p18
cell-loc
synapses
minor
params
smalldt
onsurface
migliore-1a
rallpack3
cwvclamp
vcsteps
rallpack1
smartrec
ivconv
ivconvm
mean-variance-iv-stoch
stochdet
channel-functions
stimtest
functest
migliore-pass
psd
cianmar30
mean-variance
rallpack2
rallpack3-stoch
rallpack3-stoch2
chowwhite
multirec
mainen
soma-spikes-stochastic
soma-spikes-continuous
p1-f1-mean-variance
rallpack1-IE
rallpack2-IE
singlecpt
synstim
resonance
manychannels

rallpack2-IE (run-ie.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 2.740 seconds; at 12:48:10 Thu 24 Sep 2009

CompartmentsStochastic
channels / cpmts
Continuous
channels / cpmts
Non Gated
channels / cpmts
time/mstimeStepCPU Time / s
10240 / 00 / 0392298 / 1024250.020 1.59
10240 / 00 / 0392298 / 1024250.050 0.610
10240 / 00 / 0392298 / 1024250.0100 0.310
10240 / 00 / 0392298 / 1024250.0200 0.170
10240 / 00 / 0392298 / 1024250.0500 0.0600

Morphology: cell

 

 

 

 

 

Predefined views

whole

midrange

end

All files

ModelPreprocessedOutupt dataReference data etc
run-ie.xml
cell.xml
membrane.xml
environment.xml
recording.xml
leak.xml
out-20.txt.ppp
out-50.txt.ppp
out-100.txt.ppp
out-200.txt.ppp
out-500.txt.ppp
log.txt
out-20.txt.sum
out-50.txt.sum
out-100.txt.sum
out-200.txt.sum
out-500.txt.sum
out-20.txt.dat
out-20.txt.txt
out-50.txt.dat
out-50.txt.txt
out-100.txt.dat
out-100.txt.txt
out-200.txt.dat
out-200.txt.txt
out-500.txt.dat
out-500.txt.txt
ref_branch_0.txt
ref_branch_x.txt
README
README.upi

Model

Archive file of the complete model: rallpack2-IE.jar

run-ie.xml

<PSICSRun timeStep="0.1ms" runTime="250ms" startPotential="-65mV"
	method="implicit_euler"
	morphology="cell"
	environment="environment"
	properties="membrane"
	access="recording">
	<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>