PSICS - stochastic cell and ion channel simulator

Examples

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.

rallpack1 Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
rallpack2 Regular branched cable with 9 levels of branching (512 terminals) varying timestep
rallpack3 Cable with HH sodium and potassium channels, different timesteps
wcspikes Cable with propagating spikes, varying discretization, stochastic
ralpack2-dev Regular branched cable with 9 levels of branching (512 terminals) varying timestep
soma-spikes-stochastic Cable with channels only for first 50 um, varying time step, stochatic
soma-spikes-continuous Cable with channels only for first 50 um, varying time step
multirec Cable with HH sodium and potassium channels, different timesteps
smartrec Cable with HH sodium and potassium channels, different timesteps
vcsteps
p1-f1-mean-variance
mean-variance null
p1-f2-rp1-det Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
p1-f2-rp2-det Regular branched cable with 9 levels of branching (512 terminals) varying timestep
p1-f2-rp3-det Cable with HH sodium and potassium channels, different timesteps
p1-f2-rp1-stoch null
p1-f2-rp2-stoch Regular branched cable with 9 levels of branching (512 terminals)
p1-f2-rp3-stoch Cable with HH sodium and potassium channels
cwvclamp Chow and White (1996), Biophys J
p1-f3-1c-det Migliore et al CA1 pyramidal cell
p1-f3-1a-det Migliore et al CA1 pyramidal cell
p1-f3-1a-stoch Migliore et al CA1 pyramidal cell
chowwhite null
rallpack1-IE Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
rallpack2-IE Regular branched cable with 9 levels of branching (512 terminals) varying timestep
migliore-devel Migliore et al CA1 pyramidal cell
ralpack-dev Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
mean-var-iv
mean-variance-iv
mean-variance-iv-stoch
migliore-1a Migliore et al CA1 pyramidal cell
migliore-1c Migliore et al CA1 pyramidal cell
mean-variance-iv-det
step-onset
step-onset-avg
stimtest
mainen null

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.

rallpack3/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>

rallpack3/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>

rallpack3/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>

rallpack3/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>

rallpack3/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>

rallpack3/recording.xml

<Access id="recording">

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

	</CurrentClamp>

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

</Access>

rallpack3/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>