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Off-by-one NeuroML bug

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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="1" 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.   <cell name="TestCell_1">
  118.     <meta:notes>Cell: TestCell_1 exported from NEURON ModelView</meta:notes>
  119.     <segments  xmlns="http://morphml.org/morphml/schema"> <!-- Changing the namespace from neuroml to morphml-->
  120. <!-- Section: TestCell[1].soma which has 2 3D points, so 1 segment(s)-->
  121.       <segment id="14" name = "Seg0_soma" cable = "13">
  122.         <proximal x="-59" y="90" z="0" diameter="1"/>
  123.         <distal x="-44" y="120" z="0" diameter="1"/>
  124.       </segment>
  125. <!-- Section: TestCell[1].dend[0] which has 2 3D points, so 1 segment(s)-->
  126.       <segment id="15" name = "Seg0_dend_0" parent="13" cable = "14">  <!-- Connected at 0 on parent section: TestCell[1].soma  -->
  127.         <proximal x="-59" y="90" z="0" diameter="1"/>
  128.         <distal x="-104" y="90" z="0" diameter="1"/>
  129.       </segment>
  130. <!-- Section: TestCell[1].dend[1] which has 2 3D points, so 1 segment(s)-->
  131.       <segment id="16" name = "Seg0_dend_1" parent="15" cable = "15">  <!-- Parent section: TestCell[1].dend[0] -->
  132.         <proximal x="-104" y="90" z="0" diameter="1"/>
  133.         <distal x="-149" y="165" z="0" diameter="1"/>
  134.       </segment>
  135. <!-- Section: TestCell[1].dend[2] which has 2 3D points, so 1 segment(s)-->
  136.       <segment id="17" name = "Seg0_dend_2" parent="16" cable = "16">  <!-- Parent section: TestCell[1].dend[1] -->
  137.         <proximal x="-149" y="165" z="0" diameter="1"/>
  138.         <distal x="-104" y="210" z="0" diameter="1"/>
  139.       </segment>
  140. <!-- Section: TestCell[1].dend[3] which has 2 3D points, so 1 segment(s)-->
  141.       <segment id="18" name = "Seg0_dend_3" parent="17" cable = "17">  <!-- Parent section: TestCell[1].dend[2] -->
  142.         <proximal x="-104" y="210" z="0" diameter="1"/>
  143.         <distal x="-59" y="210" z="0" diameter="1"/>
  144.       </segment>
  145. <!-- Section: TestCell[1].dend[4] which has 2 3D points, so 1 segment(s)-->
  146.       <segment id="19" name = "Seg0_dend_4" parent="18" cable = "18">  <!-- Parent section: TestCell[1].dend[3] -->
  147.         <proximal x="-59" y="210" z="0" diameter="1"/>
  148.         <distal x="15" y="195" z="0" diameter="1"/>
  149.       </segment>
  150. <!-- Section: TestCell[1].dend[5] which has 2 3D points, so 1 segment(s)-->
  151.       <segment id="20" name = "Seg0_dend_5" parent="19" cable = "19">  <!-- Parent section: TestCell[1].dend[4] -->
  152.         <proximal x="15" y="195" z="0" diameter="1"/>
  153.         <distal x="30" y="150" z="0" diameter="1"/>
  154.       </segment>
  155. <!-- Section: TestCell[1].dend[6] which has 2 3D points, so 1 segment(s)-->
  156.       <segment id="21" name = "Seg0_dend_6" parent="20" cable = "20">  <!-- Parent section: TestCell[1].dend[5] -->
  157.         <proximal x="30" y="150" z="0" diameter="1"/>
  158.         <distal x="60" y="75" z="0" diameter="1"/>
  159.       </segment>
  160. <!-- Section: TestCell[1].dend[7] which has 2 3D points, so 1 segment(s)-->
  161.       <segment id="22" name = "Seg0_dend_7" parent="21" cable = "21">  <!-- Parent section: TestCell[1].dend[6] -->
  162.         <proximal x="60" y="75" z="0" diameter="1"/>
  163.         <distal x="60" y="0" z="0" diameter="1"/>
  164.       </segment>
  165. <!-- Section: TestCell[1].dend[8] which has 2 3D points, so 1 segment(s)-->
  166.       <segment id="23" name = "Seg0_dend_8" parent="22" cable = "22">  <!-- Parent section: TestCell[1].dend[7] -->
  167.         <proximal x="60" y="0" z="0" diameter="1"/>
  168.         <distal x="-14" y="-29" z="0" diameter="1"/>
  169.       </segment>
  170. <!-- Section: TestCell[1].dend[9] which has 2 3D points, so 1 segment(s)-->
  171.       <segment id="24" name = "Seg0_dend_9" parent="23" cable = "23">  <!-- Parent section: TestCell[1].dend[8] -->
  172.         <proximal x="-14" y="-29" z="0" diameter="1"/>
  173.         <distal x="-89" y="-29" z="0" diameter="1"/>
  174.       </segment>
  175. <!-- Section: TestCell[1].dend[10] which has 2 3D points, so 1 segment(s)-->
  176.       <segment id="25" name = "Seg0_dend_10" parent="24" cable = "24">  <!-- Parent section: TestCell[1].dend[9] -->
  177.         <proximal x="-89" y="-29" z="0" diameter="1"/>
  178.         <distal x="-164" y="15" z="0" diameter="1"/>
  179.       </segment>
  180. <!-- Section: TestCell[1].dend[11] which has 2 3D points, so 1 segment(s)-->
  181.       <segment id="26" name = "Seg0_dend_11" parent="25" cable = "25">  <!-- Parent section: TestCell[1].dend[10] -->
  182.         <proximal x="-164" y="15" z="0" diameter="1"/>
  183.         <distal x="-194" y="60" z="0" diameter="1"/>
  184.       </segment>
  185.     </segments>
  186.     <cables  xmlns="http://morphml.org/morphml/schema"> <!-- Changing namespace from neuroml to morphml-->
  187.       <cable id = "13" name = "soma" fract_along_parent = "0"/>
  188.       <cable id = "14" name = "dend_0" fract_along_parent = "0"/>
  189.       <cable id = "15" name = "dend_1"/>
  190.       <cable id = "16" name = "dend_2"/>
  191.       <cable id = "17" name = "dend_3"/>
  192.       <cable id = "18" name = "dend_4"/>
  193.       <cable id = "19" name = "dend_5"/>
  194.       <cable id = "20" name = "dend_6"/>
  195.       <cable id = "21" name = "dend_7"/>
  196.       <cable id = "22" name = "dend_8"/>
  197.       <cable id = "23" name = "dend_9"/>
  198.       <cable id = "24" name = "dend_10"/>
  199.       <cable id = "25" name = "dend_11"/>
  200.       <cablegroup name="ModelViewParmSubset_3">
  201.         <cable id = "13"/>
  202.         <cable id = "14"/>
  203.         <cable id = "15"/>
  204.         <cable id = "16"/>
  205.         <cable id = "17"/>
  206.         <cable id = "18"/>
  207.         <cable id = "19"/>
  208.         <cable id = "20"/>
  209.         <cable id = "21"/>
  210.         <cable id = "22"/>
  211.         <cable id = "23"/>
  212.         <cable id = "24"/>
  213.         <cable id = "25"/>
  214.       </cablegroup>
  215.       <cablegroup name="OneSecGrp_SectionRef_27"> <!-- Creating a group containing a single section: TestCell[1].soma... -->
  216.         <cable id = "13"/>
  217.       </cablegroup>
  218.       <cablegroup name="OneSecGrp_SectionRef_28"> <!-- Creating a group containing a single section: TestCell[1].dend[0]... -->
  219.         <cable id = "14"/>
  220.       </cablegroup>
  221.       <cablegroup name="OneSecGrp_SectionRef_29"> <!-- Creating a group containing a single section: TestCell[1].dend[1]... -->
  222.         <cable id = "15"/>
  223.       </cablegroup>
  224.       <cablegroup name="OneSecGrp_SectionRef_30"> <!-- Creating a group containing a single section: TestCell[1].dend[2]... -->
  225.         <cable id = "16"/>
  226.       </cablegroup>
  227.       <cablegroup name="OneSecGrp_SectionRef_31"> <!-- Creating a group containing a single section: TestCell[1].dend[3]... -->
  228.         <cable id = "17"/>
  229.       </cablegroup>
  230.       <cablegroup name="OneSecGrp_SectionRef_32"> <!-- Creating a group containing a single section: TestCell[1].dend[4]... -->
  231.         <cable id = "18"/>
  232.       </cablegroup>
  233.       <cablegroup name="OneSecGrp_SectionRef_33"> <!-- Creating a group containing a single section: TestCell[1].dend[5]... -->
  234.         <cable id = "19"/>
  235.       </cablegroup>
  236.       <cablegroup name="OneSecGrp_SectionRef_34"> <!-- Creating a group containing a single section: TestCell[1].dend[6]... -->
  237.         <cable id = "20"/>
  238.       </cablegroup>
  239.       <cablegroup name="OneSecGrp_SectionRef_35"> <!-- Creating a group containing a single section: TestCell[1].dend[7]... -->
  240.         <cable id = "21"/>
  241.       </cablegroup>
  242.       <cablegroup name="OneSecGrp_SectionRef_36"> <!-- Creating a group containing a single section: TestCell[1].dend[8]... -->
  243.         <cable id = "22"/>
  244.       </cablegroup>
  245.       <cablegroup name="OneSecGrp_SectionRef_37"> <!-- Creating a group containing a single section: TestCell[1].dend[9]... -->
  246.         <cable id = "23"/>
  247.       </cablegroup>
  248.       <cablegroup name="OneSecGrp_SectionRef_38"> <!-- Creating a group containing a single section: TestCell[1].dend[10]... -->
  249.         <cable id = "24"/>
  250.       </cablegroup>
  251.       <cablegroup name="OneSecGrp_SectionRef_39"> <!-- Creating a group containing a single section: TestCell[1].dend[11]... -->
  252.         <cable id = "25"/>
  253.       </cablegroup>
  254.     </cables>
  255.   </cell>
  256. </cells>
  257. </neuroml>
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