Regenerated main cells with <spikeThresh>

pgleeson · pgleeson · commit 14f451eb64d2 · 2024-05-14T14:40:39.000+01:00
diff --git a/NMC/NeuroML2/LEMS_L1_HAC_cNAC187_1.xml b/NMC/NeuroML2/LEMS_L1_HAC_cNAC187_1.xml
@@ -7,7 +7,7 @@
      -->
 
     <!-- Specify which component to run -->
-    <Target component="L1_HAC_cNAC187_1" reportFile="report.l1.__SIMULATOR__.txt"/>
+    <Target component="L1_HAC_cNAC187_1" reportFile="report.L1_HAC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
diff --git a/NMC/NeuroML2/LEMS_L23_LBC_cSTUT189_1.xml b/NMC/NeuroML2/LEMS_L23_LBC_cSTUT189_1.xml
@@ -7,7 +7,7 @@
      -->
 
     <!-- Specify which component to run -->
-    <Target component="L23_LBC_cSTUT189_1" reportFile="report.l23.__SIMULATOR__.txt"/>
+    <Target component="L23_LBC_cSTUT189_1" reportFile="report.L23_LBC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
diff --git a/NMC/NeuroML2/LEMS_L23_NBC_cNAC187_1.xml b/NMC/NeuroML2/LEMS_L23_NBC_cNAC187_1.xml
@@ -7,7 +7,7 @@
      -->
 
     <!-- Specify which component to run -->
-    <Target component="L23_NBC_cNAC187_1" reportFile="report.l23.__SIMULATOR__.txt"/>
+    <Target component="L23_NBC_cNAC187_1" reportFile="report.L23_NBC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
diff --git a/NMC/NeuroML2/LEMS_L23_PC_cADpyr229_1.xml b/NMC/NeuroML2/LEMS_L23_PC_cADpyr229_1.xml
@@ -7,7 +7,7 @@
      -->
 
     <!-- Specify which component to run -->
-    <Target component="L23_PC_cADpyr229_1" reportFile="report.l23.__SIMULATOR__.txt"/>
+    <Target component="L23_PC_cADpyr229_1" reportFile="report.L23_PC.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
diff --git a/NMC/NeuroML2/LEMS_L5_TTPC1_cADpyr232_1.xml b/NMC/NeuroML2/LEMS_L5_TTPC1_cADpyr232_1.xml
@@ -7,7 +7,7 @@
      -->
 
     <!-- Specify which component to run -->
-    <Target component="L5_TTPC1_cADpyr232_1" reportFile="report.l5.__SIMULATOR__.txt"/>
+    <Target component="L5_TTPC1_cADpyr232_1" reportFile="report.L5_TTPC1.__SIMULATOR__.txt"/>
 
     <!-- Include core NeuroML2 ComponentType definitions -->
     <Include file="Cells.xml"/>
diff --git a/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml b/NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml
@@ -7223,6 +7223,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003100))*0.000080)"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
                 <specificCapacitance value="2 uF_per_cm2" segmentGroup="basal"/>
diff --git a/NMC/NeuroML2/cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml b/NMC/NeuroML2/cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml
@@ -43554,6 +43554,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003100))*0.000080)"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
                 <specificCapacitance value="2 uF_per_cm2" segmentGroup="basal"/>
diff --git a/NMC/NeuroML2/cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml b/NMC/NeuroML2/cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml
@@ -9658,6 +9658,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003000))*0.000052)"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="basal"/>
diff --git a/NMC/NeuroML2/cNAC187_L23_NBC_9d37c4b1f8_0_0.cell.nml b/NMC/NeuroML2/cNAC187_L23_NBC_9d37c4b1f8_0_0.cell.nml
@@ -5455,6 +5455,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003000))*0.000052)"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="basal"/>
diff --git a/NMC/NeuroML2/cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml b/NMC/NeuroML2/cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml
@@ -7102,6 +7102,7 @@ For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/micr
                         <inhomogeneousValue inhomogeneousParameter="PathLengthOver_apical" value="1e4 * ((-0.869600 + 2.087000*exp((p-0.000000)*0.003000))*0.000052)"/>
                     </variableParameter>
                 </channelDensityNonUniform>
+                <spikeThresh value="10mV"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="axonal"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="somatic"/>
                 <specificCapacitance value="1.0 uF_per_cm2" segmentGroup="basal"/>
diff --git a/NMC/parser/Biophysics.py b/NMC/parser/Biophysics.py
@@ -272,13 +272,18 @@ def parse_templates_json(templates_json="templates.json",
         init_memb_potentials = [neuroml.InitMembPotential(
             value="-80 mV", segment_groups='all')]
 
+        # 10mV is default for Neuron spike threshold in NetCon
+        # https://www.neuron.yale.edu/neuron/static/py_doc/modelspec/programmatic/network/netcon.html
+        spike_threshes = [neuroml.SpikeThresh(value="10mV", segment_groups='all')]
+
         membrane_properties = neuroml.MembraneProperties(
             channel_densities=channel_densities,
             channel_density_nernsts=channel_density_nernsts,
             channel_density_non_uniform_nernsts=channel_density_non_uniform_nernsts,
             channel_density_non_uniforms=channel_density_non_uniforms,
             specific_capacitances=specific_capacitances,
-            init_memb_potentials=init_memb_potentials)
+            init_memb_potentials=init_memb_potentials,
+            spike_threshes=spike_threshes)
 
         # Intracellular Properties
         #
diff --git a/NMC/parser/ParseAll.py b/NMC/parser/ParseAll.py
@@ -416,7 +416,7 @@ def process_celldir(inputs):
                                        local_nml2_cell_dir,
                                        copy_neuroml=False,
                                        simulation_seed=1234,
-                                       report_file_name='report.%s.__SIMULATOR__.txt'%(cell_dir.split('_')[0]).lower())
+                                       report_file_name='report.%s_%s.__SIMULATOR__.txt'%(cell_dir.split('_')[0],cell_dir.split('_')[1]))
 
         pynml.nml2_to_svg(nml_net_loc)
 
