psd (run.xml)
Total CPU time 58.75 seconds; at 11:58:39 Thu 24 Sep 2009
Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | time/ms | timestep/ms | napop:density | CPU Time / s |
1 | 25 / 1 | 0 / 0 | 0 / 0 | 1.50e+04 | 0.00200 | 2 | 14.6 |
1 | 50 / 1 | 0 / 0 | 0 / 0 | 1.50e+04 | 0.00200 | 4 | 21.9 |
1 | 101 / 1 | 0 / 0 | 0 / 0 | 1.50e+04 | 0.00200 | 8 | 10.3 |
1 | 201 / 1 | 0 / 0 | 0 / 0 | 1.50e+04 | 0.00200 | 16 | 12.0 |
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Predefined views
whole

mva

mvb

mvc

All files
Model | Preprocessed | Outupt data | Reference data etc |
run.xml cell.xml membrane.xml environment.xml recording.xml na1.xml |
out-2.ppp out-4.ppp out-8.ppp out-16.ppp |
log.txt out-2.sum out-4.sum out-8.sum out-16.sum out-2.dat out-2.txt out-4.dat out-4.txt out-8.dat out-8.txt out-16.dat out-16.txt |
Model
Archive file of the complete model: psd.jarrun.xml
<PSICSRun timeStep="0.002ms" runTime="15000ms" startPotential="-65mV" morphology="cell" environment="environment" properties="membrane" access="recording" stochThreshold="1000"> <StructureDiscretization baseElementSize="3um"/> <RunSet vary="napop:density" values="[2, 4, 8, 16]per_um2" filepattern="out-$"> </RunSet> <About> </About> <ViewConfig morphology="false"> <LineGraph width="500" height="400"> <XAxis min="0" max="250" label="time / ms"/> <YAxis min="-80" max="60" label="current / nA"/> <LineSet file="out-2.txt" color="red" maxshow="6"/> <LineSet file="out-4.txt" color="orange" maxshow="6"/> <LineSet file="out-8.txt" color="blue" maxshow="6"/> <LineSet file="out-16.txt" color="green" maxshow="6"/> <View id="whole" xmin="0." xmax="25." ymin="-160." ymax="20."/> </LineGraph> <LineGraph> <XAxis label="frequency/Hz"/> <YAxis label="Spectral Density"/> <PowerSpectrum file="out-2.txt" color="red"/> <PowerSpectrum file="out-4.txt" color="orange"/> <PowerSpectrum file="out-8.txt" color="blue"/> <PowerSpectrum file="out-16.txt" color="green"/> <View id="mva" xmin="-20" xmax="400" ymin = "0." ymax="60"/> <View id="mvb" xmin="-20" xmax="2000" ymin = "0." ymax="60"/> </LineGraph> <LineGraph> <XAxis label="Log10 frequency/Hz"/> <YAxis label="Log10 Spectral Density"/> <PowerSpectrum loglog="true" file="out-2.txt" color="red"/> <PowerSpectrum loglog="true" file="out-4.txt" color="orange"/> <PowerSpectrum loglog="true" file="out-8.txt" color="blue"/> <PowerSpectrum loglog="true" file="out-16.txt" color="green"/> <View id="mvc" xmin="1" xmax="4" ymin = "-3" ymax="2"/> </LineGraph> </ViewConfig> </PSICSRun>
cell.xml
<CellMorphology id="cell"> <Point id="p0" x="0" y="0" z="0" r="1."/> </CellMorphology>
membrane.xml
<CellProperties id="membrane" cytoplasmResistivity="100ohm_cm" membraneCapacitance="1uF_per_cm2"> <ChannelPopulation id="napop" channel="na1" density="16per_um2"/> </CellProperties>
environment.xml
<CellEnvironment id="environment"> <Ion id="Na" name="Sodium" reversalPotential="80mV"/> <Ion id="K" name="Potassium" reversalPotential="-80mV"/> </CellEnvironment>
recording.xml
<Access id="recording" saveInterval="0.05ms"> <VoltageClamp at="p0" lineColor="red" hold="-60.0mV"> </VoltageClamp> </Access>
na1.xml
<KSChannel id="na1" gSingle="30pS" permeantIon="Na"> <ClosedState id="c1"/> <OpenState id="o1"/> <ClosedState id="c2"/> <VHalfTransition from="c1" to="o1" vHalf = "-35mV" z="4.5e" gamma="0.8" tau="0.55ms" tauMin="0.1ms"/> <VHalfTransition from="o1" to="c2" vHalf = "-70mV" z="1.1e" gamma="0.90" tau="12.0ms" tauMin="1.5ms"/> </KSChannel>