PSICS Results for CA1PyramidalCell.xml

smalldt (CA1PyramidalCell.xml)

PSICS project generated from: CA1PyramidalCell.ncx

Total CPU time 0.2400 seconds; at 10:35:41 Thu 24 Sep 2009

Compartments	Stochastic channels / cpmts	Continuous channels / cpmts	Non Gated channels / cpmts	CPU Time / s
2	0 / 0	38793 / 2	6 / 2	0.240

Morphology: SomaOnly_allCml

Predefined views

CG_CML_v

All files

Model	Preprocessed	Outupt data	Reference data etc
CA1PyramidalCell.xml SomaOnly_allCml.xml membrane_SomaOnly_allCml.xml environment.xml recording.xml kad.xml kap.xml pasCA1.xml nax.xml kdr.xml hd__vhalfl_-73.xml na3.xml hd.xml	psics-out.ppp	log.txt psics-out.sum psics-out.dat psics-out.txt	time.txt Seg0_soma_0.txt CG_CML_0.dat.txt

Model

Archive file of the complete model: smalldt.jar

CA1PyramidalCell.xml

<PSICSRun timeStep="1.0E-2ms" runTime="50.0ms" startPotential="-65.0mV" environment="environment" morphology="SomaOnly_allCml" properties="membrane_SomaOnly_allCml" access="recording" stochThreshold="0" squareCaps="true" >
<info>PSICS project generated from: CA1PyramidalCell.ncx</info>
<StructureDiscretization baseElementSize="3.0"/>
<ViewConfig>
    <LineGraph width="500" height="400">
        <XAxis min="0" max="100.0" label="time / ms"/>
    <YAxis min="-90.0" max="50.0"/>
    <View id="CG_CML_v" xmin="0" xmax="100.0" ymin="-90.0" ymax="50.0"/>
<Line file="psics-out.txt" color="#000000" show="2"/>
    </LineGraph>

</ViewConfig>
</PSICSRun>

SomaOnly_allCml.xml

<CellMorphology id="SomaOnly_allCml">
    <Point id="Seg0_soma_0_root" x="0.0" y="0.0" z="0.0" r="3.7455" label="~all~~soma_group~~ModelViewParmSubset_2~~ModelViewParmSubset_6~~ModelViewParmSubset_9~~OneSecGrp_SectionRef_1~"/>
    <Point parent="Seg0_soma_0_root" id="Seg0_soma_0" x="0.0" y="7.4909997" z="0.0" r="3.7455" label="~all~~soma_group~~ModelViewParmSubset_2~~ModelViewParmSubset_6~~ModelViewParmSubset_9~~OneSecGrp_SectionRef_1~"/>
    
</CellMorphology>

membrane_SomaOnly_allCml.xml

<CellProperties id="membrane_SomaOnly_allCml" cytoplasmResistivity="1.5ohm_m" membraneCapacitance="0.01F_per_m2">
<ChannelPopulation channel="kad" density="30.000001907349per_um2" color="0xff0000"/>

<ChannelPopulation channel="kap" density="30.000001907349per_um2" color="0x0000ff"/>

<ChannelPopulation channel="pasCA1" density="0.035714302212per_um2" color="0x009b00"/>

<ChannelPopulation channel="nax" density="125per_um2" color="0xffc800"/>

<ChannelPopulation channel="kdr" density="10per_um2" color="0x8c6400"/>

<ChannelPopulation channel="hd__vhalfl_-73" density="0.04999999702per_um2" color="0xff00ff"/>

<ChannelPopulation channel="na3" density="25per_um2" color="0xffff00">
    <RegionMask action="include" where="region = *soma_group*"/>
</ChannelPopulation>

</CellProperties>

environment.xml

<CellEnvironment id="environment" temperature="35.0Celsius">
    <Ion id="k" name="k_ion" reversalPotential="-90mV"/>
    <Ion id="k" name="k_ion" reversalPotential="-90mV"/>
    <Ion id="non_specific" name="non_specific_ion" reversalPotential="-58mV"/>
    <Ion id="na" name="na_ion" reversalPotential="50mV"/>
    <Ion id="k" name="k_ion" reversalPotential="-90mV"/>
    <Ion id="hd" name="hd_ion" reversalPotential="-30mV"/>
    <Ion id="na" name="na_ion" reversalPotential="50mV"/>
    
</CellEnvironment>

recording.xml

<Access id="recording" saveInterval="1.0E-4ms" separateFiles="true" recordClamps="true">
    <CurrentClamp at="Seg0_soma_0" lineColor="red">
        <CurrentPulse start="20.0ms" duration="60.0ms" to="0.0038nA"/>
</CurrentClamp>


<VoltageRecorder at="Seg0_soma_0" lineColor="0x000000" label="CG_CML_0.dat"/>

</Access>

kad.xml

<KSChannel id="kad" permeantIon="k" gSingle="9.99999993922529pS">
<KSComplex instances="1">
<ClosedState id="n0"/>
<OpenState id="n"/>
<TauInfCodedTransition from="n0" to="n" tauvar="ntau" infvar="ninf"><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_n = Math.pow(5, (temperature - 24)/10);
                                    
    
    
    double alpha = 0;
                            alpha = (Math.exp ( (1e-3 * (-1.8 + (-1)/(1 + (Math.exp ((v-(-40))/5)))) * (v - (-1)) * 9.648e4) / (8.315*(273.16 + (temperature) )) ));
        
    double beta = 0;
                            beta = (Math.exp ( (1e-3 * (-1.8 + (-1)/(1 + (Math.exp ((v-(-40))/5)))) * 0.39 * (v - (-1)) * 9.648e4) / (8.315*(273.16 + (temperature) )) ));
        
    

    if (beta/(0.1 * (1 + alpha) * temp_adj_n) < 0.2 ) {
        ntau =  (0.2 * temp_adj_n) ;
    } else {
        ntau =  beta/(0.1 * (1 + alpha)) ;
    }
        ntau = ntau/temp_adj_n;
            
    ninf = 1/(1 + alpha);
        
    ]]></TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<ClosedState id="l0"/>
<OpenState id="l"/>
<TauInfCodedTransition from="l0" to="l" tauvar="ltau" infvar="linf"><![CDATA[
    
    
    double temp_adj_l = 1;
                                    
    
    
    

    if (0.26*(v + 50) < 2 ) {
        ltau =  2 ;
    } else {
        ltau =  0.26*(v + 50);
    }
        ltau = ltau/temp_adj_l;
            
    linf = 1/(1 + (Math.exp ( (1e-3 * (3) * (v - (-56)) * 9.648e4) / (8.315*(273.16 + (temperature) )) )));
        
    ]]></TauInfCodedTransition>
</KSComplex>
</KSChannel>

kap.xml

<KSChannel id="kap" permeantIon="k" gSingle="9.99999993922529pS">
<KSComplex instances="1">
<ClosedState id="n0"/>
<OpenState id="n"/>
<TauInfCodedTransition from="n0" to="n" tauvar="ntau" infvar="ninf"><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_n = Math.pow(5, (temperature - 24)/10);
                                    
    
    
    double alpha = 0;
                            alpha = (Math.exp ( (1e-3 * (-1.5 + (-1)/(1 + (Math.exp ((v-(-40))/5)))) * (v - 11) * 9.648e4) / (8.315*(273.16 + (temperature) )) ));
        
    double beta = 0;
                            beta = (Math.exp ( (1e-3 * (-1.5 + (-1)/(1 + (Math.exp ((v-(-40))/5)))) * 0.55 * (v - 11) * 9.648e4) / (8.315*(273.16 + (temperature) )) ));
        
    

    if (beta/(0.05 * (1 + alpha) * temp_adj_n) < 0.1 ) {
        ntau =  (0.1 * temp_adj_n) ;
    } else {
        ntau =  beta/(0.05 * (1 + alpha)) ;
    }
        ntau = ntau/temp_adj_n;
            
    ninf = 1/(1 + alpha);
        
    ]]></TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<ClosedState id="l0"/>
<OpenState id="l"/>
<TauInfCodedTransition from="l0" to="l" tauvar="ltau" infvar="linf"><![CDATA[
    
    
    double temp_adj_l = 1;
                                    
    
    
    

    if (0.26*(v + 50) < 2 ) {
        ltau =  2 ;
    } else {
        ltau =  0.26*(v + 50);
    }
        ltau = ltau/temp_adj_l;
            
    linf = 1/(1 + (Math.exp ( (1e-3 * (3) * (v - (-56)) * 9.648e4) / (8.315*(273.16 + (temperature) )) )));
        
    ]]></TauInfCodedTransition>
</KSComplex>
</KSChannel>

pasCA1.xml

<KSChannel id="pasCA1" permeantIon="non_specific" gSingle="9.99999993922529pS">
<OpenState id="o1"/>
</KSChannel>

nax.xml

<KSChannel id="nax" permeantIon="na" gSingle="9.99999993922529pS">
<KSComplex instances="3">
<ClosedState id="m0"/>
<OpenState id="m"/>
<TauInfCodedTransition from="m0" to="m" tauvar="mtau" infvar="minf"><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_m = Math.pow(2, (temperature - 24)/10);
                                    
    
    
    double alpha = 0;
    rate = 2.88;
        
    scale = 7.2;
    midpoint = -30;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        alpha = rate * (1 + (v - midpoint)/scale/2);
    } else {
        alpha = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }

        
    double beta = 0;
    rate = 0.8928;
        
    scale = -7.2;
    midpoint = -30;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        beta = rate * (1 + (v - midpoint)/scale/2);
    } else {
        beta = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }

        
    

    if (1/( (alpha + beta) * temp_adj_m ) < 0.02 ) {
        mtau =  (0.02 * temp_adj_m) ;
    } else {
        mtau =  1/(alpha + beta) ;
    }
        mtau = mtau/temp_adj_m;
            
    minf = alpha/(alpha + beta);
                    
    ]]></TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<ClosedState id="h0"/>
<OpenState id="h"/>
<TauInfCodedTransition from="h0" to="h" tauvar="htau" infvar="hinf"><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_h = Math.pow(2, (temperature - 24)/10);
                                    
    
    
    double alpha = 0;
    rate = 0.045;
        
    scale = 1.5;
    midpoint = -45;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        alpha = rate * (1 + (v - midpoint)/scale/2);
    } else {
        alpha = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }

        
    double beta = 0;
    rate = 0.015;
        
    scale = -1.5;
    midpoint = -45;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        beta = rate * (1 + (v - midpoint)/scale/2);
    } else {
        beta = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }

        
    

    if (1/( (alpha + beta) * temp_adj_h ) < 0.5 ) {
        htau =  (0.5 * temp_adj_h) ;
    } else {
        htau =  1/(alpha + beta) ;
    }
        htau = htau/temp_adj_h;
            
    hinf = 1/(1 + (Math.exp ((v-(-50))/4 )) );
        
    ]]></TauInfCodedTransition>
</KSComplex>
</KSChannel>

kdr.xml

<KSChannel id="kdr" permeantIon="k" gSingle="9.99999993922529pS">
<KSComplex instances="1">
<ClosedState id="n0"/>
<OpenState id="n"/>
<TauInfCodedTransition from="n0" to="n" tauvar="ntau" infvar="ninf"><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_n = 1;
                    
    
    
    double alpha = 0;
                            alpha = (Math.exp ( (1e-3 * -3 * (v - 13) * 9.648e4) / (8.315*(273.16 + (temperature) )) ));
        
    double beta = 0;
                            beta = (Math.exp ( (1e-3 * -3 * 0.7 * (v - 13) * 9.648e4) / (8.315*(273.16 + (temperature) ))) );
        
    

    if (beta/(0.02 * (1 + alpha)) < 2 ) {
        ntau =  2 ;
    } else {
        ntau =  beta/(0.02 * (1 + alpha)) ;
    }
        ntau = ntau/temp_adj_n;
            
    ninf = 1/(1 + alpha);
        
    ]]></TauInfCodedTransition>
</KSComplex>
</KSChannel>

hd__vhalfl_-73.xml

<?xml version="1.0" encoding="UTF-8"?>
<DerivedKSChannel id="hd__vhalfl_-73" from="hd">
    <ParameterChange to="vhalfl" attribute="value" newText="-73.0"/>
</DerivedKSChannel>

na3.xml (truncated)

<KSChannel id="na3" permeantIon="na" gSingle="9.99999993922529pS">
<KSComplex instances="3">
<ClosedState id="m0"/>
<OpenState id="m"/>
<TauInfCodedTransition from="m0" to="m" tauvar="mtau" infvar="minf">
<Constant id="ar" name="ar" value="1"/><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;
    
    double temp_adj_m = Math.pow(2, (temperature - 24)/10);
                                    
    
    
    double alpha = 0;
    rate = 2.88;
        
    scale = 7.2;
    midpoint = -30;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        alpha = rate * (1 + (v - midpoint)/scale/2);
    } else {
        alpha = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }
        
    double beta = 0;
    rate = 0.8928;
        
    scale = -7.2;
    midpoint = -30;
    
    if ( 1e-6 > (Math.abs((v - midpoint)/ scale))) {
        beta = rate * (1 + (v - midpoint)/scale/2);
    } else {
        beta = rate * ((v - midpoint) / scale) /(1 - (Math.exp(-1 * (v - midpoint)/scale)));
    }
        
    
    if (1/( (alpha + beta) * temp_adj_m ) < 0.02 ) {
        mtau =  (0.02 * temp_adj_m) ;
    } else {
        mtau =  1/(alpha + beta) ;
    }
        mtau = mtau/temp_adj_m;
            
    minf = alpha/(alpha + beta);
                    
    ]]></TauInfCodedTransition>
</KSComplex>
<KSComplex instances="1">
<ClosedState id="h0"/>
<OpenState id="h"/>
<TauInfCodedTransition from="h0" to="h" tauvar="htau" infvar="hinf">
<Constant id="ar" name="ar" value="1"/><![CDATA[
    
    double rate = 0;
    double scale = 0;
    double midpoint = 0;

 - and 42 more lines -

hd.xml

<KSChannel id="hd" permeantIon="hd" gSingle="9.99999993922529pS">
<KSComplex instances="1">
<ClosedState id="l0"/>
<OpenState id="l"/>
<TauInfCodedTransition from="l0" to="l" tauvar="ltau" infvar="linf">
<Constant id="vhalfl" name="vhalfl" value="-81"/><![CDATA[
    
    
    double temp_adj_l = Math.pow(4.5, (temperature - 33)/10);
                                    
    
    
    ltau = (Math.exp (0.033264 * (v - (-75))))/(0.011 * (1 + (Math.exp (0.08316 * (v - (-75)))))) ;
        ltau = ltau/temp_adj_l;
            
    linf = 1/(1 + (Math.exp (- (v-(vhalfl))/ (-8) )) );
        
    ]]></TauInfCodedTransition>
</KSComplex>
</KSChannel>