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custom_muscle_components.xml
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custom_muscle_components.xml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="cell_C">
<ionChannel id="slo-2" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="m" instances="1">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="10.237 mV"/>
</gateHHtauInf>
<!--<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="5.237 mV"/>
</gateHHtauInf>-->
</ionChannel>
<ionChannel id="shk-1" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="m" instances="1">
<timeCourse type="fixedTimeCourse" tau="10 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="13.237 mV"/>
</gateHHtauInf>
<!--<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="10.237 mV"/>
</gateHHtauInf>-->
</ionChannel>
<ionChannel id="egl-19" conductance="10pS" type="ionChannelHH" species="ca">
<notes></notes>
<gateHHtauInf id="m" instances="2">
<timeCourse type="fixedTimeCourse" tau="30 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="-5.7 mV"/>
</gateHHtauInf>
<gateHHtauInf id="n" instances="2">
<timeCourse type="fixedTimeCourse" tau="50 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="0.7 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes></notes>
<gateHHtauInf id="n" instances="4">
<timeCourse type="fixedTimeCourse" tau="190 ms"/>
<steadyState type="MuscleSigmoidVariable" rate="1" scale="6.859 mV" midpoint="1.237 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_fast_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes>K fast channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="p" instances="4">
<timeCourse type="fixedTimeCourse" tau="2.25518 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="7.42636 mV" midpoint="-8.05232 mV"/>
</gateHHtauInf>
<gateHHtauInf id="q" instances="1">
<timeCourse type="fixedTimeCourse" tau="149.963 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="-9.97468 mV" midpoint="-15.6456 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="k_slow_muscle" conductance="10pS" type="ionChannelHH" species="k">
<notes>K slow channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="n" instances="1">
<timeCourse type="fixedTimeCourse" tau="25.0007 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="15.8512 mV" midpoint="19.8741 mV"/>
</gateHHtauInf>
</ionChannel>
<ionChannel id="ca_boyle_muscle" conductance="10pS" type="ionChannelHH" species="ca">
<notes>Ca channel from Boyle and Cohen 2008</notes>
<gateHHtauInf id="e" instances="2">
<timeCourse type="fixedTimeCourse" tau="0.100027 ms"/>
<steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/>
</gateHHtauInf>
<gateHHtauInf id="f" instances="1">
<timeCourse type="fixedTimeCourse" tau="150.88 ms"/>
<!-- Note!!!
f gate is "inactivation" a/c B&C 2008 p172
but the scale value from Table A1 (kf) is positive (5mV), i.e. steady
state is zero for v << midpoint and 1 for v >> midpoint
Couple this with a very slow time course & the ion channel never
conducts as e^2 x f is always ~0
Using -5.03176mV NOT 5mV for k/scale to make this INACTIVATION
This is suggested by the value used here:
https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/MatlabSupport/Main_Version/data/input.csv#L20
see also
https://github.com/openworm/muscle_model/blob/master/BoyleCohen2008/PythonSupport/Main_Version/compareToNeuroML2.py
-->
<steadyState type="HHSigmoidVariable" rate="1" scale="-5.03176 mV" midpoint="25.1815 mV"/>
</gateHHtauInf>
<customHGate id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/>
</ionChannel>
<ionChannel id="ca_muscle" conductance="10pS" type="ionChannelHH" species="ca">
<notes></notes>
<gateHHtauInf id="m" instances="2">
<timeCourse type="fixedTimeCourse" tau="1 ms"/>
<steadyState type="MuscleSigmoidVariable" scale="4.5 mV" midpoint="6.7 mV"/>
</gateHHtauInf>
<gateHHtauInf id="h" instances="1">
<timeCourse type="fixedTimeCourse" tau="7 ms"/>
<steadyState type="MuscleSigmoidVariableCaInact" a="0.516" b="13.508 mV" c="19.48 mV"/>
</gateHHtauInf>
</ionChannel>
<ComponentType name="MuscleSigmoidVariable"
extends="baseVoltageDepVariable"
description="Sigmoidal form for variable equation">
<Parameter name="midpoint" dimension="voltage" />
<Parameter name="scale" dimension="voltage" />
<Dynamics>
<DerivedVariable name="x" dimension="none" exposure="x" value="1 / (1 + exp((-(v-midpoint)) / scale))"/>
</Dynamics>
</ComponentType>
<ComponentType name="MuscleSigmoidVariableCaInact"
extends="baseVoltageDepVariable"
description="Sigmoidal form for variable equation">
<Parameter name="a" dimension="none" />
<Parameter name="b" dimension="voltage" />
<Parameter name="c" dimension="voltage" />
<Dynamics>
<DerivedVariable name="x" dimension="none" exposure="x" value="1 - a * exp((-(v - b)*(v - b)) / (2 * c * c))"/>
</Dynamics>
</ComponentType>
<ComponentType name="muscleConcentrationModel"
extends="fixedFactorConcentrationModel"
description="Model of buffering of concentration of an ion (currently hard coded to be calcium, due to requirement for _iCa) which has a baseline level _restingConc and tends to this value with time course _decayConstant. A fixed factor _rho is used to scale the incoming current INDEPENDENTLY OF THE SIZE OF THE COMPARTMENT to produce a concentration change.">
<Parameter name="restingConc" dimension="concentration"/>
<Parameter name="decayConstant" dimension="time"/>
<Parameter name="rho" dimension="rho_factor"/>
<Requirement name="iCa" dimension="current"/>
<Requirement name="surfaceArea" dimension="area"/>
<Text name="ion"/> <!-- TODO: check why this isn't inherited from concentrationModel -->
<Dynamics>
<StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
<!--<StateVariable name="x" dimension="concentration"/>
<StateVariable name="iCaSigmoid" dimension="none"/>
<StateVariable name="iCaSigmoidMid" dimension="current"/>
<StateVariable name="iCaSigmoidSlope" dimension="current"/>
<StateVariable name="xSigmoid" dimension="none"/>
<StateVariable name="xSigmoidMid" dimension="concentration"/>
<StateVariable name="xSigmoidSlope" dimension="concentration"/>
<StateVariable name="xDecay" dimension="time"/>-->
<!--<DerivedVariable name="iCaSigmoid" dimension="none" value="1 / (1 + exp((iCaSigmoidMid - iCa) / iCaSigmoidSlope))"/>
<DerivedVariable name="xSigmoid" dimension="none" value="1 / (1 + exp((xSigmoidMid - x) / xSigmoidSlope))"/>
<TimeDerivative variable="x" value="iCaSigmoid * (iCa/surfaceArea) * rho/10 - (x / xDecay)"/>-->
<TimeDerivative variable="concentration" value="(iCa/surfaceArea) * rho - ((concentration - restingConc) / decayConstant)"/>
<OnStart>
<StateAssignment variable="concentration" value="initialConcentration"/>
<StateAssignment variable="extConcentration" value="initialExtConcentration"/>
<!--<StateAssignment variable="x" value="initialConcentration"/>
<StateAssignment variable="iCaSigmoidMid" value="0.1"/>
<StateAssignment variable="iCaSigmoidSlope" value="0.1"/>
<StateAssignment variable="xSigmoidMid" value="0.1"/>
<StateAssignment variable="xSigmoidSlope" value="0.1"/>
<StateAssignment variable="xDecay" value="0.1"/>-->
</OnStart>
<OnCondition test="concentration .lt. 0">
<StateAssignment variable="concentration" value="0"/>
</OnCondition>
<!--<OnCondition test="x .lt. 0">
<StateAssignment variable="x" value="0"/>
</OnCondition>-->
</Dynamics>
</ComponentType>
<!-- <ComponentType name="muscleConcentrationModel2"
extends="concentrationModel"
description="">
<Parameter name="restingConc" dimension="concentration"/>
<Parameter name="decayConstant" dimension="time"/>
<Parameter name="rho" dimension="rho_factor"/>
<Parameter name="xRho" dimension="rho_factor"/>
<Parameter name="iCaSigmoidMid" dimension="current"/>
<Parameter name="iCaSigmoidSlope" dimension="current"/>
<Parameter name="xSigmoidMid" dimension="concentration"/>
<Parameter name="xSigmoidSlope" dimension="concentration"/>
<Parameter name="xDecay" dimension="time"/>
<Parameter name="xrest" dimension="concentration"/>
<Requirement name="iCa" dimension="current"/>
<Requirement name="v" dimension="voltage"/>
<Requirement name="surfaceArea" dimension="area"/>
<Exposure name="xx" dimension="concentration" />
<Text name="ion"/>
<Dynamics>
<StateVariable name="concentration" exposure="concentration" dimension="concentration"/>
<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
<StateVariable name="xx" exposure="xx" dimension="concentration"/>
<StateVariable name="tmpConc" dimension="concentration"/>
<StateVariable name="tmpX" dimension="concentration"/>
<DerivedVariable name="tmp" dimension="concentration" value="concentration" />
<DerivedVariable name="z" dimension="none" value="0" />
<DerivedVariable name="iCaSigmoid" dimension="none" value="(1 / (1 + exp((iCaSigmoidMid - iCa) / iCaSigmoidSlope)))"/>
<DerivedVariable name="xSigmoid" dimension="none" value="(1 / (1 + exp((xSigmoidMid - tmpConc) / xSigmoidSlope)))"/>
<TimeDerivative variable="xx" value="((iCa)/surfaceArea) * xRho - ((xx-xrest) / xDecay)"/>
<TimeDerivative variable="concentration" value="((iCa)/surfaceArea) * xRho - ((concentration-xrest) / xDecay)"/>
<OnStart>
<StateAssignment variable="concentration" value="initialConcentration"/>
<StateAssignment variable="extConcentration" value="initialExtConcentration"/>
<StateAssignment variable="xx" value="initialConcentration"/>
</OnStart>
<OnCondition test="concentration .lt. 0">
<StateAssignment variable="concentration" value="0"/>
</OnCondition>
<OnCondition test="t .gt. 0">
<StateAssignment variable="tmpConc" value="concentration"/>
<StateAssignment variable="tmpX" value="xx"/>
</OnCondition>
<OnCondition test="xx .lt. 0">
<StateAssignment variable="xx" value="0"/>
</OnCondition>
</Dynamics>
</ComponentType>
-->
</neuroml>