resonance (run-sr.xml)
Spruston CA1 pyramidal neuron (with Ih)
Total CPU time 1.544 seconds; at 11:37:01 Tue 26 Jan 2010
| Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | CPU Time / s |
| 1506 | 0 / 0 | 487260 / 1506 | 0 / 0 | 1.54 |
 |
Morphology: ri06psics
Predefined views
zoom100ms
whole
All files
Model
Archive file of the complete model: resonance.jarrun-sr.xml
<PSICSRun timeStep="0.02ms" runTime="50ms" startPotential="-70mV" environment="environment" properties="membrane2" access="recordri06" stochThreshold="0" quickChannels="false" morphology="ri06psics" repeats="1"> <!-- activity="activity-sr" --> <StructureDiscretization baseElementSize="10um"/> <info>Spruston CA1 pyramidal neuron (with Ih)</info> <!--<RunSet vary="timeStep" values="[0.02]ms" filepattern="out"> <CommandSet vary="ipulse:to" values="[0.05 0.1 0.15 0.2 0.3 0.35 0.4 0.45]nA"/> </RunSet>--> <!--<ChannelStochThreshold channel="Nax-Mig-tuft" threshold="100000000"/> <ChannelStochThreshold channel="Kdr-Mig-tuft" threshold="100000000"/> <ChannelStochThreshold channel="Ih-Spru-tuft" threshold="100000000"/> <ChannelStochThreshold channel="Kaprox-Mig-tuft" threshold="100000000"/> <ChannelStochThreshold channel="Kadist-Mig-tuft" threshold="100000000"/> <ChannelStochThreshold channel="leak-na-tuft" threshold="100000000"/> <ChannelStochThreshold channel="leak-k-tuft" threshold="100000000"/>--> <ViewConfig> <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"/> <!--<Line file="psics-out.txt" show="2" color="#ffffcc"/> <Line file="psics-out.txt" show="3" color="#ffff99"/> <Line file="psics-out.txt" show="4" color="#ffff66"/> <Line file="psics-out.txt" show="5" color="#ffff33"/> <Line file="psics-out.txt" show="6" color="#ffff00"/> <Line file="psics-out.txt" show="7" color="#ffcc33"/> <Line file="psics-out.txt" show="8" color="#ffcc00"/> <Line file="psics-out.txt" show="9" color="#ff9933"/>--> <View id="zoom100ms" xmin="200." xmax="300." ymin="-80." ymax="-20."/> <View id="whole" xmin="-10." xmax="1110" ymin="-80." ymax="-40."/> </LineGraph> </ViewConfig> </PSICSRun>
ri06psics.xml (truncated)
<CellMorphology id="ri06psics"> <Point id="rootpoint" x="0.000" y="10.200" z="0.000" r="2.468" label="Seg0_somaA"/> <Point id="0" x="0.000" y="10.384" z="0.000" r="2.500" parent="rootpoint" label="Seg0_somaA"/> <Point id="1" x="0.000" y="9.824" z="0.000" r="2.517" parent="0" label="Seg1_somaA"/> <Point id="2" x="0.000" y="9.074" z="0.000" r="2.567" parent="1" label="Seg2_somaA"/> <Point id="3" x="0.000" y="8.413" z="0.000" r="2.986" parent="2" label="Seg3_somaA"/> <Point id="4" x="0.000" y="7.096" z="0.000" r="5.191" parent="3" label="Seg4_somaA"/> <Point id="5" x="0.000" y="6.399" z="0.000" r="5.465" parent="4" label="Seg5_somaA"/> <Point id="6" x="0.000" y="5.583" z="0.000" r="5.854" parent="5" label="Seg6_somaA"/> <Point id="7" x="0.000" y="4.946" z="0.000" r="6.267" parent="6" label="Seg7_somaA"/> <Point id="8" x="0.000" y="4.215" z="0.000" r="6.559" parent="7" label="Seg8_somaA"/> <Point id="9" x="0.000" y="3.520" z="0.000" r="6.852" parent="8" label="Seg9_somaA"/> <Point id="10" x="0.000" y="2.639" z="0.000" r="7.239" parent="9" label="Seg10_somaA"/> <Point id="11" x="0.000" y="1.855" z="0.000" r="7.354" parent="10" label="Seg11_somaA"/> <Point id="12" x="0.000" y="1.009" z="0.000" r="7.674" parent="11" label="Seg12_somaA"/> <Point id="13" x="0.000" y="0.224" z="0.000" r="7.479" parent="12" label="Seg13_somaA"/> <Point id="14" x="0.000" y="-0.504" z="0.000" r="7.736" parent="13" label="Seg14_somaA"/> <Point id="15" x="0.000" y="-1.162" z="0.000" r="7.375" parent="14" label="Seg15_somaA"/> <Point id="16" x="0.000" y="-1.926" z="0.000" r="7.394" parent="15" label="Seg16_somaA"/> <Point id="17" x="0.000" y="-2.706" z="0.000" r="7.076" parent="16" label="Seg17_somaA"/> <Point id="18" x="0.000" y="-3.370" z="0.000" r="6.736" parent="17" label="Seg18_somaA"/> <Point id="19" x="0.000" y="-4.099" z="0.000" r="6.028" parent="18" label="Seg19_somaA"/> <Point id="20" x="0.000" y="-4.734" z="0.000" r="5.656" parent="19" label="Seg20_somaA"/> <Point id="21" x="0.000" y="-5.484" z="0.000" r="5.458" parent="20" label="Seg21_somaA"/> <Point id="22" x="0.000" y="-6.261" z="0.000" r="5.116" parent="21" label="Seg22_somaA"/> <Point id="23" x="0.000" y="-7.062" z="0.000" r="4.436" parent="22" label="Seg23_somaA"/> <Point id="24" x="0.000" y="-7.866" z="0.000" r="3.920" parent="23" label="Seg24_somaA"/> <Point id="25" x="0.000" y="-8.659" z="0.000" r="3.918" parent="24" label="Seg25_somaA"/> <Point id="26" x="0.000" y="-9.447" z="0.000" r="3.371" parent="25" label="Seg26_somaA"/> <Point id="27" x="0.000" y="-10.208" z="0.000" r="3.211" parent="26" label="Seg27_somaA"/> <Point id="28" x="0.000" y="-10.962" z="0.000" r="3.100" parent="27" label="Seg28_somaA"/> <Point id="29" x="0.000" y="-11.694" z="0.000" r="2.687" parent="28" label="Seg29_somaA"/> <Point id="30" x="0.000" y="-12.436" z="0.000" r="2.405" parent="29" label="Seg30_somaA"/> <Point id="31" x="0.000" y="-13.095" z="0.000" r="1.948" parent="30" label="Seg31_somaA"/> <Point id="32" x="0.000" y="-13.770" z="0.000" r="2.300" parent="31" label="Seg32_somaA"/> <Point id="33" x="0.000" y="-14.120" z="0.000" r="1.500" parent="32" label="Seg33_somaA"/> <Point id="34" x="0.000" y="-14.872" z="0.000" r="1.500" parent="33" label="Seg34_somaA"/> <Point id="35" x="0.000" y="-15.406" z="0.000" r="1.500" parent="34" label="Seg35_somaA"/> <Point id="36" x="0.000" y="-15.670" z="0.000" r="1.500" parent="35" label="Seg36_somaA"/> <Point id="2124" x="0.000" y="13.430" z="0.000" r="2.000" parent="35" label="Seg0_dendA5_0"/> <Point id="1415" x="0.970" y="-1.273" z="0.000" r="0.970" parent="35" label="Seg0_dendA3_0"/> <Point id="5624" x="-0.250" y="-3.735" z="0.000" r="1.865" parent="35" label="Seg0_hill"/> <Point id="562" x="-1.690" y="-8.898" z="0.000" r="0.600" parent="35" label="Seg0_dendA2_0"/> <Point id="1799" x="0.000" y="-15.670" z="-0.010" r="0.970" parent="36" label="Seg0_dendA4_0"/> <Point id="37" x="0.000" y="-17.410" z="0.000" r="1.100" parent="36" label="Seg0_dendA1_0"/> <Point id="2125" x="0.000" y="16.170" z="0.000" r="1.900" parent="2124" label="Seg1_dendA5_0"/> <Point id="1416" x="2.180" y="-1.763" z="0.000" r="0.970" parent="1415" label="Seg1_dendA3_0"/> <Point id="5625" x="-0.790" y="-4.775" z="0.000" r="1.720" parent="5624" label="Seg1_hill"/> <Point id="563" x="-4.340" y="-9.138" z="0.000" r="0.600" parent="562" label="Seg1_dendA2_0"/> <Point id="1800" x="2.650" y="-16.910" z="-0.010" r="0.970" parent="1799" label="Seg1_dendA4_0"/> <Point id="38" x="0.000" y="-21.390" z="0.000" r="1.000" parent="37" label="Seg1_dendA1_0"/> <Point id="2126" x="-0.480" y="19.900" z="0.190" r="1.900" parent="2125" label="Seg2_dendA5_0"/> <Point id="1417" x="2.660" y="-1.763" z="0.000" r="0.970" parent="1416" label="Seg2_dendA3_0"/> <Point id="5626" x="-1.270" y="-5.755" z="0.000" r="1.555" parent="5625" label="Seg2_hill"/> <Point id="591" x="-4.100" y="-12.378" z="0.230" r="0.600" parent="563" label="Seg0_dendA2_01"/> <Point id="564" x="-6.040" y="-7.148" z="0.000" r="0.480" parent="563" label="Seg0_dendA2_00"/> <Point id="1801" x="2.900" y="-16.910" z="-0.010" r="0.970" parent="1800" label="Seg2_dendA4_0"/> <Point id="39" x="0.000" y="-23.380" z="0.000" r="0.980" parent="38" label="Seg2_dendA1_0"/> <Point id="2127" x="0.000" y="24.130" z="0.200" r="1.900" parent="2126" label="Seg3_dendA5_0"/> <Point id="1418" x="3.870" y="-2.263" z="0.000" r="0.970" parent="1417" label="Seg3_dendA3_0"/> - and 5734 more lines -
membrane.xml
<CellProperties id="membrane" membraneCapacitance="0.75uF_per_cm2"
cytoplasmResistivity="200.0ohm_cm">
<PassiveProperties region="*_node*" cytoplasmResistivity="50.0ohm_cm"/>
<PassiveProperties region="*inode*" membraneCapacitance="0.04uF_per_cm2"/>
<PassiveProperties region="*dend*" membraneCapacitance="1.5uF_per_cm2"/>
<CellRegion match="*soma*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24"/>
<ChannelPopulation id="Ih-Spru" channel="Ih-Spru" color="0x33ccff" density="1.5969"/>
</CellRegion>
<CellRegion match="*dend*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24">
<RegionMask action="exclude" where="region=*dendA5*"/>
</ChannelPopulation>
<ChannelPopulation id="Ih-Spru" channel="Ih-Spru" color="0x33ccff" density="1.5969 + ((2.1582-1.5969)/(1+exp((p - 98.753)/50.07)))"/>
<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="0.02"/>
<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="0.02"/>
</CellRegion>
<SynapsePopulation id="synpop" synapse="syn1" density="0.1per_um2" seed="1010">
<RegionMask action="include" where="region=*dend*"/>
<RegionMask action="exclude" where="p .lt. 30"/>
<NormalWeights min="0.9" max="1.1" sd="0.01"/>
<!--<UniformWeights min="0.1" max="3"/>
<LogUniformWeights min="0.1" max="3"/>
<LogNormalWeights min="0.1" max="3" sd="0.5"/>-->
</SynapsePopulation>
<CellRegion match="*dendA5*">
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24 * (1 + p/100) per_um2">
<RegionMask action="exclude" where="p .gt. 100"/>
</ChannelPopulation>
<ChannelPopulation id="Kadist-Mig1" channel="Kadist-Mig" color="0x33ccff" density="24 * (1 + p/100) per_um2">
<RegionMask action="exclude" where="p .lt. 100"/>
<RegionMask action="exclude" where="p .gt. 500"/>
</ChannelPopulation>
<ChannelPopulation id="Kadist-Mig2" channel="Kadist-Mig" color="0x33ccff" density="24 * 6 per_um2">
<RegionMask action="exclude" where="p .lt. 500"/>
</ChannelPopulation>
</CellRegion>
<CellRegion match="*hill*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24"/>
</CellRegion>
<CellRegion match="*iseg*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="24"/>
</CellRegion>
<CellRegion match="*inode*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="20"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="5"/>
</CellRegion>
<CellRegion match="*_node*">
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="1500"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="20"/>
<ChannelPopulation id="Kaprox-Mig" channel="Kaprox-Mig" color="0x33ccff" density="5"/>
</CellRegion>
<ChannelPopulation id="leak-na" channel="leak-na" color="0xffff00" density="0.02per_um2">
<RegionMask action="exclude" where="region=*node*"/>
</ChannelPopulation>
<ChannelPopulation id="leak-k" channel="leak-k" color="0xff33cc" density="0.02per_um2">
<RegionMask action="exclude" where="region=*node*"/>
</ChannelPopulation>
<DensityAdjustment maintain="-70mV" vary="leak-na, leak-k"/>
</CellProperties>
environment.xml
<CellEnvironment id="environment" temperature="34Celsius"> <Ion id="K" name="Potassium" reversalPotential="-90mV"/> <Ion id="Na" name="Sodium" reversalPotential="55mV"/> <Ion id="H" name="MixedCation" reversalPotential="-25mV"/> <Ion id="AMPAion" name="MixedAMPA" reversalPotential="0mV"/> </CellEnvironment>
recordri06.xml (truncated)
<Access id="recordri06" saveInterval="0.1ms"> <CellLocation id="pa0" path="100" rankBy="radius" sequenceIndex="0"/> <CellLocation id="pa1" path="100" rankBy="radius" sequenceIndex="1"/> <CellLocation id="pa2" path="100" rankBy="radius" sequenceIndex="2"/> <CellLocation id="pa3" path="100" rankBy="radius" sequenceIndex="3"/> <CellLocation id="pa4" path="100" rankBy="radius" sequenceIndex="4"/> <CellLocation id="pa5" path="100" rankBy="radius" sequenceIndex="5"/> <CellLocation id="pa6" path="100" rankBy="radius" sequenceIndex="6"/> <CellLocation id="pa7" path="100" rankBy="radius" sequenceIndex="7"/> <CellLocation id="pa8" path="100" rankBy="radius" sequenceIndex="8"/> <CellLocation id="pa9" path="100" rankBy="radius" sequenceIndex="9"/> <CellLocation id="pa10" path="100" rankBy="radius" sequenceIndex="10"/> <CellLocation id="pa11" path="100" rankBy="radius" sequenceIndex="11"/> <CellLocation id="pa12" path="100" rankBy="radius" sequenceIndex="12"/> <CellLocation id="pa13" path="100" rankBy="radius" sequenceIndex="13"/> <CellLocation id="pa14" path="100" rankBy="radius" sequenceIndex="14"/> <CellLocation id="pa15" path="100" rankBy="radius" sequenceIndex="15"/> <CellLocation id="pa16" path="100" rankBy="radius" sequenceIndex="16"/> <CellLocation id="pa17" path="100" rankBy="radius" sequenceIndex="17"/> <CellLocation id="pa18" path="100" rankBy="radius" sequenceIndex="18"/> <CellLocation id="pa19" path="100" rankBy="radius" sequenceIndex="19"/> <CellLocation id="pa20" path="100" rankBy="radius" sequenceIndex="20"/> <CellLocation id="pa21" path="100" rankBy="radius" sequenceIndex="21"/> <CellLocation id="pb0" path="200" rankBy="radius" sequenceIndex="0"/> <CellLocation id="pb1" path="200" rankBy="radius" sequenceIndex="1"/> <CellLocation id="pb2" path="200" rankBy="radius" sequenceIndex="2"/> <CellLocation id="pb3" path="200" rankBy="radius" sequenceIndex="3"/> <CellLocation id="pb4" path="200" rankBy="radius" sequenceIndex="4"/> <CellLocation id="pb5" path="200" rankBy="radius" sequenceIndex="5"/> <CellLocation id="pb6" path="200" rankBy="radius" sequenceIndex="6"/> <CellLocation id="pb7" path="200" rankBy="radius" sequenceIndex="7"/> <CellLocation id="pb8" path="200" rankBy="radius" sequenceIndex="8"/> <CellLocation id="pb9" path="200" rankBy="radius" sequenceIndex="9"/> <CellLocation id="pb10" path="200" rankBy="radius" sequenceIndex="10"/> <CellLocation id="pb11" path="200" rankBy="radius" sequenceIndex="11"/> <CellLocation id="pb12" path="200" rankBy="radius" sequenceIndex="12"/> <CellLocation id="pb13" path="200" rankBy="radius" sequenceIndex="13"/> <CellLocation id="pb14" path="200" rankBy="radius" sequenceIndex="14"/> <CellLocation id="pb15" path="200" rankBy="radius" sequenceIndex="15"/> <CellLocation id="pb16" path="200" rankBy="radius" sequenceIndex="16"/> <CellLocation id="pb17" path="200" rankBy="radius" sequenceIndex="17"/> <CellLocation id="pb18" path="200" rankBy="radius" sequenceIndex="18"/> <CellLocation id="pb19" path="200" rankBy="radius" sequenceIndex="19"/> <CellLocation id="pb20" path="200" rankBy="radius" sequenceIndex="20"/> <CellLocation id="pb21" path="200" rankBy="radius" sequenceIndex="21"/> <CellLocation id="pb22" path="200" rankBy="radius" sequenceIndex="22"/> <CellLocation id="pb23" path="200" rankBy="radius" sequenceIndex="23"/> <CellLocation id="pb24" path="200" rankBy="radius" sequenceIndex="24"/> <CellLocation id="pb25" path="200" rankBy="radius" sequenceIndex="25"/> <CellLocation id="pb26" path="200" rankBy="radius" sequenceIndex="26"/> <CellLocation id="pb27" path="200" rankBy="radius" sequenceIndex="27"/> <CellLocation id="pb28" path="200" rankBy="radius" sequenceIndex="28"/> <CellLocation id="pb29" path="200" rankBy="radius" sequenceIndex="29"/> <CellLocation id="pb30" path="200" rankBy="radius" sequenceIndex="30"/> <!--<CellLocation id="pb31" path="200" rankBy="radius" sequenceIndex="31"/> (axon)--> <CellLocation id="pc0" path="300" rankBy="radius" sequenceIndex="0"/> <CellLocation id="pc1" path="300" rankBy="radius" sequenceIndex="1"/> <CellLocation id="pc2" path="300" rankBy="radius" sequenceIndex="2"/> <CellLocation id="pc3" path="300" rankBy="radius" sequenceIndex="3"/> - and 148 more lines -
activity-sr.xml
<Activity id="activity-sr">
<AfferentEvents population="synpop">
<!--
<PoissonGenerator frequency="4Hz" seed="102"/>
<UniformGenerator frequency="20Hz"/>
<GammaGenerator theta="5ms" k="4"/>
-->
<EventSequence file="spiketimes.txt"/>
</AfferentEvents>
<!--
<AfferentEvents population="synpop2">
<PoissonGenerator frequency="2Hz" seed="101"/>
<!--
<UniformGenerator frequency="20Hz"/>
<GammaGenerator theta="5ms" k="4"/>
</AfferentEvents>
-->
Nax-Mig.xml
<KSChannel id="Nax-Mig" permeantIon="Na" gSingle="20pS">
<CodedTransitionFunction name="trap0" returnVariable="rate" type="double">
<Argument name="v" type="double"/>
<Argument name="th" type="double"/>
<Argument name="a" type="double"/>
<Argument name="q" type="double"/>
<![CDATA[
if (Math.abs(v - th) > 1.e-6) {
rate = a * (v - th) / (1 - Math.exp(-(v - th)/q));
} else {
rate = a * q;
}
]]>
</CodedTransitionFunction>
<KSComplex instances="3">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="mtau" infvar="minf">
<Constant name="q10" value="2"/>
<Constant name="tha" value="-30" info="vhalf, mV"/>
<Constant name="Ra" value="0.4" info="opening rate, per ms"/>
<Constant name="qa" value="7.2" info="activation slope, mV"/>
<Constant name="Rb" value="0.124" info="closing rate, per ms"/>
<Constant name="mmin" value="0.02" info="minimum time constant"/>
<![CDATA[
double qt = Math.pow(q10, ((temperature-24)/10));
double a = trap0(v ,tha,Ra,qa);
double b = trap0(-v ,-tha,Rb,qa);
mtau = 1 / (a + b) / qt;
if (mtau < mmin) mtau=mmin;
minf = a / (a + b);
]]>
</TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="htau" infvar="hinf">
<Constant name="q10" value="2"/>
<Constant name="thi1" value="-45" info="vhalf, mV"/>
<Constant name="thi2" value="-45" info="vhalf, mV"/>
<Constant name="Rd" value="0.03" info="opening rate, per ms"/>
<Constant name="Rg" value="0.01" info="closing rate, per ms"/>
<Constant name="qd" value="1.5" info="activation slope, mV"/>
<Constant name="qg" value="1.5" info="activation slope, mV"/>
<Constant name="hmin" value="0.5" info="minimum time constant"/>
<Constant name="thinf" value="-50" info="inact inf slope, mV"/>
<Constant name="qinf" value="4"/>
<![CDATA[
double qt = Math.pow(q10, ((temperature-24)/10));
double a = trap0(v, thi1,Rd,qd);
double b = trap0(-v, -thi2,Rg,qg);
htau = 1 / (a + b) / qt;
if (htau < hmin) htau=hmin;
hinf = 1/(1+Math.exp((v-thinf)/qinf));
]]>
</TauInfCodedTransition>
</KSComplex>
</KSChannel>
Kdr-Mig.xml
<KSChannel id="Kdr-Mig" permeantIon="K" gSingle="20pS">
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="ntau" infvar="ninf">
<Constant name="q10" value="1"/>
<Constant name="zetan" value="-3"/>
<Constant name="vhalfn" value="13" info="mV"/>
<Constant name="a0n" value="0.02"/>
<Constant name="gmn" value="0.7"/>
<Constant name="nmin" value="2"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-24)/10));
double a = Math.exp(1.e-3*zetan*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ninf = 1/(1 + a);
double betn = Math.exp(1.e-3*zetan*gmn*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ntau = betn /(qt*a0n*(1+a));
if (ntau < nmin) ntau = nmin;
]]>
</TauInfCodedTransition>
</KSComplex>
</KSChannel>
Kaprox-Mig.xml
<KSChannel id="Kaprox-Mig" permeantIon="K" gSingle="20pS">
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="ntau" infvar="ninf">
<Constant name="q10" value="5"/>
<Constant name="zetan" value="-1.5"/>
<Constant name="pw" value="-1" info=""/>
<Constant name="tq" value="-40" info=""/>
<Constant name="qq" value="5" info=""/>
<Constant name="vhalfn" value="11" info="mV"/>
<Constant name="gmn" value="0.55"/>
<Constant name="nmin" value="0.1" info="minimum time constant"/>
<Constant name="a0n" value="0.05"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-24)/10));
double zeta=zetan+pw/(1+Math.exp((v-tq)/qq));
double a = Math.exp(1.e-3*zeta*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ninf = 1/(1 + a);
double betn = Math.exp(1.e-3*zeta*gmn*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ntau = betn /(qt*a0n*(1+a));
if (ntau < nmin) ntau = nmin;
]]>
</TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<OpenState id="o"/>
<ClosedState id="c"/>
<TauInfCodedTransition from="c" to="o" tauvar="ltau" infvar="linf">
<Constant name="q10" value="5"/>
<Constant name="zetal" value="3"/>
<Constant name="vhalfl" value="-56" info="mV"/>
<Constant name="qtl" value="1" info=""/>
<Constant name="lmin" value="2" info="minimum time constant"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-24)/10));
double a = Math.exp(1.e-3*zetal*(v-vhalfl)*9.648e4/(8.315*(273.16+temperature)));
linf = 1 / (1 + a);
ltau = 0.26 * (v + 50) / qtl;
if (ltau < lmin / qtl) ltau = lmin / qtl;
]]>
</TauInfCodedTransition>
</KSComplex>
</KSChannel>
Ih-Spru.xml
<KSChannel id="Ih-Spru" permeantIon="H" gSingle="1pS">
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="ntau" infvar="ninf">
<Constant name="q10" value="4.5"/>
<Constant name="zeta" value="7"/>
<Constant name="vhalf" value="-81" info="mV"/>
<Constant name="a0" value="0.00057"/>
<Constant name="gas" value="8.315"/>
<Constant name="far" value="9.648e4"/>
<Constant name="a" value="0.4"/>
<Constant name="nmin" value="2"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-33)/10));
double alphan = qt*a0*Math.exp(1.e-3*zeta*(-a)*(v-vhalf)*far/(gas*(273.16+temperature)));
double betan = qt*a0*Math.exp(1.e-3*zeta*(1-a)*(v-vhalf)*far/(gas*(273.16+temperature)));
ninf = alphan/(alphan + betan);
ntau = 1 /(alphan+betan);
if (ntau < nmin) ntau = nmin;
]]>
</TauInfCodedTransition>
</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>
Kadist-Mig.xml
<KSChannel id="Kadist-Mig" permeantIon="K" gSingle="20pS">
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="ntau" infvar="ninf">
<Constant name="q10" value="5"/>
<Constant name="zetan" value="-1.8"/>
<Constant name="pw" value="-1" info=""/>
<Constant name="tq" value="-40" info=""/>
<Constant name="qq" value="5" info=""/>
<Constant name="vhalfn" value="-1" info="mV"/>
<Constant name="gmn" value="0.39"/>
<Constant name="nmin" value="0.2" info="minimum time constant"/>
<Constant name="a0n" value="0.1"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-24)/10));
double zeta=zetan+pw/(1+Math.exp((v-tq)/qq));
double a = Math.exp(1.e-3*zeta*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ninf = 1/(1 + a);
double betn = Math.exp(1.e-3*zeta*gmn*(v-vhalfn)*9.648e4/(8.315*(273.16+temperature)));
ntau = betn /(qt*a0n*(1+a));
if (ntau < nmin) ntau = nmin;
]]>
</TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<OpenState id="o"/>
<ClosedState id="c"/>
<TauInfCodedTransition from="c" to="o" tauvar="ltau" infvar="linf">
<Constant name="q10" value="5"/>
<Constant name="zetal" value="3"/>
<Constant name="vhalfl" value="-56" info="mV"/>
<Constant name="qtl" value="1" info=""/>
<Constant name="lmin" value="2" info="minimum time constant"/>
<![CDATA[
double qt=Math.pow(q10, ((temperature-24)/10));
double a = Math.exp(1.e-3*zetal*(v-vhalfl)*9.648e4/(8.315*(273.16+temperature)));
linf = 1 / (1 + a);
ltau = 0.26 * (v + 50) / qtl;
if (ltau < lmin / qtl) ltau = lmin / qtl;
]]>
</TauInfCodedTransition>
</KSComplex>
</KSChannel>
syn1.xml
<Synapse id="syn1" permeantIon="AMPAion" baseConductance="200pS"> <!--<ExponentialTimecourse tau="4ms"/>--> <BiExponentialTimecourse rise="0.2ms" tau="2ms"/> <!--<AlphaTimecourse tau="4ms"/> <ProfileTimecourse file="stim1.txt" timeUnit="1ms"/>--> </Synapse>
membrane2.xml
<CellProperties id="membrane2" membraneCapacitance="0.75uF_per_cm2"
cytoplasmResistivity="200.0ohm_cm">
<PassiveProperties region="*_node*" cytoplasmResistivity="50.0ohm_cm"/>
<PassiveProperties region="*inode*" membraneCapacitance="0.04uF_per_cm2"/>
<PassiveProperties region="*dend*" membraneCapacitance="1.5uF_per_cm2"/>
<ChannelPopulation id="Nax-Mig" channel="Nax-Mig" color="0xff4040" density="10"/>
<ChannelPopulation id="Kdr-Mig" channel="Kdr-Mig" color="0x33ccff" density="10"/>
<CellRegion match="*dendA1*">
<ChannelPopulation id="leak-na1" channel="leak-na1" color="0xffff00" density="0.02"/>
<ChannelPopulation id="leak-k1" channel="leak-k1" color="0xff33cc" density="0.02"/>
</CellRegion>
<CellRegion match="*dendA5*">
<ChannelPopulation id="leak-na2" channel="leak-na2" color="0xffff00" density="0.02"/>
<ChannelPopulation id="leak-k2" channel="leak-k2" color="0xff33cc" density="0.02"/>
</CellRegion>
<ChannelPopulation id="leak-na3" channel="leak-na3" color="0xffff00" density="0.02per_um2">
<RegionMask action="exclude" where="region=*dendA1*"/>
<RegionMask action="exclude" where="region=*dendA5*"/>
</ChannelPopulation>
<ChannelPopulation id="leak-k3" channel="leak-k3" color="0xff33cc" density="0.02per_um2">
<RegionMask action="exclude" where="region=*dendA1*"/>
<RegionMask action="exclude" where="region=*dendA5*"/>
</ChannelPopulation>
<!--
<DensityAdjustment maintain="-70mV" vary="leak-na, leak-k"/>
-->
<DensityAdjustment maintain="-65mV" vary="leak-na1, leak-k1"/>
<DensityAdjustment maintain="-65mV" vary="leak-na2, leak-k2"/>
<DensityAdjustment maintain="-65mV" vary="leak-na3, leak-k3"/>
</CellProperties>
leak-na1.xml
<KSChannel id="leak-na1" 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-k1.xml
<KSChannel id="leak-k1" gSingle="20pS" permeantIon="K"> <OpenState id="o1"/> <ClosedState id="c1"/> <FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/> </KSChannel>
leak-na2.xml
<KSChannel id="leak-na2" 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-k2.xml
<KSChannel id="leak-k2" gSingle="20pS" permeantIon="K"> <OpenState id="o1"/> <ClosedState id="c1"/> <FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/> </KSChannel>
leak-na3.xml
<KSChannel id="leak-na3" 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-k3.xml
<KSChannel id="leak-k3" gSingle="20pS" permeantIon="K"> <OpenState id="o1"/> <ClosedState id="c1"/> <FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/> </KSChannel>