rallpack1
rallpack2
rallpack3
wcspikes
ralpack2-dev
soma-spikes-stochastic
soma-spikes-continuous
multirec
smartrec
vcsteps
cianmar30
p1-f1-mean-variance
mean-variance
p1-f2-rp1-det
p1-f2-rp2-det
p1-f2-rp3-det
p1-f2-rp1-stoch
p1-f2-rp2-stoch
p1-f2-rp3-stoch
cwvclamp
p1-f3-1c-det
p1-f3-1a-det
p1-f3-1a-stoch
chowwhite
rallpack3-stoch
rallpack1-IE
rallpack2-IE
migliore-devel
ralpack-dev
mean-var-iv
mean-variance-iv
mean-variance-iv-stoch
migliore-1a
migliore-1c
mean-variance-iv-det
step-onset
step-onset-avg
stimtest
mainen

p1-f2-rp3-det (run.xml)

Cable with HH sodium and potassium channels, different timesteps

Uniform unbranched cable with Hodgkin-Huxley sodium and potassium channels showing a prpoagating action potential. The task specification and reference results come from Upi Bhalla's 1992 Rallpack distribution, part of which is included below. The rest in the file README.upi.

The model produces three graphs showing the reference data computed by Neuron (green) and Genesis (orange) and calculated curves in other colors according to the timestep used: magenta : 1ms, cyan : 20us, blue : 1us. The only difference between the graphs are the axis ranges: they all show the same data. The reference data was computed with 1us timesteps.

If the system performs correctly, the blue line (1us timestep) and reference green and orange should be almost coincident at the beginning and differ by less than 0.2ms after 250ms.

The magenta and cyan lines show how increasing the timestep makes very little change to the spike shape, but changes the period slightly such that by the end of the calculation the longer timestep calculation has spikes a few milliseconds behind. This is a normal feature of the implicit euler method arising from the use of forward differencing for the time derivative.

Total CPU time 15.98 seconds; at 21:34:55 Tue 28 Aug 2007

CompartmentsStochastic
channels / cpmts
Continuous
channels / cpmts
time/mstimeStepCPU Time / s
10020 / 0245043 / 1002250.010 8.80
10020 / 0245045 / 1002250.020 4.42
10020 / 0245044 / 1002250.050 1.82
10020 / 0245044 / 1002250.0100 0.944

Predefined views

whole

start

end

All files

ModelPreprocessedOutupt dataReference data etc
run.xml
cell.xml
membrane.xml
environment.xml
recording.xml
leak.xml
HH_Na.xml
HH_K.xml
summary.xml
view.xml
stoch-membrane.xml
stoch-leak.xml
ts-20-fdata.txt
ts-50-fdata.txt
ts-100-fdata.txt
ts-200-fdata.txt
ts-500-fdata.txt
ts-10-fdata.txt
ts-20-f.dat
ts-20-f.txt
ts-50-f.dat
ts-50-f.txt
ts-100-f.dat
ts-100-f.txt
ts-200-f.dat
ts-200-f.txt
ts-500-f.dat
ts-500-f.txt
ref_axon_0_neuron.txt
ref_axon_x_neuron.txt
ts-10-f.dat
ts-10-f.txt
README
README.upi
p1-f2-rp3-det.jar

Model

Archive file of the complete model: p1-f2-rp3-det.jar

run.xml

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

	<info>Cable with HH sodium and potassium channels, different timesteps</info>

	<RunSet vary="timeStep" values="[10, 20, 50, 100]us"
		filepattern="ts-$.txt"/>


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

		<Line file="ref_axon_0_neuron.txt" color="white" width="1" rescale="[1000, 1000.]"/>
		<Line file="ref_axon_x_neuron.txt" color="white" width="1" rescale="[1000, 1000.]"/>


		<LineSet file="ts-10-f.txt" color="red"/>
		<LineSet file="ts-20-f.txt" color="blue"/>
		<LineSet file="ts-50-f.txt" color="cyan"/>
	    <LineSet file="ts-100-f.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 at="p1" lineColor="blue"/>

</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>

stoch-membrane.xml

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

 	 <ChannelPopulation id="leakpop" channel="stoch-leak" density="0.0357143per_um2"/>

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

</CellProperties>

stoch-leak.xml

<KSChannel id="stoch-leak" gSingle="10pS" permeantIon="K">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>