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pgleeson committed May 14, 2024
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Showing 35 changed files with 62 additions and 62 deletions.
4 changes: 2 additions & 2 deletions examples/ACNet.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Balanced.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Balanced_240cells_36926conns.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Balanced_610cells_0conns.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Balanced_610cells_213550conns.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Complex.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/Deterministic.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/GapJunctions.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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Binary file modified examples/HDF5/ACNet.net.nml.h5
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Binary file modified examples/HDF5/IClamps.net.nml.h5
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4 changes: 2 additions & 2 deletions examples/HDF5/LEMS_ACNet.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="ACNet/Na_bask.channel.nml"/>
<Include file="ACNet.net.nml.h5"/>

<Simulation id="Sim_ACNet" length="250ms" step="0.025ms" target="ACNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_ACNet" length="250.0ms" step="0.025ms" target="ACNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="Display_pop_bask_v" title="Plots of Display_pop_bask_v" timeScale="1ms" xmin="-25.0" xmax="275.0" ymin="-80" ymax="40">
<Line id="pop_bask_0_bask_0_v" quantity="pop_bask/0/bask/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_bask_1_bask_0_v" quantity="pop_bask/1/bask/0/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/HDF5/LEMS_IClamps.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="IClamps/Na_pyr.channel.nml"/>
<Include file="IClamps.net.nml.h5"/>

<Simulation id="Sim_IClamps" length="500ms" step="0.005ms" target="IClamps" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_IClamps" length="500.0ms" step="0.005ms" target="IClamps" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__popHH" title="Membrane potentials of cells in popHH" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="popHH[0]: v" quantity="popHH/0/pyr_4_sym_soma/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
</Display>
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4 changes: 2 additions & 2 deletions examples/HDF5/LEMS_SpikingNet.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="SpikingNet/RS.cell.nml"/>
<Include file="SpikingNet.net.nml.h5"/>

<Simulation id="Sim_SpikingNet" length="1000ms" step="0.01ms" target="SpikingNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_SpikingNet" length="1000.0ms" step="0.01ms" target="SpikingNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__pop_post" title="Membrane potentials of cells in pop_post" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-90" ymax="50">
<Line id="pop_post[0]: v" quantity="pop_post/0/RS/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_post[1]: v" quantity="pop_post/1/RS/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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Binary file modified examples/HDF5/SpikingNet.net.nml.h5
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Binary file modified examples/HDF5/Weights.net.nml.h5
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4 changes: 2 additions & 2 deletions examples/IClamps.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/L23TraubDemo.net.nml
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<notes>

This NeuroML 2 file was generated by OpenCortex v0.1.18 using:
libNeuroML v0.5.8
pyNeuroML v1.1.14
libNeuroML v0.5.9
pyNeuroML v1.2.13

</notes>
<property tag="Network seed" value="1234"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_ACNet.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="ACNet/Na_bask.channel.nml"/>
<Include file="ACNet.net.nml"/>

<Simulation id="Sim_ACNet" length="250ms" step="0.025ms" target="ACNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_ACNet" length="250.0ms" step="0.025ms" target="ACNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="Display_pop_bask_v" title="Plots of Display_pop_bask_v" timeScale="1ms" xmin="-25.0" xmax="275.0" ymin="-80" ymax="40">
<Line id="pop_bask_0_bask_0_v" quantity="pop_bask/0/bask/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_bask_1_bask_0_v" quantity="pop_bask/1/bask/0/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_Balanced.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="Balanced/Ca_LVAst.channel.nml"/>
<Include file="Balanced.net.nml"/>

<Simulation id="Sim_Balanced" length="1000ms" step="0.025ms" target="Balanced" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Balanced" length="1000.0ms" step="0.025ms" target="Balanced" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="popBBP" title="Plots of popBBP" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="popBBP_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="popBBP/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
</Display>
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4 changes: 2 additions & 2 deletions examples/LEMS_Balanced_610cells_0conns.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="Balanced/Ca_LVAst.channel.nml"/>
<Include file="Balanced_610cells_0conns.net.nml"/>

<Simulation id="Sim_Balanced_610cells_0conns" length="1000ms" step="0.025ms" target="Balanced_610cells_0conns" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Balanced_610cells_0conns" length="1000.0ms" step="0.025ms" target="Balanced_610cells_0conns" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="popBBP" title="Plots of popBBP" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="popBBP_0_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="popBBP/0/cADpyr229_L23_PC_5ecbf9b163_0_0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="popBBP_1_cADpyr229_L23_PC_5ecbf9b163_0_0_v" quantity="popBBP/1/cADpyr229_L23_PC_5ecbf9b163_0_0/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_Complex.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="Complex/pyr_4_sym.cell.nml"/>
<Include file="Complex.net.nml"/>

<Simulation id="Sim_Complex" length="500ms" step="0.025ms" target="Complex" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Complex" length="500.0ms" step="0.025ms" target="Complex" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__popIaf" title="Membrane potentials of cells in popIaf" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="popIaf[0]: v" quantity="popIaf/0/iaf/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="popIaf[1]: v" quantity="popIaf/1/iaf/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_Deterministic.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="Deterministic/iaf.cell.nml"/>
<Include file="Deterministic.net.nml"/>

<Simulation id="Sim_Deterministic" length="500ms" step="0.005ms" target="Deterministic" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Deterministic" length="500.0ms" step="0.005ms" target="Deterministic" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__pop_iaf" title="Membrane potentials of cells in pop_iaf" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="pop_iaf[0]: v" quantity="pop_iaf/0/iaf/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_iaf[1]: v" quantity="pop_iaf/1/iaf/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_GapJunctions.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="GapJunctions/Na_pyr.channel.nml"/>
<Include file="GapJunctions.net.nml"/>

<Simulation id="Sim_GapJunctions" length="1000ms" step="0.025ms" target="GapJunctions" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_GapJunctions" length="1000.0ms" step="0.025ms" target="GapJunctions" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="Display_pop_post_v" title="Plots of Display_pop_post_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop_post_0_pyr_4_sym_0_v" quantity="pop_post/0/pyr_4_sym/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_post_1_pyr_4_sym_0_v" quantity="pop_post/1/pyr_4_sym/0/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_IClamps.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

Expand All @@ -24,7 +24,7 @@
<Include file="IClamps/Na_pyr.channel.nml"/>
<Include file="IClamps.net.nml"/>

<Simulation id="Sim_IClamps" length="500ms" step="0.005ms" target="IClamps" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_IClamps" length="500.0ms" step="0.005ms" target="IClamps" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__popIzh" title="Membrane potentials of cells in popIzh" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="popIzh[0]: v" quantity="popIzh/0/RS/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
</Display>
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4 changes: 2 additions & 2 deletions examples/LEMS_L23TraubDemo.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="L23TraubDemo/naf2__a0__b0__c0__d0__fastNa_shiftmin2_5.channel.nml"/>
<Include file="L23TraubDemo.net.nml"/>

<Simulation id="Sim_L23TraubDemo" length="300ms" step="0.025ms" target="L23TraubDemo" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_L23TraubDemo" length="300.0ms" step="0.025ms" target="L23TraubDemo" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="Display_pop_bask_0_v" title="Plots of Display_pop_bask_0_v" timeScale="1ms" xmin="-30.0" xmax="330.0" ymin="-80" ymax="40">
<Line id="pop_bask_0_SupBasket_0_v" quantity="pop_bask/0/SupBasket/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
</Display>
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4 changes: 2 additions & 2 deletions examples/LEMS_Recording.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

Expand All @@ -23,7 +23,7 @@
<Include file="Recording/Na_pyr.channel.nml"/>
<Include file="Recording.net.nml"/>

<Simulation id="Sim_Recording" length="500ms" step="0.005ms" target="Recording" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Recording" length="500.0ms" step="0.005ms" target="Recording" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__pop0" title="Membrane potentials of cells in pop0" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="pop0[0] seg 0: v" quantity="pop0/0/pyr_4_sym/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop0[0] seg 1: v" quantity="pop0/0/pyr_4_sym/1/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_SimpleNet.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

Expand All @@ -17,7 +17,7 @@
<Include file="SimpleNet/RS.cell.nml"/>
<Include file="SimpleNet.net.nml"/>

<Simulation id="Sim_SimpleNet" length="500ms" step="0.025ms" target="SimpleNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_SimpleNet" length="500.0ms" step="0.025ms" target="SimpleNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__RS_pop" title="Membrane potentials of cells in RS_pop" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-90" ymax="50">
<Line id="RS_pop[0]: v" quantity="RS_pop/0/RS/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="RS_pop[1]: v" quantity="RS_pop/1/RS/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_SpikingNet.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

Expand All @@ -17,7 +17,7 @@
<Include file="SpikingNet/RS.cell.nml"/>
<Include file="SpikingNet.net.nml"/>

<Simulation id="Sim_SpikingNet" length="1000ms" step="0.01ms" target="SpikingNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_SpikingNet" length="1000.0ms" step="0.01ms" target="SpikingNet" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__pop_pre" title="Membrane potentials of cells in pop_pre" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-90" ymax="50">
<Line id="pop_pre[0]: v" quantity="pop_pre/0/RS/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_pre[1]: v" quantity="pop_pre/1/RS/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_VClamp.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

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<Include file="VClamp/pas.channel.nml"/>
<Include file="VClamp.net.nml"/>

<Simulation id="Sim_VClamp" length="500ms" step="0.025ms" target="VClamp" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_VClamp" length="500.0ms" step="0.025ms" target="VClamp" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="Display_popRS_0_v" title="Plots of Display_popRS_0_v" timeScale="1ms" xmin="-50.0" xmax="550.0" ymin="-80" ymax="40">
<Line id="popRS_0_L23PyrRS_0_v" quantity="popRS/0/L23PyrRS/0/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="popRS_0_L23PyrRS_142_v" quantity="popRS/0/L23PyrRS/142/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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4 changes: 2 additions & 2 deletions examples/LEMS_Weights.xml
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<!--
This LEMS file has been automatically generated using PyNeuroML v1.1.14 (libNeuroML v0.5.8)
This LEMS file has been automatically generated using PyNeuroML v1.2.13 (libNeuroML v0.5.9)
-->

Expand All @@ -21,7 +21,7 @@
<Include file="Weights/Na.channel.nml"/>
<Include file="Weights.net.nml"/>

<Simulation id="Sim_Weights" length="1000ms" step="0.025ms" target="Weights" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Simulation id="Sim_Weights" length="1000.0ms" step="0.025ms" target="Weights" seed="12345"> <!-- Note seed: ensures same random numbers used every run -->
<Display id="DispPop__pop_pre" title="Membrane potentials of cells in pop_pre" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-90" ymax="50">
<Line id="pop_pre[0]: v" quantity="pop_pre/0/HH_477127614/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop_pre[1]: v" quantity="pop_pre/1/HH_477127614/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
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