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pgleesonpgleeson
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Restructure cell
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‎NeuroML2/L23_cADpyr.cell.nml‎

Lines changed: 20 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -7046,35 +7046,47 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
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</morphology>
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<biophysicalProperties id="biophys">
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<membraneProperties>
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<channelDensity id="all_g_pas" ionChannel="pas" condDensity="3e-5 S_per_cm2" erev="-75 mV" ion="non_specific"/>
7050-
<channelDensity id="basal_gIhbar_Ih" ionChannel="Ih" condDensity="8e-05 S_per_cm2" erev="-45.0 mV" segmentGroup="basal" ion="hcn"/>
7051+
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<channelDensity id="apical_gNaTs2_tbar_NaTs2_t" ionChannel="NaTs2_t" condDensity="0.012009 S_per_cm2" erev="50.0 mV" segmentGroup="apical" ion="na"/>
7053+
<channelDensity id="axonal_gNaTa_tbar_NaTa_t" ionChannel="NaTa_t" condDensity="3.429725 S_per_cm2" erev="50.0 mV" segmentGroup="axonal" ion="na"/>
7054+
<channelDensity id="axonal_gNap_Et2bar_Nap_Et2" ionChannel="Nap_Et2" condDensity="0.009803 S_per_cm2" erev="50.0 mV" segmentGroup="axonal" ion="na"/>
7055+
<channelDensity id="somatic_gNaTs2_tbar_NaTs2_t" ionChannel="NaTs2_t" condDensity="0.926705 S_per_cm2" erev="50.0 mV" segmentGroup="somatic" ion="na"/>
7056+
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<channelDensity id="apical_gSKv3_1bar_SKv3_1" ionChannel="SKv3_1" condDensity="0.000513 S_per_cm2" erev="-85.0 mV" segmentGroup="apical" ion="k"/>
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<channelDensity id="apical_gImbar_Im" ionChannel="Im" condDensity="0.00074 S_per_cm2" erev="-85.0 mV" segmentGroup="apical" ion="k"/>
7054-
<channelDensity id="axonal_gNaTa_tbar_NaTa_t" ionChannel="NaTa_t" condDensity="3.429725 S_per_cm2" erev="50.0 mV" segmentGroup="axonal" ion="na"/>
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<channelDensity id="axonal_gK_Tstbar_K_Tst" ionChannel="K_Tst" condDensity="0.001035 S_per_cm2" erev="-85.0 mV" segmentGroup="axonal" ion="k"/>
7056-
<channelDensity id="axonal_gNap_Et2bar_Nap_Et2" ionChannel="Nap_Et2" condDensity="0.009803 S_per_cm2" erev="50.0 mV" segmentGroup="axonal" ion="na"/>
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<channelDensity id="axonal_gSK_E2bar_SK_E2" ionChannel="SK_E2" condDensity="0.008085 S_per_cm2" erev="-85.0 mV" segmentGroup="axonal" ion="k"/>
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<channelDensity id="axonal_gK_Pstbar_K_Pst" ionChannel="K_Pst" condDensity="0.959296 S_per_cm2" erev="-85.0 mV" segmentGroup="axonal" ion="k"/>
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<channelDensity id="axonal_gSKv3_1bar_SKv3_1" ionChannel="SKv3_1" condDensity="0.094971 S_per_cm2" erev="-85.0 mV" segmentGroup="axonal" ion="k"/>
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<channelDensity id="somatic_gSKv3_1bar_SKv3_1" ionChannel="SKv3_1" condDensity="0.102517 S_per_cm2" erev="-85.0 mV" segmentGroup="somatic" ion="k"/>
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<channelDensity id="somatic_gSK_E2bar_SK_E2" ionChannel="SK_E2" condDensity="0.099433 S_per_cm2" erev="-85.0 mV" segmentGroup="somatic" ion="k"/>
7062-
<channelDensity id="somatic_gNaTs2_tbar_NaTs2_t" ionChannel="NaTs2_t" condDensity="0.926705 S_per_cm2" erev="50.0 mV" segmentGroup="somatic" ion="na"/>
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<channelDensity id="somatic_gIhbar_Ih" ionChannel="Ih" condDensity="8e-05 S_per_cm2" erev="-45.0 mV" segmentGroup="somatic" ion="hcn"/>
7064-
<channelDensityNernst id="axonal_gCa_HVAbar_Ca_HVA" ionChannel="Ca_HVA" condDensity="0.000306 S_per_cm2" segmentGroup="axonal" ion="ca"/>
7065-
<channelDensityNernst id="axonal_gCa_LVAstbar_Ca_LVAst" ionChannel="Ca_LVAst" condDensity="5e-05 S_per_cm2" segmentGroup="axonal" ion="ca"/>
7066-
<channelDensityNernst id="somatic_gCa_HVAbar_Ca_HVA" ionChannel="Ca_HVA" condDensity="0.000374 S_per_cm2" segmentGroup="somatic" ion="ca"/>
7067-
<channelDensityNernst id="somatic_gCa_LVAstbar_Ca_LVAst" ionChannel="Ca_LVAst" condDensity="0.000778 S_per_cm2" segmentGroup="somatic" ion="ca"/>
7069+
<channelDensity id="basal_gIhbar_Ih" ionChannel="Ih" condDensity="8e-05 S_per_cm2" erev="-45.0 mV" segmentGroup="basal" ion="hcn"/>
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<channelDensityNonUniform id="apical_gIhbar_Ih" ionChannel="Ih" erev="-45.0 mV" ion="hcn">
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<variableParameter parameter="condDensity" segmentGroup="apical">
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<inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003100))*0.000080)"/>
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</variableParameter>
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</channelDensityNonUniform>
7075+
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<channelDensityNernst id="axonal_gCa_HVAbar_Ca_HVA" ionChannel="Ca_HVA" condDensity="0.000306 S_per_cm2" segmentGroup="axonal" ion="ca"/>
7078+
<channelDensityNernst id="axonal_gCa_LVAstbar_Ca_LVAst" ionChannel="Ca_LVAst" condDensity="5e-05 S_per_cm2" segmentGroup="axonal" ion="ca"/>
7079+
<channelDensityNernst id="somatic_gCa_HVAbar_Ca_HVA" ionChannel="Ca_HVA" condDensity="0.000374 S_per_cm2" segmentGroup="somatic" ion="ca"/>
7080+
<channelDensityNernst id="somatic_gCa_LVAstbar_Ca_LVAst" ionChannel="Ca_LVAst" condDensity="0.000778 S_per_cm2" segmentGroup="somatic" ion="ca"/>
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<specificCapacitance value="2 uF_per_cm2" segmentGroup="basal"/>
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<specificCapacitance value="2 uF_per_cm2" segmentGroup="apical"/>
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<specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
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<specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
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<initMembPotential value="-80 mV"/>
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</membraneProperties>
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<intracellularProperties>
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<species segmentGroup="axonal" id="ca" concentrationModel="CaDynamics_E2_NML2__cADpyr_229_axonal" ion="ca" initialConcentration="5.0E-11 mol_per_cm3" initialExtConcentration="2.0E-6 mol_per_cm3"/>

‎NeuroML2/osbSessions/15.html‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,18 @@
11
<div>
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3-
<p><strong>Changing the conductance densities</strong></p>
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<p><strong>Changing the conductance densities and passive properties of the cell</strong></p>
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<p>Try changing the conductance densities of some of the ion channels and other cellular properties below. Some scenarios to try:</p>
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<p><strong>&nbsp;> Remove the high transient Na<sup>+</sup> conductance on the axon</strong> <br/>
9-
Setting this value to 0 should lead to reduced firing frequency. However there is still a persistent Na<sup>+</sup> conductance on the axon and so a gradual depolarisation leading to spiking...</p>
9+
Setting this value to 0 should lead to reduced firing frequency. However, there is still a persistent Na<sup>+</sup> conductance on the axon and so a gradual depolarisation leading to spiking...</p>
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<p><strong>&nbsp;> Remove the persistent Na<sup>+</sup> conductance on the axon also</strong> <br/>
12-
This removes all spiking in the cell</p>
12+
This removes all spiking activity in the cell</p>
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1414
<p><strong>&nbsp;> Change the axial resistance of the cytoplasm</strong> <br/>
15-
Increasing this (e.g. to 100 Ohm cm) will confine spiking to axon/soma and suppress spread to rest of cell</p>
15+
Increasing this (e.g. to 1000 Ohm cm) will confine spiking to axon/soma and suppress spread to rest of cell; decreasing it (e.g. to 10 Ohm cm) will lead to the cell being almost isopotential.</p>
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<div class="tutorialForm center">
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