<?xml version="1.0" encoding="ISO-8859-1"?>

<!--
       This file has been generated by neuroConstruct because a cell mechanism (ChannelMLCell Mechanism [InstanceName: naf_tcr, channelMLFile: NaF_tcr_Chan.xml])
      has a different set of parameters (sh_h = -7.0, sh_m_i = -3.0, sh_m_r = -2.5) on a group of sections.

      Conversion of the original NML2 file to use the updated parameters is implemented in handleExtraParamsForNml2()
      in https://github.com/NeuralEnsemble/neuroConstruct/blob/master/src/ucl/physiol/neuroconstruct/neuroml/NeuroMLFileManager.java
      See that file to check/improve this conversion
-->

<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="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5">

    <notes>ChannelML file based on Traub et al. 2003</notes>

    <ionChannel id="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5" conductance="10pS" type="ionChannelHH" species="na">

        <notes>Fast Sodium transient (inactivating) current. Channel used in Traub et al 2005, slight modification of naf from Traub et al 2003</notes>
                
        <annotation>
            <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description rdf:about="naf_tcr">
                    
                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                        <rdf:Bag>
                            <rdf:li>Roger D. Traub, Eberhard H. Buhl, Tengis Gloveli, and Miles A. Whittington                
Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na+ Conductance or by Blocking BK Channels
J Neurophysiol 89: 909-921, 2003</rdf:li>
                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=12574468"/>
                        </rdf:Bag>
                    </bqmodel:isDescribedBy>

                
                    <bqmodel:isDescribedBy xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
                        <rdf:Bag>
                            <rdf:li>Roger D. Traub, Diego Contreras, Mark O. Cunningham, Hilary Murray, Fiona E. N. LeBeau, Anita Roopun, Andrea Bibbig, W. Bryan Wilent, Michael J. Higley, and Miles A. Whittington
Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts.
J. Neurophysiol. 93, 2194-2232, 2005</rdf:li>
                            <rdf:li rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/15525801?dopt=Abstract"/>
                        </rdf:Bag>
                    </bqmodel:isDescribedBy>

                
                    <bqbiol:isVersionOf xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                        <rdf:Bag>
                            <rdf:li>Na channels</rdf:li>
                            <rdf:li rdf:resource="http://senselab.med.yale.edu/senselab/NeuronDB/channelGene2.htm#table2"/>
                        </rdf:Bag>
                    </bqbiol:isVersionOf>

                </rdf:Description>
            </rdf:RDF>
        </annotation>

        <gate id="m" type="gateHHtauInf" instances="3">
            <timeCourse type="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_m_tau_tau"/>
            <steadyState type="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_m_inf_inf"/>
        </gate>

        <gate id="h" type="gateHHtauInf" instances="1">
            <timeCourse type="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_h_tau_tau"/>
            <steadyState type="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_h_inf_inf"/>
        </gate>
                            
    </ionChannel>

    <ComponentType name="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_m_tau_tau" extends="baseVoltageDepTime">
        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
        <!--Note: this parameter (sh_m_i) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_i" dimension="none" value="-3.0"/>
        <!--Note: this parameter (sh_m_r) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_r" dimension="none" value="-2.5"/>
        <!--Note: this parameter (sh_h) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_h" dimension="none" value="-7.0"/>

        <Dynamics>
            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
            <ConditionalDerivedVariable name="t" exposure="t" dimension="time">
                <Case condition="( V + sh_m_i + sh_m_r )  .lt. ( -30 )" value="( 0.025 + 0.14 * ( exp ( ((V + sh_m_i + sh_m_r) + 30) / 10) ) ) * TIME_SCALE"/>
                <Case value="( 0.02 + (0.145) * ( exp ( -1 * ((V + sh_m_i + sh_m_r) + 30) / 10) )) * TIME_SCALE"/>
            </ConditionalDerivedVariable>
        </Dynamics>

    </ComponentType>

    <ComponentType name="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_m_inf_inf" extends="baseVoltageDepVariable">
        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
        <!--Note: this parameter (sh_m_i) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_i" dimension="none" value="-3.0"/>
        <!--Note: this parameter (sh_m_r) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_r" dimension="none" value="-2.5"/>
        <!--Note: this parameter (sh_h) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_h" dimension="none" value="-7.0"/>

        <Dynamics>
            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
            <DerivedVariable name="x" exposure="x" dimension="none" value=" 1 / ( 1 + (exp ( ( -1 * (V + sh_m_i + sh_m_r) - 38) / 10)) ) "/>
        </Dynamics>

    </ComponentType>

    <ComponentType name="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_h_tau_tau" extends="baseVoltageDepTime">
        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
        <!--Note: this parameter (sh_m_i) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_i" dimension="none" value="-3.0"/>
        <!--Note: this parameter (sh_m_r) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_r" dimension="none" value="-2.5"/>
        <!--Note: this parameter (sh_h) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_h" dimension="none" value="-7.0"/>

        <Dynamics>
            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
            <DerivedVariable name="t" exposure="t" dimension="time" value="(0.15 + 1.15 / ( 1 + ( exp (( V + 37 ) / 15) ) )) * TIME_SCALE"/>
        </Dynamics>

    </ComponentType>

    <ComponentType name="naf_tcr__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5__sh_hmin7__sh_m_imin3__sh_m_rmin2_5_h_inf_inf" extends="baseVoltageDepVariable">
        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
        <!--Note: this parameter (sh_m_i) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_i" dimension="none" value="-3.0"/>
        <!--Note: this parameter (sh_m_r) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_m_r" dimension="none" value="-2.5"/>
        <!--Note: this parameter (sh_h) should ideally be defined only once within the ionChannel! Work in progress...-->
        <Constant name="sh_h" dimension="none" value="-7.0"/>

        <Dynamics>
            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
            <DerivedVariable name="x" exposure="x" dimension="none" value="1 / ( 1 + (exp (( ( V + sh_h ) + 62.9 ) / 10.7)) )"/>
        </Dynamics>

    </ComponentType>

</neuroml>
