git-annex in atlas

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"/>
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+    <Include file="rotated_cells/HL23PV_sim.cell.nml"/>
+    <Include file="rotated_cells/HL23VIP_sim.cell.nml"/>
     <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_1" quantity="HL23PYR_pop/1/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_2" quantity="HL23PYR_pop/2/HL23PYR_sim/0/v"/>
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+            <OutputColumn id="HL23PYR_pop_4" quantity="HL23PYR_pop/4/HL23PYR_sim/0/v"/>
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+            <OutputColumn id="HL23PYR_pop_22" quantity="HL23PYR_pop/22/HL23PYR_sim/0/v"/>
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+            <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="HL23PYR_pop_40" quantity="HL23PYR_pop/40/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_41" quantity="HL23PYR_pop/41/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_42" quantity="HL23PYR_pop/42/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_43" quantity="HL23PYR_pop/43/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_44" quantity="HL23PYR_pop/44/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_45" quantity="HL23PYR_pop/45/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_46" quantity="HL23PYR_pop/46/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_47" quantity="HL23PYR_pop/47/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_48" quantity="HL23PYR_pop/48/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_49" quantity="HL23PYR_pop/49/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_50" quantity="HL23PYR_pop/50/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_51" quantity="HL23PYR_pop/51/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_52" quantity="HL23PYR_pop/52/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_53" quantity="HL23PYR_pop/53/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_54" quantity="HL23PYR_pop/54/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_55" quantity="HL23PYR_pop/55/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_56" quantity="HL23PYR_pop/56/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_57" quantity="HL23PYR_pop/57/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_58" quantity="HL23PYR_pop/58/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_59" quantity="HL23PYR_pop/59/HL23PYR_sim/0/v"/>
+            <OutputColumn id="HL23PYR_pop_60" quantity="HL23PYR_pop/60/HL23PYR_sim/0/v"/>
+            <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/create_simulate.py

@@ -1199,8 +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>