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.
- p18 Channel noise in dendrites
- cell-loc Current clamp stimulation profile read from a file, varying the stimulation scale factor
- synapses Simple cell with distributions of synapses and event generators to activate them
- minor PSICS project generated from: CA1PyramidalCell.ncx
- params
- smalldt PSICS project generated from: CA1PyramidalCell.ncx
- onsurface Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
- migliore-1a Migliore et al CA1 pyramidal cell
- rallpack3 Cable with HH sodium and potassium channels, different timesteps
- cwvclamp Chow and White (1996), Biophys J
- vcsteps
- rallpack1 Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
- smartrec Cell with smart recorders accessing channel population conductances independently
- ivconv
- ivconvm
- mean-variance-iv-stoch
- stochdet
- channel-functions test for channels with xml coded functions
- stimtest Current clamp stimulation profile read from a file, varying the stimulation scale factor
- functest test for channels with xml coded functions
- migliore-pass Migliore et al CA1 pyramidal cell
- psd
- cianmar30 Channel noise in dendrites
- mean-variance
- rallpack2 Regular branched cable with 9 levels of branching (512 terminals) varying timestep
- rallpack3-stoch Cable with HH sodium and potassium channels
- rallpack3-stoch2 Cable with HH sodium and potassium channels, 20pS single channel conductance
- chowwhite Chow and White (1996), Biophys J. Showing spontaneous spiking with varying numbers of channels
- multirec Different ways of positioning recorders along the cell between defined points
- mainen
- 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
- p1-f1-mean-variance
- 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
- singlecpt Cable with channels only for first 50 um, varying time step
- synstim Simple cell with distributions of synapses and event generators to activate them
- resonance Spruston CA1 pyramidal neuron (with Ih)
- manychannels
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" recordClamps="false"> <CurrentClamp label="start" at="p0" lineColor="red" hold="0.1nA" record="true"> </CurrentClamp> <VoltageRecorder label="end" at="p1" lineColor="blue" /> </Access>
rallpack3/run.xml
<PSICSRun 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="[50, 100]us" filepattern="ts-$" /> <ViewConfig> <LineGraph width="500" height="400"> <XAxis label="time / ms" /> <YAxis 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.txt" color="red" /> <LineSet file="ts-20.txt" color="blue" /> <LineSet file="ts-50.txt" color="cyan" /> <LineSet file="ts-100.txt" color="green" /> <View id="whole" /> <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>