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Ignoring file on mac #9

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Aug 19, 2024
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Ignoring file on mac #9

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e232218
Ignoring on mac
pgleeson Aug 13, 2024
4a3275f
Regenerated
pgleeson Aug 19, 2024
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4 changes: 4 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -28,3 +28,7 @@ arm64
/NeuroML2/Sim_Fig4C_AWCon.json
/NeuroML2/Fig7B_RMD.json
/NeuroML2/Sim_Fig7B_RMD.json
/NeuroML2/.DS_Store
/NeuroML2/*.hoc
/NeuroML2/*.mod
/NeuroML2/*_nrn.py
48 changes: 24 additions & 24 deletions NeuroML2/AWCon_bk.channel.nml
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Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/Fig4C_AWCon.net.nml
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Original file line number Diff line number Diff line change
@@ -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"/>
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/Fig7B_RMD.net.nml
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Original file line number Diff line number Diff line change
@@ -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"/>
Expand Down
8 changes: 4 additions & 4 deletions NeuroML2/GenerateNeuroML.py
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Expand Up @@ -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",
Expand All @@ -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",
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/IClamp_AWCon.json
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@@ -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",
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/IClamp_RMD.json
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@@ -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",
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/IClamp_RMD.net.nml
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Original file line number Diff line number Diff line change
@@ -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:
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/LEMS_Sim_Fig4C_AWCon.xml
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Expand Up @@ -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)

-->

Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/LEMS_Sim_Fig7B_RMD.xml
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Expand Up @@ -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)

-->

Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/LEMS_Sim_IClamp_RMD.xml
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Expand Up @@ -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)

-->

Expand Down
48 changes: 24 additions & 24 deletions NeuroML2/RMD_bk.channel.nml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/Sim_IClamp_AWCon.json
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Original file line number Diff line number Diff line change
@@ -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,
Expand Down
2 changes: 1 addition & 1 deletion NeuroML2/Sim_IClamp_RMD.json
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Original file line number Diff line number Diff line change
@@ -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,
Expand Down
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