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

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 package
This 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

CompartmentsStochastic
channels / cpmts
Continuous
channels / cpmts
Non Gated
channels / cpmts
time/mstimeStepCPU Time / s
10010 / 00 / 078579 / 1001250.020 1.65
10010 / 00 / 078579 / 1001250.050 0.670
10010 / 00 / 078579 / 1001250.0100 0.330
10010 / 00 / 078579 / 1001250.0200 0.170
10010 / 00 / 078579 / 1001250.0500 0.0700

Morphology: cell

 

 

 

 

 

Predefined views

whole

end

midrange

All files

ModelPreprocessedOutupt dataReference data etc
run-ie.xml
cell.xml
membrane.xml
environment.xml
recording.xml
leak.xml
ts-20.txt.ppp
ts-50.txt.ppp
ts-100.txt.ppp
ts-200.txt.ppp
ts-500.txt.ppp
log.txt
ts-20.txt.sum
ts-50.txt.sum
ts-100.txt.sum
ts-200.txt.sum
ts-500.txt.sum
ts-20.txt.dat
ts-20.txt.txt
ts-50.txt.dat
ts-50.txt.txt
ts-100.txt.dat
ts-100.txt.txt
ts-200.txt.dat
ts-200.txt.txt
ts-500.txt.dat
ts-500.txt.txt
ref_cable_0.txt
ref_cable_x.txt
README
README.upi

Model

Archive file of the complete model: rallpack1-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="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>