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 |
 |
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>