PSICS Results for runiv.xml

ivconv (runiv.xml)

Continuous I-V curve for testing stochastic convergence.

Total CPU time 0.01000 seconds; at 11:43:24 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	CPU Time / s
1	0 / 0	201 / 1	0 / 0	0.0100

Morphology: cell

Predefined views

16

All files

Model	Preprocessed	Outupt data	Reference data etc
runiv.xml cell.xml membrane.xml environment.xml recording-iv.xml na1.xml runiv-mstoch.xml	psics-out.ppp	log.txt psics-out.sum psics-out.dat psics-out.txt	ref_continuous.txt ref-continuous.txt

Model

Archive file of the complete model: ivconv.jar

runiv.xml

<PSICSRun timeStep="0.01ms" runTime="15ms" startPotential="-80mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording-iv"
	stochThreshold="0">

	<StructureDiscretization baseElementSize="3um"/>



<About>
  	Continuous I-V curve for testing stochastic convergence.
 </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="psics-out.txt" color="green"/>
		 <View id="16" xmin="0." xmax="40." ymin="-500." ymax="20."/>
		</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="1.e-8uF_per_um2">

	<ChannelPopulation id="napop" channel="na1" density="16per_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>

runiv-mstoch.xml

<PSICSRun timeStep="0.01ms" runTime="15ms" startPotential="-80mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording-iv"
	stochThreshold="1000"
	repeats="100000">

	<StructureDiscretization baseElementSize="3um"/>



<About>
  	Continuous I-V curve for testing stochastic convergence.
 </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="psics-out.txt" color="blue" maxshow="100"/>
		 	 
		 
		
		 <Line file="ref-continuous.txt" color="white" width="1"/>
		
		<LineSet file="psics-out.txt" color="green" function="mean">
		 		 <DataComparison file="ref-continuous.txt" line="0"/>
		 </LineSet>
		 
		 
		 
		 <View id="16" xmin="0." xmax="40." ymin="-500." ymax="20."/>
		 
		 <View id="zoom" xmin="5" xmax="6" ymin="-440." ymax="-340."/>
		 
		  <View id="start" xmin="0" xmax="5" ymin="-10." ymax="1."/>
		</LineGraph>
	</ViewConfig>
</PSICSRun>