migliore-1a (run1a.xml)
Migliore et al CA1 pyramidal cell
Model corresponding to figure 1a with a steady current injection at the soma and recording from two points on the apical dendrite, 200um and 400um from the soma. It shows some backpropagation to 200um but very little at 400um.
N.B. the cell looks odd because it is the exported compartmentalization from Neuron that has lost the original positions. There are just straight segments and a systematic branching angle that makes it curl up.
This uses the coded channel transition rate option in several of the channels in order to use exactly the same expressions as in the Migliore paper. The leaks are stochastic with open probability 0.7 and conductance 20pS.
Total CPU time 1.140 seconds; at 10:35:49 Thu 24 Sep 2009
| Compartments | Stochastic channels / cpmts | Continuous channels / cpmts | Non Gated channels / cpmts | CPU Time / s |
| 493 | 0 / 0 | 686857 / 493 | 0 / 0 | 1.14 |
 |
Morphology: morph59
Predefined views
whole
first
All files
| Model | Preprocessed | Outupt data | Reference data etc |
| run1a.xml morph59.xml membrane.xml environment.xml recording-a.xml Nax-coded.xml Kdr-coded.xml Kaprox-coded.xml leak-Na.xml leak-K.xml Na3-coded-basal.xml Na3-coded-apical.xml Kadist-coded.xml Na3-coded-soma.xml |
psics-out.ppp |
log.txt psics-out.sum psics-out.dat psics-out.txt |
Model
Archive file of the complete model: migliore-1a.jarrun1a.xml
<PSICSRun timeStep="0.05ms" runTime="120ms" startPotential="-65mV"
morphology="morph59"
environment="environment"
properties="membrane"
access="recording-a"
stochThreshold="0">
<StructureDiscretization baseElementSize="45.um">
<LocalRefinement from="752" elementSize="5um"/>
</StructureDiscretization>
<ChannelDiscretization vMin="-100mV" vMax="60mV" deltaV="2mV"/>
<info>Migliore et al CA1 pyramidal cell</info>
<About>
Model corresponding to figure 1a with a steady current injection at the soma
and recording from two points on the apical dendrite, 200um and 400um from the soma.
It shows some backpropagation to 200um but very little at 400um.
</About>
<About>
N.B. the cell looks odd because it is the exported compartmentalization from Neuron
that has lost the original positions. There are just straight segments and a
systematic branching angle that makes it curl up.
</About>
<About>
This uses the coded channel transition rate option in several of the channels in order
to use exactly the same expressions as in the Migliore paper. The leaks are stochastic
with open probability 0.7 and conductance 20pS.
</About>
<ViewConfig>
<LineGraph width="500" height="400">
<XAxis min="0" max="250" label="time / ms"/>
<YAxis min="-80" max="60" label="potential / mV"/>
<LineSet file="psics-out.txt" color="red" show="1"/>
<LineSet file="psics-out.txt" color="blue" show="2"/>
<!--
<LineSet file="psics-out.txt" color="green" show="3"/>
-->
<View id="whole" xmin="-10." xmax="120." ymin="-80." ymax="20."/>
<View id="first" xmin="-2" xmax="20" ymin="-80." ymax="20."/>
</LineGraph>
</ViewConfig>
</PSICSRun>
morph59.xml (truncated)
<morphml id="morph59">
<!-- XML file generated by NEURON 5.9 ModelViewer -->
<!-- Authors: Michael Hines and Sushil Kambampati -->
<!-- Yale University -->
<!-- Date: Fri Sep 7 12:52:05 BST 2007 -->
<cells>
<cell name="soma[0]">
<segments>
<segment id="1" name = "Seg0_soma[0]" cable = "0">
<proximal x="0" y="0" z="0" diameter="3.4"/>
<distal x="0.25" y="0" z="0" diameter="3.4"/>
</segment>
<segment id="2" name = "Seg1_soma[0]" parent="1" cable = "0">
<distal x="0.5" y="0" z="0" diameter="3.4"/>
</segment>
<segment id="671" name = "Seg0_basal[41]" parent="1" cable = "181">
<proximal x="0" y="0" z="0" diameter="1"/>
<distal x="-4.38737" y="1.85495" z="0" diameter="1"/>
</segment>
<segment id="672" name = "Seg1_basal[41]" parent="671" cable = "181">
<distal x="-8.77474" y="3.7099" z="0" diameter="1"/>
</segment>
<segment id="606" name = "Seg0_basal[23]" parent="1" cable = "163">
<proximal x="0" y="0" z="0" diameter="1"/>
<distal x="-5.95875" y="0.799243" z="0" diameter="1"/>
</segment>
<segment id="607" name = "Seg1_basal[23]" parent="606" cable = "163">
<distal x="-11.9175" y="1.59849" z="0" diameter="1"/>
</segment>
<segment id="593" name = "Seg0_basal[20]" parent="1" cable = "160">
<proximal x="0" y="0" z="0" diameter="0.4"/>
<distal x="-8.98517" y="-1.20517" z="0" diameter="0.4"/>
</segment>
<segment id="594" name = "Seg1_basal[20]" parent="593" cable = "160">
<distal x="-26.9555" y="-3.61552" z="0" diameter="0.4"/>
</segment>
<segment id="595" name = "Seg2_basal[20]" parent="594" cable = "160">
<distal x="-35.9407" y="-4.82069" z="0" diameter="0.4"/>
</segment>
<segment id="517" name = "Seg0_basal[0]" parent="1" cable = "140">
<proximal x="0" y="0" z="0" diameter="0.8"/>
<distal x="-1.33023" y="-0.562414" z="0" diameter="0.8"/>
</segment>
<segment id="518" name = "Seg1_basal[0]" parent="517" cable = "140">
<distal x="-2.66047" y="-1.12483" z="0" diameter="0.8"/>
</segment>
<segment id="3" name = "Seg0_soma[1]" parent="2" cable = "1">
<proximal x="0.5" y="0" z="0" diameter="3.4"/>
<distal x="0.55" y="0" z="0" diameter="3.4"/>
</segment>
<segment id="4" name = "Seg1_soma[1]" parent="3" cable = "1">
<distal x="0.6" y="0" z="0" diameter="3.4"/>
</segment>
<segment id="736" name = "Seg0_basal[59]" parent="672" cable = "199">
<proximal x="-8.77474" y="3.7099" z="0" diameter="0.4"/>
<distal x="-15.8252" y="10.9693" z="0" diameter="0.4"/>
</segment>
<segment id="737" name = "Seg1_basal[59]" parent="736" cable = "199">
<distal x="-29.9261" y="25.4881" z="0" diameter="0.4"/>
</segment>
- and 2829 more lines -membrane.xml
<CellProperties id="membrane"
cytoplasmResistivity="150ohm_cm"
membraneCapacitance="1.0uF_per_cm2">
<Exclusion winner="*soma*" loser="*apical*"/>
<Exclusion winner="*soma*" loser="*basal*"/>
<Exclusion winner="*soma*" loser="*axon*"/>
<PassiveProperties region="*apical*" membraneCapacitance="2uF_per_cm2"/>
<PassiveProperties region="*basal*" membraneCapacitance="2uF_per_cm2"/>
<PassiveProperties region="*axon*" cytoplasmResistivity="50ohm_cm"/>
<PassiveProperties region="*soma*" membraneCapacitance="1uF_per_cm2"/>
<ChannelPopulation channel="leak-Na" density="0.0512per_um2"/>
<ChannelPopulation channel="leak-K" density="0.0512per_um2"/>
<CellRegion match="*axon*">
<ChannelPopulation channel="Nax-coded" density="21.33per_um2"/>
<ChannelPopulation channel="Kdr-coded" density="3.33per_um2"/>
<ChannelPopulation channel="Kaprox-coded" density="3.2per_um2"/>
</CellRegion>
<CellRegion match="*basal*">
<ChannelPopulation channel="leak-Na" density="0.0512per_um2"/>
<ChannelPopulation channel="leak-K" density="0.0512per_um2"/>
<ChannelPopulation channel="Na3-coded-basal" density="10.67per_um2"/>
<ChannelPopulation channel="Kdr-coded" density="3.33per_um2"/>
<ChannelPopulation channel="Kaprox-coded" density="16per_um2"/>
</CellRegion>
<CellRegion match="*apical*">
<ChannelPopulation channel="leak-Na" density="0.0512per_um2"/>
<ChannelPopulation channel="leak-K" density="0.0512per_um2"/>
<ChannelPopulation channel="Na3-coded-apical" density="10.67per_um2">
<RegionMask action="exclude" where="d .lt. 0.5"/>
<RegionMask action="exclude" where="p .gt. 500"/>
</ChannelPopulation>
<ChannelPopulation channel="Kdr-coded" density="3.33per_um2">
<RegionMask action="exclude" where="d .lt. 0.5"/>
<RegionMask action="exclude" where="p .gt. 500"/>
</ChannelPopulation>
<ChannelPopulation channel="Kaprox-coded" density="16 * (1 + p/100) per_um2">
<RegionMask action="exclude" where="p .gt. 100"/>
</ChannelPopulation>
<ChannelPopulation channel="Kadist-coded" density="16 * (1 + p / 100)per_um2">
<RegionMask action="exclude" where="p .lt. 100"/>
<RegionMask action="exclude" where="p .gt. 500"/>
</ChannelPopulation>
</CellRegion>
<CellRegion match="*soma*">
<ChannelPopulation channel="Na3-coded-soma" density="10.67per_um2"/>
<ChannelPopulation channel="Kdr-coded" density="3.33per_um2"/>
<ChannelPopulation channel="Kaprox-coded" density="16per_um2"/>
</CellRegion>
<DensityAdjustment maintain="-65mV" 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"/> </CellEnvironment>
recording-a.xml
<Access id="recording-a"> <CurrentClamp at="5" id="clampat5" hold="0.15nA"/> <VoltageRecorder at="Seg0_apical[12]"/> <VoltageRecorder at="Seg0_apical[27]"/> </Access>
Nax-coded.xml
<KSChannel id="Nax-coded" permeantIon="Na" gSingle="30pS">
<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-coded.xml
<KSChannel id="Kdr-coded" permeantIon="K" gSingle="30pS">
<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-coded.xml
<KSChannel id="Kaprox-coded" permeantIon="K" gSingle="30pS">
<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>
leak-Na.xml
<KSChannel id="leak-Na" gSingle="5pS" 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="5pS" permeantIon="K"> <OpenState id="o1"/> <ClosedState id="c1"/> <FixedRateTransition from="o1" to="c1" forward="3.per_ms" reverse="7.per_ms"/> </KSChannel>
Na3-coded-basal.xml
<DerivedKSChannel id="Na3-coded-basal" from="Na3-coded-soma"> <ParameterChange to="Na3-a2-semiconstant" attribute="value" newText="1"/> </DerivedKSChannel>
Na3-coded-apical.xml
<DerivedKSChannel id="Na3-coded-apical" from="Na3-coded-soma"> <ParameterChange to="Na3-a2-semiconstant" attribute="value" newText="0.5"/> </DerivedKSChannel>
Kadist-coded.xml
<KSChannel id="Kadist-coded" permeantIon="K" gSingle="30pS">
<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>
Na3-coded-soma.xml
<KSChannel id="Na3-coded-soma" permeantIon="Na" gSingle="30pS">
<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"/>
<Constant name ="Ra" value="0.4"/>
<Constant name="Rb" value="0.124"/>
<Constant name="qa" value="7.2"/>
<Constant name="mmin" value="0.02"/>
<![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"/>
<Constant name="thi2" value="-45"/>
<Constant name="thinf" value="-50"/>
<Constant name ="Rd" value="0.03"/>
<Constant name="Rg" value="0.01"/>
<Constant name="qd" value="1.5"/>
<Constant name="qg" value="1.5"/>
<Constant name="hmin" value="0.5"/>
<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>
<KSComplex instances="1">
<ClosedState id="c"/>
<OpenState id="o"/>
<TauInfCodedTransition from="c" to="o" tauvar="stau" infvar="sinf">
<Constant name="q10" value="2"/>
<Constant name="vvh" value="-58"/>
<Constant name="vvs" value="2"/>
<Constant name ="a2" value="0.8" id="Na3-a2-semiconstant"/> <!-- a2 is the only change between soma, apical basal. -->
<Constant name="zetas" value="12"/>
<Constant name="gms" value="0.2"/>
<Constant name="vhalfs" value="-60"/>
<Constant name="a0s" value="0.0003"/>
<Constant name="smax" value="10"/>
<![CDATA[
double qt = Math.pow(q10, ((temperature-24)/10));
double c = 1 / (1+Math.exp((v-vvh)/vvs));
sinf = c+a2*(1-c);
double bets = Math.exp(1.e-3*zetas*gms*(v-vhalfs)*9.648e4/(8.315*(273.16+temperature)));
double alps = Math.exp(1.e-3*zetas*(v-vhalfs)*9.648e4/(8.315*(273.16+temperature)));
stau = bets / (a0s * (1 + alps));
if (stau<smax) stau=smax;
]]>
</TauInfCodedTransition>
</KSComplex>
</KSChannel>