rallpack1-IE (run-ie.xml)
Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds
Uniform unbranched cable. The task specification and reference results come from Upi Bhalla's 1992 Rallpack distribution, part of which is included below. The rest in the file 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.
If the system performs correctly, the results should be almost superimposed with less than 0.01 mV difference from the reference, for any of the timesteps.
From Upi Bhalla's 1992 Rallpack packageThis simulation models a simple uniform unbranched cable with 1000 identical compartments, with a length constant of 1, a diameter of 1 micron, and a total length of 1 mm. The membrane properties are : RA = 1.0 ohms meter = 100 ohms cm RM = 4.0 ohms meter^2 = 40000 ohms cm^2 CM = 0.01 Farads/meter^2 = 1.0 uf/cm^2 EM = -0.065 Volts = -65 mV ELEAK = EREST = EM A current of 0.1 nA is injected in the first compartment. Membrane voltages are recorded for the first and last compartments. This model is run for a simulated time of 0.25 seconds.
Total CPU time 2.890 seconds; at 12:47:56 Thu 24 Sep 2009
Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | time/ms | timeStep | CPU Time / s |
1001 | 0 / 0 | 0 / 0 | 78579 / 1001 | 250.0 | 20 | 1.65 |
1001 | 0 / 0 | 0 / 0 | 78579 / 1001 | 250.0 | 50 | 0.670 |
1001 | 0 / 0 | 0 / 0 | 78579 / 1001 | 250.0 | 100 | 0.330 |
1001 | 0 / 0 | 0 / 0 | 78579 / 1001 | 250.0 | 200 | 0.170 |
1001 | 0 / 0 | 0 / 0 | 78579 / 1001 | 250.0 | 500 | 0.0700 |
Morphology: cell
Predefined views
whole
end
midrange
All files
Model
Archive file of the complete model: rallpack1-IE.jarrun-ie.xml
<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV" method="implicit_euler" morphology="cell" environment="environment" properties="membrane" access="recording"> <StructureDiscretization baseElementSize="1um"/> <RunSet vary="timeStep" values="[20, 50, 100, 200, 500]us" filepattern="ts-$.txt"/> <info>Cable, 100um long, run for 250ms with different timesteps between 20 and 500 microseconds</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_cable_0.txt" color="white" width="2" rescale="[1000, 1000.]"/> <Line file="ref_cable_x.txt" color="white" width="2" rescale="[1000, 1000.]"/> <LineSet file="ts-500-f.txt" color="orange" label="500"> <DataComparison file="ref_cable_0.txt" line="0"rescale="[1000, 1000.]"/> <DataComparison file="ref_cable_x.txt" line="1"rescale="[1000, 1000.]"/> </LineSet> <LineSet file="ts-200-f.txt" color="yellow" label="200"> <DataComparison file="ref_cable_0.txt" line="0" rescale="[1000, 1000.]"/> <DataComparison file="ref_cable_x.txt" line="1" rescale="[1000, 1000.]"/> </LineSet> <LineSet file="ts-100-f.txt" color="green" label="100"> <DataComparison file="ref_cable_0.txt" line="0" rescale="[1000, 1000.]"/> <DataComparison file="ref_cable_x.txt" line="1" rescale="[1000, 1000.]"/> </LineSet> <LineSet file="ts-50-f.txt" color="cyan" label="50"> <DataComparison file="ref_cable_0.txt" line="0" rescale="[1000, 1000.]"/> <DataComparison file="ref_cable_x.txt" line="1" rescale="[1000, 1000.]"/> </LineSet> <LineSet file="ts-20-f.txt" color="blue" label="20"> <DataComparison file="ref_cable_0.txt" line="0" rescale="[1000, 1000.]"/> <DataComparison file="ref_cable_x.txt" line="1" rescale="[1000, 1000.]"/> </LineSet> <View id="whole" xmin="-10." xmax="260." ymin="-100." ymax="100."/> <View id="end" xmin="249" xmax="250.2" ymin="101.93" ymax="101.94"/> <View id="midrange" xmin="80" xmax="90" ymin="25" ymax="30"/> </LineGraph> </ViewConfig> </PSICSRun>
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>
membrane.xml
<CellProperties id="membrane" membraneCapacitance="1.0uF_per_cm2" cytoplasmResistivity="100.0ohm_cm"> <ChannelPopulation id="population_1" channel="leak" density="25per_um2"/> </CellProperties>
environment.xml
<CellEnvironment id="environment"> <Ion id="K" name="Potassium" reversalPotential="-65mV"/> </CellEnvironment>
recording.xml
<Access id="recording" recordClamps="true"> <CurrentClamp at="p0" lineColor="red" hold="0.1nA"> </CurrentClamp> <VoltageRecorder at="p1" lineColor="blue"/> </Access>
leak.xml
<KSChannel id="leak" gSingle="0.01pS" permeantIon="K"> <OpenState id="o1"/> </KSChannel>