p1-f3-1a-stoch (run1a-stoch.xml)

Migliore et al CA1 pyramidal cell

Model corresponding to figure 1a with a steady current injection at the soma and recording from two points on the apical dendrite, 200um and 400um from the soma. It shows some backpropagation to 200um but very little at 400um.

This is not an exact reimplementation of the Migliore et al model but rather a nearby equivalent in PSICS using only the standard channel transition equation. Slow inactivation of the sodium channel has not been modelled as an independent gate that only partially closes (closing to 20 % in the soma and to 50 % in the dendrites) since the kinetics of this process do not appear to affect the model. Instead, the inactivated dendritic channels are simply left out of the model by providing two populations: one population, at 50 % of maximum, that covers all active compartments and another, overlapping population, just for the soma.

Total CPU time 4.276 seconds; at 10:35:45 Fri 3 Aug 2007

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	CPU Time / s
325	883556 / 325	0 / 0	4.28

Predefined views

whole

first

All files

Model	Preprocessed	Outupt data	Reference data etc
run1a-stoch.xml morph.xml membrane.xml environment.xml recording-a.xml leak.xml Nax.xml Kdrca1.xml Kaprox.xml Kadist.xml summary.xml view.xml ns-leak.xml	psics-out-fdata.txt	psics-out-f.dat psics-out-f.txt

Model

run1a-stoch.xml

<PSICSRun   lib="." timeStep="0.1ms" runTime="120ms" startPotential="-65mV"
	morphology="morph"
	environment="environment"
	properties="membrane"
	access="recording-a"
	stochThreshold="50000">
	<StructureDiscretization baseElementSize="10um"/>

	<info>Migliore et al CA1 pyramidal cell</info>

<About>
		Model corresponding to figure 1a with a steady current injection at the soma
		and recording from two points on the apical dendrite, 200um and 400um from the soma.
		It shows some backpropagation to 200um but very little at 400um.
	</About>

	<About>
		This is not an exact reimplementation of the Migliore et al model but rather a nearby
		equivalent in PSICS using only the standard channel transition equation.
	    Slow inactivation of the sodium channel
	    has not been modelled as an independent gate that only partially closes
		(closing to 20% in the soma and to 50% in the dendrites) since the kinetics of this process do
		not appear to affect the model. Instead, the inactivated dendritic channels are simply left
		out of the model by providing two populations: one population, at 50% of maximum,
		that covers all active compartments and another, overlapping population, just for the soma.
	</About>

	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="potential / mV"/>

	    <LineSet file="psics-out-f.txt" color="green"/>

		<View id="whole" xmin="-10." xmax="120." ymin="-80." ymax="20."/>

		<View id="first" xmin="15" xmax="30." ymin="-80." ymax="20."/>
		</LineGraph>
	</ViewConfig>
</PSICSRun>

morph.xml (truncated)

<!-- /tmp/cell.xml -->
<!-- XML file generated by NEURON 5.6 ModelViewer -->
<!-- Authors: Michael Hines and Sushil Kambampati -->
<!-- Yale University -->
<!-- Date: Tue Jul 31 11:15:50 BST 2007
 -->
<model>
<morphology xmlns="http://morphml.org/namespace">
  <setOfPoints>
  <point id="1" x="0" y="0" z="0" diam="3.4"/>
  <point id="2" x="0.25" y="0" z="0" diam="3.4"/>
  <point id="3" x="0.5" y="0" z="0" diam="3.4"/>
  <point id="4" x="0.5" y="0" z="0" diam="3.4"/>
  <point id="5" x="0.55" y="0" z="0" diam="3.4"/>
  <point id="6" x="0.6" y="0" z="0" diam="3.4"/>
  <point id="7" x="0.6" y="0" z="0" diam="5.8"/>
  <point id="8" x="0.892617" y="0" z="0" diam="5.8"/>
  <point id="9" x="1.18523" y="0" z="0" diam="5.8"/>
  <point id="10" x="1.18523" y="0" z="0" diam="7.4"/>
  <point id="11" x="2.36643" y="0" z="0" diam="7.4"/>
  <point id="12" x="3.54763" y="0" z="0" diam="7.4"/>
  <point id="13" x="3.54763" y="0" z="0" diam="8.4"/>
  <point id="14" x="4.06309" y="0" z="0" diam="8.4"/>
  <point id="15" x="4.57855" y="0" z="0" diam="8.4"/>
  <point id="16" x="4.57855" y="0" z="0" diam="9"/>
  <point id="17" x="7.12341" y="0" z="0" diam="9"/>
  <point id="18" x="9.66828" y="0" z="0" diam="9"/>
  <point id="19" x="9.66828" y="0" z="0" diam="8.4"/>
  <point id="20" x="10.749" y="0" z="0" diam="8.4"/>
  <point id="21" x="11.8297" y="0" z="0" diam="8.4"/>
  <point id="22" x="11.8297" y="0" z="0" diam="7.4"/>
  <point id="23" x="12.5256" y="0" z="0" diam="7.4"/>
  <point id="24" x="13.2215" y="0" z="0" diam="7.4"/>
  <point id="25" x="13.2215" y="0" z="0" diam="7"/>
  <point id="26" x="13.5837" y="0" z="0" diam="7"/>
  <point id="27" x="13.946" y="0" z="0" diam="7"/>
  <point id="28" x="13.946" y="0" z="0" diam="6.8"/>
  <point id="29" x="14.4567" y="0" z="0" diam="6.8"/>
  <point id="30" x="14.9674" y="0" z="0" diam="6.8"/>
  <point id="31" x="14.9674" y="0" z="0" diam="5.8"/>
  <point id="32" x="15.3851" y="0" z="0" diam="5.8"/>
  <point id="33" x="15.8028" y="0" z="0" diam="5.8"/>
  <point id="34" x="15.8028" y="0" z="0" diam="4.8"/>
  <point id="35" x="16.1278" y="0" z="0" diam="4.8"/>
  <point id="36" x="16.4528" y="0" z="0" diam="4.8"/>
  <point id="37" x="16.4528" y="0" z="0" diam="4.2"/>
  <point id="38" x="17.4266" y="0" z="0" diam="4.2"/>
  <point id="39" x="18.4003" y="0" z="0" diam="4.2"/>
  <point id="40" x="18.4003" y="0" z="0" diam="3.8"/>
  <point id="41" x="19.7579" y="0" z="0" diam="3.8"/>
  <point id="42" x="21.1156" y="0" z="0" diam="3.8"/>
  <point id="43" x="21.1156" y="0" z="0" diam="3.6"/>
  <point id="44" x="23.8164" y="0" z="0" diam="3.6"/>
  <point id="45" x="26.5173" y="0" z="0" diam="3.6"/>
  <point id="46" x="26.5173" y="0" z="0" diam="3"/>
  <point id="47" x="28.4558" y="0" z="0" diam="3"/>
  <point id="48" x="30.3943" y="0" z="0" diam="3"/>
  <point id="49" x="30.3943" y="0" z="0" diam="3"/>
  <point id="50" x="32.3851" y="0.841732" z="0" diam="3"/>
  <point id="51" x="34.376" y="1.68346" z="0" diam="3"/>

 - and 2082 more lines -

membrane.xml

<CellProperties id="membrane"
      cytoplasmResistivity="150ohm_cm"
      membraneCapacitance="1uF_per_cm2">

	<ChannelPopulation channel="leak" density="0.00per_um2"/>

	<ChannelPopulation channel="Nax" density="7per_um2" distribution="main"/>
	<ChannelPopulation channel="Nax" density="12per_um2" distribution="soma"/>

    <ChannelPopulation channel="Kdrca1" density="3.3per_um2"/>

    <ChannelPopulation channel="Kaprox" density="16per_um2" distribution="prox"/>
   	<ChannelPopulation channel="Kadist" density="16per_um2" distribution="dist"/>

	<ChannelPopulation channel="ns-leak" density="0.004per_um2" distribution="prox"/>
	<ChannelPopulation channel="ns-leak" density="0.004per_um2" distribution="dist"/>


	<DistributionRule id="main">
    	<RegionMask action="include" where="diameter .gt. 0.5"/>
    </DistributionRule>


	<DistributionRule id="soma">
		<RegionMask action="include" where="path .lt. 40"/>
	</DistributionRule>


	<DistributionRule id="prox" expression="(1 + path / 100)">
		<RegionMask action="exclude" where="path .gt. 100"/>
	</DistributionRule>

	<DistributionRule id="dist" expression="(1 + path / 100)">
		<RegionMask action="exclude" where="path .lt. 100"/>
		<RegionMask action="exclude" where="path .gt. 600"/>
	</DistributionRule>

</CellProperties>

environment.xml

<CellEnvironment id="environment">
    <Ion id="NSCAT" name="Non-specific cationic leak" reversalPotential="-40mV"/>
	<Ion id="LEAK" name="Non-specific leak" reversalPotential="-65mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-90mV"/>
	<Ion id="Na" name="Sodium" reversalPotential="55mV"/>
</CellEnvironment>

recording-a.xml

<Access id="recording-a">

	<CurrentClamp at="2" hold="0.23nA">

	</CurrentClamp>

	<VoltageRecorder at="80"/>

	<VoltageRecorder at="150"/>

</Access>

leak.xml

<KSChannel id="leak" gSingle="30pS" permeantIon="LEAK">
	<OpenState id="o1"/>
</KSChannel>

Nax.xml

<KSChannel id="Nax" permeantIon="Na" gSingle="30pS">

  <KSComplex instances="3">
      <ClosedState id="c"/>
      <OpenState id="o"/>
 	  <VHalfTransition from="c" to="o" z="4.82e" vHalf="-35.08mV" gamma="0.49" tau="0.569ms"
 		tauMinFwd="0.0304ms" tauMinRev="0.1773ms"/>
 </KSComplex>


<KSComplex instances="1">
      <ClosedState id="c"/>
      <OpenState id="o"/>
        <VHalfTransition from="o" to="c" z="7.55e" vHalf="-46.40mV" gamma="0.6"
           tau="11.4ms" tauMinFwd="0.564ms" tauMinRev="1.42ms"/>
 </KSComplex>

 </KSChannel>

Kdrca1.xml

<KSChannel id="Kdrca1" permeantIon="K" gSingle="30pS">

<KSComplex instances="1">
      <ClosedState id="c"/>
      <OpenState id="o"/>
    <VHalfTransition from="c" to="o" z="2.70e" vHalf="13.00mV" gamma="0.700" tau="50ms"
           tauMinFwd="0.ms" tauMinRev="0.ms"/>
 </KSComplex>


 </KSChannel>

Kaprox.xml

<KSChannel id="Kaprox" permeantIon="K" gSingle="30pS">

	<KSComplex instances="1">
      <ClosedState id="c"/>
      <OpenState id="o"/>
       <VHalfTransition from="c" to="o" z="3.42e" vHalf="0.15mV" gamma="0.655" tau="2.52ms"
       			tauMinFwd="1.58ms" tauMinRev="0.0ms"/>

 </KSComplex>


<KSComplex instances="1">
      <OpenState id="o"/>
      <ClosedState id="c"/>
       <VHalfTransition from="o" to="c" z="5.64e" vHalf="-57.64mV" gamma="0.443"
                tau="3.17ms" tauMinFwd="3.17ms" tauMinRev="1.8ms"/>
 </KSComplex>



 </KSChannel>

Kadist.xml

<KSChannel id="Kadist" permeantIon="K" gSingle="30pS">

<KSComplex instances="1">
      <ClosedState id="c"/>
      <OpenState id="o"/>
    <VHalfTransition from="c" to="o" z="4.57e" vHalf="-13.43mV" gamma="0.673" tau="0.825ms"
         tauMinFwd="0.819ms" tauMinRev="0.153ms"/>
 </KSComplex>


<KSComplex instances="1">
      <OpenState id="o"/>
      <ClosedState id="c"/>
    <VHalfTransition from="o" to="c" z="5.64e" vHalf="-57.64mV" gamma="0.443" tau="3.17ms"
    		tauMinFwd="3.17ms" tauMinRev="1.8ms"/>
 </KSComplex>



 </KSChannel>

ns-leak.xml

<KSChannel id="ns-leak" gSingle="30pS" permeantIon="NSCAT">
	<OpenState id="o1"/>
</KSChannel>