Merge branch 'sanjayankur31-neuroml-ankur-dev' into development

OpenSourceBrain · Apr 10, 2024 · b044d69 · b044d69
2 parents 9cd5e8c + bb27e41
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diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,5 @@
 arm64
 __pycache__
 *.log
+*.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_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_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/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/...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/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/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>