Permalink
Switch branches/tags
Nothing to show
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
79 lines (48 sloc) 3 KB
<?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">
<ionChannel id="ca_boyle" 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>
<gateHHtauInf type="customHGate" id="h" instances="1" alpha="0.282473" ca_half="6.41889e-8 mM" k="-1.00056e-8 mM"/>
</ionChannel>
<ComponentType name="customHGate"
extends="gateHHtauInf"
description="Custom gate for h">
<Parameter name="alpha" dimension="none"/>
<Parameter name="k" dimension="concentration"/>
<Parameter name="ca_half" dimension="concentration"/>
<Constant name="SEC" dimension="time" value="1s"/>
<Exposure name="tau" dimension="time"/>
<Exposure name="inf" dimension="none"/>
<Requirement name="caConc" dimension="concentration"/>
<Dynamics>
<DerivedVariable name="rateScale" exposure="rateScale" dimension="none" value="1"/>
<DerivedVariable name="inf" dimension="none" exposure="inf" value="1 / (1 + (exp( (ca_half - caConc) / k)))"/>
<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)"/>
</Dynamics>
</ComponentType>
</neuroml>