Use smaller l23 net for testing

OpenSourceBrain · Jul 31, 2024 · 779c6c1 · 779c6c1
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Showing 9 changed files with 5,015 additions and 8,265 deletions.
diff --git a/.gitignore b/.gitignore
@@ -80,3 +80,4 @@ neuroConstruct/generatedNeuroML2/html
 *code.gen.so
 *_eden.py
 arm64
+/neuroConstruct/generatedNeuroML2/*netpyne.py
diff --git a/NeuroML2/pythonScripts/netbuild/LEMS_TestL23.xml b/NeuroML2/pythonScripts/netbuild/LEMS_TestL23.xml
@@ -0,0 +1,112 @@
+<Lems>
+
+    <!-- 
+
+        This LEMS file has been automatically generated using PyNeuroML v1.3.5 (libNeuroML v0.6.1)
+
+     -->
+
+    <!-- Specify which component to run -->
+    <Target component="Sim_TestL23"/>
+
+    <!-- Include core NeuroML2 ComponentType definitions -->
+    <Include file="Cells.xml"/>
+    <Include file="Networks.xml"/>
+    <Include file="Simulation.xml"/>
+
+    <Include file="TestL23/Syn_AMPA_SupPyr_SupFS.synapse.nml"/>
+    <Include file="TestL23/Syn_AMPA_SupPyr_SupLTS.synapse.nml"/>
+    <Include file="TestL23/Syn_AMPA_SupPyr_SupPyr.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupAxAx_SupPyr.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupBask_SupAxAx.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupBask_SupBask.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupBask_SupLTS.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupBask_SupPyr.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupLTS_FS.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupLTS_LTS.synapse.nml"/>
+    <Include file="TestL23/Syn_GABAA_SupLTS_SupPyr.synapse.nml"/>
+    <Include file="TestL23/Syn_NMDA_RSPyr_SupFS.synapse.nml"/>
+    <Include file="TestL23/Syn_NMDA_RSPyr_SupLTS.synapse.nml"/>
+    <Include file="TestL23/Syn_NMDA_SupPyr_SupPyr.synapse.nml"/>
+    <Include file="TestL23/SynForEctStim.synapse.nml"/>
+    <Include file="TestL23/L23PyrRS.cell.nml"/>
+    <Include file="TestL23/ar__m00_25.channel.nml"/>
+    <Include file="TestL23/cad__beta0_01__phi26000.nml"/>
+    <Include file="TestL23/cad__beta0_05__phi52000.nml"/>
+    <Include file="TestL23/cal.channel.nml"/>
+    <Include file="TestL23/cat.channel.nml"/>
+    <Include file="TestL23/k2.channel.nml"/>
+    <Include file="TestL23/ka.channel.nml"/>
+    <Include file="TestL23/kahp.channel.nml"/>
+    <Include file="TestL23/kc.channel.nml"/>
+    <Include file="TestL23/kdr.channel.nml"/>
+    <Include file="TestL23/km.channel.nml"/>
+    <Include file="TestL23/naf__a0__b0__c0__d0__fastNa_shiftmin3_5.channel.nml"/>
+    <Include file="TestL23/nap.channel.nml"/>
+    <Include file="TestL23/pas.channel.nml"/>
+    <Include file="TestL23/SupLTSInter.cell.nml"/>
+    <Include file="TestL23/cad__beta0_02__phi260000.nml"/>
+    <Include file="TestL23/cad__beta0_05__phi520000.nml"/>
+    <Include file="TestL23/cat_a.channel.nml"/>
+    <Include file="TestL23/kahp_slower.channel.nml"/>
+    <Include file="TestL23/kc_fast.channel.nml"/>
+    <Include file="TestL23/kdr_fs.channel.nml"/>
+    <Include file="TestL23/naf2__a0__b0__c0__d0__fastNa_shiftmin2_5.channel.nml"/>
+    <Include file="TestL23/SupAxAx.cell.nml"/>
+    <Include file="TestL23/SupBasket.cell.nml"/>
+    <Include file="TestL23.net.nml"/>
+
+    <Simulation id="Sim_TestL23" length="20.0ms" step="0.025ms" target="TestL23" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
+        <Display id="DispPop__CG3D_L23PyrRS" title="Membrane potentials of cells in CG3D_L23PyrRS" timeScale="1ms" xmin="-2.0" xmax="22.0" ymin="-90" ymax="50">
+            <Line id="CG3D_L23PyrRS[0]: v" quantity="CG3D_L23PyrRS/0/L23PyrRS/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[1]: v" quantity="CG3D_L23PyrRS/1/L23PyrRS/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[2]: v" quantity="CG3D_L23PyrRS/2/L23PyrRS/v" scale="1mV" color="#98e752" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[3]: v" quantity="CG3D_L23PyrRS/3/L23PyrRS/v" scale="1mV" color="#bca074" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[4]: v" quantity="CG3D_L23PyrRS/4/L23PyrRS/v" scale="1mV" color="#632794" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[5]: v" quantity="CG3D_L23PyrRS/5/L23PyrRS/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[6]: v" quantity="CG3D_L23PyrRS/6/L23PyrRS/v" scale="1mV" color="#df5954" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[7]: v" quantity="CG3D_L23PyrRS/7/L23PyrRS/v" scale="1mV" color="#52c8bf" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[8]: v" quantity="CG3D_L23PyrRS/8/L23PyrRS/v" scale="1mV" color="#bf0239" timeScale="1ms"/>
+            <Line id="CG3D_L23PyrRS[9]: v" quantity="CG3D_L23PyrRS/9/L23PyrRS/v" scale="1mV" color="#3f9fe8" timeScale="1ms"/>
+        </Display>
+
+        <Display id="DispPop__CG3D_SupBask" title="Membrane potentials of cells in CG3D_SupBask" timeScale="1ms" xmin="-2.0" xmax="22.0" ymin="-90" ymax="50">
+            <Line id="CG3D_SupBask[0]: v" quantity="CG3D_SupBask/0/SupBasket/v" scale="1mV" color="#dda9d2" timeScale="1ms"/>
+        </Display>
+
+        <Display id="DispPop__CG3D_SupAxAx" title="Membrane potentials of cells in CG3D_SupAxAx" timeScale="1ms" xmin="-2.0" xmax="22.0" ymin="-90" ymax="50">
+            <Line id="CG3D_SupAxAx[0]: v" quantity="CG3D_SupAxAx/0/SupAxAx/v" scale="1mV" color="#85ad96" timeScale="1ms"/>
+        </Display>
+
+        <Display id="DispPop__CG3D_SupLTS" title="Membrane potentials of cells in CG3D_SupLTS" timeScale="1ms" xmin="-2.0" xmax="22.0" ymin="-90" ymax="50">
+            <Line id="CG3D_SupLTS[0]: v" quantity="CG3D_SupLTS/0/SupLTSInter/v" scale="1mV" color="#59438f" timeScale="1ms"/>
+        </Display>
+
+        <OutputFile id="Volts_file__CG3D_L23PyrRS" fileName="Sim_TestL23.CG3D_L23PyrRS.v.dat">
+            <OutputColumn id="v_CG3D_L23PyrRS_0_L23PyrRS_v" quantity="CG3D_L23PyrRS/0/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_1_L23PyrRS_v" quantity="CG3D_L23PyrRS/1/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_2_L23PyrRS_v" quantity="CG3D_L23PyrRS/2/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_3_L23PyrRS_v" quantity="CG3D_L23PyrRS/3/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_4_L23PyrRS_v" quantity="CG3D_L23PyrRS/4/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_5_L23PyrRS_v" quantity="CG3D_L23PyrRS/5/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_6_L23PyrRS_v" quantity="CG3D_L23PyrRS/6/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_7_L23PyrRS_v" quantity="CG3D_L23PyrRS/7/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_8_L23PyrRS_v" quantity="CG3D_L23PyrRS/8/L23PyrRS/v"/>
+            <OutputColumn id="v_CG3D_L23PyrRS_9_L23PyrRS_v" quantity="CG3D_L23PyrRS/9/L23PyrRS/v"/>
+        </OutputFile>
+
+        <OutputFile id="Volts_file__CG3D_SupBask" fileName="Sim_TestL23.CG3D_SupBask.v.dat">
+            <OutputColumn id="v_CG3D_SupBask_0_SupBasket_v" quantity="CG3D_SupBask/0/SupBasket/v"/>
+        </OutputFile>
+
+        <OutputFile id="Volts_file__CG3D_SupAxAx" fileName="Sim_TestL23.CG3D_SupAxAx.v.dat">
+            <OutputColumn id="v_CG3D_SupAxAx_0_SupAxAx_v" quantity="CG3D_SupAxAx/0/SupAxAx/v"/>
+        </OutputFile>
+
+        <OutputFile id="Volts_file__CG3D_SupLTS" fileName="Sim_TestL23.CG3D_SupLTS.v.dat">
+            <OutputColumn id="v_CG3D_SupLTS_0_SupLTSInter_v" quantity="CG3D_SupLTS/0/SupLTSInter/v"/>
+        </OutputFile>
+
+    </Simulation>
+
+</Lems>
diff --git a/NeuroML2/pythonScripts/netbuild/RunColumn.py b/NeuroML2/pythonScripts/netbuild/RunColumn.py
@@ -500,11 +500,11 @@ def RunColumnSimulation(net_id="TestRunColumn",
 
                   if check_type and (check_group_1 or check_group_2 or check_group_3):
 
-	             opencortex.print_comment_v("Changing offset current in 'PulseGenerators' for %s to %f"%(cell_group, deep_bias_current))
-	      
-	             input_params_final[cell_group][input_group]['SmallestAmplitudeList']=[ (deep_bias_current-0.05)/1000 ] 
-	              
-	             input_params_final[cell_group][input_group]['LargestAmplitudeList']=[ (deep_bias_current+0.05)/1000 ]
+                     opencortex.print_comment_v("Changing offset current in 'PulseGenerators' for %s to %f"%(cell_group, deep_bias_current))
+               
+                     input_params_final[cell_group][input_group]['SmallestAmplitudeList']=[ (deep_bias_current-0.05)/1000 ] 
+                     
+                     input_params_final[cell_group][input_group]['LargestAmplitudeList']=[ (deep_bias_current+0.05)/1000 ]
 
     input_list_array_final, input_synapse_list=oc_utils.build_inputs(nml_doc=nml_doc,
                                                                      net=network,