p18
cell-loc
synapses
minor
params
smalldt
onsurface
migliore-1a
rallpack3
cwvclamp
vcsteps
rallpack1
smartrec
ivconv
ivconvm
mean-variance-iv-stoch
stochdet
channel-functions
stimtest
functest
migliore-pass
psd
cianmar30
mean-variance
rallpack2
rallpack3-stoch
rallpack3-stoch2
chowwhite
multirec
mainen
soma-spikes-stochastic
soma-spikes-continuous
p1-f1-mean-variance
rallpack1-IE
rallpack2-IE
singlecpt
synstim
resonance
manychannels

rallpack3-stoch2 (run-stoch2.xml)

Cable with HH sodium and potassium channels, 20pS single channel conductance

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 121.4 seconds; at 12:35:06 Thu 24 Sep 2009

CompartmentsStochastic
channels / cpmts
Continuous
channels / cpmts
Non Gated
channels / cpmts
time/mstimeStepCPU Time / s
1001245167 / 10010 / 078579 / 1001250.020 84.9
1001245167 / 10010 / 078579 / 1001250.050 36.5

Morphology: cell

 

 

Predefined views

whole

start

end

All files

ModelPreprocessedOutupt dataReference data etc
run-stoch2.xml
cell.xml
membrane2.xml
environment.xml
recording.xml
leak.xml
HH_Na2.xml
HH_K2.xml
ts-20.ppp
ts-50.ppp
log.txt
ts-20.sum
ts-50.sum
ts-20.dat
ts-20.txt
ts-50.dat
ts-50.txt
ref_axon_0_neuron.txt
ref_axon_x_neuron.txt
README
README.upi

Model

Archive file of the complete model: rallpack3-stoch2.jar

run-stoch2.xml

<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane2"
	access="recording"
	stochThreshold="10000">
	<StructureDiscretization baseElementSize="1um"/>

	<info>Cable with HH sodium and potassium channels, 20pS single channel conductance</info>

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


	<ViewConfig>
		<LineGraph width="800" 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-50.txt" color="blue"/>
		<LineSet file="ts-20.txt" color="red"/>


		<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>

membrane2.xml

<CellProperties id="membrane2"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">

	<ChannelPopulation channel="leak" density="25per_um2"/>
 
	<ChannelPopulation channel="HH_Na2" density="60per_um2"/>
    <ChannelPopulation channel="HH_K2" 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_Na2.xml

<KSChannel id="HH_Na2" 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_K2.xml

<KSChannel id="HH_K2" 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>