"/>
<include segmentGroup="basal_0"/>
<include segmentGroup="apical_0"/>
<include segmentGroup="tuft_0"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="soma_0">
<member segment="0"/>
<member segment="1"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="hillock_0">
<property tag="numberInternalDivisions" value="5"/>
<member segment="2"/>
<member segment="3"/>
<member segment="4"/>
<member segment="5"/>
<member segment="6"/>
<member segment="7"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="basal_0">
<member segment="8"/>
<member segment="9"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="apical_0">
<property tag="numberInternalDivisions" value="5"/>
<member segment="10"/>
<member segment="11"/>
<member segment="12"/>
<member segment="13"/>
<member segment="14"/>
<member segment="15"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="iseg_0">
<property tag="numberInternalDivisions" value="5"/>
<member segment="16"/>
<member segment="17"/>
<member segment="18"/>
<member segment="19"/>
<member segment="20"/>
<member segment="21"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="tuft_0">
<property tag="numberInternalDivisions" value="2"/>
<member segment="22"/>
<member segment="23"/>
<member segment="24"/>
</segmentGroup>
<segmentGroup neuroLexId="sao864921383" id="axon_0">
<member segment="25"/>
<member segment="26"/>
</segmentGroup>
<segmentGroup id="basal_group">
<include segmentGroup="basal_0"/>
</segmentGroup>
<segmentGroup id="apical_group">
<include segmentGroup="apical_0"/>
<inhomogeneousParameter id="PathLengthOver_apical_group" variable="p" metric="Path Length from root">
<proximal translationStart="0.0"/>
</inhomogeneousParameter>
</segmentGroup>
<segmentGroup id="tuft_group">
<include segmentGroup="tuft_0"/>
</segmentGroup>
<segmentGroup id="hillock_group">
<include segmentGroup="hillock_0"/>
</segmentGroup>
<segmentGroup id="iseg_group">
<include segmentGroup="iseg_0"/>
</segmentGroup>
<segmentGroup id="axosomatic_list">
<include segmentGroup="soma_0"/>
<include segmentGroup="hillock_0"/>
<include segmentGroup="basal_0"/>
<include segmentGroup="iseg_0"/>
<include segmentGroup="axon_0"/>
</segmentGroup>
<segmentGroup id="apicaltree_list">
<include segmentGroup="apical_0"/>
<include segmentGroup="tuft_0"/>
<inhomogeneousParameter id="PathLengthOver_apicaltree_list" variable="p" metric="Path Length from root">
<proximal translationStart="0.0"/>
</inhomogeneousParameter>
</segmentGroup>
</morphology>
<biophysicalProperties id="biophys">
<membraneProperties>
<channelDensity id="axosomatic_gpas" ionChannel="pas" condDensity="0.8624864686729613 S_per_m2" erev="-80.735127 mV" segmentGroup="axosomatic_list" ion="non_specific"/>
<channelDensity id="apicaltree_gpas" ionChannel="pas" condDensity="0.43124323433648065 S_per_m2" erev="-80.735127 mV" segmentGroup="apicaltree_list" ion="non_specific"/>
<channelDensity id="kfast_soma" ionChannel="kfast" condDensity="41.35183 S_per_m2" erev="-80mV" segmentGroup="soma_group" ion="k"/>
<channelDensity id="kslow_soma" ionChannel="kslow" condDensity="264.78782 S_per_m2" erev="-80mV" segmentGroup="soma_group" ion="k"/>
<channelDensity id="nap_soma" ionChannel="nap" condDensity="4.179878 S_per_m2" erev="55mV" segmentGroup="soma_group" ion="na"/>
<channelDensity id="km_soma" ionChannel="km" condDensity="14.917361 S_per_m2" erev="-80mV" segmentGroup="soma_group" ion="k"/>
<channelDensity id="ih_basal" ionChannel="ih" condDensity="11.921506 S_per_m2" erev="-47mV" segmentGroup="basal_group" ion="hcn"/>
<channelDensity id="tuft_kca" ionChannel="kca" condDensity="9.6 S_per_m2" erev="-80mV" segmentGroup="tuft_group" ion="k"/>
<channelDensityVShift id="nat_soma" ionChannel="nat" condDensity="402.172079 S_per_m2" erev="55 mV" segmentGroup="soma_group" ion="na" vShift="10mV"/>
<channelDensityVShift id="nat_hillock" ionChannel="nat" condDensity="8030.326751 S_per_m2" erev="55 mV" segmentGroup="hillock_group" ion="na" vShift="10mV"/>
<channelDensityVShift id="nat_iseg" ionChannel="nat" condDensity="17591.201145 S_per_m2" erev="55 mV" segmentGroup="iseg_group" ion="na" vShift="4.017831 mV"/>
<channelDensityVShift id="nat_tuft" ionChannel="nat" condDensity="11.555568 S_per_m2" erev="55 mV" segmentGroup="tuft_group" ion="na" vShift="10 mV"/>
<channelDensityVShift id="tuft_sca" ionChannel="sca" condDensity="3.86 S_per_m2" erev="140 mV" segmentGroup="tuft_group" ion="ca" vShift="3.79 mV"/>
<channelDensityNonUniform id="apicaltree_g_kfast" ionChannel="kfast" erev="-80 mV" ion="k">
<variableParameter parameter="condDensity" segmentGroup="apicaltree_list">
<inhomogeneousValue inhomogeneousParameter="PathLengthOver_apicaltree_list" value="41.35183*exp(-p/91.798929)"/>
</variableParameter>
</channelDensityNonUniform>
<channelDensityNonUniform id="apicaltree_g_kslow" ionChannel="kslow" erev="-80mV" ion="k">
<variableParameter parameter="condDensity" segmentGroup="apicaltree_list">
<inhomogeneousValue inhomogeneousParameter="PathLengthOver_apicaltree_list" value="264.78782*exp(-p/75.607992)"/>
</variableParameter>
</channelDensityNonUniform>
<channelDensityNonUniform id="apical_g_nat" ionChannel="nat" erev="55 mV" ion="na">
<variableParameter parameter="condDensity" segmentGroup="apical_group">
<inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical_group" value="-0.781233022*p + 402.172079"/>
</variableParameter>
</channelDensityNonUniform>
<channelDensityNonUniform id="apical_g_ih" ionChannel="ih" erev="-47 mV" ion="hcn">
<variableParameter parameter="condDensity" segmentGroup="apical_group">
<inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical_group" value="0.030533276*p"/>
</variableParameter>
</channelDensityNonUniform>
<spikeThresh value="-20mV"/>
<specificCapacitance value="2.336857 uF_per_cm2" segmentGroup="axosomatic_list"/>
<specificCapacitance value="1.1684285 uF_per_cm2" segmentGroup="apicaltree_list"/>
<initMembPotential value="-67mV"/>
</membraneProperties>
<intracellularProperties>
<species id="ca" concentrationModel="cad" ion="ca" initialConcentration="100e-6 mM" initialExtConcentration="2 mM" segmentGroup="tuft_group"/>
<resistivity value="0.082 kohm_cm" segmentGroup="soma_group"/>
<resistivity value="0.082 kohm_cm" segmentGroup="axon_group"/>
<resistivity value="0.734 kohm_cm" segmentGroup="basal_group"/>
<resistivity value="0.527 kohm_cm" segmentGroup="tuft_group"/>
<resistivity value="0.35847 kohm_cm" segmentGroup="apical_group"/>
</intracellularProperties>
</biophysicalProperties>
</cell>
</neuroml>