Merge pull request #1 from openworm/development

Latest NeuroML version
openworm · Apr 25, 2024 · c4fbde2 · c4fbde2
2 parents 4ed2bcf + 3b0a781
commit c4fbde2
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diff --git a/.gitignore b/.gitignore
@@ -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
diff --git a/NeuroML2/AWCon.cell.nml b/NeuroML2/AWCon.cell.nml
@@ -1,12 +1,17 @@
 <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>
@@ -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"/>

diff --git a/NeuroML2/AWCon_cca.channel.nml b/NeuroML2/AWCon_cca.channel.nml
@@ -0,0 +1,66 @@
+<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>
diff --git a/NeuroML2/AWCon_kir.channel.nml b/NeuroML2/AWCon_kir.channel.nml
@@ -0,0 +1,33 @@
+<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>
diff --git a/NeuroML2/AWCon_leak.channel.nml b/NeuroML2/AWCon_leak.channel.nml
@@ -0,0 +1,6 @@
+<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>
diff --git a/NeuroML2/AWCon_shak.channel.nml b/NeuroML2/AWCon_shak.channel.nml
@@ -0,0 +1,57 @@
+<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>
diff --git a/NeuroML2/AWCon_shal.channel.nml b/NeuroML2/AWCon_shal.channel.nml
@@ -0,0 +1,91 @@
+<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>