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Off-by-one NeuroML bug one cell

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Mar 21st, 2019
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  1. <?xml version="1.0" encoding="UTF-8"?>
  2. <neuroml xmlns="http://morphml.org/neuroml/schema"
  3.    xmlns:mml="http://morphml.org/morphml/schema"
  4.    xmlns:meta="http://morphml.org/metadata/schema"
  5.    xmlns:bio="http://morphml.org/biophysics/schema"
  6.    xmlns:cml="http://morphml.org/channelml/schema"
  7.    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  8.    xsi:schemaLocation="http://morphml.org/neuroml/schema http://www.neuroml.org/NeuroMLValidator/NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1.xsd"
  9.    name = "NeuroML Level 1 file exported from NEURON"
  10.    lengthUnits="micron">
  11.  
  12. <meta:notes>NeuroML Level 1 file generated from ModelView by: NEURON -- VERSION 7.5 master (6b4c19f) 2017-09-25
  13. Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson,
  14. Yale University and UCL</meta:notes>
  15.  
  16. <cells>
  17.   <cell name="TestCell_0">
  18.     <meta:notes>Cell: TestCell_0 exported from NEURON ModelView</meta:notes>
  19.     <segments  xmlns="http://morphml.org/morphml/schema"> <!-- Changing the namespace from neuroml to morphml-->
  20. <!-- Section: TestCell[0].soma which has 2 3D points, so 1 segment(s)-->
  21.       <segment id="0" name = "Seg0_soma" cable = "0">
  22.         <proximal x="-59" y="90" z="0" diameter="1"/>
  23.         <distal x="-44" y="120" z="0" diameter="1"/>
  24.       </segment>
  25. <!-- Section: TestCell[0].dend[0] which has 2 3D points, so 1 segment(s)-->
  26.       <segment id="2" name = "Seg0_dend_0" parent="0" cable = "1">  <!-- Connected at 0 on parent section: TestCell[0].soma  -->
  27.         <proximal x="-59" y="90" z="0" diameter="1"/>
  28.         <distal x="-104" y="90" z="0" diameter="1"/>
  29.       </segment>
  30. <!-- Section: TestCell[0].dend[1] which has 2 3D points, so 1 segment(s)-->
  31.       <segment id="3" name = "Seg0_dend_1" parent="2" cable = "2">  <!-- Parent section: TestCell[0].dend[0] -->
  32.         <proximal x="-104" y="90" z="0" diameter="1"/>
  33.         <distal x="-149" y="165" z="0" diameter="1"/>
  34.       </segment>
  35. <!-- Section: TestCell[0].dend[2] which has 2 3D points, so 1 segment(s)-->
  36.       <segment id="4" name = "Seg0_dend_2" parent="3" cable = "3">  <!-- Parent section: TestCell[0].dend[1] -->
  37.         <proximal x="-149" y="165" z="0" diameter="1"/>
  38.         <distal x="-104" y="210" z="0" diameter="1"/>
  39.       </segment>
  40. <!-- Section: TestCell[0].dend[3] which has 2 3D points, so 1 segment(s)-->
  41.       <segment id="5" name = "Seg0_dend_3" parent="4" cable = "4">  <!-- Parent section: TestCell[0].dend[2] -->
  42.         <proximal x="-104" y="210" z="0" diameter="1"/>
  43.         <distal x="-59" y="210" z="0" diameter="1"/>
  44.       </segment>
  45. <!-- Section: TestCell[0].dend[4] which has 2 3D points, so 1 segment(s)-->
  46.       <segment id="6" name = "Seg0_dend_4" parent="5" cable = "5">  <!-- Parent section: TestCell[0].dend[3] -->
  47.         <proximal x="-59" y="210" z="0" diameter="1"/>
  48.         <distal x="15" y="195" z="0" diameter="1"/>
  49.       </segment>
  50. <!-- Section: TestCell[0].dend[5] which has 2 3D points, so 1 segment(s)-->
  51.       <segment id="7" name = "Seg0_dend_5" parent="6" cable = "6">  <!-- Parent section: TestCell[0].dend[4] -->
  52.         <proximal x="15" y="195" z="0" diameter="1"/>
  53.         <distal x="30" y="150" z="0" diameter="1"/>
  54.       </segment>
  55. <!-- Section: TestCell[0].dend[6] which has 2 3D points, so 1 segment(s)-->
  56.       <segment id="8" name = "Seg0_dend_6" parent="7" cable = "7">  <!-- Parent section: TestCell[0].dend[5] -->
  57.         <proximal x="30" y="150" z="0" diameter="1"/>
  58.         <distal x="60" y="75" z="0" diameter="1"/>
  59.       </segment>
  60. <!-- Section: TestCell[0].dend[7] which has 2 3D points, so 1 segment(s)-->
  61.       <segment id="9" name = "Seg0_dend_7" parent="8" cable = "8">  <!-- Parent section: TestCell[0].dend[6] -->
  62.         <proximal x="60" y="75" z="0" diameter="1"/>
  63.         <distal x="60" y="0" z="0" diameter="1"/>
  64.       </segment>
  65. <!-- Section: TestCell[0].dend[8] which has 2 3D points, so 1 segment(s)-->
  66.       <segment id="10" name = "Seg0_dend_8" parent="9" cable = "9">  <!-- Parent section: TestCell[0].dend[7] -->
  67.         <proximal x="60" y="0" z="0" diameter="1"/>
  68.         <distal x="-14" y="-29" z="0" diameter="1"/>
  69.       </segment>
  70. <!-- Section: TestCell[0].dend[9] which has 2 3D points, so 1 segment(s)-->
  71.       <segment id="11" name = "Seg0_dend_9" parent="10" cable = "10">  <!-- Parent section: TestCell[0].dend[8] -->
  72.         <proximal x="-14" y="-29" z="0" diameter="1"/>
  73.         <distal x="-89" y="-29" z="0" diameter="1"/>
  74.       </segment>
  75. <!-- Section: TestCell[0].dend[10] which has 2 3D points, so 1 segment(s)-->
  76.       <segment id="12" name = "Seg0_dend_10" parent="11" cable = "11">  <!-- Parent section: TestCell[0].dend[9] -->
  77.         <proximal x="-89" y="-29" z="0" diameter="1"/>
  78.         <distal x="-164" y="15" z="0" diameter="1"/>
  79.       </segment>
  80. <!-- Section: TestCell[0].dend[11] which has 2 3D points, so 1 segment(s)-->
  81.       <segment id="13" name = "Seg0_dend_11" parent="12" cable = "12">  <!-- Parent section: TestCell[0].dend[10] -->
  82.         <proximal x="-164" y="15" z="0" diameter="1"/>
  83.         <distal x="-194" y="60" z="0" diameter="1"/>
  84.       </segment>
  85.     </segments>
  86.     <cables  xmlns="http://morphml.org/morphml/schema"> <!-- Changing namespace from neuroml to morphml-->
  87.       <cable id = "0" name = "soma" fract_along_parent = "0"/>
  88.       <cable id = "1" name = "dend_0" fract_along_parent = "0"/>
  89.       <cable id = "2" name = "dend_1"/>
  90.       <cable id = "3" name = "dend_2"/>
  91.       <cable id = "4" name = "dend_3"/>
  92.       <cable id = "5" name = "dend_4"/>
  93.       <cable id = "6" name = "dend_5"/>
  94.       <cable id = "7" name = "dend_6"/>
  95.       <cable id = "8" name = "dend_7"/>
  96.       <cable id = "9" name = "dend_8"/>
  97.       <cable id = "10" name = "dend_9"/>
  98.       <cable id = "11" name = "dend_10"/>
  99.       <cable id = "12" name = "dend_11"/>
  100.       <cablegroup name="all"> <!-- Replacing subset name ModelViewParmSubset_0 with all, as it contains all sections -->
  101.         <cable id = "0"/>
  102.         <cable id = "1"/>
  103.         <cable id = "2"/>
  104.         <cable id = "3"/>
  105.         <cable id = "4"/>
  106.         <cable id = "5"/>
  107.         <cable id = "6"/>
  108.         <cable id = "7"/>
  109.         <cable id = "8"/>
  110.         <cable id = "9"/>
  111.         <cable id = "10"/>
  112.         <cable id = "11"/>
  113.         <cable id = "12"/>
  114.       </cablegroup>
  115.     </cables>
  116.   </cell>
  117. </cells>
  118. </neuroml>
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