PSICS Results for runfunc.xml

functest (runfunc.xml)

test for channels with xml coded functions

Total CPU time 1.050 seconds; at 11:55:07 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	CPU Time / s
1	0 / 0	3396 / 1	0 / 0	1.05

Morphology: cmmorph

Predefined views

whole

first

All files

Model	Preprocessed	Outupt data	Reference data etc
runfunc.xml cmmorph.xml cmmembrane.xml environment.xml cmrec.xml stoch-leak.xml Na3-function-soma.xml Kdrca1.xml	psics-out.ppp	log.txt psics-out.sum psics-out.dat psics-out.txt

Model

Archive file of the complete model: functest.jar

runfunc.xml

<PSICSRun   timeStep="0.1ms" runTime="120ms" startPotential="-65mV"
	morphology="cmmorph"
	environment="environment"
	properties="cmmembrane"
	access="cmrec"
	stochThreshold="0">
	<StructureDiscretization baseElementSize="10um"/>

	<info>test for channels with xml coded functions</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.txt" color="green"/>

		<View id="whole" xmin="-10." xmax="120." ymin="-80." ymax="20."/>

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

cmmorph.xml

<CellMorphology id="cmmorph">

    <Point id="p0" x="0" y="0" z="0" r="3."/>

</CellMorphology>

cmmembrane.xml

<CellProperties id="cmmembrane"
      cytoplasmResistivity="150ohm_cm"
      membraneCapacitance="2uF_per_cm2">

	<ChannelPopulation channel="stoch-leak" density="0.03per_um2"/>

	<ChannelPopulation channel="Na3-function-soma" density="10per_um2"/>
    <ChannelPopulation channel="Kdrca1" density="20per_um2"/>



</CellProperties>

environment.xml

<CellEnvironment id="environment" temperature="34Celsius">
	<Ion id="K" name="Potassium" reversalPotential="-90mV"/>
	<Ion id="Na" name="Sodium" reversalPotential="55mV"/>
</CellEnvironment>

cmrec.xml

<Access id="cmrec">

	<CurrentClamp at="p0" hold="0nA">
		<CurrentPulse start="10ms" duration="2ms" to="0.05nA"/>
	</CurrentClamp>



</Access>

stoch-leak.xml

<KSChannel id="stoch-leak" gSingle="30pS" permeantIon="K">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>

Na3-function-soma.xml (truncated)

<KSChannel id="Na3-function-soma" permeantIon="Na" gSingle="30pS">
<Function name="explinear" args="v, th, a, q">
	<Sum name="vmth">
		<Val>v</Val>
		<Minus>
			<Val>th</Val>
		</Minus>
	</Sum>
	<Product name="full">
			<Val>a</Val>
			<Val>vmth</Val>
			<Reciprocol>
				<Sum>
					<Con>1</Con>
					<Minus>
						<Exp>
							<Product>
								<Con>-1</Con>
								<Val>vmth</Val>
								<Reciprocol>
									<Val>q</Val>
								</Reciprocol>
							</Product>
						</Exp>
					</Minus>
				</Sum>
			</Reciprocol>
		</Product>
		<Condition name="cond">
			<Lesser>
				<Con>1.e-6</Con>
			</Lesser>
			<Greater>
			<Sum>
				<Abs>
					<Val>vmth</Val>
				</Abs>
			</Sum>
			</Greater>
		</Condition>
	<Return>
		<Choose>
			<When test="cond">
				<Val>full</Val>
			</When>
			<Otherwise>
				<Product>
					<Val>a</Val>
					<Val>q</Val>
				</Product>
			</Otherwise>
		</Choose>
	</Return>
</Function>
<KSComplex instances="3">
      <ClosedState id="c"/>
      <OpenState id="o"/>
 	<TauInfTransition from="c" to="o" id="tr1">
 		<Constant name="q10">2</Constant>
 		<Constant name="tha">-30</Constant>

 - and 342 more lines -

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>