Index
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

p18 (run_distrib.xml)

Channel noise in dendrites

Total CPU time 0.2000 seconds; at 10:35:08 Thu 24 Sep 2009

CompartmentsStochastic
channels / cpmts		Continuous
channels / cpmts		Non Gated
channels / cpmts		CPU Time / s
20850 / 0158616 / 18810 / 0 0.200

Morphology: p18p

 

Predefined views

zoom100ms

whole

All files

ModelPreprocessedOutupt dataReference data etc
run_distrib.xml
p18p.xml
membrane_distrib.xml
environment.xml
record_p18.xml
NaMS.xml
KvMS.xml
KmMS.xml
CaMS.xml
leak-na.xml
leak-k.xml
 psics-out.ppp
 log.txt
psics-out.sum
psics-out.dat
psics-out.txt
 psics-out.morph

Model

Archive file of the complete model: p18.jar

run_distrib.xml

<PSICSRun   timeStep="0.01ms" runTime="1ms" startPotential="-60mV"
	environment="environment"
	properties="membrane_distrib"
	access="record_p18"
	stochThreshold="0"
	quickChannels="false"
	morphology="p18p"
	repeats="1">
	
	<StructureDiscretization baseElementSize="5um"/>
	<info>Channel noise in dendrites</info>

	<ViewConfig morphologyData="true">
		<LineGraph width="500" height="400">
		<XAxis min="0" max="100" label="time / ms"/>
		<YAxis min="-80" max="60" label="potential / mV"/>

		<Line file="psics-out.txt" show="1" color="#ffffff"/>

		<View id="zoom100ms" xmin="200." xmax="300." ymin="-70." ymax="-20."/>
		<View id="whole" xmin="-10." xmax="1010" ymin="-70." ymax="-20."/>
		</LineGraph>
	</ViewConfig>
</PSICSRun>

p18p.xml (truncated)

<CellMorphology id="p18p">
   <Point id="rootpoint" x="0.200" y="5.000" z="0.400" r="10.125" label="Seg0_soma_0"/>
   <Point id="0" x="0.200" y="6.000" z="0.400" r="9.550" parent="rootpoint" label="Seg0_soma_0"/>
   <Point id="6" x="0.200" y="3.800" z="0.400" r="9.585" parent="rootpoint" label="Seg0_soma_3"/>
   <Point id="1086" x="-0.800" y="5.500" z="0.400" r="0.441" parent="0" label="Seg0_hill"/>
   <Point id="13" x="0.200" y="6.531" z="1.346" r="1.200" parent="0" label="Seg0_dend_0"/>
   <Point id="1" x="0.200" y="9.700" z="1.000" r="8.430" parent="0" label="Seg0_soma_1"/>
   <Point id="161" x="0.200" y="4.192" z="1.238" r="0.700" parent="6" label="Seg0_dend_22"/>
   <Point id="7" x="0.200" y="0.900" z="2.500" r="7.895" parent="6" label="Seg0_soma_4"/>
   <Point id="1087" x="-2.800" y="5.500" z="0.400" r="0.369" parent="1086" label="Seg1_hill"/>
   <Point id="14" x="-6.100" y="7.531" z="1.346" r="1.200" parent="13" label="Seg1_dend_0"/>
   <Point id="129" x="0.200" y="8.869" z="1.454" r="0.700" parent="1" label="Seg0_dend_17"/>
   <Point id="2" x="0.200" y="14.400" z="2.100" r="6.585" parent="1" label="Seg0_soma_2"/>
   <Point id="162" x="1.800" y="-1.908" z="-5.162" r="0.700" parent="161" label="Seg1_dend_22"/>
   <Point id="196" x="0.200" y="1.854" z="1.131" r="0.700" parent="7" label="Seg0_dend_29"/>
   <Point id="8" x="0.200" y="0.000" z="4.100" r="7.275" parent="7" label="Seg0_soma_5"/>
   <Point id="1088" x="-4.800" y="5.500" z="0.400" r="0.298" parent="1087" label="Seg2_hill"/>
   <Point id="15" x="-12.700" y="10.531" z="1.346" r="1.250" parent="14" label="Seg2_dend_0"/>
   <Point id="130" x="9.100" y="8.869" z="1.454" r="0.700" parent="129" label="Seg1_dend_17"/>
   <Point id="3" x="0.200" y="16.600" z="2.100" r="5.660" parent="2" label="Seg1_soma_2"/>
   <Point id="163" x="-5.900" y="-9.308" z="-5.162" r="1.000" parent="162" label="Seg2_dend_22"/>
   <Point id="197" x="10.400" y="-3.046" z="0.531" r="0.700" parent="196" label="Seg1_dend_29"/>
   <Point id="9" x="0.200" y="-2.200" z="2.300" r="5.315" parent="8" label="Seg1_soma_5"/>
   <Point id="1089" x="-6.800" y="5.500" z="0.400" r="0.226" parent="1088" label="Seg3_hill"/>
   <Point id="16" x="-20.400" y="8.131" z="1.346" r="1.250" parent="15" label="Seg3_dend_0"/>
   <Point id="131" x="13.300" y="11.269" z="1.454" r="0.550" parent="130" label="Seg2_dend_17"/>
   <Point id="4" x="0.200" y="19.500" z="2.100" r="4.350" parent="3" label="Seg2_soma_2"/>
   <Point id="167" x="-1.000" y="-19.808" z="-5.062" r="0.700" parent="163" label="Seg0_dend_24"/>
   <Point id="164" x="-13.200" y="-3.208" z="-10.462" r="0.300" parent="163" label="Seg0_dend_23"/>
   <Point id="198" x="13.700" y="-5.046" z="0.531" r="0.600" parent="197" label="Seg2_dend_29"/>
   <Point id="246" x="0.200" y="-2.823" z="0.915" r="0.850" parent="9" label="Seg0_dend_36"/>
   <Point id="10" x="0.200" y="-3.600" z="3.400" r="4.620" parent="9" label="Seg0_soma_6"/>
   <Point id="1090" x="-8.800" y="5.500" z="0.400" r="0.155" parent="1089" label="Seg4_hill"/>
   <Point id="88" x="-22.600" y="2.931" z="1.346" r="0.650" parent="16" label="Seg0_dend_12"/>
   <Point id="17" x="-28.300" y="12.831" z="1.646" r="0.800" parent="16" label="Seg0_dend_1"/>
   <Point id="132" x="28.100" y="14.969" z="3.354" r="0.700" parent="131" label="Seg3_dend_17"/>
   <Point id="5" x="0.200" y="20.900" z="2.100" r="3.540" parent="4" label="Seg3_soma_2"/>
   <Point id="171" x="2.200" y="-31.608" z="-5.062" r="0.650" parent="167" label="Seg0_dend_26"/>
   <Point id="168" x="5.000" y="-21.208" z="-5.062" r="0.350" parent="167" label="Seg0_dend_25"/>
   <Point id="165" x="-24.900" y="2.692" z="-13.662" r="0.300" parent="164" label="Seg1_dend_23"/>
   <Point id="199" x="20.500" y="-3.746" z="0.531" r="0.750" parent="198" label="Seg3_dend_29"/>
   <Point id="247" x="-9.600" y="-8.623" z="0.915" r="0.850" parent="246" label="Seg1_dend_36"/>
   <Point id="11" x="0.200" y="-5.600" z="3.400" r="3.040" parent="10" label="Seg1_soma_6"/>
   <Point id="1091" x="-9.800" y="5.500" z="0.400" r="0.155" parent="1090" label="Seg5_hill"/>
   <Point id="89" x="-30.100" y="4.231" z="1.346" r="0.650" parent="88" label="Seg1_dend_12"/>
   <Point id="24" x="-41.200" y="16.231" z="1.646" r="0.750" parent="17" label="Seg0_dend_3"/>
   <Point id="18" x="-35.000" y="20.431" z="7.146" r="0.400" parent="17" label="Seg0_dend_2"/>
   <Point id="133" x="31.900" y="14.969" z="5.054" r="0.600" parent="132" label="Seg4_dend_17"/>
   <Point id="332" x="0.200" y="22.900" z="2.100" r="3.800" parent="5" label="Seg0_apic_0"/>
   <Point id="172" x="0.300" y="-37.508" z="-5.062" r="0.600" parent="171" label="Seg1_dend_26"/>
   <Point id="169" x="9.100" y="-31.708" z="-5.062" r="0.350" parent="168" label="Seg1_dend_25"/>
   <Point id="166" x="-27.500" y="4.892" z="-12.662" r="0.300" parent="165" label="Seg2_dend_23"/>
   <Point id="200" x="24.400" y="-5.646" z="-0.969" r="0.600" parent="199" label="Seg4_dend_29"/>
   <Point id="248" x="-9.600" y="-16.423" z="0.915" r="0.650" parent="247" label="Seg2_dend_36"/>
   <Point id="296" x="0.200" y="-5.162" z="0.808" r="1.000" parent="11" label="Seg0_dend_39"/>
   <Point id="12" x="0.200" y="-7.500" z="0.700" r="1.615" parent="11" label="Seg0_soma_7"/>
   <Point id="1080" x="-11.300" y="5.500" z="0.400" r="0.119" parent="1091" label="Seg0_iseg"/>
   <Point id="90" x="-39.300" y="-1.669" z="1.046" r="0.650" parent="89" label="Seg2_dend_12"/>
   <Point id="73" x="-46.100" y="13.031" z="1.446" r="0.400" parent="24" label="Seg0_dend_9"/>
   <Point id="25" x="-49.300" y="16.231" z="5.146" r="0.550" parent="24" label="Seg0_dend_4"/>

 - and 1075 more lines -

membrane_distrib.xml

<CellProperties id="membrane_distrib" membraneCapacitance="0.75uF_per_cm2"
    cytoplasmResistivity="150.0ohm_cm">

  	<PassiveProperties region="*myelin*" membraneCapacitance="0.02uF_per_cm2"/>
  	<PassiveProperties region="*dend*" membraneCapacitance="1.125uF_per_cm2"/>
	<PassiveProperties region="*apic*" membraneCapacitance="1.125uF_per_cm2"/>

	<CellRegion match="*soma*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1"/>
		<ChannelPopulation id="KvMS" channel="KvMS" color="0x33ccff" density="10"/>
		<ChannelPopulation id="KmMS" channel="KmMS" color="0x33ccff" density="0.005"/>
		<ChannelPopulation id="CaMS" channel="CaMS" color="0x66ff33" density="0.015"/>
	</CellRegion>

	<CellRegion match="*dend*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1.5"/>
		<ChannelPopulation id="KmMS" channel="KmMS" color="0x33ccff" density="0.0075"/>
		<ChannelPopulation id="CaMS" channel="CaMS" color="0x66ff33" density="0.02"/>
		<ChannelPopulation id="leak-na" channel="leak-na" density="0.00415"/>
		<ChannelPopulation id="leak-k" channel="leak-k" density="0.00415"/>
	</CellRegion>

	<CellRegion match="*apic*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1.5"/>
		<ChannelPopulation id="KmMS" channel="KmMS" color="0x33ccff" density="0.0075"/>
		<ChannelPopulation id="CaMS" channel="CaMS" color="0x66ff33" density="0.02"/>
		<ChannelPopulation id="leak-na" channel="leak-na" density="0.00415"/>
		<ChannelPopulation id="leak-k" channel="leak-k" density="0.00415"/>
	</CellRegion>

	<CellRegion match="*hill*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1500"/>
		<ChannelPopulation id="KvMS" channel="KvMS" color="0x33ccff" density="100"/>
	</CellRegion>

	<CellRegion match="*iseg*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1500"/>
		<ChannelPopulation id="KvMS" channel="KvMS" color="0x33ccff" density="100"/>
	</CellRegion>

	<CellRegion match="*node*">
		<ChannelPopulation id="NaMS" channel="NaMS" color="0xff4040" density="1000"/>
		<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="80"/>
		<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="80"/>
	</CellRegion>

	<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="0.0083per_um2">
		<RegionMask action="exclude" where="region=*myelin*"/>
	</ChannelPopulation>

	<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="0.0083per_um2">
		<RegionMask action="exclude" where="region=*myelin*"/>
	</ChannelPopulation>



	<DensityAdjustment maintain="-60mV" vary="leak-na, leak-k"/>
</CellProperties>

environment.xml

<CellEnvironment id="environment" temperature="37.0Celsius">
	<Ion id="Na" name="Sodium" reversalPotential="50mV"/>
	<Ion id="K" name="Potassium" reversalPotential="-90mV"/>
	<Ion id="Ca" name="Calcium" reversalPotential="140mV"/>
	<Ion id="AMPARion" name="AMPAR_mixed" reversalPotential="0mV"/>
	</CellEnvironment>

record_p18.xml (truncated)

<Access id="record_p18" saveInterval="0.1ms" recordClamps="no">
<VoltageRecorder at="Seg3_iseg" lineColor="blue"/>
	<CellLocation id="syn1" path="100" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn2" path="200" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn3" path="300" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn4" path="400" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn5" path="500" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn6" path="700" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn7" path="200" rankBy="radius" sequenceIndex="11"/>
	<CellLocation id="syn8" path="200" rankBy="radius" sequenceIndex="10"/>
	<CellLocation id="syn9" path="250" rankBy="radius" sequenceIndex="5"/>
	<CellLocation id="syn10" path="800" rankBy="radius" sequenceIndex="5"/>
	<CellLocation id="syn11" path="100" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn12" path="200" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn13" path="300" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn14" path="800" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn15" path="200" rankBy="radius" sequenceIndex="9"/>
	<CellLocation id="syn16" path="200" rankBy="radius" sequenceIndex="8"/>
	<CellLocation id="syn17" path="200" rankBy="radius" sequenceIndex="7"/>
	<CellLocation id="syn18" path="200" rankBy="radius" sequenceIndex="6"/>
	<CellLocation id="syn19" path="250" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn20" path="350" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn21" path="100" rankBy="radius" sequenceIndex="3"/>
	<CellLocation id="syn22" path="200" rankBy="radius" sequenceIndex="3"/>
	<CellLocation id="syn23" path="300" rankBy="radius" sequenceIndex="3"/>
	<CellLocation id="syn24" path="300" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn25" path="800" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn26" path="200" rankBy="radius" sequenceIndex="5"/>
	<CellLocation id="syn27" path="200" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn28" path="150" rankBy="radius" sequenceIndex="8"/>
	<CellLocation id="syn29" path="250" rankBy="radius" sequenceIndex="3"/>
	<CellLocation id="syn30" path="250" rankBy="radius" sequenceIndex="8"/>
	<CellLocation id="syn31" path="100" rankBy="radius" sequenceIndex="7"/>
	<CellLocation id="syn32" path="100" rankBy="radius" sequenceIndex="9"/>
	<CellLocation id="syn33" path="100" rankBy="radius" sequenceIndex="10"/>
	<CellLocation id="syn34" path="100" rankBy="radius" sequenceIndex="8"/>
	<CellLocation id="syn35" path="150" rankBy="radius" sequenceIndex="14"/>
	<CellLocation id="syn36" path="150" rankBy="radius" sequenceIndex="13"/>
	<CellLocation id="syn37" path="150" rankBy="radius" sequenceIndex="12"/>
	<CellLocation id="syn38" path="150" rankBy="radius" sequenceIndex="11"/>
	<CellLocation id="syn39" path="150" rankBy="radius" sequenceIndex="10"/>
	<CellLocation id="syn40" path="125" rankBy="radius" sequenceIndex="15"/>
	<CellLocation id="syn41" path="100" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn42" path="200" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn43" path="300" rankBy="radius" sequenceIndex="4"/>
	<CellLocation id="syn44" path="800" rankBy="radius" sequenceIndex="1"/>
	<CellLocation id="syn45" path="700" rankBy="radius" sequenceIndex="2"/>
	<CellLocation id="syn46" path="210" rankBy="radius" sequenceIndex="13"/>
	<CellLocation id="syn47" path="200" rankBy="radius" sequenceIndex="10"/>
	<CellLocation id="syn48" path="230" rankBy="radius" sequenceIndex="6"/>
	<CellLocation id="syn49" path="700" rankBy="radius" sequenceIndex="3"/>
	<CellLocation id="syn50" path="150" rankBy="radius" sequenceIndex="7"/>
	
	
	<ConductanceClamp location="syn1">
		<TimeSeries id="epsp" file="epsp.txt" timeUnit="1ms" valueUnit="1nS" scaleFactor="1.2" column="1"/>
	</ConductanceClamp>
	<ConductanceClamp location="syn2">
		<TimeSeries id="epsp" file="epsp.txt" timeUnit="1ms" valueUnit="1nS" scaleFactor="1.2" column="2"/>
	</ConductanceClamp>

 - and 145 more lines -

NaMS.xml

<KSChannel id="NaMS" permeantIon="Na" gSingle="20pS">

	<KSComplex id="m" instances="3">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="1.638per_ms" midpoint ="-30mV" scale="9mV" q10="2.3" baseTemperature="23Celsius"/>
		<ExpLinearTransition from="o" to = "c" rate="1.116per_ms" midpoint="-30mV" scale="-9mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>

	<KSComplex id="h">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="o" to="c" rate="0.12per_ms" midpoint="-45mV" scale="5mV" q10="2.3" baseTemperature="23Celsius"/>
		<ExpLinearTransition from="c" to="o" rate="0.0455per_ms" midpoint="-70mV" scale="-5mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>

</KSChannel>

KvMS.xml

<KSChannel id="KvMS" permeantIon="K" gSingle="20pS">

	<KSComplex id="n">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.18per_ms" midpoint ="25mV" scale="9mV" q10="2.3" baseTemperature="23Celsius"/>
		<ExpLinearTransition from="o" to = "c" rate="0.018per_ms" midpoint="25mV" scale="-9mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>


</KSChannel>

KmMS.xml

<KSChannel id="KmMS" permeantIon="K" gSingle="20pS">

	<KSComplex id="n">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.009per_ms" midpoint ="-30mV" scale="9mV" q10="2.3" baseTemperature="23Celsius"/>
		<ExpLinearTransition from="o" to = "c" rate="0.009per_ms" midpoint="-30mV" scale="-9mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>


</KSChannel>

CaMS.xml

<KSChannel id="CaMS" permeantIon="Ca" gSingle="20pS">

	<KSComplex id="m" instances="2">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpLinearTransition from="c" to="o" rate="0.209per_ms" midpoint ="-27mV" scale="3.8mV" q10="2.3" baseTemperature="23Celsius"/>
		<ExpTransition from="o" to = "c" rate="0.94per_ms" midpoint="-75mV" scale="-17mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>

	<KSComplex id="h">
		<ClosedState id="c"/>
		<OpenState id="o"/>
		<ExpTransition from="c" to="o" rate="0.000457per_ms" midpoint="-13mV" scale="-50mV" q10="2.3" baseTemperature="23Celsius"/>
		<SigmoidTransition from="o" to="c" rate="0.0065per_ms" midpoint="-15mV" scale="28mV" q10="2.3" baseTemperature="23Celsius"/>
	</KSComplex>

</KSChannel>

leak-na.xml

<KSChannel id="leak-na" gSingle="20pS" permeantIon="Na">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>

leak-k.xml

<KSChannel id="leak-k" gSingle="20pS" permeantIon="K">
	<OpenState id="o1"/>
	<ClosedState id="c1"/>
	<FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/>
</KSChannel>