p1-f2-rp2-stoch (run-stoch.xml)
Regular branched cable with 9 levels of branching (512 terminals)
Branched tree with ten levels of branching obeying the Rall 3/2 power law. This gives a tree with 512 terminal segments and 1023 segments in total. Electrical properties are as for Rallpack 1. Full details in README.upi.
The model produces three graphs showing the reference data (correct solution) in white, and calculated curves in other colors according to the timestep used. The only difference between the graphs are the axis ranges: they all show the same data.
For each timestep (and for the reference) there are two curves: the potentail at the root of the tree and the potential at a terminal. Note that for this set of cell properties, the two potentials are very close throughout the simulation and are barely distinguishable in the first figure.
If the system performs correctly, the lines should be almost on top of each other at these scales (well within 0.01mV).
Total CPU time 25.05 seconds; at 18:36:51 Mon 30 Jul 2007
| Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | time/ms | timestep/ms | stoch-leak:gSingle | CPU Time / s |
| 1044 | 4892 / 792 | 852 / 7 | 250.0 | 0.05 | 1 | 11.4 |
| 1044 | 1149 / 435 | 0 / 0 | 250.0 | 0.05 | 5 | 5.86 |
| 1044 | 575 / 285 | 0 / 0 | 250.0 | 0.05 | 10 | 4.36 |
| 1044 | 287 / 181 | 0 / 0 | 250.0 | 0.05 | 20 | 3.40 |
 |
Predefined views
whole
midrange
end
All files
| Model | Preprocessed | Outupt data | Reference data etc |
| run-stoch.xml cell.xml stoch-membrane.xml environment.xml recording.xml stoch-leak.xml summary.xml view.xml |
g-1-fdata.txt g-5-fdata.txt g-10-fdata.txt g-20-fdata.txt |
g-1-f.dat g-1-f.txt g-5-f.dat g-5-f.txt g-10-f.dat g-10-f.txt g-20-f.dat g-20-f.txt ref_branch_0.txt ref_branch_x.txt |
README README.upi |
Model
run-stoch.xml
<PSICSRun lib="." timeStep="50us" runTime="250ms" startPotential="-65mV"
method="weighted_crank_nicolson"
morphology="cell"
environment="environment"
properties="stoch-membrane"
access="recording"
repeats="4"
stochThreshold="100">
<StructureDiscretization baseElementSize="10um" merge="false" squareCaps="true"/>
<RunSet vary="stoch-leak:gSingle" values="[1, 5, 10, 20]pS"
covary="leakpop:density" covalues="[0.357143, 0.0714286, 0.0357143, 0.0178571]per_um2"
filepattern="g-$.txt"/>
<info>Regular branched cable with 9 levels of branching (512 terminals)</info>
<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_branch_0.txt" color="white" width="2" rescale="[1000, 1000.]"/>
<Line file="ref_branch_x.txt" color="white" width="2" rescale="[1000, 1000.]"/>
<LineSet file="g-1-f.txt" color="red" label="1"/>
<LineSet file="g-5-f.txt" color="yellow" label="5"/>
<LineSet file="g-10-f.txt" color="green" label="10"/>
<LineSet file="g-20-f.txt" color="blue" label="20"/>
<View id="whole" xmin="-10." xmax="260." ymin="-70." ymax="-35."/>
<View id="midrange" xmin="66" xmax="73" ymin="-45.2" ymax="-44.2"/>
<View id="end" xmin="230." xmax="255." ymin="-40.25" ymax="-40.12"/>
</LineGraph>
</ViewConfig>
</PSICSRun>
cell.xml (truncated)
<CellMorphology id="cell"> <Point id="p0" x="0" y="0" z="0" r="8.0"/> <Point id="p1" parent="p0" x="32.0" y="0" z="0" r="8.0"/> <Point id="p2" parent="p1" minor="true" x="47.65501764758427" y="-20.0" z="0" r="5.039684199579492"/> <Point id="p3" parent="p1" minor="true" x="47.65501764758427" y="20.0" z="0" r="5.039684199579492"/> <Point id="p4" parent="p2" minor="true" x="65.15857926526252" y="-30.0" z="0" r="3.1748021039363983"/> <Point id="p5" parent="p2" minor="true" x="65.15857926526252" y="-10.0" z="0" r="3.1748021039363983"/> <Point id="p6" parent="p3" minor="true" x="65.15857926526252" y="10.0" z="0" r="3.1748021039363983"/> <Point id="p7" parent="p3" minor="true" x="65.15857926526252" y="30.0" z="0" r="3.1748021039363983"/> <Point id="p8" parent="p4" minor="true" x="80.35726341883318" y="-35.0" z="0" r="1.9999999999999993"/> <Point id="p9" parent="p4" minor="true" x="80.35726341883318" y="-25.0" z="0" r="1.9999999999999993"/> <Point id="p10" parent="p5" minor="true" x="80.35726341883318" y="-15.0" z="0" r="1.9999999999999993"/> <Point id="p11" parent="p5" minor="true" x="80.35726341883318" y="-5.0" z="0" r="1.9999999999999993"/> <Point id="p12" parent="p6" minor="true" x="80.35726341883318" y="5.0" z="0" r="1.9999999999999993"/> <Point id="p13" parent="p6" minor="true" x="80.35726341883318" y="15.0" z="0" r="1.9999999999999993"/> <Point id="p14" parent="p7" minor="true" x="80.35726341883318" y="25.0" z="0" r="1.9999999999999993"/> <Point id="p15" parent="p7" minor="true" x="80.35726341883318" y="35.0" z="0" r="1.9999999999999993"/> <Point id="p16" parent="p8" minor="true" x="92.80796196897661" y="-37.5" z="0" r="1.2599210498948727"/> <Point id="p17" parent="p8" minor="true" x="92.80796196897661" y="-32.5" z="0" r="1.2599210498948727"/> <Point id="p18" parent="p9" minor="true" x="92.80796196897661" y="-27.5" z="0" r="1.2599210498948727"/> <Point id="p19" parent="p9" minor="true" x="92.80796196897661" y="-22.5" z="0" r="1.2599210498948727"/> <Point id="p20" parent="p10" minor="true" x="92.80796196897661" y="-17.5" z="0" r="1.2599210498948727"/> <Point id="p21" parent="p10" minor="true" x="92.80796196897661" y="-12.5" z="0" r="1.2599210498948727"/> <Point id="p22" parent="p11" minor="true" x="92.80796196897661" y="-7.5" z="0" r="1.2599210498948727"/> <Point id="p23" parent="p11" minor="true" x="92.80796196897661" y="-2.5" z="0" r="1.2599210498948727"/> <Point id="p24" parent="p12" minor="true" x="92.80796196897661" y="2.5" z="0" r="1.2599210498948727"/> <Point id="p25" parent="p12" minor="true" x="92.80796196897661" y="7.5" z="0" r="1.2599210498948727"/> <Point id="p26" parent="p13" minor="true" x="92.80796196897661" y="12.5" z="0" r="1.2599210498948727"/> <Point id="p27" parent="p13" minor="true" x="92.80796196897661" y="17.5" z="0" r="1.2599210498948727"/> <Point id="p28" parent="p14" minor="true" x="92.80796196897661" y="22.5" z="0" r="1.2599210498948727"/> <Point id="p29" parent="p14" minor="true" x="92.80796196897661" 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r="0.7937005259840995"/> <Point id="p58" parent="p29" minor="true" x="102.8095202138685" y="26.25" z="0" r="0.7937005259840995"/> - and 966 more lines -
stoch-membrane.xml
<CellProperties id="stoch-membrane"
cytoplasmResistivity="100ohm_cm"
membraneCapacitance="1uF_per_cm2">
<ChannelPopulation id="leakpop" channel="stoch-leak" density="0.357143per_um2"/>
</CellProperties>
environment.xml
<CellEnvironment id="environment"> <Ion id="K" name="Potassium" reversalPotential="-65mV"/> </CellEnvironment>
recording.xml
<Access id="recording">
<CurrentClamp at="p0" lineColor="red" hold="0.1nA">
</CurrentClamp>
<VoltageRecorder at="p1023" lineColor="blue"/>
</Access>
stoch-leak.xml
<KSChannel id="stoch-leak" gSingle="1pS" permeantIon="K"> <OpenState id="o1"/> <ClosedState id="c1"/> <FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/> </KSChannel>