Merge pull request #5 from sanjayankur31/neuroml-ankur

Convert ion channels, KC cell
OpenSourceBrain · Apr 10, 2024 · d1c86af · d1c86af
2 parents 7809e3d + c3bfccd
commit d1c86af
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Showing 26 changed files with 286 additions and 184 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+*.dat
+x86_64/
diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_ka_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_ka_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kst_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kst_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kv_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_kv_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_naf_at_6.3_degC.png b/NEURON/mb/mod/Steady_state(s)_of_activation_variables_in_naf_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_ka_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_ka_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kst_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kst_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kv_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_kv_at_6.3_degC.png
diff --git a/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_naf_at_6.3_degC.png b/NEURON/mb/mod/Time_course(s)_of_activation_variables_in_naf_at_6.3_degC.png
diff --git a/NeuroML2/.test.validate.omt b/NeuroML2/.test.validate.omt
@@ -0,0 +1,7 @@
+# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation 
+# Still in development, subject to change without notice!!
+
+
+# This test will validate MOST all of the NeuroML 2 files in the current directory
+target: "*.c*.nml"
+engine: jNeuroML_validate
diff --git a/NeuroML2/KC.cell.nml b/NeuroML2/KC.cell.nml
@@ -0,0 +1,39 @@
+<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="KC_doc">
+    <include href="channels/pas.channel.nml"/>
+    <include href="channels/nas.channel.nml"/>
+    <include href="channels/naf.channel.nml"/>
+    <include href="channels/kv.channel.nml"/>
+    <include href="channels/ka.channel.nml"/>
+    <include href="channels/kst.channel.nml"/>
+    <cell id="KC">
+        <morphology id="morphology">
+            <segment id="0" name="Seg0">
+                <proximal x="0.0" y="0.0" z="0.0" diameter="20.0"/>
+                <distal x="0.0" y="0.0" z="6.366" diameter="20.0"/>
+            </segment>
+            <segmentGroup id="soma_group" neuroLexId="GO:0043025">
+                <notes>Default soma segment group for the cell</notes>
+                <member segment="0"/>
+            </segmentGroup>
+            <segmentGroup id="all">
+                <notes>Default segment group for all segments in the cell</notes>
+                <member segment="0"/>
+            </segmentGroup>
+        </morphology>
+        <biophysicalProperties id="biophys">
+            <membraneProperties>
+                <channelDensity id="pas" ionChannel="pas" condDensity=".0000975 S_per_cm2" erev="-70 mV" ion="non_specific"/>
+                <channelDensity id="nas" ionChannel="nas" condDensity="3e-3 S_per_cm2" erev="-58 mV" ion="na"/>
+                <channelDensity id="naf" ionChannel="naf" condDensity="3.5e-2 S_per_cm2" erev="-58 mV" ion="na"/>
+                <channelDensity id="kv" ionChannel="kv" condDensity="1.5e-3 S_per_cm2" erev="-81 mV" ion="k"/>
+                <channelDensity id="ka" ionChannel="ka" condDensity="1.4525e-2 S_per_cm2" erev="-81 mV" ion="k"/>
+                <channelDensity id="kst" ionChannel="kst" condDensity="2.0275e-3 S_per_cm2" erev="-81 mV" ion="k"/>
+                <specificCapacitance value="1 uF_per_cm2"/>
+                <initMembPotential value="-80mV"/>
+            </membraneProperties>
+            <intracellularProperties>
+                <resistivity value="35.4 ohm_cm"/>
+            </intracellularProperties>
+        </biophysicalProperties>
+    </cell>
+</neuroml>
diff --git a/NeuroML2/channels/RaySigmoid.nml b/NeuroML2/channels/RaySigmoid.nml
@@ -0,0 +1,42 @@
+<?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="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing variations of steady state and tau expressions for ion channels used in Ray et al 2020. These are required because in the mod files, the tables stop at 40, and so we need to tweak our implementations.</notes>
+
+    <ComponentType name="Ray_inf"
+        extends="baseVoltageDepVariable"
+        description="Inf parameter to describe naf" >
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 s"/>
+        <Constant name="table_max" dimension="voltage" value="40 mV"/>
+        <Parameter name="rate" dimension="none"/>
+        <Parameter name="midpoint" dimension="voltage"/>
+        <Parameter name="scale" dimension="voltage"/>
+        <Dynamics>
+            <ConditionalDerivedVariable name="x" dimension="per_time" exposure="x">
+                <Case condition="v .gt. table_max" value="(rate / (1 + exp(0 - (table_max - midpoint) / scale)))/TIME_SCALE"/>
+                <Case value="(rate / (1 + exp(0 - (v - midpoint) / scale)))/TIME_SCALE"/>
+            </ConditionalDerivedVariable>
+        </Dynamics>
+    </ComponentType>
+
+     <ComponentType name="Ray_tau"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe naf">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="table_max" dimension="voltage" value="40 mV"/>
+        <Parameter name="max_tau" dimension="per_time"/>
+        <Parameter name="min_tau" dimension="per_time"/>
+        <Parameter name="midpoint" dimension="voltage"/>
+        <Parameter name="scale" dimension="voltage"/>
+        <Dynamics>
+            <ConditionalDerivedVariable name="t" dimension="per_time" exposure="t" >
+                <Case condition="v .gt. table_max" value="((max_tau - min_tau) / (1 + exp(0 - (table_max - midpoint) / scale))) + min_tau"/>
+                <Case value="((max_tau - min_tau) / (1 + exp(0 - (v - midpoint) / scale))) + min_tau"/>
+            </ConditionalDerivedVariable>
+
+        </Dynamics>
+
+    </ComponentType>
+</neuroml>
diff --git a/...dy_state(s)_of_activation_variables_of_Nas_from_nas.channel.nml_at_6.3_degC.png b/...dy_state(s)_of_activation_variables_of_Nas_from_nas.channel.nml_at_6.3_degC.png
diff --git a/...eady_state(s)_of_activation_variables_of_ka_from_ka.channel.nml_at_6.3_degC.png b/...eady_state(s)_of_activation_variables_of_ka_from_ka.channel.nml_at_6.3_degC.png
diff --git a/...eady_state(s)_of_activation_variables_of_kv_from_kv.channel.nml_at_6.3_degC.png b/...eady_state(s)_of_activation_variables_of_kv_from_kv.channel.nml_at_6.3_degC.png
diff --git a/...dy_state(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png b/...dy_state(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png
diff --git a/...e_Course(s)_of_activation_variables_of_Nas_from_nas.channel.nml_at_6.3_degC.png b/...e_Course(s)_of_activation_variables_of_Nas_from_nas.channel.nml_at_6.3_degC.png
diff --git a/...ime_Course(s)_of_activation_variables_of_ka_from_ka.channel.nml_at_6.3_degC.png b/...ime_Course(s)_of_activation_variables_of_ka_from_ka.channel.nml_at_6.3_degC.png
diff --git a/...ime_Course(s)_of_activation_variables_of_kv_from_kv.channel.nml_at_6.3_degC.png b/...ime_Course(s)_of_activation_variables_of_kv_from_kv.channel.nml_at_6.3_degC.png
diff --git a/...e_Course(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png b/...e_Course(s)_of_activation_variables_of_naf_from_naf.channel.nml_at_6.3_degC.png
diff --git a/NeuroML2/channels/ka.channel.nml b/NeuroML2/channels/ka.channel.nml
@@ -0,0 +1,65 @@
+<?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="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
+
+    <ionChannel id="ka" conductance="1pS" type="ionChannelHH" species="k">
+
+        <notes>
+                Implementation of A type K+ channel ( KA ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA.
+                This is transient A type K+ channel in Apis mellifera Kenyon cells (cultured).
+        </notes>
+
+        <!-- custom component types because the tables in the mod files only go to 40 -->
+        <gate id="m" type="gateHHtauInf" instances="3">
+            <steadyState type="Ray_inf" rate="1.0" midpoint="-20.1mV" scale="16.1mV"/>
+            <timeCourse type="Ray_ka_taum"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <steadyState type="Ray_inf" rate="1.0" midpoint="-74.7mV" scale="-7.0mV"/>
+            <timeCourse type="Ray_ka_tauh"/>
+        </gate>
+
+    </ionChannel>
+
+    <ComponentType name="Ray_ka_taum"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe ka">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="max_tau" dimension="per_time" value="1.65 per_s"/>
+        <Constant name="min_tau" dimension="per_time" value="0.35 per_s"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <ConditionalDerivedVariable name="t" dimension="per_time" exposure="t" >
+                <Case condition="V .gt. 40" value="(max_tau - min_tau) / ((1 + exp(-(40. + 70.0) / 4.0)) * ( 1 + exp((40. + 2.0) / 12.0))) + min_tau"/>
+                <Case value="(max_tau - min_tau) / ((1 + exp(-(V + 70.0) / 4.0)) * ( 1 + exp((V + 2.0) / 12.0))) + min_tau"/>
+
+            </ConditionalDerivedVariable>
+        </Dynamics>
+
+    </ComponentType>
+
+    <ComponentType name="Ray_ka_tauh"
+                   extends="baseVoltageDepTime"
+                   description="Tau parameter to describe ka">
+
+        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
+        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
+        <Constant name="max_tau" dimension="per_time" value="90.0 per_s"/>
+        <Constant name="min_tau" dimension="per_time" value="2.5 per_s"/>
+        <Dynamics>
+            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
+            <ConditionalDerivedVariable name="t" dimension="per_time" exposure="t" >
+                <Case condition="V .gt. 40" value="(max_tau - min_tau) / ((1 + exp(-(40. + 60.) / 25.0)) * (1 + exp((40. + 62.0) / 16.0))) + min_tau"/>
+                <Case value="(max_tau - min_tau) / ((1 + exp(-(V + 60.) / 25.0)) * (1 + exp((V + 62.0) / 16.0))) + min_tau"/>
+            </ConditionalDerivedVariable>
+
+        </Dynamics>
+
+    </ComponentType>
+
+</neuroml>
diff --git a/NeuroML2/channels/kst.channel.nml b/NeuroML2/channels/kst.channel.nml
@@ -0,0 +1,25 @@
+<?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="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
+
+    <ionChannel id="kst" conductance="1pS" type="ionChannelHH" species="k">
+
+        <notes>
+            NEURON implementation of slow transient K+ channel ( KST ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA
+
+            This is slow transient K+ channel in Apis mellifera Kenyon cells (cultured).
+        </notes>
+
+        <gate id="m" type="gateHHtauInf" instances="3">
+            <steadyState type="Ray_inf" rate="1" midpoint="-20.1mV" scale="16.1mV"/>
+            <timeCourse type="Ray_tau" min_tau="0.5 per_s" max_tau="5.0 per_s" midpoint="20.0 mV" scale="-20.0mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <steadyState type="Ray_inf" rate="1" midpoint="-74.7mV" scale="-7.0mV"/>
+            <timeCourse type="Ray_tau" min_tau="150.0 per_s" max_tau="200.0 per_s" midpoint="52.0 mV" scale="-15.0mV"/>
+        </gate>
+    </ionChannel>
+</neuroml>
diff --git a/NeuroML2/channels/kv.channel.nml b/NeuroML2/channels/kv.channel.nml
@@ -0,0 +1,21 @@
+<?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="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
+
+    <ionChannel id="kv" conductance="1pS" type="ionChannelHH" species="k">
+
+        <notes>
+                Implementation of A type K+ channel ( KV ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA.
+                This is a delayed rectifier type K+ channel in Apis mellifera Kenyon cells (cultured).
+        </notes>
+
+        <!-- custom component types because the tables in the mod files only go to 40 -->
+        <gate id="m" type="gateHHtauInf" instances="4">
+            <steadyState type="Ray_inf" rate="1.0" midpoint="-37.6mV" scale="27.24mV"/>
+            <timeCourse type="Ray_tau" min_tau="1.85 per_s" max_tau="3.53 per_s" midpoint="45.0 mV" scale="-13.71mV"/>
+        </gate>
+
+    </ionChannel>
+</neuroml>
diff --git a/NeuroML2/channels/naf.channel.nml b/NeuroML2/channels/naf.channel.nml
@@ -0,0 +1,26 @@
+<?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="NeuroML_ionChannel">
+
+    <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
+
+    <ionChannel id="naf" conductance="1pS" type="ionChannelHH" species="na">
+
+        <notes>
+            Implementation of fast Na+ channel ( NAF ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA
+
+            This is fast Na+ channel in Apis mellifera Kenyon cells :(cultured).
+        </notes>
+
+        <gate id="m" type="gateHHtauInf" instances="3">
+            <steadyState type="Ray_inf" rate="1.0" midpoint="-30.1mV" scale="6.65mV"/>
+            <timeCourse type="Ray_tau" min_tau="0.83 per_s" max_tau="0.093 per_s" midpoint="-20.3 mV" scale="6.45mV"/>
+        </gate>
+
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <steadyState type="Ray_inf" rate="1.0" midpoint="-51.4mV" scale="-5.9mV"/>
+            <timeCourse type="Ray_tau" min_tau="0.12 per_s" max_tau="1.660 per_s" midpoint="-8.03 mV" scale="-8.69mV"/>
+        </gate>
+
+    </ionChannel>
+</neuroml>
diff --git a/NeuroML2/channels/nas.channel.nml b/NeuroML2/channels/nas.channel.nml
@@ -2,136 +2,24 @@
 <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="NeuroML_ionChannel">
 
     <notes>NeuroML file containing a single ion channel</notes>
+    <include href="RaySigmoid.nml" />
 
-    <ionChannel id="Navp" conductance="1pS" type="ionChannelHH" species="na">
+    <ionChannel id="nas" conductance="1pS" type="ionChannelHH" species="na">
 
         <notes>
             Implementation of slow Na+ channel ( NAS ) from Wustenberg DG, Boytcheva M, Grunewald B, Byrne JH, Menzel R, Baxter DA
 
             This is slow Na+ channel in Apis mellifera Kenyon cells :(cultured).
         </notes>
 
-        <gate id="m" type="gateHHratesTau" instances="3">
-            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-30.1mV" scale="6.65mV"/>
-            <timeCourse type="Ray_nas_taum"/>
+        <gate id="m" type="gateHHtauInf" instances="3">
+            <steadyState type="Ray_inf" rate="1" midpoint="-30.1mV" scale="6.65mV"/>
+            <timeCourse type="Ray_tau" min_tau="0.83 per_s" max_tau="0.093 per_s" midpoint="-20.3 mV" scale="6.45mV"/>
         </gate>
 
-        <gate id="h" type="gateHHratesTau" instances="1">
-            <forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-51.4mV" scale="5.9mV"/>
-            <timeCourse type="Ray_nas_tauh"/>
+        <gate id="h" type="gateHHtauInf" instances="1">
+            <steadyState type="Ray_inf" rate="1" midpoint="-51.4mV" scale="-5.9mV"/>
+            <timeCourse type="Ray_tau" min_tau="1.9 per_s" max_tau="12.24 per_s" midpoint="-32.6 mV" scale="-8.0mV"/>
         </gate>
-
     </ionChannel>
-
-     <ComponentType name="Ray_nas_taum"
-                   extends="baseVoltageDepTime"
-                   description="Tau parameter to describe Navp">
-
-        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
-        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
-        <Constant name="max_tau" dimension="per_time" value="0.83 per_time"/>
-        <Constant name="min_tau" dimension="per_time" value="0.093 per_time"/>
-        <Dynamics>
-            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
-            <ConditionalDerivedVariable name="t" dimension="time" exposure="t">
-                <Case condition="(ALPHA + BETA) .eq. 0" value="( 0 ) * TIME_SCALE"/>
-                <Case condition="1/( (ALPHA + BETA) * rateScale )  .lt. ( 0.02 )" value="( (0.02 * rateScale) ) * TIME_SCALE"/>
-                <Case value="( 1/(ALPHA + BETA) ) * TIME_SCALE"/>
-            </ConditionalDerivedVariable>
-
-        </Dynamics>
-
-    </ComponentType>
-
-    <ComponentType name="Ray_nas_tauh"
-                   extends="baseVoltageDepTime"
-                   description="Tau parameter to describe Navp">
-
-        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
-        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
-
-        <Requirement name="alpha" dimension="per_time"/>
-        <Requirement name="beta" dimension="per_time"/>
-        <Requirement name="rateScale" dimension="none"/>
-
-        <Dynamics>
-            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
-            <DerivedVariable name="ALPHA" dimension="none" value="alpha * TIME_SCALE"/>
-            <DerivedVariable name="BETA" dimension="none" value="beta * TIME_SCALE"/>
-
-            <ConditionalDerivedVariable name="t" exposure="t" dimension="time">
-                <Case condition="(ALPHA + BETA) .eq. 0" value="( 0 ) * TIME_SCALE"/>
-                <Case condition="1/( (ALPHA + BETA) * rateScale )  .lt. ( 0.5 )" value="( (0.5 * rateScale) ) * TIME_SCALE"/>
-                <Case value="( 1/(ALPHA + BETA) ) * TIME_SCALE"/>
-            </ConditionalDerivedVariable>
-
-        </Dynamics>
-
-    </ComponentType>
-
-    <ComponentType name="Ray_nas_taus"
-                   extends="baseVoltageDepTime"
-                   description="Tau parameter to describe Navp">
-
-        <Constant name="TIME_SCALE" dimension="time" value="1 ms"/>
-        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
-        <Constant name="TEMP_SCALE" dimension="temperature" value="1 K"/>
-        <Constant name="R" dimension="none" value="8.315"/>
-        <Constant name="F" dimension="none" value="96480"/>
-
-        <Requirement name="rateScale" dimension="none"/>
-        <Requirement name="temperature" dimension="temperature"/>
-
-        <Dynamics>
-            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
-            <DerivedVariable name="T" dimension="none" value="temperature / TEMP_SCALE"/>
-
-            <DerivedVariable name="alpha" dimension="none" value="exp((1e-3*12*(V+45)*F) / (R*(T+0.01)))"/> <!-- NEURON code: 273.16 + celsius-->
-            <DerivedVariable name="beta" dimension="none" value="exp((1e-3*12*0.2*(V+45)*F) / (R*(T+0.01)))"/> <!-- NEURON code: 273.16 + celsius-->
-
-            <DerivedVariable name="tmp" value="beta / (3e-4*(1 + alpha))" dimension="none"/>
-            <ConditionalDerivedVariable name="t" dimension="time" exposure="t" >
-                <Case condition="(tmp / rateScale) .lt. 10" value="10 * rateScale * TIME_SCALE"/>
-                <Case value="tmp * TIME_SCALE"/>
-            </ConditionalDerivedVariable>
-
-        </Dynamics>
-
-    </ComponentType>
-
-    <ComponentType name="Ray_nas_sss_ar2_1"
-                   extends="baseVoltageDepVariable"
-                   description="steadyState parameter to describe Navp">
-
-        <Constant name="no_inact" dimension="none" value="1"/> <!-- 1: no inact, 0: max inact-->
-        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
-
-        <Dynamics>
-            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
-
-            <DerivedVariable name="alpha" dimension="none" value="1 / (1 + exp((V+43)/2))"/>
-
-            <DerivedVariable name="x" exposure="x" dimension="none" value="alpha + no_inact*(1 - alpha)"/>
-        </Dynamics>
-
-    </ComponentType>
-
-
-    <ComponentType name="Ray_nas_sss_ar2_0_8"
-                   extends="baseVoltageDepVariable"
-                   description="steadyState parameter to describe Navp">
-
-        <Constant name="no_inact" dimension="none" value="0.8"/> <!-- 1: no inact, 0: max inact-->
-        <Constant name="VOLT_SCALE" dimension="voltage" value="1 mV"/>
-
-        <Dynamics>
-            <DerivedVariable name="V" dimension="none" value="v / VOLT_SCALE"/>
-
-            <DerivedVariable name="alpha" dimension="none" value="1 / (1 + exp((V+43)/2))"/>
-
-            <DerivedVariable name="x" exposure="x" dimension="none" value="alpha + no_inact*(1 - alpha)"/>
-        </Dynamics>
-
-    </ComponentType>
-
 </neuroml>