PSICS Results for run.xml

multirec (run.xml)

Different ways of positioning recorders along the cell between defined points

Total CPU time 1.090 seconds; at 12:36:12 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timeStep	CPU Time / s
1001	0 / 0	245167 / 1001	78579 / 1001	250.0	100	1.09

Morphology: cell

Predefined views

whole

start

end

All files

Model	Preprocessed	Outupt data	Reference data etc
run.xml cell.xml membrane.xml environment.xml recording.xml leak.xml HH_Na.xml HH_K.xml	ts-100.ppp	log.txt ts-100.sum ts-100.dat ts-100.txt

Model

Archive file of the complete model: multirec.jar

run.xml

<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	stochThreshold="0">
	<StructureDiscretization baseElementSize="1um"/>

	<info>Different ways of positioning recorders along the cell between defined points</info>

	<RunSet vary="timeStep" values="[100]us"
		filepattern="ts-$"/>


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

		 <LineSet file="ts-100.txt" color="green"/>

		<View id="whole" xmin="-10." xmax="260." ymin="-100." ymax="80."/>
		<View id="start"   xmin="0." xmax="30." ymin="-100." ymax="80."/>
		 <View id="end"   xmin="210." xmax="255." ymin="-100." ymax="80."/>

		</LineGraph>
	</ViewConfig>

</PSICSRun>

cell.xml

<CellMorphology id="cell">
	<Point id="p0" x="0" y="0" z="0" r="0.5"/>
	<Point parent="p0" id="p1" x="1000" y="0" z = "0" r="0.5"/>
</CellMorphology>

membrane.xml

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

	<ChannelPopulation channel="leak" density="25per_um2"/>

	<ChannelPopulation channel="HH_Na" density="60per_um2"/>
    <ChannelPopulation channel="HH_K" density="18per_um2"/>

</CellProperties>

environment.xml

<CellEnvironment id="environment">
	<Ion id="LEAK" name="Non-specific leak" reversalPotential="-65mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-77mV"/>
	<Ion id="Na" name="Sodium" reversalPotential="50mV"/>
</CellEnvironment>

recording.xml

<Access id="recording">

    <CurrentClamp at="p0" lineColor="red" hold="0.1nA">

    </CurrentClamp>
    

    <VoltageRecorder distance="100um"/>
    <VoltageRecorder distance="200um" towards="p1"/>
    <VoltageRecorder distance="300um"/>
    <VoltageRecorder distance="-100um" from="p1"/>
    <VoltageRecorder at="p1"/>

</Access>

leak.xml

<KSChannel id="leak" gSingle="0.01pS" permeantIon="LEAK">
	<OpenState id="o1"/>
</KSChannel>

HH_Na.xml

<KSChannel id="HH_Na" permeantIon="Na" gSingle="20pS">

	<KSComplex id="m" instances="3">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="1.per_ms" midpoint ="-40.mV" scale="10mV"/>
		<ExpTransition from="o" to = "c" rate="4.per_ms" midpoint="-65.mV" scale="-18mV"/>
	</KSComplex>


	<KSComplex id="h">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpTransition from="c" to="o" rate="0.07per_ms" midpoint="-65.mV" scale="-20.mV"/>
		<SigmoidTransition from="o" to="c" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
	</KSComplex>

</KSChannel>

HH_K.xml

<KSChannel id="HH_K" permeantIon="K" gSingle="20pS">

	<KSComplex id="n" instances="4">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.1per_ms" midpoint ="-55.mV" scale="10mV"/>
		<ExpTransition from="o" to = "c" rate="0.125per_ms" midpoint="-65.mV" scale="-80mV"/>
	</KSComplex>


</KSChannel>