feat: regenerate cells

OpenSourceBrain · Apr 23, 2024 · f4f59b7 · f4f59b7
1 parent 6b02e83
commit f4f59b7
Show file tree

Hide file tree

Showing 14 changed files with 1,438 additions and 1,424 deletions.
diff --git a/CellTypesDatabase/models/NeuroML2/497232312.net.nml b/CellTypesDatabase/models/NeuroML2/497232312.net.nml
@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <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"
+    xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.xsd"
     id = "NeuroML2_file_exported_from_NEURON">
 
-  <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.1.0 HEAD (047dd824) 2022-03-25
+  <notes> NeuroML 2 file generated from ModelView by: NEURON -- VERSION 8.2.4 HEAD (1d87d5d39) 2024-02-09
           Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
           Yale University and UCL 
   </notes>

diff --git a/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_472450023.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_483108201.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_486556811.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/Cell_497232312.cell.nml b/CellTypesDatabase/models/NeuroML2/Cell_497232312.cell.nml
diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_472450023.xml b/CellTypesDatabase/models/NeuroML2/LEMS_472450023.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.1 (libNeuroML v0.4.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.10 (libNeuroML v0.5.8)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="472450023"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="Network_472450023.net.nml"/>
     <Include file="Cell_472450023.cell.nml"/>
     <Include file="Im.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="Ca_LVA.channel.nml"/>
     <Include file="CaDynamics_all.nml"/>
     <Include file="CaDynamics.nml"/>
-
-    <Simulation id="472450023" length="2500ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="472450023" length="2500.0ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_Cell_472450023" title="Membrane potentials of cells in Pop_Cell_472450023" timeScale="1ms" xmin="-250.0" xmax="2750.0" ymin="-90" ymax="50">
             <Line id="Pop_Cell_472450023[0]: v" quantity="Pop_Cell_472450023/0/Cell_472450023/v" scale="1mV" color="#e1a7b4" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_Cell_472450023" fileName="472450023.Pop_Cell_472450023.v.dat">
-            <OutputColumn id="v_Pop_Cell_472450023_0_Cell_472450023_v" quantity="Pop_Cell_472450023/0/Cell_472450023/v"/> 
+            <OutputColumn id="v_Pop_Cell_472450023_0_Cell_472450023_v" quantity="Pop_Cell_472450023/0/Cell_472450023/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_483108201.xml b/CellTypesDatabase/models/NeuroML2/LEMS_483108201.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.1 (libNeuroML v0.4.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.10 (libNeuroML v0.5.8)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="483108201"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="Network_483108201.net.nml"/>
     <Include file="Cell_483108201.cell.nml"/>
     <Include file="Im.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="Ca_LVA.channel.nml"/>
     <Include file="CaDynamics_all.nml"/>
     <Include file="CaDynamics.nml"/>
-
-    <Simulation id="483108201" length="2500ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="483108201" length="2500.0ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_Cell_483108201" title="Membrane potentials of cells in Pop_Cell_483108201" timeScale="1ms" xmin="-250.0" xmax="2750.0" ymin="-90" ymax="50">
             <Line id="Pop_Cell_483108201[0]: v" quantity="Pop_Cell_483108201/0/Cell_483108201/v" scale="1mV" color="#e1a7b4" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_Cell_483108201" fileName="483108201.Pop_Cell_483108201.v.dat">
-            <OutputColumn id="v_Pop_Cell_483108201_0_Cell_483108201_v" quantity="Pop_Cell_483108201/0/Cell_483108201/v"/> 
+            <OutputColumn id="v_Pop_Cell_483108201_0_Cell_483108201_v" quantity="Pop_Cell_483108201/0/Cell_483108201/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_486556811.xml b/CellTypesDatabase/models/NeuroML2/LEMS_486556811.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.1 (libNeuroML v0.4.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.10 (libNeuroML v0.5.8)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="486556811"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="Network_486556811.net.nml"/>
     <Include file="Cell_486556811.cell.nml"/>
     <Include file="Im.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="Ca_LVA.channel.nml"/>
     <Include file="CaDynamics_all.nml"/>
     <Include file="CaDynamics.nml"/>
-
-    <Simulation id="486556811" length="2500ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="486556811" length="2500.0ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_Cell_486556811" title="Membrane potentials of cells in Pop_Cell_486556811" timeScale="1ms" xmin="-250.0" xmax="2750.0" ymin="-90" ymax="50">
             <Line id="Pop_Cell_486556811[0]: v" quantity="Pop_Cell_486556811/0/Cell_486556811/v" scale="1mV" color="#e1a7b4" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_Cell_486556811" fileName="486556811.Pop_Cell_486556811.v.dat">
-            <OutputColumn id="v_Pop_Cell_486556811_0_Cell_486556811_v" quantity="Pop_Cell_486556811/0/Cell_486556811/v"/> 
+            <OutputColumn id="v_Pop_Cell_486556811_0_Cell_486556811_v" quantity="Pop_Cell_486556811/0/Cell_486556811/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/CellTypesDatabase/models/NeuroML2/LEMS_497232312.xml b/CellTypesDatabase/models/NeuroML2/LEMS_497232312.xml
@@ -1,19 +1,19 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.1 (libNeuroML v0.4.0)
+        This LEMS file has been automatically generated using PyNeuroML v1.2.10 (libNeuroML v0.5.8)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="497232312"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="Network_497232312.net.nml"/>
     <Include file="Cell_497232312.cell.nml"/>
     <Include file="pas.channel.nml"/>
@@ -29,17 +29,16 @@
     <Include file="Ca_LVA.channel.nml"/>
     <Include file="CaDynamics_all.nml"/>
     <Include file="CaDynamics.nml"/>
-
-    <Simulation id="497232312" length="2500ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-
+
+    <Simulation id="497232312" length="2500.0ms" step="0.005ms" target="network" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
         <Display id="DispPop__Pop_Cell_497232312" title="Membrane potentials of cells in Pop_Cell_497232312" timeScale="1ms" xmin="-250.0" xmax="2750.0" ymin="-90" ymax="50">
             <Line id="Pop_Cell_497232312[0]: v" quantity="Pop_Cell_497232312/0/Cell_497232312/v" scale="1mV" color="#e1a7b4" timeScale="1ms"/>
         </Display>
-        
+
         <OutputFile id="Volts_file__Pop_Cell_497232312" fileName="497232312.Pop_Cell_497232312.v.dat">
-            <OutputColumn id="v_Pop_Cell_497232312_0_Cell_497232312_v" quantity="Pop_Cell_497232312/0/Cell_497232312/v"/> 
+            <OutputColumn id="v_Pop_Cell_497232312_0_Cell_497232312_v" quantity="Pop_Cell_497232312/0/Cell_497232312/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>
diff --git a/CellTypesDatabase/models/NeuroML2/ManyCells.net.nml b/CellTypesDatabase/models/NeuroML2/ManyCells.net.nml
@@ -6,22 +6,22 @@
     <network id="ManyCells">
         <population id="Pop_472450023" component="Cell_472450023" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <population id="Pop_483108201" component="Cell_483108201" type="populationList">
             <instance id="0">
-                <location x="300." y="0." z="0."/>
+                <location x="300.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <population id="Pop_486556811" component="Cell_486556811" type="populationList">
             <instance id="0">
-                <location x="600." y="0." z="0."/>
+                <location x="600.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <population id="Pop_497232312" component="Cell_497232312" type="populationList">
             <instance id="0">
-                <location x="900." y="0." z="0."/>
+                <location x="900.0" y="0.0" z="0.0"/>
             </instance>
         </population>
     </network>

diff --git a/CellTypesDatabase/models/NeuroML2/Network_472450023.net.nml b/CellTypesDatabase/models/NeuroML2/Network_472450023.net.nml
@@ -29,7 +29,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
         <property tag="recommended_dt_ms" value="0.005"/>
         <population id="Pop_Cell_472450023" component="Cell_472450023" size="1" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim_input" population="Pop_Cell_472450023" component="stim">

diff --git a/CellTypesDatabase/models/NeuroML2/Network_483108201.net.nml b/CellTypesDatabase/models/NeuroML2/Network_483108201.net.nml
@@ -29,7 +29,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
         <property tag="recommended_dt_ms" value="0.005"/>
         <population id="Pop_Cell_483108201" component="Cell_483108201" size="1" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim_input" population="Pop_Cell_483108201" component="stim">

diff --git a/CellTypesDatabase/models/NeuroML2/Network_486556811.net.nml b/CellTypesDatabase/models/NeuroML2/Network_486556811.net.nml
@@ -29,7 +29,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
         <property tag="recommended_dt_ms" value="0.005"/>
         <population id="Pop_Cell_486556811" component="Cell_486556811" size="1" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim_input" population="Pop_Cell_486556811" component="stim">

diff --git a/CellTypesDatabase/models/NeuroML2/Network_497232312.net.nml b/CellTypesDatabase/models/NeuroML2/Network_497232312.net.nml
@@ -29,7 +29,7 @@ Electrophysiology on which this model is based: http://celltypes.brain-map.org/m
         <property tag="recommended_dt_ms" value="0.005"/>
         <population id="Pop_Cell_497232312" component="Cell_497232312" size="1" type="populationList">
             <instance id="0">
-                <location x="0." y="0." z="0."/>
+                <location x="0.0" y="0.0" z="0.0"/>
             </instance>
         </population>
         <inputList id="stim_input" population="Pop_Cell_497232312" component="stim">