PSICS Results for run.xml

ralpack2-dev (run.xml)

Regular branched cable with 9 levels of branching (512 terminals) varying timestep

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 2.999 seconds; at 13:59:52 Fri 4 Jan 2008

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	time/ms	timeStep	CPU Time / s
1024	0 / 0	0 / 0	402124 / 1024	250.0	20	1.676
1024	0 / 0	0 / 0	402124 / 1024	250.0	50	0.687
1024	0 / 0	0 / 0	402124 / 1024	250.0	100	0.359
1024	0 / 0	0 / 0	402124 / 1024	250.0	200	0.188
1024	0 / 0	0 / 0	402124 / 1024	250.0	500	0.089

Predefined views

whole

midrange

end

out-500-f.txt, line 0, deviation: mean = -0.000521, rms= 0.00406
out-500-f.txt, line 1, deviation: mean = -0.000578, rms= 0.00148
out-200-f.txt, line 0, deviation: mean = -0.000318, rms= 0.00174
out-200-f.txt, line 1, deviation: mean = -0.000327, rms= 0.000559
out-100-f.txt, line 0, deviation: mean = -0.000230, rms= 0.000851
out-100-f.txt, line 1, deviation: mean = -0.000225, rms= 0.000270
out-50-f.txt, line 0, deviation: mean = -0.000187, rms= 0.000415
out-50-f.txt, line 1, deviation: mean = -0.000175, rms= 0.000182
out-20-f.txt, line 0, deviation: mean = -0.000138, rms= 0.000301
out-20-f.txt, line 1, deviation: mean = -0.000127, rms= 0.000137

All files

Model

Archive file of the complete model: ralpack2-dev.jar

run.xml

<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording"
	quickChannels="false">
	<StructureDiscretization baseElementSize="100um" merge="false" squareCaps="true"/>

	<RunSet vary="timeStep" values="[20, 50, 100, 200, 500]us"
		filepattern="out-$.txt"/>
  	<info>Regular branched cable with 9 levels of branching (512 terminals) varying timestep</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="out-500-f.txt" color="orange" label="500">
			<DataComparison file="ref_branch_0.txt" line="0" rescale="[1000, 1000.]"/>
			<DataComparison file="ref_branch_x.txt" line="1" rescale="[1000, 1000.]"/>
		</LineSet>

		<LineSet file="out-200-f.txt" color="yellow" label="200">
			<DataComparison file="ref_branch_0.txt" line="0" rescale="[1000, 1000.]"/>
			<DataComparison file="ref_branch_x.txt" line="1" rescale="[1000, 1000.]"/>
		</LineSet>

		<LineSet file="out-100-f.txt" color="green" label="100">
			<DataComparison file="ref_branch_0.txt" line="0" rescale="[1000, 1000.]"/>
			<DataComparison file="ref_branch_x.txt" line="1" rescale="[1000, 1000.]"/>
		</LineSet>
		<LineSet file="out-50-f.txt" color="cyan" label="100">
			<DataComparison file="ref_branch_0.txt" line="0" rescale="[1000, 1000.]"/>
			<DataComparison file="ref_branch_x.txt" line="1" rescale="[1000, 1000.]"/>
		</LineSet>
		<LineSet file="out-20-f.txt" color="blue" label="20">
			<DataComparison file="ref_branch_0.txt" line="0" rescale="[1000, 1000.]"/>
			<DataComparison file="ref_branch_x.txt" line="1" rescale="[1000, 1000.]"/>
		</LineSet>

		<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" y="27.5" z="0" r="1.2599210498948727"/>
<Point id="p30" parent="p15" minor="true" x="92.80796196897661" y="32.5" z="0" r="1.2599210498948727"/>
<Point id="p31" parent="p15" minor="true" x="92.80796196897661" y="37.5" z="0" r="1.2599210498948727"/>
<Point id="p32" parent="p16" minor="true" x="102.8095202138685" y="-38.75" z="0" r="0.7937005259840995"/>
<Point id="p33" parent="p16" minor="true" x="102.8095202138685" y="-36.25" z="0" r="0.7937005259840995"/>
<Point id="p34" parent="p17" minor="true" x="102.8095202138685" y="-33.75" z="0" r="0.7937005259840995"/>
<Point id="p35" parent="p17" minor="true" x="102.8095202138685" y="-31.25" z="0" r="0.7937005259840995"/>
<Point id="p36" parent="p18" minor="true" x="102.8095202138685" y="-28.75" z="0" r="0.7937005259840995"/>
<Point id="p37" parent="p18" minor="true" x="102.8095202138685" y="-26.25" z="0" r="0.7937005259840995"/>
<Point id="p38" parent="p19" minor="true" x="102.8095202138685" y="-23.75" z="0" r="0.7937005259840995"/>
<Point id="p39" parent="p19" minor="true" x="102.8095202138685" y="-21.25" z="0" r="0.7937005259840995"/>
<Point id="p40" parent="p20" minor="true" x="102.8095202138685" y="-18.75" z="0" r="0.7937005259840995"/>
<Point id="p41" parent="p20" minor="true" x="102.8095202138685" y="-16.25" z="0" r="0.7937005259840995"/>
<Point id="p42" parent="p21" minor="true" x="102.8095202138685" y="-13.75" z="0" r="0.7937005259840995"/>
<Point id="p43" parent="p21" minor="true" x="102.8095202138685" y="-11.25" z="0" r="0.7937005259840995"/>
<Point id="p44" parent="p22" minor="true" x="102.8095202138685" y="-8.75" z="0" r="0.7937005259840995"/>
<Point id="p45" parent="p22" minor="true" x="102.8095202138685" y="-6.25" z="0" r="0.7937005259840995"/>
<Point id="p46" parent="p23" minor="true" x="102.8095202138685" y="-3.75" z="0" r="0.7937005259840995"/>
<Point id="p47" parent="p23" minor="true" x="102.8095202138685" y="-1.25" z="0" r="0.7937005259840995"/>
<Point id="p48" parent="p24" minor="true" x="102.8095202138685" y="1.25" z="0" r="0.7937005259840995"/>
<Point id="p49" parent="p24" minor="true" x="102.8095202138685" y="3.75" z="0" r="0.7937005259840995"/>
<Point id="p50" parent="p25" minor="true" x="102.8095202138685" y="6.25" z="0" r="0.7937005259840995"/>
<Point id="p51" parent="p25" minor="true" x="102.8095202138685" y="8.75" z="0" r="0.7937005259840995"/>
<Point id="p52" parent="p26" minor="true" x="102.8095202138685" y="11.25" z="0" r="0.7937005259840995"/>
<Point id="p53" parent="p26" minor="true" x="102.8095202138685" y="13.75" z="0" r="0.7937005259840995"/>
<Point id="p54" parent="p27" minor="true" x="102.8095202138685" y="16.25" z="0" r="0.7937005259840995"/>
<Point id="p55" parent="p27" minor="true" x="102.8095202138685" y="18.75" z="0" r="0.7937005259840995"/>
<Point id="p56" parent="p28" minor="true" x="102.8095202138685" y="21.25" z="0" r="0.7937005259840995"/>
<Point id="p57" parent="p28" minor="true" x="102.8095202138685" y="23.75" z="0" 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 -

membrane.xml

<CellProperties id="membrane"
      cytoplasmResistivity="100ohm_cm"
      membraneCapacitance="1uF_per_cm2">

	<ChannelPopulation channel="leak" density="25per_um2" allocation="regular"/>

</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>

leak.xml

<KSChannel id="leak" gSingle="0.01pS" permeantIon="K">
	<OpenState id="o1"/>
</KSChannel>

Model	Preprocessed	Outupt data	Reference data etc
run.xml cell.xml membrane.xml environment.xml recording.xml leak.xml summary.xml view.xml	out-20-fdata.txt out-50-fdata.txt out-100-fdata.txt out-200-fdata.txt out-500-fdata.txt	out-20-f.dat out-20-f.txt out-50-f.dat out-50-f.txt out-100-f.dat out-100-f.txt out-200-f.dat out-200-f.txt out-500-f.dat out-500-f.txt ref_branch_0.txt ref_branch_x.txt end.txt	README README.upi ralpack2-dev.jar