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openworm · Aug 19, 2024 · 4a3275f · 4a3275f
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diff --git a/.gitignore b/.gitignore
@@ -29,3 +29,6 @@ arm64
 /NeuroML2/Fig7B_RMD.json
 /NeuroML2/Sim_Fig7B_RMD.json
 /NeuroML2/.DS_Store
+/NeuroML2/*.hoc
+/NeuroML2/*.mod
+/NeuroML2/*_nrn.py
diff --git a/NeuroML2/AWCon_bk.channel.nml b/NeuroML2/AWCon_bk.channel.nml
@@ -19,6 +19,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -35,12 +41,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -79,6 +79,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -95,12 +101,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -137,6 +137,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -153,12 +159,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -191,6 +191,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -207,12 +213,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>

diff --git a/NeuroML2/Fig4C_AWCon.net.nml b/NeuroML2/Fig4C_AWCon.net.nml
@@ -1,5 +1,5 @@
 <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_v2.3.1.xsd" id="Fig4C_AWCon">
-    <notes>Generated by NeuroMLlite v0.5.9
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Fig4C_AWCon
     Generation seed: 1234</notes>
     <include href="AWCon.cell.nml"/>

diff --git a/NeuroML2/Fig7B_RMD.net.nml b/NeuroML2/Fig7B_RMD.net.nml
@@ -1,5 +1,5 @@
 <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_v2.3.1.xsd" id="Fig7B_RMD">
-    <notes>Generated by NeuroMLlite v0.5.9
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: Fig7B_RMD
     Generation seed: 1234</notes>
     <include href="RMD.cell.nml"/>

diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py
@@ -818,6 +818,10 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
             extra_params = [
                 "backgr",
                 "cac_nano",
+                "cao_nano",
+                "kcm",
+                "kom",
+                "kop",
                 "wom",
                 "wyx",
                 "kyx",
@@ -836,10 +840,6 @@ def create_cells(channels_to_include, duration=700, stim_delay=310, stim_duratio
                 "b",
                 "gsc",
                 "eca",
-                "cao_nano",
-                "kcm",
-                "kom",
-                "kop",
                 "minf_unc2",
                 "alpha",
                 "beta",

diff --git a/NeuroML2/IClamp_AWCon.json b/NeuroML2/IClamp_AWCon.json
@@ -1,6 +1,6 @@
 {
     "IClamp_AWCon": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "A network model: IClamp_AWCon",
         "parameters": {
             "stim_amp": "10pA",

diff --git a/NeuroML2/IClamp_RMD.json b/NeuroML2/IClamp_RMD.json
@@ -1,6 +1,6 @@
 {
     "IClamp_RMD": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "notes": "A network model: IClamp_RMD",
         "parameters": {
             "stim_amp": "10pA",

diff --git a/NeuroML2/IClamp_RMD.net.nml b/NeuroML2/IClamp_RMD.net.nml
@@ -1,5 +1,5 @@
 <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_v2.3.1.xsd" id="IClamp_RMD">
-    <notes>Generated by NeuroMLlite v0.5.9
+    <notes>Generated by NeuroMLlite v0.6.0
     Generated network: IClamp_RMD
     Generation seed: 1234
     NeuroMLlite parameters: 

diff --git a/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml b/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.15 (libNeuroML v0.6.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)
 
      -->
 

diff --git a/NeuroML2/LEMS_Sim_Fig7B_RMD.xml b/NeuroML2/LEMS_Sim_Fig7B_RMD.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.15 (libNeuroML v0.6.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)
 
      -->
 

diff --git a/NeuroML2/LEMS_Sim_IClamp_RMD.xml b/NeuroML2/LEMS_Sim_IClamp_RMD.xml
@@ -2,7 +2,7 @@
 
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.2.15 (libNeuroML v0.6.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.3.7 (libNeuroML v0.6.3)
 
      -->
 

diff --git a/NeuroML2/RMD_bk.channel.nml b/NeuroML2/RMD_bk.channel.nml
@@ -19,6 +19,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -35,12 +41,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -79,6 +79,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -95,12 +101,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -137,6 +137,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -153,12 +159,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>
@@ -191,6 +191,12 @@
         <Constant name="backgr" dimension="none" value="0.05"/>
         <Constant name="r" dimension="none" value="1.3e-08"/>
         <Constant name="b" dimension="none" value="3e-05"/>
+        <Constant name="pi" dimension="none" value="3.14159265359"/>
+        <Constant name="d" dimension="none" value="2.5e-10"/>
+        <Constant name="F" dimension="none" value="96485.0"/>
+        <Constant name="kb" dimension="none" value="500000000.0"/>
+        <Constant name="gsc" dimension="none" value="4e-11"/>
+        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="wom" dimension="none" value="3.152961"/>
         <Constant name="wyx" dimension="none" value="0.012643"/>
         <Constant name="kyx" dimension="none" value="34.338784"/>
@@ -207,12 +213,6 @@
         <Constant name="p5tmunc2" dimension="none" value="0.1029"/>
         <Constant name="shiftmunc2" dimension="none" value="30.0"/>
         <Constant name="constmunc2" dimension="none" value="3.0"/>
-        <Constant name="pi" dimension="none" value="3.14159265359"/>
-        <Constant name="d" dimension="none" value="2.5e-10"/>
-        <Constant name="F" dimension="none" value="96485.0"/>
-        <Constant name="kb" dimension="none" value="500000000.0"/>
-        <Constant name="gsc" dimension="none" value="4e-11"/>
-        <Constant name="eca" dimension="none" value="60.0"/>
         <Constant name="stm2" dimension="none" value="25.0"/>
         <Constant name="va_unc2" dimension="none" value="-12.17"/>
         <Constant name="ka_unc2" dimension="none" value="3.97"/>

diff --git a/NeuroML2/Sim_IClamp_AWCon.json b/NeuroML2/Sim_IClamp_AWCon.json
@@ -1,6 +1,6 @@
 {
     "Sim_IClamp_AWCon": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "network": "IClamp_AWCon.json",
         "duration": 2400.0,
         "dt": 0.025,

diff --git a/NeuroML2/Sim_IClamp_RMD.json b/NeuroML2/Sim_IClamp_RMD.json
@@ -1,6 +1,6 @@
 {
     "Sim_IClamp_RMD": {
-        "version": "NeuroMLlite v0.5.9",
+        "version": "NeuroMLlite v0.6.0",
         "network": "IClamp_RMD.json",
         "duration": 2400.0,
         "dt": 0.025,