Index
rallpack1
rallpack2
rallpack3
wcspikes
ralpack2-dev
soma-spikes-stochastic
soma-spikes-continuous
multirec
smartrec
vcsteps
cianmar30
p1-f1-mean-variance
mean-variance
p1-f2-rp1-det
p1-f2-rp2-det
p1-f2-rp3-det
p1-f2-rp1-stoch
p1-f2-rp2-stoch
p1-f2-rp3-stoch
cwvclamp
p1-f3-1c-det
p1-f3-1a-det
p1-f3-1a-stoch
chowwhite
rallpack3-stoch
rallpack1-IE
rallpack2-IE
migliore-devel
ralpack-dev
mean-var-iv
mean-variance-iv
mean-variance-iv-stoch
migliore-1a
migliore-1c
mean-variance-iv-det
step-onset
step-onset-avg
stimtest
mainen

p1-f3-1c-det (run1c.xml)

Migliore et al CA1 pyramidal cell

Total CPU time 0.3080 seconds; at 11:52:42 Fri 3 Aug 2007

CompartmentsStochastic
channels / cpmts		Continuous
channels / cpmts		CPU Time / s
3250 / 0883556 / 325 0.308

Predefined views

whole

first

later

All files

ModelPreprocessedOutupt dataReference data etc
run1c.xml
morph.xml
membrane.xml
environment.xml
leak.xml
Nax.xml
Kdrca1.xml
Kaprox.xml
Kadist.xml
summary.xml
view.xml
recording-c.xml
ns-leak.xml
 psics-out-fdata.txt
 psics-out-f.dat
psics-out-f.txt

Model

run1c.xml

<PSICSRun   lib="." timeStep="0.1ms" runTime="200ms" startPotential="-65mV"
	morphology="morph"
	environment="environment"
	properties="membrane"
	access="recording-c"
	stochThreshold="0">
	<StructureDiscretization baseElementSize="10um"/>

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

	<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="200." ymin="-80." ymax="20."/>

		<View id="first" xmin="5" xmax="20." ymin="-80." ymax="20."/>

		<View id="later" xmin="125" xmax="145." 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="0.006per_um2" distribution="prox"/>
	<ChannelPopulation channel="ns-leak" density="0.006per_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>

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="-63.64mV" gamma="0.443"
                tau="6.17ms" 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="4.47e" 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="-63.64mV" gamma="0.443" tau="3.17ms"
    		tauMinFwd="3.17ms" tauMinRev="1.8ms"/>
 </KSComplex>



 </KSChannel>

recording-c.xml

<Access id="recording-c">

	<CurrentClamp at="2" hold="0nA">
		<CurrentPulse start="10ms" duration="1ms" to="2nA"/>
		<CurrentPulse start="50ms" duration="1ms" to="2nA"/>
		<CurrentPulse start="90ms" duration="1ms" to="2nA"/>
		<CurrentPulse start="130ms" duration="1ms" to="2nA"/>
		<CurrentPulse start="170ms" duration="1ms" to="2nA"/>
	</CurrentClamp>


	<ConductanceClamp at="81" potential="0mV">
		<ConductancePulse start="70ms" duration="8ms" to="3nS" repeatAfter="10ms"/>
	</ConductanceClamp>


	<VoltageRecorder at="80"/>

</Access>

ns-leak.xml

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