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Clean up, and update NeuroML to reflect block->blockMechanism rename.
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The default simulation configuration here is an example of various
problems with NEURON export:
- broken conversion of temperature parameters
- no support of idealGasConstantDims
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@epiasini
epiasini committed Jul 3, 2013
1 parent e0178bb commit 562e759
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Showing 19 changed files with 72 additions and 8,214 deletions.
148 changes: 41 additions & 107 deletions neuroConstruct/GranCellRothmanIF.ncx
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Expand Up @@ -241,65 +241,6 @@ part of NeuroML or any standardised XML specification. -->
</void>
</object>
</void>
<void method="add">
<object class="ucl.physiol.neuroconstruct.project.SimPlot">
<void property="cellGroup">
<string>GrCs_156</string>
</void>
<void property="cellNumber">
<string>*</string>
</void>
<void property="graphWindow">
<string>GrCs_156_v</string>
</void>
<void property="maxValue">
<float>50.0</float>
</void>
<void property="minValue">
<float>-90.0</float>
</void>
<void property="plotAndOrSave">
<string>Plot and save</string>
</void>
<void property="plotReference">
<string>GrCs_156_v</string>
</void>
<void property="segmentId">
<string>0</string>
</void>
</object>
</void>
<void method="add">
<object class="ucl.physiol.neuroconstruct.project.SimPlot">
<void property="cellGroup">
<string>GrCs_156</string>
</void>
<void property="cellNumber">
<string>0</string>
</void>
<void property="graphWindow">
<string>GraphWin_2</string>
</void>
<void property="maxValue">
<float>50.0</float>
</void>
<void property="minValue">
<float>-90.0</float>
</void>
<void property="plotAndOrSave">
<string>Save only</string>
</void>
<void property="plotReference">
<string>GrCs_156_spikes</string>
</void>
<void property="segmentId">
<string>0</string>
</void>
<void property="valuePlotted">
<string>SPIKE:-40</string>
</void>
</object>
</void>
<void method="add">
<object class="ucl.physiol.neuroconstruct.project.SimPlot">
<void property="cellGroup">
Expand Down Expand Up @@ -378,7 +319,7 @@ part of NeuroML or any standardised XML specification. -->
<float>100.0</float>
</void>
<void property="reference">
<string>Sim_161</string>
<string>Sim_167</string>
</void>
<void property="saveCopyGenSimFiles">
<boolean>true</boolean>
Expand Down Expand Up @@ -468,15 +409,36 @@ part of NeuroML or any standardised XML specification. -->
<void method="add">
<string>GrCs</string>
</void>
<void method="add">
<string>stims</string>
</void>
</void>
<void property="description">
<string>This is the default configuration of the Cell Groups, stimulations, plots, etc for this project</string>
<string>Default simulation configuration: the granule cell is stimulated with four independent (AMPA+NMDA) Poisson spike trains.</string>
</void>
<void property="inputs">
<void method="add">
<string>relay_stim</string>
</void>
</void>
<void property="name">
<string>Default Simulation Configuration</string>
</void>
<void property="netConns">
<void method="add">
<string>stims_to_GrCs_AMPA</string>
</void>
<void method="add">
<string>stims_to_GrCs_NMDA</string>
</void>
</void>
<void property="plots">
<void method="add">
<string>GrCs_v</string>
</void>
</void>
<void property="simDuration">
<float>100.0</float>
<float>1000.0</float>
</void>
</object>
</void>
Expand All @@ -503,7 +465,10 @@ part of NeuroML or any standardised XML specification. -->
</void>
<void property="netConns">
<void method="add">
<string>stims_to_GrCs</string>
<string>stims_to_GrCs_AMPA</string>
</void>
<void method="add">
<string>stims_to_GrCs_NMDA</string>
</void>
</void>
<void property="plots">
Expand Down Expand Up @@ -540,11 +505,6 @@ part of NeuroML or any standardised XML specification. -->
<void property="name">
<string>rate_IO</string>
</void>
<void property="netConns">
<void method="add">
<string>stims_to_GrCs</string>
</void>
</void>
<void property="plots">
<void method="add">
<string>GrCs_spikes</string>
Expand Down Expand Up @@ -604,11 +564,6 @@ part of NeuroML or any standardised XML specification. -->
<void property="name">
<string>rate_IO_156</string>
</void>
<void property="plots">
<void method="add">
<string>GrCs_156_spikes</string>
</void>
</void>
<void property="simDuration">
<float>1000.0</float>
</void>
Expand Down Expand Up @@ -688,13 +643,13 @@ part of NeuroML or any standardised XML specification. -->
<void method="get">
<string>Name</string>
<void method="add">
<string>stims_to_GrCs</string>
<string>GrCs_dummy_to_Grcs</string>
</void>
<void method="add">
<string>GrCs_dummy_to_Grcs</string>
<string>stims_to_GrCs_AMPA</string>
</void>
<void method="add">
<string>NetConn_GrCs_dummy_GrCs</string>
<string>stims_to_GrCs_NMDA</string>
</void>
</void>
<void method="get">
Expand Down Expand Up @@ -728,6 +683,9 @@ part of NeuroML or any standardised XML specification. -->
<void property="synapseType">
<string>RothmanMFToGrCAMPA</string>
</void>
<void property="threshold">
<double>-40.0</double>
</void>
<void property="weightsGenerator">
<object class="ucl.physiol.neuroconstruct.utils.WeightGenerator">
<void property="numberType">
Expand All @@ -752,6 +710,9 @@ part of NeuroML or any standardised XML specification. -->
<void property="synapseType">
<string>RothmanMFToGrCNMDA</string>
</void>
<void property="threshold">
<double>-40.0</double>
</void>
<void property="weightsGenerator">
<object class="ucl.physiol.neuroconstruct.utils.WeightGenerator">
<void property="numberType">
Expand Down Expand Up @@ -792,33 +753,6 @@ part of NeuroML or any standardised XML specification. -->
</void>
</object>
</void>
<void method="add">
<object class="ucl.physiol.neuroconstruct.project.SynapticProperties">
<void property="delayGenerator">
<object class="ucl.physiol.neuroconstruct.utils.NumberGenerator">
<void property="fixedNum">
<float>0.0</float>
</void>
<void property="numberType">
<int>11</int>
</void>
</object>
</void>
<void property="synapseType">
<string>RothmanMFToGrCNMDA</string>
</void>
<void property="threshold">
<double>-40.0</double>
</void>
<void property="weightsGenerator">
<object class="ucl.physiol.neuroconstruct.utils.WeightGenerator">
<void property="numberType">
<int>11</int>
</void>
</object>
</void>
</object>
</void>
</object>
</void>
<void method="add">
Expand All @@ -836,7 +770,7 @@ part of NeuroML or any standardised XML specification. -->
</object>
</void>
<void property="synapseType">
<string>SingleExpSyn</string>
<string>RothmanMFToGrCNMDA</string>
</void>
<void property="threshold">
<double>-40.0</double>
Expand Down Expand Up @@ -892,13 +826,13 @@ part of NeuroML or any standardised XML specification. -->
<void method="get">
<string>Source</string>
<void method="add">
<string>stims</string>
<string>GrCs_dummy</string>
</void>
<void method="add">
<string>GrCs_dummy</string>
<string>stims</string>
</void>
<void method="add">
<string>GrCs_dummy</string>
<string>stims</string>
</void>
</void>
<void method="get">
Expand Down

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