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HengyeZhuHengyeZhu
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Merge pull request #15 from OpenSourceBrain/feat-validate
Update files and test config to ensure that CI passes
2 parents 3b822e6 + 1db31d7 commit 837a1e1

35 files changed

+217
-201
lines changed

‎.pre-commit-config.yaml‎

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# See https://pre-commit.com for more information
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# See https://pre-commit.com/hooks.html for more hooks
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.12.3
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hooks:
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- id: ruff
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args: [ "--select", "I", "--fix" ]
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- id: ruff-format

‎NeuroML2/channels/.test.validate.omt‎

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# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation
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# exclude a few that use new component types and are so not valid against the schema
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target: "*.channel.nml"
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# - exclude a few that use new component types and are so not valid against the schema
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# - exclude new concentration models
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target: "ch_CavN.channel.nml; ch_KCaS.channel.nml; ch_Kdrfastngf.channel.nml; ch_KvAngf.channel.nml; ch_KvCaB.channel.nml; ch_Navngf.channel.nml; k*.channel.nml; hin.channel.nml; h_kole.channel.nml; h_migliore.channel.nml; I*channel.nml; i*channel.nml; n*channel.nml; N*channel.nml; p*channel.nml; t*channel.nml"
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engine: jNeuroML_validate

‎NeuroML2/channels/IKsin.channel.nml‎

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<ionChannel id="IKsin" conductance="10pS" type="ionChannelHH" species="k">
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<gate id="a" type="gateHHtauInf" instances="1">
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-34mV" scale="6.5mV"/>
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<timeCourse type="fixedTimeCourse" tau="10 ms"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-34mV" scale="6.5mV"/>
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</gate>
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<gate id="b" type="gateHHtauInf" instances="1">
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-65mV" scale="-6.6mV"/>
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<timeCourse type="IKsin_b_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-65mV" scale="-6.6mV"/>
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</gate>
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</ionChannel>
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<ComponentType name="IKsin_b_tau" extends="baseVoltageDepTime">
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</ComponentType>
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</neuroml>
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</neuroml>

‎NeuroML2/channels/IL.channel.nml‎

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<forwardRate type="HHSigmoidRate" rate="1.6per_ms" scale="13.888888889mV" midpoint="-5.0mV"/>
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<reverseRate type="HHExpLinearRate" rate="0.1072per_ms" scale="-5.36mV" midpoint="1.31mV"/>
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</gate>
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</ionChannel>
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</neuroml>
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</neuroml>

‎NeuroML2/channels/IT.channel.nml‎

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<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="ittc">
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<ionChannel id="ittc" conductance="10pS" type="ionChannelHH" species="ca">
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<gate id="m" type="gateHHtauInf" instances="2">
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<q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="24degC"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-59mV" scale="6.2mV"/>
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<timeCourse type="ittc_m_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-59mV" scale="6.2mV"/>
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</gate>
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<gate id="h" type="gateHHtauInf" instances="1">
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<q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="24degC"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-83mV" scale="-4mV"/>
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<timeCourse type="ittc_h_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-83mV" scale="-4mV"/>
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</gate>
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</ionChannel>
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<ComponentType name="ittc_m_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<DerivedVariable name="t" exposure="t" dimension="time" value="(1 / (exp(-(V + shift + 129.6) / 16.7)
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<DerivedVariable name="t" exposure="t" dimension="time" value="(1 / (exp(-(V + shift + 129.6) / 16.7)
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+ exp((V + shift + 14.8) / 18.2)) + 0.612) * TIME_SCALE"/>
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</Dynamics>
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<ComponentType name="ittc_h_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<DerivedVariable name="t" exposure="t" dimension="time" value="(30.8 + (211.4 + exp((V + shift + 113.2) / 5))
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<DerivedVariable name="t" exposure="t" dimension="time" value="(30.8 + (211.4 + exp((V + shift + 113.2) / 5))
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/ (1+exp((V + shift + 84) / 3.2))) * TIME_SCALE"/>
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</Dynamics>
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</ComponentType>
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</neuroml>
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‎NeuroML2/channels/IT2.channel.nml‎

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<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="itre">
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<notes>GHK</notes>
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<ionChannel id="itre" conductance="10pS" type="ionChannelHH" species="ca">
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<gate id="m" type="gateHHtauInf" instances="2">
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<q10Settings type="q10ExpTemp" q10Factor="2.5" experimentalTemp="24degC"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-52mV" scale="7.4mV"/>
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<timeCourse type="itre_m_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-52mV" scale="7.4mV"/>
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</gate>
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<gate id="h" type="gateHHtauInf" instances="1">
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<q10Settings type="q10ExpTemp" q10Factor="2.5" experimentalTemp="24degC"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-80mV" scale="-5mV"/>
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<timeCourse type="itre_h_tau"/>
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<steadyState type="HHSigmoidVariable" rate="1" midpoint="-80mV" scale="-5mV"/>
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</gate>
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</ionChannel>
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<ComponentType name="itre_m_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Constant name="phim" dimension="none" value="2"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<ComponentType name="itre_h_tau" extends="baseVoltageDepTime">
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Constant name="shift" dimension="none" value="2"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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</ComponentType>
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</neuroml>
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</neuroml>

‎NeuroML2/channels/Iahp.channel.nml‎

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<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="iahp">
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<ionChannel id="iahp" conductance="10pS" type="ionChannelHH" species="k2">
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<gate id="m" type="gateHHtauInf" instances="2">
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<q10Settings type="q10ExpTemp" q10Factor="3" experimentalTemp="22degC"/>
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<steadyState type="iahp_m_inf"/>
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<timeCourse type="iahp_m_tau"/>
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<steadyState type="iahp_m_inf"/>
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</gate>
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</ionChannel>
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<Dynamics>
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<DerivedVariable name="ca_conc" dimension="none" value="caConc / CONC_SCALE"/>
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<DerivedVariable name="x" exposure="x" dimension="none" value="car / ( 1 + car )"/>
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</Dynamics>
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</ComponentType>
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</Dynamics>
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</ComponentType>
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</neuroml>

‎NeuroML2/channels/Nafx.channel.nml‎

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<gate id="m" type="gateHHrates" instances="3">
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<forwardRate type="Nafx_m_alpha_rate"/>
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<reverseRate type="Nafx_m_beta_rate"/>
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</gate>
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</gate>
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<gate id="h" type="gateHHrates" instances="1">
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<forwardRate type="Nafx_h_alpha_rate"/>
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<reverseRate type="Nafx_h_beta_rate"/>
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</gate>
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</gate>
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<gate id="s" type="gateHHtauInf" instances="1">
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<steadyState type="Nafx_s_inf"/>
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<timeCourse type="Nafx_s_tau"/>
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<steadyState type="Nafx_s_inf"/>
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</gate>
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</ionChannel>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<ConditionalDerivedVariable name="r" exposure="r" dimension="per_time">
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<Case condition=" (V+28) .gt. 1e-4" value="-0.2816*(V+28)/(-1+exp(-(V+28)/9.3)) / TIME_SCALE"/>
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<Case condition=" (V+28) .lt. -1e-4" value="-0.2816*(V+28)/(-1+exp(-(V+28)/9.3)) / TIME_SCALE"/>
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<Case value="-0.2816*(V+28)/(-1+exp(-(V+28)/9.3)) / TIME_SCALE"/>
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</ConditionalDerivedVariable>
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</Dynamics>
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</ComponentType>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<ConditionalDerivedVariable name="r" exposure="r" dimension="per_time">
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<Case condition=" (V+1) .gt. 1e-4" value="0.2464*(V+1)/(-1+exp((V+1)/6)) / TIME_SCALE"/>
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<Case condition=" (V+1) .lt. -1e-4" value="0.2464*(V+1)/(-1+exp((V+1)/6)) / TIME_SCALE"/>
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<Case value="0.2464*(V+1)/(-1+exp((V+1)/6)) / TIME_SCALE"/>
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</ConditionalDerivedVariable>
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</Dynamics>
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</ComponentType>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Dynamics>
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<DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
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<ConditionalDerivedVariable name="r" exposure="r" dimension="per_time">
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<Case condition=" (V+40.1) .gt. 1e-4" value="0.098/exp((V+40.1+43.1)/20) / TIME_SCALE"/>
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<Case condition=" (V+40.1) .lt. -1e-4" value="0.098/exp((V+40.1+43.1)/20) / TIME_SCALE"/>
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<Case value="0.098/exp((V+40.1+43.1)/20) / TIME_SCALE"/>
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</ConditionalDerivedVariable>
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</Dynamics>
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<ComponentType name="Nafx_s_inf" extends="baseVoltageDepVariable">
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="zetan" dimension="none" value="-3"/>
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<Constant name="vvh" dimension="none" value="-58"/>
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<Constant name="vvs" dimension="none" value="2"/>
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<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
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<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
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<Constant name="taumin" dimension="time" value="30 ms"/>
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<Constant name="taumin" dimension="time" value="30 ms"/>
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<Constant name="a0r" dimension="none" value="0.0003"/>
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<Constant name="zetar" dimension="none" value="12"/>
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<Constant name="vhalfr" dimension="none" value="-60"/>
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</neuroml>
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NeuroML2/channels/iconc_Ca.channel.nml renamed to NeuroML2/channels/cadad.nml

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
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id="cadad">
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<concentrationModel id="cadad_IT2_dend_all" ion="ca" type="cadad" cainf="2.4e-4 mM" taur="99.1146852282 ms" depth="0.119408607923 um"/>
8-
<concentrationModel id="cadad_IT2_somatic" ion="ca" type="cadad" cainf="2.4e-4 mM" taur="99.1146852282 ms" depth="0.119408607923 um"/>
7+
<concentrationModel id="cadad_IT2_dend_all" ion="ca" type="cadad" cainf="2.4e-4 mM" taur="99.1146852282 ms" depth="0.119408607923 um"/>
8+
<concentrationModel id="cadad_IT2_somatic" ion="ca" type="cadad" cainf="2.4e-4 mM" taur="99.1146852282 ms" depth="0.119408607923 um"/>
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<ComponentType name="cadad" extends="concentrationModel">
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<Parameter name="cainf" dimension="concentration"/>
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<Parameter name="taur" dimension="time"/>
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<Parameter name="depth" dimension="length"/>
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<Constant name="Faraday" dimension="charge_per_mole" value="96485.3C_per_mol"/>
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<Constant name="AREA_SCALE" dimension="area" value="1m2"/>
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<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
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<DerivedVariable name="currDensCa" dimension="currentDensity" value="iCa / surfaceArea"/>
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<TimeDerivative variable="concentration" value="(currDensCa/(2*Faraday*depth)) - ((concentration - cainf) / taur)"/>
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</ComponentType>
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</neuroml>
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</neuroml>

NeuroML2/channels/cadyn.channel.nml renamed to NeuroML2/channels/cadyn.nml

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<?xml version="1.0" encoding="ISO-8859-1"?>
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
55
id="cadyn">
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7-
<concentrationModel id="cadyn_" ion="ca" type="cadyn" cainf="5e-5 mM" taur="200 ms" depth="0.1 um"/>
7+
<concentrationModel id="cadyn_" ion="ca" type="cadyn" cainf="5e-5 mM" taur="200 ms" depth="0.1 um"/>
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<ComponentType name="cadyn" extends="concentrationModel">
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<Parameter name="cainf" dimension="concentration"/>
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<Parameter name="taur" dimension="time"/>
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<Parameter name="depth" dimension="length"/>
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<Constant name="Faraday" dimension="charge_per_mole" value="96485.3C_per_mol"/>
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<Constant name="AREA_SCALE" dimension="area" value="1m2"/>
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2727
<StateVariable name="extConcentration" exposure="extConcentration" dimension="concentration"/>
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2929
<DerivedVariable name="currDensCa" dimension="currentDensity" value="iCa / surfaceArea"/>
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<TimeDerivative variable="concentration" value="(currDensCa/(2*Faraday*depth)) / 18 - ((concentration - cainf) / taur * 11)"/>
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</ComponentType>
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</neuroml>
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</neuroml>

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