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<?xml version="1.0" encoding="UTF-8"?> | ||
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" | ||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" | ||
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/master/Schemas/NeuroML2/NeuroML_v2beta.xsd" | ||
id="ca_boyle"> | ||
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<ionChannel id="ca_boyle" conductance="10pS" type="ionChannelHH" species="ca"> | ||
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<notes>Ca channel from Boyle and Cohen 2008</notes> | ||
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<gateHHtauInf id="e" instances="2"> | ||
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<timeCourse type="fixedTimeCourse" tau="0.100027 ms"/> | ||
<steadyState type="HHSigmoidVariable" rate="1" scale="6.74821 mV" midpoint="-3.3568 mV"/> | ||
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</gateHHtauInf> | ||
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<gateHHtauInf id="f" instances="1"> | ||
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<timeCourse type="fixedTimeCourse" tau="150.88 ms"/> | ||
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<!-- 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"/> | ||
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</gateHHtauInf> | ||
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<customHGate id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/> | ||
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</ionChannel> | ||
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<ComponentType name="customHGate" | ||
extends="gateHHtauInf" | ||
description="Custom gate for h"> | ||
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<Parameter name="alpha" dimension="none"/> | ||
<Parameter name="k" dimension="concentration"/> | ||
<Parameter name="ca_half" dimension="concentration"/> | ||
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<Constant name="SEC" dimension="time" value="1s"/> | ||
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<Exposure name="tau" dimension="time"/> | ||
<Exposure name="inf" dimension="none"/> | ||
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<Requirement name="caConc" dimension="concentration"/> | ||
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<Dynamics> | ||
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<DerivedVariable name="rateScale" exposure="rateScale" dimension="none" value="1"/> | ||
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<DerivedVariable name="inf" dimension="none" exposure="inf" value="1 / (1 + (exp( (ca_half - caConc) / k)))"/> | ||
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<DerivedVariable name="tau" dimension="time" exposure="tau" value="0 * SEC"/> | ||
<DerivedVariable name="q" exposure="q" dimension="none" value="inf"/> | ||
<DerivedVariable name="fcond" exposure="fcond" dimension="none" value="1 +((q-1) * alpha)"/> | ||
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</Dynamics> | ||
</ComponentType> | ||
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</neuroml> |