NeuroML2/.test.pyr.jnmleden.omt

@@ -0,0 +1,18 @@
+
+# Script for running automated tests on OSB, see https://github.com/OpenSourceBrain/osb-model-validation
+
+target: LEMS_HL23PYR_sim.xml
+engine: jNeuroML_EDEN
+mep: tests/.test.pyr.mep
+experiments:
+  stepPYR:
+    observables:
+      spike times:
+        file:
+          path: HL23PYR_net.dat
+          columns: [0,1]
+          scaling: [1000,1000]
+        spike detection:
+          method: threshold
+        tolerance: 0.04034227312889255
+

NeuroML2/.test.sst.jnmleden.omt

@@ -14,5 +14,5 @@ experiments:
           scaling: [1000,1000]
         spike detection:
           method: threshold
-        tolerance: 0.014022701352305402 # Note: this is different on linux and mac!!
+        tolerance: 0.017020583283549745
 

NeuroML2/HL23.net.nml

@@ -17,31 +17,31 @@
     </pulseGenerator>
     <network id="HL23Net" type="networkWithTemperature" temperature="34 degC">
         <population id="HL23PV_pop" component="HL23PV" type="populationList">
-            <property tag="color" value="0.9211165553686066 0.14007090321945415 0.13240906273729447"/>
+            <property tag="color" value="0.8258528277092643 0.7026721292874603 0.3711218355643212"/>
             <property tag="region" value="L23"/>
             <instance id="0">
-                <location x="90." y="97." z="122."/>
+                <location x="151.0" y="107.0" z="152.0"/>
             </instance>
         </population>
         <population id="HL23PYR_pop" component="HL23PYR" type="populationList">
-            <property tag="color" value="0.3711218355643212 0.5921654881609745 0.8643564030331798"/>
+            <property tag="color" value="0.41279258530304264 0.6738038445103539 0.1692198559903848"/>
             <property tag="region" value="L23"/>
             <instance id="0">
-                <location x="82." y="166." z="49."/>
+                <location x="63.0" y="81.0" z="161.0"/>
             </instance>
         </population>
         <population id="HL23SST_pop" component="HL23SST" type="populationList">
-            <property tag="color" value="0.12784498310997972 0.6035166401204584 0.31978189671367574"/>
+            <property tag="color" value="0.401938987145538 0.7045979982277839 0.39340325762864414"/>
             <property tag="region" value="L23"/>
             <instance id="0">
-                <location x="137." y="92." z="9."/>
+                <location x="151.0" y="198.0" z="25.0"/>
             </instance>
         </population>
         <population id="HL23VIP_pop" component="HL23VIP" type="populationList">
-            <property tag="color" value="0.39340325762864414 0.5925035310986511 0.8124028526236982"/>
+            <property tag="color" value="0.29793772864771784 0.5515873792106866 0.5986193047542998"/>
             <property tag="region" value="L23"/>
             <instance id="0">
-                <location x="60." y="194." z="48."/>
+                <location x="90.0" y="184.0" z="91.0"/>
             </instance>
         </population>
         <explicitInput target="pop0[0]" input="pg_HL23PV"/>

NeuroML2/HL23Net_1.0.net.nml

@@ -0,0 +1 @@
+/annex/objects/SHA256E-s146003963--e1e00cd40bdfe3efdbf8ef8e96837574d0e95e60a3d9489cc6a243deffe01cc0.net.nml

NeuroML2/HL23PV.net.nml

@@ -5,10 +5,10 @@
     </pulseGenerator>
     <network id="HL23PVNet" type="networkWithTemperature" temperature="34 degC">
         <population id="HL23PV_pop" component="HL23PV" type="populationList">
-            <property tag="color" value="0.8249648621074325 0.027813322534632867 0.6404955383058488"/>
+            <property tag="color" value="0.5672091346475104 0.3794564714867984 0.4911688801788786"/>
             <property tag="region" value="L23"/>
             <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_iclamp_HL23PV" population="HL23PV_pop" component="pg_HL23PV">

NeuroML2/HL23PYR.cell.nml

@@ -5,11 +5,11 @@
   </notes>
     <include href="CaDynamics_E2_NML2.nml"/>
     <include href="channels/pas.channel.nml"/>
-    <include href="channels/Ih.channel.nml"/>
     <include href="channels/SK.channel.nml"/>
     <include href="channels/K_T.channel.nml"/>
     <include href="channels/K_P.channel.nml"/>
     <include href="channels/Kv3_1.channel.nml"/>
+    <include href="channels/Ih.channel.nml"/>
     <include href="channels/Im.channel.nml"/>
     <include href="channels/NaTg/NaTg.channel.nml"/>
     <include href="channels/Ca_HVA.channel.nml"/>
@@ -30341,7 +30341,6 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="pas" ionChannel="pas" condDensity="0.0000954 S_per_cm2" erev="-80 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
-                <channelDensity id="Ih" ionChannel="Ih" condDensity="0.000148 S_per_cm2" erev="-45 mV" segmentGroup="all_minus_myelin" ion="hcn"/>
                 <channelDensity id="SK_somatic" ionChannel="SK" condDensity="0.000853 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                 <channelDensity id="K_T_somatic" ionChannel="K_T" condDensity="0.0605 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
                 <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.000208 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
@@ -30357,6 +30356,7 @@
                 <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.941 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                 <channelDensity id="NaTg_axonal" ionChannel="NaTg_PYR_axonal" condDensity="1.38 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
                 <channelDensity id="Nap_axonal" ionChannel="Nap" condDensity="0.00842 S_per_cm2" erev="50 mV" segmentGroup="axon_group" ion="na"/>
+                <channelDensity id="Ih_axonal" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="axon_group" ion="hcn"/>
                 <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="0.00155 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.00296 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                 <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="0.0003060000 S_per_cm2" segmentGroup="axon_group" ion="ca"/>

NeuroML2/HL23PYR.net.nml

@@ -1,29 +1,18 @@
 <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.xsd" id="HL23PYR">
     <include href="HL23PYR.cell.nml"/>
-    <include href="HL23PYR.tonic.cell.nml"/>
     <pulseGenerator id="pg_HL23PYR" delay="50ms" duration="200ms" amplitude="0.2nA">
         <notes>Simple pulse generator</notes>
     </pulseGenerator>
     <network id="HL23PYRNet" type="networkWithTemperature" temperature="34 degC">
         <population id="HL23PYR_pop" component="HL23PYR" type="populationList">
-            <property tag="color" value="0.4911688801788786 0.8258528277092643 0.7026721292874603"/>
+            <property tag="color" value="0.3220229197377431 0.19279726280626452 0.37635392246534727"/>
             <property tag="region" value="L23"/>
             <instance id="0">
-                <location x="0." y="0." z="0."/>
-            </instance>
-        </population>
-        <population id="HL23PYR_pop_tonic" component="HL23PYR_tonic" type="populationList">
-            <property tag="color" value="0.4911688801788786 0.8258528277092643 0.7026721292874603"/>
-            <property tag="region" value="L23"/>
-            <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_iclamp_HL23PYR" population="HL23PYR_pop" component="pg_HL23PYR">
             <input id="0" target="../HL23PYR_pop/0" destination="synapses"/>
         </inputList>
-        <inputList id="stim_iclamp_HL23PYR_tonic" population="HL23PYR_pop_tonic" component="pg_HL23PYR">
-            <input id="0" target="../HL23PYR_pop_tonic/0" destination="synapses"/>
-        </inputList>
     </network>
 </neuroml>

NeuroML2/HL23SST.cell.nml

@@ -5,8 +5,8 @@
   </notes>
     <include href="CaDynamics_E2_NML2.nml"/>
     <include href="channels/pas.channel.nml"/>
-    <include href="channels/Ih.channel.nml"/>
     <include href="channels/NaTg/NaTg.channel.nml"/>
+    <include href="channels/Ih.channel.nml"/>
     <include href="channels/K_P.channel.nml"/>
     <include href="channels/K_T.channel.nml"/>
     <include href="channels/Kv3_1.channel.nml"/>
@@ -17407,7 +17407,6 @@
         <biophysicalProperties id="biophys">
             <membraneProperties>
                 <channelDensity id="pas" ionChannel="pas" condDensity="0.0000232 S_per_cm2" erev="-81.5 mV" segmentGroup="all_minus_myelin" ion="non_specific"/>
-                <channelDensity id="Ih" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="all_minus_myelin" ion="hcn"/>
                 <channelDensity id="NaTg_somatic" ionChannel="NaTg_SST_somatic" condDensity="0.127 S_per_cm2" erev="50 mV" segmentGroup="soma_group" ion="na"/>
                 <channelDensity id="Ih_somatic" ionChannel="Ih" condDensity="0.0000431 S_per_cm2" erev="-45 mV" segmentGroup="soma_group" ion="hcn"/>
                 <channelDensity id="K_P_somatic" ionChannel="K_P" condDensity="0.0111 S_per_cm2" erev="-85 mV" segmentGroup="soma_group" ion="k"/>
@@ -17423,6 +17422,7 @@
                 <channelDensity id="Kv3_1_axonal" ionChannel="Kv3_1" condDensity="0.984 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                 <channelDensity id="Im_axonal" ionChannel="Im" condDensity="0.000317 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
                 <channelDensity id="SK_axonal" ionChannel="SK" condDensity="0.00113 S_per_cm2" erev="-85 mV" segmentGroup="axon_group" ion="k"/>
+                <channelDensity id="Ih_axonal" ionChannel="Ih" condDensity="0.00001 S_per_cm2" erev="-45 mV" segmentGroup="axon_group" ion="hcn"/>
                 <channelDensityNernst id="Ca_HVA_somatic" ionChannel="Ca_HVA" condDensity="0.00355 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                 <channelDensityNernst id="Ca_LVA_somatic" ionChannel="Ca_LVA" condDensity="0.00314 S_per_cm2" segmentGroup="soma_group" ion="ca"/>
                 <channelDensityNernst id="Ca_HVA_axonal" ionChannel="Ca_HVA" condDensity="0.00145 S_per_cm2" segmentGroup="axon_group" ion="ca"/>

NeuroML2/HL23SST.net.nml

@@ -5,10 +5,10 @@
     </pulseGenerator>
     <network id="HL23SSTNet" type="networkWithTemperature" temperature="34 degC">
         <population id="HL23SST_pop" component="HL23SST" type="populationList">
-            <property tag="color" value="0.5784757388856554 0.39718707958454325 0.9346205865875172"/>
+            <property tag="color" value="0.535471639452566 0.3604778501284934 0.5663043989204367"/>
             <property tag="region" value="L23"/>
             <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_iclamp_HL23SST" population="HL23SST_pop" component="pg_HL23SST">

NeuroML2/HL23VIP.net.nml

@@ -5,10 +5,10 @@
     </pulseGenerator>
     <network id="HL23VIPNet" type="networkWithTemperature" temperature="34 degC">
         <population id="HL23VIP_pop" component="HL23VIP" type="populationList">
-            <property tag="color" value="0.5663043989204367 0.401938987145538 0.7045979982277839"/>
+            <property tag="color" value="0.9794101583806073 0.9037718829562477 0.18968218720673302"/>
             <property tag="region" value="L23"/>
             <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_iclamp_HL23VIP" population="HL23VIP_pop" component="pg_HL23VIP">

NeuroML2/LEMS_HL23PV_sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.9 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23PV_sim"/>
 
@@ -13,7 +13,7 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23PV.net.nml"/>
     <Include file="HL23PV.cell.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
@@ -28,13 +28,12 @@
     <Include file="channels/SK.channel.nml"/>
     <Include file="channels/Ca_HVA.channel.nml"/>
     <Include file="channels/Ca_LVA.channel.nml"/>
-   
+
     <Simulation id="HL23PV_sim" length="300.0ms" step="0.01ms" target="HL23PVNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
         <OutputFile id="HL23PV_net_output" fileName="HL23PV_net.dat">
-            <OutputColumn id="HL23PV_pop_0_v" quantity="HL23PV_pop/0/HL23PV/0/v"/> 
+            <OutputColumn id="HL23PV_pop_0_v" quantity="HL23PV_pop/0/HL23PV/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23PYR_sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.9 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23PYR_sim"/>
 
@@ -13,31 +13,27 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23PYR.net.nml"/>
     <Include file="HL23PYR.cell.nml"/>
-    <Include file="HL23PYR.tonic.cell.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="channels/pas.channel.nml"/>
-    <Include file="channels/Ih.channel.nml"/>
     <Include file="channels/SK.channel.nml"/>
     <Include file="channels/K_T.channel.nml"/>
     <Include file="channels/K_P.channel.nml"/>
     <Include file="channels/Kv3_1.channel.nml"/>
+    <Include file="channels/Ih.channel.nml"/>
     <Include file="channels/Im.channel.nml"/>
     <Include file="channels/NaTg/NaTg.channel.nml"/>
     <Include file="channels/Ca_HVA.channel.nml"/>
     <Include file="channels/Ca_LVA.channel.nml"/>
     <Include file="channels/Nap.channel.nml"/>
-    <Include file="channels/Tonic.nml"/>
-   
+
     <Simulation id="HL23PYR_sim" length="300.0ms" step="0.01ms" target="HL23PYRNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
         <OutputFile id="HL23PYR_net_output" fileName="HL23PYR_net.dat">
-            <OutputColumn id="HL23PYR_pop_0_v" quantity="HL23PYR_pop/0/HL23PYR/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_0_v_tonic" quantity="HL23PYR_pop_tonic/0/HL23PYR_tonic/0/v"/> 
+            <OutputColumn id="HL23PYR_pop_0_v" quantity="HL23PYR_pop/0/HL23PYR/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23SST_sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.9 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23SST_sim"/>
 
@@ -13,13 +13,13 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23SST.net.nml"/>
     <Include file="HL23SST.cell.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
     <Include file="channels/pas.channel.nml"/>
-    <Include file="channels/Ih.channel.nml"/>
     <Include file="channels/NaTg/NaTg.channel.nml"/>
+    <Include file="channels/Ih.channel.nml"/>
     <Include file="channels/K_P.channel.nml"/>
     <Include file="channels/K_T.channel.nml"/>
     <Include file="channels/Kv3_1.channel.nml"/>
@@ -28,13 +28,12 @@
     <Include file="channels/Ca_HVA.channel.nml"/>
     <Include file="channels/Ca_LVA.channel.nml"/>
     <Include file="channels/Nap.channel.nml"/>
-   
+
     <Simulation id="HL23SST_sim" length="300.0ms" step="0.01ms" target="HL23SSTNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
         <OutputFile id="HL23SST_net_output" fileName="HL23SST_net.dat">
-            <OutputColumn id="HL23SST_pop_0_v" quantity="HL23SST_pop/0/HL23SST/0/v"/> 
+            <OutputColumn id="HL23SST_pop_0_v" quantity="HL23SST_pop/0/HL23SST/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23VIP_sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v0.7.6 (libNeuroML v0.4.2)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.9 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23VIP_sim"/>
 
@@ -13,7 +13,7 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23VIP.net.nml"/>
     <Include file="HL23VIP.cell.nml"/>
     <Include file="CaDynamics_E2_NML2.nml"/>
@@ -28,13 +28,12 @@
     <Include file="channels/SK.channel.nml"/>
     <Include file="channels/Ca_HVA.channel.nml"/>
     <Include file="channels/Ca_LVA.channel.nml"/>
-   
+
     <Simulation id="HL23VIP_sim" length="300.0ms" step="0.01ms" target="HL23VIPNet" seed="12345">  <!-- Note seed: ensures same random numbers used every run -->
-        
         <OutputFile id="HL23VIP_net_output" fileName="HL23VIP_net.dat">
-            <OutputColumn id="HL23VIP_pop_0_v" quantity="HL23VIP_pop/0/HL23VIP/0/v"/> 
+            <OutputColumn id="HL23VIP_pop_0_v" quantity="HL23VIP_pop/0/HL23VIP/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23_0.01_Sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.1.5 (libNeuroML v0.5.6)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.8 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23Sim_0.01"/>
 
@@ -13,33 +13,32 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23Net_0.01.net.nml"/>
     <Include file="rotated_cells/HL23PYR_sim.cell.nml"/>
     <Include file="rotated_cells/HL23SST_sim.cell.nml"/>
     <Include file="rotated_cells/HL23PV_sim.cell.nml"/>
     <Include file="rotated_cells/HL23VIP_sim.cell.nml"/>
     <Include file="lems_components_0.01.xml"/>
-   
+
     <Simulation id="HL23Sim_0.01" length="1000.0ms" step="0.025ms" target="HL23Network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-        
         <OutputFile id="output1" fileName="HL23Net_0.01.v.dat">
-            <OutputColumn id="HL23PYR_pop_0" quantity="HL23PYR_pop/0/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_1" quantity="HL23PYR_pop/1/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_2" quantity="HL23PYR_pop/2/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_3" quantity="HL23PYR_pop/3/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_4" quantity="HL23PYR_pop/4/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_5" quantity="HL23PYR_pop/5/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_6" quantity="HL23PYR_pop/6/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_7" quantity="HL23PYR_pop/7/HL23PYR_sim/0/v"/> 
-            <OutputColumn id="HL23SST_pop_0" quantity="HL23SST_pop/0/HL23SST_sim/0/v"/> 
-            <OutputColumn id="HL23SST_pop_1" quantity="HL23SST_pop/1/HL23SST_sim/0/v"/> 
-            <OutputColumn id="HL23PV_pop_0" quantity="HL23PV_pop/0/HL23PV_sim/0/v"/> 
-            <OutputColumn id="HL23PV_pop_1" quantity="HL23PV_pop/1/HL23PV_sim/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_0" quantity="HL23VIP_pop/0/HL23VIP_sim/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_1" quantity="HL23VIP_pop/1/HL23VIP_sim/0/v"/> 
+            <OutputColumn id="HL23PYR_pop_0" quantity="HL23PYR_pop/0/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_1" quantity="HL23PYR_pop/1/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_2" quantity="HL23PYR_pop/2/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_3" quantity="HL23PYR_pop/3/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_4" quantity="HL23PYR_pop/4/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_5" quantity="HL23PYR_pop/5/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_6" quantity="HL23PYR_pop/6/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_7" quantity="HL23PYR_pop/7/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_0" quantity="HL23SST_pop/0/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_1" quantity="HL23SST_pop/1/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_0" quantity="HL23PV_pop/0/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_1" quantity="HL23PV_pop/1/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_0" quantity="HL23VIP_pop/0/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_1" quantity="HL23VIP_pop/1/HL23VIP_sim/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23_0.05_Sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.9 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23Sim_0.05"/>
 
@@ -13,117 +13,69 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23Net_0.05.net.nml"/>
-    <Include file="rotated_cells/HL23PYR_0.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_240.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_480.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_720.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_157.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_397.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_637.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_74.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_314.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_554.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_794.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_231.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_471.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_711.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_148.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_388.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_628.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_65.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_305.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_545.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_785.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_222.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_462.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_702.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_139.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_379.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_619.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_56.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_296.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_536.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_776.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_225.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_465.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_705.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_154.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_394.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_634.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_83.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_323.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_563.cell.nml"/>
-    <Include file="rotated_cells/HL23SST_804.cell.nml"/>
-    <Include file="rotated_cells/HL23SST_809.cell.nml"/>
-    <Include file="rotated_cells/HL23SST_837.cell.nml"/>
-    <Include file="rotated_cells/HL23PV_852.cell.nml"/>
-    <Include file="rotated_cells/HL23PV_879.cell.nml"/>
-    <Include file="rotated_cells/HL23PV_906.cell.nml"/>
-    <Include file="rotated_cells/HL23PV_874.cell.nml"/>
-    <Include file="rotated_cells/HL23VIP_924.cell.nml"/>
-    <Include file="rotated_cells/HL23VIP_998.cell.nml"/>
-    <Include file="rotated_cells/HL23VIP_930.cell.nml"/>
-    <Include file="rotated_cells/HL23VIP_933.cell.nml"/>
+    <Include file="rotated_cells/HL23PYR_sim.cell.nml"/>
+    <Include file="rotated_cells/HL23SST_sim.cell.nml"/>
+    <Include file="rotated_cells/HL23PV_sim.cell.nml"/>
+    <Include file="rotated_cells/HL23VIP_sim.cell.nml"/>
     <Include file="lems_components_0.05.xml"/>
-   
-    <Simulation id="HL23Sim_0.05" length="2000ms" step="0.025ms" target="HL23Network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-        
+
+    <Simulation id="HL23Sim_0.05" length="1000.0ms" step="0.025ms" target="HL23Network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
         <OutputFile id="output1" fileName="HL23Net_0.05.v.dat">
-            <OutputColumn id="HL23PYR_pop_0" quantity="HL23PYR_pop_0/0/HL23PYR_0/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_240" quantity="HL23PYR_pop_240/0/HL23PYR_240/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_480" quantity="HL23PYR_pop_480/0/HL23PYR_480/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_720" quantity="HL23PYR_pop_720/0/HL23PYR_720/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_157" quantity="HL23PYR_pop_157/0/HL23PYR_157/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_397" quantity="HL23PYR_pop_397/0/HL23PYR_397/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_637" quantity="HL23PYR_pop_637/0/HL23PYR_637/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_74" quantity="HL23PYR_pop_74/0/HL23PYR_74/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_314" quantity="HL23PYR_pop_314/0/HL23PYR_314/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_554" quantity="HL23PYR_pop_554/0/HL23PYR_554/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_794" quantity="HL23PYR_pop_794/0/HL23PYR_794/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_231" quantity="HL23PYR_pop_231/0/HL23PYR_231/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_471" quantity="HL23PYR_pop_471/0/HL23PYR_471/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_711" quantity="HL23PYR_pop_711/0/HL23PYR_711/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_148" quantity="HL23PYR_pop_148/0/HL23PYR_148/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_388" quantity="HL23PYR_pop_388/0/HL23PYR_388/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_628" quantity="HL23PYR_pop_628/0/HL23PYR_628/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_65" quantity="HL23PYR_pop_65/0/HL23PYR_65/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_305" quantity="HL23PYR_pop_305/0/HL23PYR_305/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_545" quantity="HL23PYR_pop_545/0/HL23PYR_545/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_785" quantity="HL23PYR_pop_785/0/HL23PYR_785/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_222" quantity="HL23PYR_pop_222/0/HL23PYR_222/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_462" quantity="HL23PYR_pop_462/0/HL23PYR_462/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_702" quantity="HL23PYR_pop_702/0/HL23PYR_702/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_139" quantity="HL23PYR_pop_139/0/HL23PYR_139/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_379" quantity="HL23PYR_pop_379/0/HL23PYR_379/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_619" quantity="HL23PYR_pop_619/0/HL23PYR_619/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_56" quantity="HL23PYR_pop_56/0/HL23PYR_56/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_296" quantity="HL23PYR_pop_296/0/HL23PYR_296/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_536" quantity="HL23PYR_pop_536/0/HL23PYR_536/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_776" quantity="HL23PYR_pop_776/0/HL23PYR_776/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_225" quantity="HL23PYR_pop_225/0/HL23PYR_225/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_465" quantity="HL23PYR_pop_465/0/HL23PYR_465/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_705" quantity="HL23PYR_pop_705/0/HL23PYR_705/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_154" quantity="HL23PYR_pop_154/0/HL23PYR_154/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_394" quantity="HL23PYR_pop_394/0/HL23PYR_394/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_634" quantity="HL23PYR_pop_634/0/HL23PYR_634/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_83" quantity="HL23PYR_pop_83/0/HL23PYR_83/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_323" quantity="HL23PYR_pop_323/0/HL23PYR_323/0/v"/> 
-            <OutputColumn id="HL23PYR_pop_563" quantity="HL23PYR_pop_563/0/HL23PYR_563/0/v"/> 
-            <OutputColumn id="HL23SST_pop_804" quantity="HL23SST_pop_804/0/HL23SST_804/0/v"/> 
-            <OutputColumn id="HL23SST_pop_809" quantity="HL23SST_pop_809/0/HL23SST_809/0/v"/> 
-            <OutputColumn id="HL23SST_pop_837" quantity="HL23SST_pop_837/0/HL23SST_837/0/v"/> 
-            <OutputColumn id="HL23PV_pop_852" quantity="HL23PV_pop_852/0/HL23PV_852/0/v"/> 
-            <OutputColumn id="HL23PV_pop_879" quantity="HL23PV_pop_879/0/HL23PV_879/0/v"/> 
-            <OutputColumn id="HL23PV_pop_906" quantity="HL23PV_pop_906/0/HL23PV_906/0/v"/> 
-            <OutputColumn id="HL23PV_pop_874" quantity="HL23PV_pop_874/0/HL23PV_874/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_924" quantity="HL23VIP_pop_924/0/HL23VIP_924/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_998" quantity="HL23VIP_pop_998/0/HL23VIP_998/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_930" quantity="HL23VIP_pop_930/0/HL23VIP_930/0/v"/> 
-            <OutputColumn id="HL23VIP_pop_933" quantity="HL23VIP_pop_933/0/HL23VIP_933/0/v"/> 
+            <OutputColumn id="HL23PYR_pop_0" quantity="HL23PYR_pop/0/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_1" quantity="HL23PYR_pop/1/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_2" quantity="HL23PYR_pop/2/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_3" quantity="HL23PYR_pop/3/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_4" quantity="HL23PYR_pop/4/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_5" quantity="HL23PYR_pop/5/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_6" quantity="HL23PYR_pop/6/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_7" quantity="HL23PYR_pop/7/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_8" quantity="HL23PYR_pop/8/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_9" quantity="HL23PYR_pop/9/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_10" quantity="HL23PYR_pop/10/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_11" quantity="HL23PYR_pop/11/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_12" quantity="HL23PYR_pop/12/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_13" quantity="HL23PYR_pop/13/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_14" quantity="HL23PYR_pop/14/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_15" quantity="HL23PYR_pop/15/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_16" quantity="HL23PYR_pop/16/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_17" quantity="HL23PYR_pop/17/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_18" quantity="HL23PYR_pop/18/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_19" quantity="HL23PYR_pop/19/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_20" quantity="HL23PYR_pop/20/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_21" quantity="HL23PYR_pop/21/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_22" quantity="HL23PYR_pop/22/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_23" quantity="HL23PYR_pop/23/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_24" quantity="HL23PYR_pop/24/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_25" quantity="HL23PYR_pop/25/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_26" quantity="HL23PYR_pop/26/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_27" quantity="HL23PYR_pop/27/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_28" quantity="HL23PYR_pop/28/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_29" quantity="HL23PYR_pop/29/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_30" quantity="HL23PYR_pop/30/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_31" quantity="HL23PYR_pop/31/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_32" quantity="HL23PYR_pop/32/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_33" quantity="HL23PYR_pop/33/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_34" quantity="HL23PYR_pop/34/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_35" quantity="HL23PYR_pop/35/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_36" quantity="HL23PYR_pop/36/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_37" quantity="HL23PYR_pop/37/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_38" quantity="HL23PYR_pop/38/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_39" quantity="HL23PYR_pop/39/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_0" quantity="HL23SST_pop/0/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_1" quantity="HL23SST_pop/1/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_2" quantity="HL23SST_pop/2/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_0" quantity="HL23PV_pop/0/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_1" quantity="HL23PV_pop/1/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_2" quantity="HL23PV_pop/2/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_3" quantity="HL23PV_pop/3/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_0" quantity="HL23VIP_pop/0/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_1" quantity="HL23VIP_pop/1/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_2" quantity="HL23VIP_pop/2/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_3" quantity="HL23VIP_pop/3/HL23VIP_sim/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/LEMS_HL23_0.1_Sim.xml

@@ -1,11 +1,11 @@
 <Lems>
-    
+
     <!-- 
 
-        This LEMS file has been automatically generated using PyNeuroML v1.0.10 (libNeuroML v0.5.3)
+        This LEMS file has been automatically generated using PyNeuroML v1.1.8 (libNeuroML v0.5.6)
 
      -->
-    
+
     <!-- Specify which component to run -->
     <Target component="HL23Sim_0.1"/>
 
@@ -13,215 +13,118 @@
     <Include file="Cells.xml"/>
     <Include file="Networks.xml"/>
     <Include file="Simulation.xml"/>
-    
+
     <Include file="HL23Net_0.1.net.nml"/>
-    <Include file="rotated_cells/HL23PYR_0.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_120.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_240.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_360.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_480.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_600.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_720.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_37.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_157.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_277.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_397.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_517.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_637.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_757.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_74.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_194.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_314.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_434.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_554.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_674.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_794.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_111.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_231.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_351.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_471.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_591.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_711.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_28.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_148.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_268.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_388.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_508.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_628.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_748.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_65.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_185.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_305.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_425.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_545.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_665.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_785.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_102.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_222.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_342.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_462.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_582.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_702.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_19.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_139.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_259.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_379.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_499.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_619.cell.nml"/>
-    <Include file="rotated_cells/HL23PYR_739.cell.nml"/>
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     <Include file="lems_components_0.1.xml"/>
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-    <Simulation id="HL23Sim_0.1" length="2000ms" step="0.025ms" target="HL23Network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
-        
+
+    <Simulation id="HL23Sim_0.1" length="1000.0ms" step="0.025ms" target="HL23Network" seed="123">  <!-- Note seed: ensures same random numbers used every run -->
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+            <OutputColumn id="HL23PYR_pop_61" quantity="HL23PYR_pop/61/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_62" quantity="HL23PYR_pop/62/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_63" quantity="HL23PYR_pop/63/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_64" quantity="HL23PYR_pop/64/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_65" quantity="HL23PYR_pop/65/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_66" quantity="HL23PYR_pop/66/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_67" quantity="HL23PYR_pop/67/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_68" quantity="HL23PYR_pop/68/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_69" quantity="HL23PYR_pop/69/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_70" quantity="HL23PYR_pop/70/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_71" quantity="HL23PYR_pop/71/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_72" quantity="HL23PYR_pop/72/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_73" quantity="HL23PYR_pop/73/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_74" quantity="HL23PYR_pop/74/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_75" quantity="HL23PYR_pop/75/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_76" quantity="HL23PYR_pop/76/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_77" quantity="HL23PYR_pop/77/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_78" quantity="HL23PYR_pop/78/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_79" quantity="HL23PYR_pop/79/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_0" quantity="HL23SST_pop/0/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_1" quantity="HL23SST_pop/1/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_2" quantity="HL23SST_pop/2/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_3" quantity="HL23SST_pop/3/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23SST_pop_4" quantity="HL23SST_pop/4/HL23SST_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_0" quantity="HL23PV_pop/0/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_1" quantity="HL23PV_pop/1/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_2" quantity="HL23PV_pop/2/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_3" quantity="HL23PV_pop/3/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_4" quantity="HL23PV_pop/4/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_5" quantity="HL23PV_pop/5/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23PV_pop_6" quantity="HL23PV_pop/6/HL23PV_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_0" quantity="HL23VIP_pop/0/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_1" quantity="HL23VIP_pop/1/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_2" quantity="HL23VIP_pop/2/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_3" quantity="HL23VIP_pop/3/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_4" quantity="HL23VIP_pop/4/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_5" quantity="HL23VIP_pop/5/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_6" quantity="HL23VIP_pop/6/HL23VIP_sim/0/v"/>
+            <OutputColumn id="HL23VIP_pop_7" quantity="HL23VIP_pop/7/HL23VIP_sim/0/v"/>
         </OutputFile>
-        
+
     </Simulation>
 
 </Lems>

NeuroML2/NeuroML-info-PYR.yaml

@@ -1168,7 +1168,7 @@ mechanisms:
                         values:
                             '*': 1.0e-05
             gmax_Ih:
-                ave_all_segs: 0.0015897764797549684
+                ave_all_segs: 0.00158518922246965
                 values:
                     HL23PYR_0_.apic_0:
                         id: HL23PYR[0].apic_0
@@ -1650,12 +1650,12 @@ mechanisms:
                         id: HL23PYR[0].axon_0
                         nseg: 5
                         values:
-                            '*': 0.00014799999
+                            '*': 1.0e-05
                     HL23PYR_0_.axon_1:
                         id: HL23PYR[0].axon_1
                         nseg: 7
                         values:
-                            '*': 0.00014799999
+                            '*': 1.0e-05
                     HL23PYR_0_.dend_0:
                         id: HL23PYR[0].dend_0
                         nseg: 1

NeuroML2/create_simulate.py

@@ -15,6 +15,7 @@ import random
 import sys
 import time
 import typing
+import bisect
 
 import h5py
 import lems.api as lems
@@ -40,6 +41,13 @@ logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
 
+# https://stackoverflow.com/questions/3410976/how-to-round-a-number-to-significant-figures-in-python
+# currently unused
+def round_to_sig(x):
+    one_less = round(x, int(math.floor(math.log10(abs(x))))) / 10
+    return round(x + one_less, int(math.floor(math.log10(abs(one_less)))))
+
+
 class HL23Net(object):
 
     """HL23 network"""
@@ -539,8 +547,9 @@ class HL23Net(object):
                     )  # type: neuroml.Projection
 
                 # show a progress bar so we have some idea of what's going on
-                # bar = progressbar.ProgressBar(max_value=int(conndataset.shape[0] * self.network_scale * self.network_scale))
-                bar = progressbar.ProgressBar()
+                max_value_possible = int(conndataset.shape[0])
+                # rounded = round_to_sig(approx_max_value)
+                bar = progressbar.ProgressBar(max_val=max_value_possible, poll_interval=30)
                 bar_count = 0
                 for conn in conndataset:
                     precell = conn[0]
@@ -557,8 +566,8 @@ class HL23Net(object):
                         )
                         continue
 
-                    bar_count += 1
                     bar.update(bar_count)
+                    bar_count += 1
 
                     section = (section.decode("utf-8")).split(".")[1]
                     neuroml_seggrp_id = get_segment_group_name(section)
@@ -583,11 +592,7 @@ class HL23Net(object):
                     total_len = list_cumul_lengths[-1]
 
                     section_loc = total_len * sectionx
-                    ind = 0
-                    for leng in list_cumul_lengths:
-                        if leng > section_loc:
-                            break
-                        ind += 1
+                    ind = bisect.bisect_left(list_cumul_lengths, section_loc)
 
                     post_seg = list_ord_segs[ind]
 
@@ -1096,8 +1101,8 @@ class HL23Net(object):
 
         :param engine: engine to use (jneuroml_neuron/jneuroml_netpyne)
         :type engine: str
-        :param nsg: toggle submitting to nsg
-        :type nsg: bool
+        :param nsg: toggle submitting to nsg, use "dry" for a dry run
+        :type nsg: bool or str
         :param **kwargs: other engine + nsg specific args
         """
         if nsg is False:
@@ -1194,8 +1199,8 @@ if __name__ == "__main__":
                   nsg_sim_config={
                       "number_cores_": "64",
                       "tasks_per_node_": "64",
-                      "number_nodes_": "2",
-                      "runtime_": "2",
+                      "number_nodes_": "20",
+                      "runtime_": "5",
                       'toolId': "OSBv2_EXPANSE_0_7_3",
                       'nrnivmodl_o_': "1",
                       "cmdlineopts_": "-nogui"

NeuroML2/lems_components_0.01.xml

@@ -4,15 +4,15 @@
   <Include file="synapses/ProbAMPANMDA.synapse.nml"/>
   <Include file="synapses/ProbUDF.synapse.nml"/>
   <Include file="channels/Tonic.nml"/>
+  <Include file="channels/Ca_HVA.channel.nml"/>
+  <Include file="channels/Ca_LVA.channel.nml"/>
   <Include file="channels/Ih.channel.nml"/>
-  <Include file="channels/K_T.channel.nml"/>
+  <Include file="channels/Im.channel.nml"/>
   <Include file="channels/K_P.channel.nml"/>
-  <Include file="channels/Nap.channel.nml"/>
-  <Include file="channels/Ca_LVA.channel.nml"/>
+  <Include file="channels/K_T.channel.nml"/>
   <Include file="channels/Kv3_1.channel.nml"/>
-  <Include file="channels/Im.channel.nml"/>
+  <Include file="channels/Nap.channel.nml"/>
   <Include file="channels/SK.channel.nml"/>
-  <Include file="channels/Ca_HVA.channel.nml"/>
   <Include file="channels/pas.channel.nml"/>
   <Include file="channels/NaTg/NaTg.channel.nml"/>
   <Include file="synapses/Gfluct.nml"/>

NeuroML2/lems_components_0.05.xml

@@ -32,12 +32,12 @@
   <Component id="HL23VIP_HL23SST_ProbUDFsyn" type="ProbUDFsyn" tau_r="1 ms" tau_d="10 ms" Use="0.27" Dep="760 ms" Fac="22 ms" gbase="0.00036 uS" u0="0" erev="-80 mV"/>
   <Component id="HL23VIP_HL23PV_ProbUDFsyn" type="ProbUDFsyn" tau_r="1 ms" tau_d="10 ms" Use="0.25" Dep="720 ms" Fac="21 ms" gbase="0.00034 uS" u0="0" erev="-80 mV"/>
   <Component id="HL23VIP_HL23VIP_ProbUDFsyn" type="ProbUDFsyn" tau_r="1 ms" tau_d="10 ms" Use="0.26" Dep="720 ms" Fac="21 ms" gbase="0.00034 uS" u0="0" erev="-80 mV"/>
-  <Component id="Gfluct_HL23PYR_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="46.164195579603586 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="46.164195579603586 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23SST_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="49.461638121003844 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="49.461638121003844 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23PV_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="461.6419557960359 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="461.6419557960359 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23VIP_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="108.81560386620846 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="108.81560386620846 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23PYR_0_1" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="30.944785706118136 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="30.944785706118136 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23PYR_0_3" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="37.79604661212809 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="37.79604661212809 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23PYR_0_7" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="56.385075809173344 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="56.385075809173344 pS" std_i="0pS"/>
-  <Component id="Gfluct_HL23PYR_0_9" type="Gfluct" start="0ms" stop="1000ms" dt="0.01ms" E_e="0mV" E_i="-80mV" g_e0="68.86888711239459 pS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="68.86888711239459 pS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PYR_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="0.00010881560386620847 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="0.00010881560386620847 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23SST_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="4.9461638121003845e-05 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="4.9461638121003845e-05 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PV_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="0.00046164195579603584 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="0.00046164195579603584 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23VIP_0_5" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="0.00010881560386620847 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="0.00010881560386620847 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PYR_0_1" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="7.294128059299276e-05 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="7.294128059299276e-05 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PYR_0_3" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="8.909068130001622e-05 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="8.909068130001622e-05 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PYR_0_7" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="0.00013290767869305147 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="0.00013290767869305147 uS" std_i="0pS"/>
+  <Component id="Gfluct_HL23PYR_0_9" type="Gfluct" start="0ms" stop="1000ms" dt="0.025ms" E_e="0mV" E_i="-80mV" g_e0="0.0001623338053363587 uS" g_i0="0pS" tau_e="65ms" tau_i="20ms" std_e="0.0001623338053363587 uS" std_i="0pS"/>
 </Lems>

NeuroML2/postprocess_cells.py

@@ -153,17 +153,6 @@ def postprocess_HL23PYR():
     # write passive cell
     write_neuroml2_file(celldoc, f"{cellname}.pas.cell.nml")
 
-    cell.add_channel_density(
-        nml_cell_doc=celldoc,
-        cd_id="Ih",
-        ion_channel="Ih",
-        cond_density="0.000148 S_per_cm2",
-        erev="-45 mV",
-        group_id="all_minus_myelin",
-        ion="hcn",
-        ion_chan_def_file="channels/Ih.channel.nml",
-    )
-
     # somatic
     soma_group = cell.get_segment_group("soma_group")
     sgid = soma_group.id
@@ -443,6 +432,17 @@ def postprocess_HL23PYR():
         segment_groups=sgid,
     )
 
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="Ih_axonal",
+        ion_channel="Ih",
+        cond_density="0.00001 S_per_cm2",
+        erev="-45 mV",
+        group_id=sgid,
+        ion="hcn",
+        ion_chan_def_file="channels/Ih.channel.nml",
+    )
+
     # L1 validation
     # cell.validate(recursive=True)
     # cell.summary(morph=False, biophys=True)
@@ -810,17 +810,6 @@ def postprocess_HL23SST():
     # write passive cell
     write_neuroml2_file(celldoc, f"{cellname}.pas.cell.nml")
 
-    cell.add_channel_density(
-        nml_cell_doc=celldoc,
-        cd_id="Ih",
-        ion_channel="Ih",
-        cond_density="0.00001 S_per_cm2",
-        erev="-45 mV",
-        group_id="all_minus_myelin",
-        ion="hcn",
-        ion_chan_def_file="channels/Ih.channel.nml",
-    )
-
     # somatic
     soma_group = cell.get_segment_group("soma_group")
     sgid = soma_group.id
@@ -1061,6 +1050,18 @@ def postprocess_HL23SST():
         initial_ext_concentration="2.0E-6 mol_per_cm3",
         segment_groups=sgid,
     )
+    # HCN
+    cell.add_channel_density(
+        nml_cell_doc=celldoc,
+        cd_id="Ih_axonal",
+        ion_channel="Ih",
+        cond_density="0.00001 S_per_cm2",
+        erev="-45 mV",
+        group_id=sgid,
+        ion="hcn",
+        ion_chan_def_file="channels/Ih.channel.nml",
+    )
+
     # L1 validation
     cell.validate(recursive=True)
     cell.summary(morph=True, biophys=True)
@@ -1668,6 +1669,6 @@ if __name__ == "__main__":
     analyse_HL23PV(True, True)
     postprocess_HL23PYR()
     analyse_HL23PYR(False, True)
-    postprocess_HL23SST()
     analyse_HL23SST(True, True)
     """
+    postprocess_HL23SST()