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Latest NeuroML version #1

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merged 8 commits into from
Apr 25, 2024
Merged

Latest NeuroML version #1

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c323cb1
Restructure & tst pynml
pgleeson Apr 19, 2024
d1034b0
Add initial kir, black formatting
pgleeson Apr 19, 2024
6358caf
Initial version gate parsing
pgleeson Apr 19, 2024
b6a97c0
Improved channel parsing
pgleeson Apr 19, 2024
9faa191
More tests xpp vs nml2
pgleeson Apr 19, 2024
113b1a1
2 more channels added
pgleeson Apr 22, 2024
8e001f9
Added shal egl32 unc2 channels
pgleeson Apr 23, 2024
3b0a781
Different form of <gate> to ensure valid neuroml
pgleeson Apr 25, 2024
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9 changes: 9 additions & 0 deletions .gitignore
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Expand Up @@ -9,3 +9,12 @@ report.*.txt
/NeuroML2/IClamp_AWCon.net.nml
/NeuroML2/LEMS_Sim_IClamp_AWCon.xml
/NicollettiEtAl2019.pdf
/NeuroML2/LEMS_Test_RMD_kir.xml
/NeuroML2/LEMS_RMD.xml
/NeuroML2/Test_RMD.ode
/NeuroML2/report.txt
/RMD.model.xml
/NeuroML2/LEMS_Test_RMD_cca.xml
/NeuroML2/LEMS_Test_RMD_shak.xml
/NeuroML2/LEMS_Test_*.xml
/RMD_2.ode
22 changes: 16 additions & 6 deletions NeuroML2/AWCon.cell.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon">
<notes>A cell from Nicoletti et al. 2019</notes>
<include href="leak.channel.nml"/>
<include href="AWCon_leak.channel.nml"/>
<include href="AWCon_shal.channel.nml"/>
<include href="AWCon_shak.channel.nml"/>
<include href="AWCon_kir.channel.nml"/>
<include href="AWCon_unc2.channel.nml"/>
<include href="AWCon_cca.channel.nml"/>
<cell id="AWCon">
<notes>AWCon cell from Nicoletti et al. 2019</notes>
<morphology id="morphology">
<segment id="0" name="soma">
<proximal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
<distal x="0.0" y="0.0" z="0.0" diameter="10.0"/>
<proximal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
<distal x="0.0" y="0.0" z="0.0" diameter="17.841242"/>
</segment>
<segmentGroup id="soma_group" neuroLexId="GO:0043025">
<notes>Default soma segment group for the cell</notes>
Expand All @@ -19,10 +24,15 @@
</morphology>
<biophysicalProperties id="biophys">
<membraneProperties>
<channelDensity id="leak_chans" ionChannel="leak" condDensity="3.0 S_per_m2" erev="-80mV" ion="non_specific"/>
<channelDensity id="leak_chans" ionChannel="AWCon_leak" condDensity="0.27 S_per_m2" erev="-80.0mV" ion="non_specific"/>
<channelDensity id="shal_chans" ionChannel="AWCon_shal" condDensity="2.9 S_per_m2" erev="-80.0mV" ion="k"/>
<channelDensity id="shak_chans" ionChannel="AWCon_shak" condDensity="0.1 S_per_m2" erev="-80.0mV" ion="k"/>
<channelDensity id="kir_chans" ionChannel="AWCon_kir" condDensity="0.65 S_per_m2" erev="-80.0mV" ion="k"/>
<channelDensity id="unc2_chans" ionChannel="AWCon_unc2" condDensity="1.0 S_per_m2" erev="60.0mV" ion="ca"/>
<channelDensity id="cca_chans" ionChannel="AWCon_cca" condDensity="0.7 S_per_m2" erev="60.0mV" ion="ca"/>
<spikeThresh value="0mV"/>
<specificCapacitance value="1.2 uF_per_cm2"/>
<initMembPotential value="-75mV"/>
<specificCapacitance value="0.0031000000000000003 F_per_m2"/>
<initMembPotential value="-70mV"/>
</membraneProperties>
<intracellularProperties>
<resistivity value="0.1 kohm_cm"/>
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66 changes: 66 additions & 0 deletions NeuroML2/AWCon_cca.channel.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon_cca">
<notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
<ionChannelHH id="AWCon_cca" species="ca" conductance="10pS">
<notes>AWCon_cca channel from Nicoletti et al. 2019</notes>
<gate id="m" instances="2" type="gateHHtauInf">
<timeCourse type="cca_m_tau"/>
<steadyState type="cca_m_inf"/>
</gate>
<gate id="h" instances="1" type="gateHHtauInf">
<timeCourse type="cca_h_tau"/>
<steadyState type="cca_h_inf"/>
</gate>
</ionChannelHH>
<ComponentType name="cca_m_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="va_cca1" dimension="none" value="-42.65"/>
<Constant name="ka_cca1" dimension="none" value="1.7"/>
<Constant name="sscca1" dimension="none" value="15.0"/>
<Constant name="fcca" dimension="none" value="1.4"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((1/(fcca*ka_cca1))*(-V - sscca1 + va_cca1)) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="cca_m_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="stmcca1" dimension="none" value="30.0"/>
<Constant name="constmcca1" dimension="none" value="0.5"/>
<Constant name="p1tmcca1" dimension="none" value="40.0"/>
<Constant name="p2tmcca1" dimension="none" value="-62.5393"/>
<Constant name="p3tmcca1" dimension="none" value="-12.4758"/>
<Constant name="p4tmcca1" dimension="none" value="0.6947"/>
<Constant name="f3ca" dimension="none" value="1.7"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(constmcca1*(p1tmcca1/(exp((1/(f3ca*p3tmcca1))*(-V + p2tmcca1 - stmcca1)) + 1) + p4tmcca1))/1000"/>
</Dynamics>
</ComponentType>
<ComponentType name="cca_h_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="sshcca1" dimension="none" value="15.0"/>
<Constant name="f2cca1" dimension="none" value="1.15"/>
<Constant name="vi_cca1" dimension="none" value="-58.0"/>
<Constant name="ki_cca1" dimension="none" value="7.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((1/(f2cca1*ki_cca1))*(V + sshcca1 - vi_cca1)) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="cca_h_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="sthcca1" dimension="none" value="15.0"/>
<Constant name="consthcca1" dimension="none" value="0.08"/>
<Constant name="p1thcca1" dimension="none" value="280.0"/>
<Constant name="p2thcca1" dimension="none" value="-60.7312"/>
<Constant name="p3thcca1" dimension="none" value="8.5224"/>
<Constant name="p4thcca1" dimension="none" value="19.7456"/>
<Constant name="f4ca" dimension="none" value="1.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(consthcca1*(p1thcca1/(exp((1/(f4ca*p3thcca1))*(V - p2thcca1 + sthcca1)) + 1) + p4thcca1))/1000"/>
</Dynamics>
</ComponentType>
</neuroml>
33 changes: 33 additions & 0 deletions NeuroML2/AWCon_kir.channel.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon_kir">
<notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
<ionChannelHH id="AWCon_kir" species="k" conductance="10pS">
<notes>AWCon_kir channel from Nicoletti et al. 2019</notes>
<gate id="m" instances="1" type="gateHHtauInf">
<timeCourse type="kir_m_tau"/>
<steadyState type="kir_m_inf"/>
</gate>
</ionChannelHH>
<ComponentType name="kir_m_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="va_kir" dimension="none" value="-52.0"/>
<Constant name="ka_kir" dimension="none" value="13.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V - va_kir + 30)/ka_kir) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="kir_m_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="p1tmkir" dimension="none" value="17.0752"/>
<Constant name="p2tmkir" dimension="none" value="-17.8258"/>
<Constant name="p3tmkir" dimension="none" value="20.3154"/>
<Constant name="p4tmkir" dimension="none" value="-43.4414"/>
<Constant name="p5tmkir" dimension="none" value="11.1691"/>
<Constant name="p6tmkir" dimension="none" value="3.8329"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(p1tmkir/(exp((-V + p2tmkir)/p3tmkir) + exp((V - p4tmkir)/p5tmkir)) + p6tmkir)/1000"/>
</Dynamics>
</ComponentType>
</neuroml>
6 changes: 6 additions & 0 deletions NeuroML2/AWCon_leak.channel.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon_leak">
<notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
<ionChannelHH id="AWCon_leak" species="non_specific" conductance="10pS">
<notes>AWCon_leak channel from Nicoletti et al. 2019</notes>
</ionChannelHH>
</neuroml>
57 changes: 57 additions & 0 deletions NeuroML2/AWCon_shak.channel.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon_shak">
<notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
<ionChannelHH id="AWCon_shak" species="k" conductance="10pS">
<notes>AWCon_shak channel from Nicoletti et al. 2019</notes>
<gate id="m" instances="1" type="gateHHtauInf">
<timeCourse type="shak_m_tau"/>
<steadyState type="shak_m_inf"/>
</gate>
<gate id="h" instances="1" type="gateHHtauInf">
<timeCourse type="shak_h_tau"/>
<steadyState type="shak_h_inf"/>
</gate>
</ionChannelHH>
<ComponentType name="shak_m_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="vashak" dimension="none" value="20.4"/>
<Constant name="kashak" dimension="none" value="7.7"/>
<Constant name="shiftV05" dimension="none" value="0.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((-V - shiftV05 + vashak)/kashak) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shak_m_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="ptmshak1" dimension="none" value="26.571450568169027"/>
<Constant name="ptmshak2" dimension="none" value="-33.74161180071613"/>
<Constant name="ptmshak3" dimension="none" value="15.757936311607475"/>
<Constant name="ptmshak4" dimension="none" value="15.364937728953288"/>
<Constant name="ptmshak5" dimension="none" value="1.990037272604829"/>
<Constant name="shiftV05" dimension="none" value="0.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(ptmshak1/(exp((V - (ptmshak2 + shiftV05))/ptmshak3) + exp((-V + ptmshak2 + shiftV05)/ptmshak4)) + ptmshak5)/1000"/>
</Dynamics>
</ComponentType>
<ComponentType name="shak_h_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="kishak" dimension="none" value="5.8"/>
<Constant name="vishak" dimension="none" value="-6.95"/>
<Constant name="shiftV05" dimension="none" value="0.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shiftV05 - vishak)/kishak) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shak_h_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="pthshak" dimension="none" value="1400.0"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(pthshak)/1000"/>
</Dynamics>
</ComponentType>
</neuroml>
91 changes: 91 additions & 0 deletions NeuroML2/AWCon_shal.channel.nml
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<neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" 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_v2.3.xsd" id="AWCon_shal">
<notes>An ion channel from cell AWCon from Nicoletti et al. 2019</notes>
<ionChannelHH id="AWCon_shal" species="k" conductance="10pS">
<notes>AWCon_shal channel from Nicoletti et al. 2019</notes>
<gate id="m" instances="3" type="gateHHtauInf">
<timeCourse type="shal_m_tau"/>
<steadyState type="shal_m_inf"/>
</gate>
<gate id="h" instances="1" type="gateFractional">
<subGate id="hf" fractionalConductance="0.7">
<steadyState type="shal_h_hf_inf"/>
<timeCourse type="shal_h_hf_tau"/>
</subGate>
<subGate id="hs" fractionalConductance="0.3">
<steadyState type="shal_h_hs_inf"/>
<timeCourse type="shal_h_hs_tau"/>
</subGate>
</gate>
</ionChannelHH>
<ComponentType name="shal_m_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="vashal" dimension="none" value="11.2"/>
<Constant name="kashal" dimension="none" value="14.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((-V - shalsfhit + vashal)/kashal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_m_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="ptmshal1" dimension="none" value="13.8"/>
<Constant name="ptmshal2" dimension="none" value="-17.5165"/>
<Constant name="ptmshal3" dimension="none" value="12.9213"/>
<Constant name="ptmshal4" dimension="none" value="-3.7082"/>
<Constant name="ptmshal5" dimension="none" value="6.4876"/>
<Constant name="ptmshal6" dimension="none" value="1.8849"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(ptmshal1/(exp((-V + ptmshal2)/ptmshal3) + exp((V - ptmshal4)/ptmshal5)) + ptmshal6))/1000"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hf_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="kishal" dimension="none" value="8.3"/>
<Constant name="vishal" dimension="none" value="-33.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shalsfhit - vishal)/kishal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hf_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="pthfshal1" dimension="none" value="539.1584"/>
<Constant name="pthfshal2" dimension="none" value="-28.199"/>
<Constant name="pthfshal3" dimension="none" value="4.9199"/>
<Constant name="pthfshal4" dimension="none" value="27.2811"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(pthfshal1/(exp((V - pthfshal2)/pthfshal3) + 1) + pthfshal4))/1000"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hs_inf" extends="baseVoltageDepVariable">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="shalsfhit" dimension="none" value="18.0"/>
<Constant name="kishal" dimension="none" value="8.3"/>
<Constant name="vishal" dimension="none" value="-33.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="x" dimension="none" exposure="x" value="1/(exp((V + shalsfhit - vishal)/kishal) + 1)"/>
</Dynamics>
</ComponentType>
<ComponentType name="shal_h_hs_tau" extends="baseVoltageDepTime">
<Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
<Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
<Constant name="pthsshal1" dimension="none" value="8422.0"/>
<Constant name="pthsshal2" dimension="none" value="-37.7391"/>
<Constant name="pthsshal3" dimension="none" value="6.3785"/>
<Constant name="pthsshal4" dimension="none" value="118.8983"/>
<Constant name="cshal" dimension="none" value="0.1"/>
<Dynamics>
<DerivedVariable name="V" dimension="none" value="(v) / VOLT_SCALE"/>
<DerivedVariable name="t" dimension="time" exposure="t" value="(cshal*(pthsshal1/(exp((V - pthsshal2)/pthsshal3) + 1) + pthsshal4))/1000"/>
</Dynamics>
</ComponentType>
</neuroml>
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