PSICS Results for run.xml

cell-loc (run.xml)

Current clamp stimulation profile read from a file, varying the stimulation scale factor

Total CPU time 0.9400 seconds; at 10:35:24 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timestep/ms	p2:sequenceIndex	CPU Time / s
355	0 / 0	0 / 0	0 / 0	250.0	0.05	0	0.190
355	0 / 0	0 / 0	0 / 0	250.0	0.05	2	0.190
355	0 / 0	0 / 0	0 / 0	250.0	0.05	4	0.190
355	0 / 0	0 / 0	0 / 0	250.0	0.05	6	0.190
355	0 / 0	0 / 0	0 / 0	250.0	0.05	8	0.180

Morphology: null

Predefined views

whole

enlarged

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml membrane.xml environment.xml recording.xml	out-0.ppp out-2.ppp out-4.ppp out-6.ppp out-8.ppp	log.txt out-0.sum out-2.sum out-4.sum out-6.sum out-8.sum out-0.dat out-0.txt out-2.dat out-2.txt out-4.dat out-4.txt out-6.dat out-6.txt out-8.dat out-8.txt	stim1.txt NM1.swc out-0.morph out-2.morph out-4.morph out-6.morph out-8.morph

Model

Archive file of the complete model: cell-loc.jar

run.xml

<PSICSRun timeStep="0.05ms" runTime="250ms" startPotential="-65mV"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="0">
	<MorphologySource format="swc" file="NM1.swc"/>

	<StructureDiscretization baseElementSize="25um"/>


	<RunSet vary="p2:sequenceIndex" values="[0, 2, 4, 6, 8]"
		filepattern="out-$"/>

	<info>Current clamp stimulation profile read from a file, varying the stimulation scale factor</info>


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

		<LineSet file="out-0.txt" color="red"/>
		<LineSet file="out-2.txt" color="blue"/>
		<LineSet file="out-4.txt" color="yellow"/>
		<LineSet file="out-6.txt" color="pink"/>
		<LineSet file="out-8.txt" color="orange"/>

		 <View id="whole" xmin="-10." xmax="50." ymin="-100." ymax="80."/>
		  <View id="enlarged" xmin="-10." xmax="50." ymin="-70." ymax="-50."/>
		</LineGraph>
	</ViewConfig>


</PSICSRun>

membrane.xml

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



</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="Na" name="Sodium" reversalPotential="40mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-80mV"/>
</CellEnvironment>

recording.xml

<Access id="recording">

	<CellLocation id="p0" path="10" rankBy="radius" sequenceFraction="1."/>
	<CellLocation id="p1" path="120" rankBy="radius" sequenceFraction="0.5"/>
	<CellLocation id="p2" path="240" rankBy="radius" sequenceIndex="1"/>


	<CurrentClamp location="p2" lineColor="red" hold="0.0nA">
	     <TimeSeries id="stim" file="stim1.txt" timeUnit="1ms" valueUnit="0.01nA"
	     	scaleFactor="10.0"/>
	</CurrentClamp>

    <VoltageRecorder location="p1" lineColor="blue"/>

	<VoltageRecorder location="p0" lineColor="blue"/>



</Access>