pSICS - the Parallel Stochastic Ion Channel Simulator
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PSICS comes with a range of built-in models. They can be run with the command-line argument "-e" followed by the name of the model to run. Some of the examples are also part of standard test cases that are run with specific options such as "-v" to run the rallpack validation examples.

For each model there is a single page summary that is generated automatically when the model is run.

Model specification samples

The files included below come from the rallpack3 example folder and illustrate how the various components of a model are specified. The full structure allowed for each type of model component is in the formats reference.


<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" />


<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" />


<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" />



<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" />



<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 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" />



<Access id="recording">

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


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



<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" />

		<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." />


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