From e232218d24549f2ea99e3b437e82614b5b765eab Mon Sep 17 00:00:00 2001 From: pgleeson Date: Tue, 13 Aug 2024 14:53:26 +0100 Subject: [PATCH 1/2] Ignoring on mac --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 1e4ed8c..96df504 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,4 @@ arm64 /NeuroML2/Sim_Fig4C_AWCon.json /NeuroML2/Fig7B_RMD.json /NeuroML2/Sim_Fig7B_RMD.json +/NeuroML2/.DS_Store From 4a3275f3443e545d7905d9fd16d584ebd8811fdc Mon Sep 17 00:00:00 2001 From: pgleeson Date: Mon, 19 Aug 2024 12:21:58 +0100 Subject: [PATCH 2/2] Regenerated --- .gitignore | 3 ++ NeuroML2/AWCon_bk.channel.nml | 48 +++++++++++++++---------------- NeuroML2/Fig4C_AWCon.net.nml | 2 +- NeuroML2/Fig7B_RMD.net.nml | 2 +- NeuroML2/GenerateNeuroML.py | 8 +++--- NeuroML2/IClamp_AWCon.json | 2 +- NeuroML2/IClamp_RMD.json | 2 +- NeuroML2/IClamp_RMD.net.nml | 2 +- NeuroML2/LEMS_Sim_Fig4C_AWCon.xml | 2 +- NeuroML2/LEMS_Sim_Fig7B_RMD.xml | 2 +- NeuroML2/LEMS_Sim_IClamp_RMD.xml | 2 +- NeuroML2/RMD_bk.channel.nml | 48 +++++++++++++++---------------- NeuroML2/Sim_IClamp_AWCon.json | 2 +- NeuroML2/Sim_IClamp_RMD.json | 2 +- 14 files changed, 65 insertions(+), 62 deletions(-) diff --git a/.gitignore b/.gitignore index 96df504..394d569 100644 --- 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 index 7d83fa5..fd53096 100644 --- a/NeuroML2/AWCon_bk.channel.nml +++ b/NeuroML2/AWCon_bk.channel.nml @@ -19,6 +19,12 @@ + + + + + + @@ -35,12 +41,6 @@ - - - - - - @@ -79,6 +79,12 @@ + + + + + + @@ -95,12 +101,6 @@ - - - - - - @@ -137,6 +137,12 @@ + + + + + + @@ -153,12 +159,6 @@ - - - - - - @@ -191,6 +191,12 @@ + + + + + + @@ -207,12 +213,6 @@ - - - - - - diff --git a/NeuroML2/Fig4C_AWCon.net.nml b/NeuroML2/Fig4C_AWCon.net.nml index b3000e8..d5eacdd 100644 --- a/NeuroML2/Fig4C_AWCon.net.nml +++ b/NeuroML2/Fig4C_AWCon.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.9 + Generated by NeuroMLlite v0.6.0 Generated network: Fig4C_AWCon Generation seed: 1234 diff --git a/NeuroML2/Fig7B_RMD.net.nml b/NeuroML2/Fig7B_RMD.net.nml index 15e67a7..7f5cda5 100644 --- a/NeuroML2/Fig7B_RMD.net.nml +++ b/NeuroML2/Fig7B_RMD.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.9 + Generated by NeuroMLlite v0.6.0 Generated network: Fig7B_RMD Generation seed: 1234 diff --git a/NeuroML2/GenerateNeuroML.py b/NeuroML2/GenerateNeuroML.py index 4239cac..3e9c1dc 100644 --- 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 index 7d40375..49314d5 100644 --- 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 index 0a14039..39a8338 100644 --- 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 index 014098e..7b5487a 100644 --- a/NeuroML2/IClamp_RMD.net.nml +++ b/NeuroML2/IClamp_RMD.net.nml @@ -1,5 +1,5 @@ - Generated by NeuroMLlite v0.5.9 + 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 index db186d8..3f7bce2 100644 --- a/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml +++ b/NeuroML2/LEMS_Sim_Fig4C_AWCon.xml @@ -2,7 +2,7 @@ diff --git a/NeuroML2/LEMS_Sim_Fig7B_RMD.xml b/NeuroML2/LEMS_Sim_Fig7B_RMD.xml index 4f87de5..50690cb 100644 --- a/NeuroML2/LEMS_Sim_Fig7B_RMD.xml +++ b/NeuroML2/LEMS_Sim_Fig7B_RMD.xml @@ -2,7 +2,7 @@ diff --git a/NeuroML2/LEMS_Sim_IClamp_RMD.xml b/NeuroML2/LEMS_Sim_IClamp_RMD.xml index bba11d5..a9896b8 100644 --- a/NeuroML2/LEMS_Sim_IClamp_RMD.xml +++ b/NeuroML2/LEMS_Sim_IClamp_RMD.xml @@ -2,7 +2,7 @@ diff --git a/NeuroML2/RMD_bk.channel.nml b/NeuroML2/RMD_bk.channel.nml index cfd2301..0e03628 100644 --- a/NeuroML2/RMD_bk.channel.nml +++ b/NeuroML2/RMD_bk.channel.nml @@ -19,6 +19,12 @@ + + + + + + @@ -35,12 +41,6 @@ - - - - - - @@ -79,6 +79,12 @@ + + + + + + @@ -95,12 +101,6 @@ - - - - - - @@ -137,6 +137,12 @@ + + + + + + @@ -153,12 +159,6 @@ - - - - - - @@ -191,6 +191,12 @@ + + + + + + @@ -207,12 +213,6 @@ - - - - - - diff --git a/NeuroML2/Sim_IClamp_AWCon.json b/NeuroML2/Sim_IClamp_AWCon.json index 13c819b..c40350c 100644 --- 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 index 77ea136..5344249 100644 --- 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,