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Off-by-one NeuroML buggy 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="GC_0">
  18. <meta:notes>Cell: GC_0 exported from NEURON ModelView</meta:notes>
  19. <segments xmlns="http://morphml.org/morphml/schema"> <!-- Changing the namespace from neuroml to morphml-->
  20. <!-- Section: GC[0].somagc which has 3 3D points, so 2 segment(s)-->
  21. <segment id="0" name = "Seg0_somagc" cable = "0">
  22. <proximal x="0" y="0" z="0" diameter="8"/>
  23. <distal x="4" y="0" z="0" diameter="8"/>
  24. </segment>
  25. <segment id="2" name = "Seg1_somagc" parent="0" cable = "0">
  26. <distal x="8" y="0" z="0" diameter="8"/>
  27. </segment>
  28. <!-- Section: GC[0].priden which has 3 3D points, so 2 segment(s)-->
  29. <segment id="7" name = "Seg0_priden" parent="2" cable = "3"> <!-- Parent section: GC[0].somagc -->
  30. <proximal x="8" y="0" z="0" diameter="0.5"/>
  31. <distal x="83" y="0" z="0" diameter="0.5"/>
  32. </segment>
  33. <segment id="8" name = "Seg1_priden" parent="7" cable = "3">
  34. <distal x="158" y="0" z="0" diameter="0.5"/>
  35. </segment>
  36. <!-- Section: GC[0].priden2[0] which has 3 3D points, so 2 segment(s)-->
  37. <segment id="9" name = "Seg0_priden2_0" parent="7" cable = "4"> <!-- Connected at 0.8 on parent section: GC[0].priden -->
  38. <proximal x="128" y="0" z="0" diameter="0.4"/>
  39. <distal x="128" y="50" z="0" diameter="0.4"/>
  40. </segment>
  41. <segment id="10" name = "Seg1_priden2_0" parent="9" cable = "4">
  42. <distal x="128" y="100" z="0" diameter="0.4"/>
  43. </segment>
  44. <!-- Section: GC[0].dend[1] which has 3 3D points, so 2 segment(s)-->
  45. <segment id="5" name = "Seg0_dend_1" parent="8" cable = "2"> <!-- Connected at 0.5 on parent section: GC[0].priden2[0] -->
  46. <proximal x="128" y="50" z="0" diameter="0.2"/>
  47. <distal x="127" y="50" z="0" diameter="0.2"/>
  48. </segment>
  49. <segment id="6" name = "Seg1_dend_1" parent="5" cable = "2">
  50. <distal x="126" y="50" z="0" diameter="0.2"/>
  51. </segment>
  52. <!-- Section: GC[0].dend[0] which has 3 3D points, so 2 segment(s)-->
  53. <segment id="3" name = "Seg0_dend_0" parent="6" cable = "1"> <!-- Parent section: GC[0].dend[1] -->
  54. <proximal x="126" y="50" z="0" diameter="1"/>
  55. <distal x="125.5" y="50" z="0" diameter="1"/>
  56. </segment>
  57. <segment id="4" name = "Seg1_dend_0" parent="3" cable = "1">
  58. <distal x="125" y="50" z="0" diameter="1"/>
  59. </segment>
  60. </segments>
  61. <cables xmlns="http://morphml.org/morphml/schema"> <!-- Changing namespace from neuroml to morphml-->
  62. <cable id = "0" name = "somagc" fract_along_parent = "0"/>
  63. <cable id = "3" name = "priden">
  64. <meta:properties>
  65. <meta:property>
  66. <meta:tag>numberInternalDivisions</meta:tag> <!-- Discetization of model at time of export. Can be overridden by importing application-->
  67. <meta:value>10</meta:value>
  68. </meta:property>
  69. </meta:properties>
  70. </cable>
  71. <cable id = "4" name = "priden2_0" fract_along_parent = "0.8">
  72. <meta:properties>
  73. <meta:property>
  74. <meta:tag>numberInternalDivisions</meta:tag> <!-- Discetization of model at time of export. Can be overridden by importing application-->
  75. <meta:value>10</meta:value>
  76. </meta:property>
  77. </meta:properties>
  78. </cable>
  79. <cable id = "2" name = "dend_1" fract_along_parent = "0.5"/>
  80. <cable id = "1" name = "dend_0"/>
  81. <cablegroup name="all"> <!-- Replacing subset name ModelViewParmSubset_0 with all, as it contains all sections -->
  82. <cable id = "0"/>
  83. <cable id = "3"/>
  84. <cable id = "4"/>
  85. <cable id = "2"/>
  86. <cable id = "1"/>
  87. </cablegroup>
  88. <cablegroup name="ModelViewParmSubset_1">
  89. <cable id = "0"/>
  90. </cablegroup>
  91. <cablegroup name="ModelViewParmSubset_2">
  92. <cable id = "2"/>
  93. <cable id = "1"/>
  94. </cablegroup>
  95. <cablegroup name="ModelViewParmSubset_3">
  96. <cable id = "0"/>
  97. <cable id = "3"/>
  98. <cable id = "4"/>
  99. </cablegroup>
  100. <cablegroup name="ModelViewParmSubset_4">
  101. <cable id = "3"/>
  102. <cable id = "4"/>
  103. <cable id = "2"/>
  104. <cable id = "1"/>
  105. </cablegroup>
  106. <cablegroup name="OneSecGrp_SectionRef_1"> <!-- Creating a group containing a single section: GC[0].somagc... -->
  107. <cable id = "0"/>
  108. </cablegroup>
  109. </cables>
  110. </cell>
  111. </cells>
  112. </neuroml>
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