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pgleesonpgleeson
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Regenerated with some extra property info in cells
1 parent 571a60b commit 427de74

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-30
lines changed

‎NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163.stepcurrent3.net.nml‎

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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_PC_cADpyr/details
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******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_PC_L23PC/details
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</notes>
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</notes>
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<include href="cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml"></include>
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<pulseGenerator id="stepcurrent3_hyp" delay="0ms" duration="3000ms" amplitude="-0.071777nA"/>
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<pulseGenerator id="stepcurrent3" delay="700ms" duration="2000ms" amplitude="0.1897924nA"/>

‎NMC/NeuroML2/cADpyr229_L23_PC_5ecbf9b163_0_0.cell.nml‎

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,14 +17,21 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_PC_cADpyr/details
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******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_PC_L23PC/details
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</notes>
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</notes>
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<property tag="BBP:layer" value="L3"/>
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<property tag="BBP:me-type" value="L23_PC_cADpyr"/>
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<property tag="BBP:m-type" value="L23_PC"/>
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<property tag="BBP:cell name" value="cADpyr229_L23_PC_3_dend-C170897A-P3_axon-C260897C-P4_-_Clone_4"/>
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<property tag="BBP:gid" value="35954"/>
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<property tag="BBP:e-type" value="L23PC"/>
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<property tag="BBP:morphology" value="dend-C170897A-P3_axon-C260897C-P4_-_Clone_4"/>
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<morphology id="morphology">
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<segment id="0" name="Seg0_soma_0">
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<proximal x="2.575320e-01" y="-8.049430e+00" z="0.000000e+00" diameter="3.02824"/>

‎NMC/NeuroML2/cADpyr232_L5_TTPC1_0fb1ca4724.stepcurrent3.net.nml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,14 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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6+
For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L5_TTPC1_cADpyr/details
7+
68
******************************************************
79
* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
911
******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L5_TTPC1_L5PC/details
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</notes>
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</notes>
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<include href="cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml"></include>
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<pulseGenerator id="stepcurrent3_hyp" delay="0ms" duration="3000ms" amplitude="-0.247559nA"/>
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<pulseGenerator id="stepcurrent3" delay="700ms" duration="2000ms" amplitude="0.646625nA"/>

‎NMC/NeuroML2/cADpyr232_L5_TTPC1_0fb1ca4724_0_0.cell.nml‎

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,14 +17,21 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L5_TTPC1_cADpyr/details
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******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L5_TTPC1_L5PC/details
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</notes>
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</notes>
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<property tag="BBP:layer" value="L5"/>
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<property tag="BBP:me-type" value="L5_TTPC1_cADpyr"/>
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<property tag="BBP:m-type" value="L5_TTPC1"/>
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<property tag="BBP:cell name" value="cADpyr232_L5_TTPC1_5_dend-C060114A2_axon-C060114A5"/>
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<property tag="BBP:gid" value="12858"/>
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<property tag="BBP:e-type" value="L5PC"/>
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<property tag="BBP:morphology" value="dend-C060114A2_axon-C060114A5"/>
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<morphology id="morphology">
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<segment id="0" name="Seg0_soma_0">
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<proximal x="3.947040e+00" y="-1.382970e+01" z="0.000000e+00" diameter="3.61096"/>

‎NMC/NeuroML2/cNAC187_L1_HAC_f8c9772d9d.stepcurrent3.net.nml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,14 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L1_HAC_cNAC/details
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68
******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L1_HAC_cNAC/details
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</notes>
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</notes>
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<include href="cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml"></include>
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<pulseGenerator id="stepcurrent3_hyp" delay="0ms" duration="3000ms" amplitude="-0.025513nA"/>
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<pulseGenerator id="stepcurrent3" delay="700ms" duration="2000ms" amplitude="0.0665952nA"/>

‎NMC/NeuroML2/cNAC187_L1_HAC_f8c9772d9d_0_0.cell.nml‎

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -17,14 +17,21 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L1_HAC_cNAC/details
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******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L1_HAC_cNAC/details
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</notes>
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</notes>
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<property tag="BBP:layer" value="L1"/>
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<property tag="BBP:me-type" value="L1_HAC_cNAC"/>
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<property tag="BBP:m-type" value="L1_HAC"/>
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<property tag="BBP:cell name" value="cNAC187_L1_HAC_1_sm081119a6"/>
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<property tag="BBP:gid" value="31362"/>
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<property tag="BBP:e-type" value="cNAC"/>
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<property tag="BBP:morphology" value="sm081119a6"/>
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<morphology id="morphology">
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<segment id="0" name="Seg0_soma_0">
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<proximal x="-3.809550e+00" y="-7.565470e+00" z="0.000000e+00" diameter="2.78828"/>

‎NMC/NeuroML2/cSTUT189_L23_LBC_e6e8f83407.stepcurrent3.net.nml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3,14 +3,14 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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6+
For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_LBC_cSTUT/details
7+
68
******************************************************
79
* This export to NeuroML2 has not yet been fully validated!!
810
* Use with caution!!
911
******************************************************
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11-
For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_LBC_cSTUT/details
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</notes>
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</notes>
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<include href="cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml"></include>
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<pulseGenerator id="stepcurrent3_hyp" delay="0ms" duration="3000ms" amplitude="-0.042603nA"/>
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<pulseGenerator id="stepcurrent3" delay="700ms" duration="2000ms" amplitude="0.2898434nA"/>

‎NMC/NeuroML2/cSTUT189_L23_LBC_e6e8f83407_0_0.cell.nml‎

Lines changed: 10 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -18,14 +18,21 @@
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Export of a cell model obtained from the BBP NeocorticalMicrocircuit Collaboration Portal into NeuroML2
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_LBC_cSTUT/details
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******************************************************
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* This export to NeuroML2 has not yet been fully validated!!
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* Use with caution!!
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******************************************************
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For more information on this cell model see: https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/L23_LBC_cSTUT/details
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</notes>
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</notes>
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<property tag="BBP:layer" value="L3"/>
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<property tag="BBP:me-type" value="L23_LBC_cSTUT"/>
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<property tag="BBP:m-type" value="L23_LBC"/>
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<property tag="BBP:cell name" value="cSTUT189_L23_LBC_3_C050398B-I4_-_Scale_x1.000_y1.050_z1.000"/>
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<property tag="BBP:gid" value="162947"/>
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<property tag="BBP:e-type" value="cSTUT"/>
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<property tag="BBP:morphology" value="C050398B-I4_-_Scale_x1.000_y1.050_z1.000"/>
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<morphology id="morphology">
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<segment id="0" name="Seg0_soma_0">
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<proximal x="-2.563980e+00" y="1.218560e+01" z="-3.459150e+00" diameter="3.25378"/>

‎NMC/parser/ParseAll.py‎

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Original file line numberDiff line numberDiff line change
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import neuroml
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import shutil
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import re
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import zipfile
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from Biophysics import get_biophysical_properties
@@ -310,20 +310,33 @@ def process_celldir(inputs):
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notes = ''
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notes += \
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"\n\nExport of a cell model obtained from the BBP Neocortical" \
313-
"Microcircuit Collaboration Portal into NeuroML2" \
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"\n\n******************************************************\n*" \
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" This export to NeuroML2 has not yet been fully validated!!" \
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"\n* Use with caution!!\n***********************************" \
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"*******************\n\n"
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"Microcircuit Collaboration Portal into NeuroML2\n\n"
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if len(ignore_chans) > 0:
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notes += "Ignored channels = %s\n\n" % ignore_chans
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#### Fix me-type
319+
cell_name = cell_info['cell name']
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cell_info['me-type'] = cell_info['m-type'] + '_' + re.split('[0-9]',cell_name)[0]
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322323
notes += "For more information on this cell model see: " \
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"https://bbp.epfl.ch/nmc-portal/microcircuit#/metype/%s/" \
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"details\n\n" % cell_info['me-type']
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notes += "******************************************************\n*" \
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" This export to NeuroML2 has not yet been fully validated!!" \
329+
"\n* Use with caution!!\n***********************************" \
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"*******************\n\n "
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326332
cell.notes = notes
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for k in cell_info.keys():
335+
p = neuroml.Property(tag='BBP:%s'%k, value=cell_info[k])
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cell.properties.append(p)
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for channel in incl_chans:
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nml_doc.includes.append(neuroml.IncludeType(

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