na.channel.nml

<?xml version="1.0" encoding="ISO-8859-1"?>
<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/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd" id="it">

    <notes>NeuroML file containing a single Channel description</notes>

    <ionChannel id="na" conductance="10 pS" type="ionChannelHH" species="na">

        <notes>Sodium channel, Hodgkin-Huxley style kinetics.

WARNING: Global parameter "vshift" from modfile has not been implemented.

Comments from original mod file:

26 Ago 2002 Modification of original channel to allow variable time
step and to correct an initialization error.
    Done by Michael Hines(michael.hines@yale.e) and Ruggero
Scorcioni(rscorcio@gmu.edu) at EU Advance Course in Computational
Neuroscience. Obidos, Portugal
11 Jan 2007
    Glitch in trap where (v/th) was where (v-th)/q is. (thanks Ronald
van Elburg!)

na.mod

Sodium channel, Hodgkin-Huxley style kinetics.

Kinetics were fit to data from Huguenard et al. (1988) and Hamill et
al. (1991)

qi is not well constrained by the data, since there are no points
between -80 and -55.  So this was fixed at 5 while the thi1,thi2,Rg,Rd
were optimized using a simplex least square proc

voltage dependencies are shifted approximately from the best
fit to give higher threshold

Author: Zach Mainen, Salk Institute, 1994, zach@salk.edu
</notes>

        <annotation>
            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description rdf:about="na">

                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                        <rdf:Bag>
                            <rdf:li>na3h5 Sodium channel, Hodgkin-Huxley style kinetics. Data from Huguenard et al. (1988) and Hamill et
al. (1991)</rdf:li>
                            <rdf:li>Developmental changes in Na+ conductances in rat neocortical neurons: appearance of a slowly inactivating component. Huguenard JR1, Hamill OP, Prince DA. J Neurophysiol. 1988 Mar;59(3):778-95.</rdf:li>
                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/2452862"/>
                            <rdf:li>Patch-Clamp Studies of Voltage-Gated Currents in Identified Neurons of the Rat Cerebral Cortex. O. P. Hamill⇑, J. R. Huguenard and D. A. Prince. Cereb. Cortex (1991) 1 (1): 48-61.</rdf:li>
                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/1668364"/>
                        </rdf:Bag>
                    </bqmodel:isDescribedBy>

                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                        <rdf:Bag>
                            <rdf:li>Sodium channels</rdf:li>
                            <rdf:li rdf:resource="http://senselab.med.yale.edu/neurondb/channelGene2.aspx#table2"/>
                        </rdf:Bag>
                    </bqbiol:isVersionOf>
                </rdf:Description>
            </rdf:RDF>
        </annotation>
	
	    <q10ConductanceScaling q10Factor="2.3" experimentalTemp="23degC"/>

        <gate id="m" type="gateHHrates" instances="3">
       	    <q10Settings type="q10ExpTemp" q10Factor="2.3" experimentalTemp="23degC"/>
            <forwardRate type="HHExpLinearRate" rate="1.638per_ms" scale="9mV" midpoint="-25mV"/>
            <reverseRate type="HHExpLinearRate" rate="1.116per_ms" scale="-9mV" midpoint="-25mV"/>
        </gate>

        <gate id="h" type="gateHHratesInf" instances="1">
       	    <q10Settings type="q10ExpTemp" q10Factor="2.3" experimentalTemp="23degC"/>
            <forwardRate type="HHExpLinearRate" rate="0.12per_ms" scale="5mV" midpoint="-40mV"/>
            <reverseRate type="HHExpLinearRate" rate="0.0455per_ms" scale="-5mV" midpoint="-65mV"/>
            <steadyState type="Na_h_inf" />
        </gate>

    </ionChannel>


    <ComponentType name="Na_h_inf" extends="baseVoltageDepVariable">
        <Constant name="thinf" dimension="voltage" value="-55mV"/>
        <Constant name="qinf" dimension="voltage" value="6.2 mV"/>

        <Dynamics>
          <DerivedVariable name="x" exposure="x" dimension="none" value="1/(1+exp((v-thinf)/qinf))"/>
        </Dynamics>

    </ComponentType>


</neuroml>