PSICS Results for runiv.xml

mean-var-iv (runiv.xml)

I-V curves for the same model as is used for mean variance analysis.

Total CPU time 1.286 seconds; at 15:12:29 Tue 4 Sep 2007

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	time/ms	timestep/ms	napop:density	CPU Time / s
1	5 / 1	0 / 0	40.0	0.01	0.4	0.314
1	25 / 1	0 / 0	40.0	0.01	2	0.224
1	51 / 1	0 / 0	40.0	0.01	4	0.256
1	101 / 1	0 / 0	40.0	0.01	8	0.244
1	201 / 1	0 / 0	40.0	0.01	16	0.248

Predefined views

whole

All files

Model

Archive file of the complete model: mean-var-iv.jar

runiv.xml

<PSICSRun   lib="." timeStep="0.01ms" runTime="40ms" startPotential="-80mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording-iv"
	stochThreshold="1000">

	<StructureDiscretization baseElementSize="3um"/>

<RunSet vary="napop:density" values="[0.4, 2, 4, 8, 16]per_um2"
                filepattern="out-$.txt">
 		<CommandSet vary="vstep:to" values="[-60, -40, -30, -20, -10, 0, 10, 20, 30, 40]mV"/>
	</RunSet>



<About>
  	I-V curves for the same model as is used for mean variance analysis.
 </About>



	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>
		<LineSet file="out-0.4-f.txt" color="pink"/>
		 <View id="whole" xmin="0." xmax="40." ymin="-20." ymax="160."/>
		</LineGraph>
	</ViewConfig>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>
		<LineSet file="out-2-f.txt" color="red"/>
		 <View id="whole" xmin="0." xmax="40." ymin="-20." ymax="160."/>
		</LineGraph>
	</ViewConfig>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>
		<LineSet file="out-4-f.txt" color="orange"/>
		 <View id="whole" xmin="0." xmax="40." ymin="-20." ymax="160."/>
		</LineGraph>
	</ViewConfig>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>
		<LineSet file="out-8-f.txt" color="blue"/>
		 <View id="whole" xmin="0." xmax="40." ymin="-20." ymax="160."/>
		</LineGraph>
	</ViewConfig>


	<ViewConfig>
		<LineGraph width="500" height="400">
		<XAxis min="0" max="250" label="time / ms"/>
		<YAxis min="-80" max="60" label="current / nA"/>
		<LineSet file="out-16-f.txt" color="green"/>
		 <View id="whole" xmin="0." xmax="40." ymin="-20." ymax="160."/>
		</LineGraph>
	</ViewConfig>
</PSICSRun>

cell.xml

<CellMorphology id="cell">

    <Point id="p0" x="0" y="0" z="0" r="1."/>

</CellMorphology>

membrane.xml

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">

	<ChannelPopulation id="napop" channel="na1" density="12per_um2"/>


</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="80mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

recording-iv.xml

<Access id="recording-iv" saveInterval="0.01ms">

	<VoltageClamp at="p0" lineColor="red" hold="-80.0mV">
		<VoltagePulse id="vstep" start="5ms" to="0mV"
			      duration="20ms"/>

	</VoltageClamp>

</Access>

na1.xml

<KSChannel id="na1" gSingle="30pS" permeantIon="Na">
	<ClosedState id="c1"/>
	<OpenState id="o1"/>
	<ClosedState id="c2"/>

	<VHalfTransition from="c1" to="o1" vHalf = "-35mV" z="4.5e" gamma="0.8" tau="0.55ms" tauMin="0.1ms"/>

	<VHalfTransition from="o1" to="c2" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="12.0ms" tauMin="1.5ms"/>

</KSChannel>

view1.xml

<ViewConfig package="org.psics.model.display">
   <LineGraph width="500"
       height="400">
      <LineSet color="red"
          file="out-2-f.txt"
          width="0.0"
          maxshow="20"/>
      <xaxis min="0.0"
          max="250.0"
          label="time / ms"/>
      <yaxis min="-80.0"
          max="60.0"
          label="current / nA"/>
      <View xmin="0.0"
          xmax="40.0"
          ymin="-20.0"
          ymax="160.0"
          id="whole"/>
   </LineGraph>
</ViewConfig>

view2.xml

<ViewConfig package="org.psics.model.display">
   <LineGraph width="500"
       height="400">
      <LineSet color="orange"
          file="out-4-f.txt"
          width="0.0"
          maxshow="20"/>
      <xaxis min="0.0"
          max="250.0"
          label="time / ms"/>
      <yaxis min="-80.0"
          max="60.0"
          label="current / nA"/>
      <View xmin="0.0"
          xmax="40.0"
          ymin="-20.0"
          ymax="160.0"
          id="whole"/>
   </LineGraph>
</ViewConfig>

view3.xml

<ViewConfig package="org.psics.model.display">
   <LineGraph width="500"
       height="400">
      <LineSet color="blue"
          file="out-8-f.txt"
          width="0.0"
          maxshow="20"/>
      <xaxis min="0.0"
          max="250.0"
          label="time / ms"/>
      <yaxis min="-80.0"
          max="60.0"
          label="current / nA"/>
      <View xmin="0.0"
          xmax="40.0"
          ymin="-20.0"
          ymax="160.0"
          id="whole"/>
   </LineGraph>
</ViewConfig>

view4.xml

<ViewConfig package="org.psics.model.display">
   <LineGraph width="500"
       height="400">
      <LineSet color="green"
          file="out-16-f.txt"
          width="0.0"
          maxshow="20"/>
      <xaxis min="0.0"
          max="250.0"
          label="time / ms"/>
      <yaxis min="-80.0"
          max="60.0"
          label="current / nA"/>
      <View xmin="0.0"
          xmax="40.0"
          ymin="-20.0"
          ymax="160.0"
          id="whole"/>
   </LineGraph>
</ViewConfig>

Model	Preprocessed	Outupt data	Reference data etc
runiv.xml cell.xml membrane.xml environment.xml recording-iv.xml na1.xml summary.xml view.xml view1.xml view2.xml view3.xml view4.xml	out-0.4-fdata.txt out-2-fdata.txt out-4-fdata.txt out-8-fdata.txt out-16-fdata.txt	out-0.4-f.dat out-0.4-f.txt out-2-f.dat out-2-f.txt out-4-f.dat out-4-f.txt out-8-f.dat out-8-f.txt out-16-f.dat out-16-f.txt