Transforming XML file: NeuroMLFiles/Examples/ChannelML/PyramidalCell.xml using XSL file: NeuroMLFiles/Schemata/v1.8.1/Level3/NeuroML_Level3_v1.8.1_HTML.xsl

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Converting the file: PyramidalCell.xml

NeuroML Level 3 file

General notesNeuroML Level 2 file generated by NEURON 6.1 ModelViewer Authors: Michael Hines, Sushil Kambampati and Padraig Gleeson, Yale University and UCL

Cell: soma

Namesoma
Description
As described in the NeuroML file
Cell: soma exported from NEURON ModelView
Total number of segments2037
Total number of cables79 with 0 soma cable(s), 0 dendritic cable(s) and 0 axonal cable(s)
Cable details soma (id:0), fraction along parent cable: 0, number of segments in cable: 27

dendrite_8_0 (id:78), fraction along parent cable: 0.5, number of segments in cable: 37

dendrite_7_0 (id:69), fraction along parent cable: 0.5, number of segments in cable: 5

dendrite_6_0 (id:60), fraction along parent cable: 0.5, number of segments in cable: 5

dendrite_5_0 (id:59), fraction along parent cable: 0.5, number of segments in cable: 86

dendrite_4_0 (id:46), fraction along parent cable: 0.5, number of segments in cable: 8

dendrite_3_0 (id:35), fraction along parent cable: 0.5, number of segments in cable: 11

dendrite_2_0 (id:32), fraction along parent cable: 0.5, number of segments in cable: 6

dendrite_1_0 (id:1), fraction along parent cable: 0.5, number of segments in cable: 3

dendrite_7_4 (id:73), number of segments in cable: 6

dendrite_7_1 (id:70), number of segments in cable: 15

dendrite_6_6 (id:66), number of segments in cable: 17

dendrite_6_1 (id:61), number of segments in cable: 17

dendrite_4_6 (id:52), number of segments in cable: 12

dendrite_4_1 (id:47), number of segments in cable: 23

dendrite_3_4 (id:39), number of segments in cable: 2

dendrite_3_1 (id:36), number of segments in cable: 33

dendrite_2_2 (id:34), number of segments in cable: 84

dendrite_2_1 (id:33), number of segments in cable: 68

dendrite_1_2 (id:3), number of segments in cable: 4

dendrite_1_1 (id:2), number of segments in cable: 63

dendrite_7_6 (id:75), number of segments in cable: 7

dendrite_7_5 (id:74), number of segments in cable: 61

dendrite_7_3 (id:72), number of segments in cable: 15

dendrite_7_2 (id:71), number of segments in cable: 12

dendrite_6_8 (id:68), number of segments in cable: 5

dendrite_6_7 (id:67), number of segments in cable: 4

dendrite_6_3 (id:63), number of segments in cable: 3

dendrite_6_2 (id:62), number of segments in cable: 13

dendrite_4_10 (id:56), number of segments in cable: 16

dendrite_4_7 (id:53), number of segments in cable: 11

dendrite_4_5 (id:51), number of segments in cable: 4

dendrite_4_2 (id:48), number of segments in cable: 13

dendrite_3_10 (id:45), number of segments in cable: 12

dendrite_3_5 (id:40), number of segments in cable: 6

dendrite_3_3 (id:38), number of segments in cable: 62

dendrite_3_2 (id:37), number of segments in cable: 24

dendrite_1_4 (id:5), number of segments in cable: 3

dendrite_1_3 (id:4), number of segments in cable: 22

dendrite_7_8 (id:77), number of segments in cable: 7

dendrite_7_7 (id:76), number of segments in cable: 7

dendrite_6_5 (id:65), number of segments in cable: 8

dendrite_6_4 (id:64), number of segments in cable: 20

dendrite_4_12 (id:58), number of segments in cable: 65

dendrite_4_11 (id:57), number of segments in cable: 79

dendrite_4_9 (id:55), number of segments in cable: 10

dendrite_4_8 (id:54), number of segments in cable: 18

dendrite_4_4 (id:50), number of segments in cable: 4

dendrite_4_3 (id:49), number of segments in cable: 4

dendrite_3_9 (id:44), number of segments in cable: 77

dendrite_3_6 (id:41), number of segments in cable: 10

dendrite_1_6 (id:7), number of segments in cable: 3

dendrite_1_5 (id:6), number of segments in cable: 8

dendrite_3_8 (id:43), number of segments in cable: 9

dendrite_3_7 (id:42), number of segments in cable: 6

dendrite_1_8 (id:9), number of segments in cable: 122

dendrite_1_7 (id:8), number of segments in cable: 61

dendrite_1_14 (id:15), number of segments in cable: 99

dendrite_1_9 (id:10), number of segments in cable: 115

dendrite_1_22 (id:23), number of segments in cable: 47

dendrite_1_15 (id:16), number of segments in cable: 50

dendrite_1_13 (id:14), number of segments in cable: 87

dendrite_1_10 (id:11), number of segments in cable: 10

dendrite_1_28 (id:29), number of segments in cable: 48

dendrite_1_23 (id:24), number of segments in cable: 52

dendrite_1_19 (id:20), number of segments in cable: 22

dendrite_1_16 (id:17), number of segments in cable: 31

dendrite_1_12 (id:13), number of segments in cable: 7

dendrite_1_11 (id:12), number of segments in cable: 8

dendrite_1_30 (id:31), number of segments in cable: 10

dendrite_1_29 (id:30), number of segments in cable: 39

dendrite_1_25 (id:26), number of segments in cable: 1

dendrite_1_24 (id:25), number of segments in cable: 6

dendrite_1_21 (id:22), number of segments in cable: 7

dendrite_1_20 (id:21), number of segments in cable: 5

dendrite_1_18 (id:19), number of segments in cable: 12

dendrite_1_17 (id:18), number of segments in cable: 16

dendrite_1_27 (id:28), number of segments in cable: 11

dendrite_1_26 (id:27), number of segments in cable: 11

Cable Groups
Groups of cables defined, for example, to allow easier specification of channel location
all contains 79 cables: soma (id:0) dendrite_8_0 (id:78) dendrite_7_0 (id:69) dendrite_6_0 (id:60) dendrite_5_0 (id:59) dendrite_4_0 (id:46) dendrite_3_0 (id:35) dendrite_2_0 (id:32) dendrite_1_0 (id:1) dendrite_7_4 (id:73) dendrite_7_1 (id:70) dendrite_6_6 (id:66) dendrite_6_1 (id:61) dendrite_4_6 (id:52) dendrite_4_1 (id:47) dendrite_3_4 (id:39) dendrite_3_1 (id:36) dendrite_2_2 (id:34) dendrite_2_1 (id:33) dendrite_1_2 (id:3) dendrite_1_1 (id:2) dendrite_7_6 (id:75) dendrite_7_5 (id:74) dendrite_7_3 (id:72) dendrite_7_2 (id:71) dendrite_6_8 (id:68) dendrite_6_7 (id:67) dendrite_6_3 (id:63) dendrite_6_2 (id:62) dendrite_4_10 (id:56) dendrite_4_7 (id:53) dendrite_4_5 (id:51) dendrite_4_2 (id:48) dendrite_3_10 (id:45) dendrite_3_5 (id:40) dendrite_3_3 (id:38) dendrite_3_2 (id:37) dendrite_1_4 (id:5) dendrite_1_3 (id:4) dendrite_7_8 (id:77) dendrite_7_7 (id:76) dendrite_6_5 (id:65) dendrite_6_4 (id:64) dendrite_4_12 (id:58) dendrite_4_11 (id:57) dendrite_4_9 (id:55) dendrite_4_8 (id:54) dendrite_4_4 (id:50) dendrite_4_3 (id:49) dendrite_3_9 (id:44) dendrite_3_6 (id:41) dendrite_1_6 (id:7) dendrite_1_5 (id:6) dendrite_3_8 (id:43) dendrite_3_7 (id:42) dendrite_1_8 (id:9) dendrite_1_7 (id:8) dendrite_1_14 (id:15) dendrite_1_9 (id:10) dendrite_1_22 (id:23) dendrite_1_15 (id:16) dendrite_1_13 (id:14) dendrite_1_10 (id:11) dendrite_1_28 (id:29) dendrite_1_23 (id:24) dendrite_1_19 (id:20) dendrite_1_16 (id:17) dendrite_1_12 (id:13) dendrite_1_11 (id:12) dendrite_1_30 (id:31) dendrite_1_29 (id:30) dendrite_1_25 (id:26) dendrite_1_24 (id:25) dendrite_1_21 (id:22) dendrite_1_20 (id:21) dendrite_1_18 (id:19) dendrite_1_17 (id:18) dendrite_1_27 (id:28) dendrite_1_26 (id:27)
ModelViewParmSubset_1 contains 77 cables: dendrite_8_0 (id:78) dendrite_7_0 (id:69) dendrite_6_0 (id:60) dendrite_4_0 (id:46) dendrite_3_0 (id:35) dendrite_2_0 (id:32) dendrite_1_0 (id:1) dendrite_7_4 (id:73) dendrite_7_1 (id:70) dendrite_6_6 (id:66) dendrite_6_1 (id:61) dendrite_4_6 (id:52) dendrite_4_1 (id:47) dendrite_3_4 (id:39) dendrite_3_1 (id:36) dendrite_2_2 (id:34) dendrite_2_1 (id:33) dendrite_1_2 (id:3) dendrite_1_1 (id:2) dendrite_7_6 (id:75) dendrite_7_5 (id:74) dendrite_7_3 (id:72) dendrite_7_2 (id:71) dendrite_6_8 (id:68) dendrite_6_7 (id:67) dendrite_6_3 (id:63) dendrite_6_2 (id:62) dendrite_4_10 (id:56) dendrite_4_7 (id:53) dendrite_4_5 (id:51) dendrite_4_2 (id:48) dendrite_3_10 (id:45) dendrite_3_5 (id:40) dendrite_3_3 (id:38) dendrite_3_2 (id:37) dendrite_1_4 (id:5) dendrite_1_3 (id:4) dendrite_7_8 (id:77) dendrite_7_7 (id:76) dendrite_6_5 (id:65) dendrite_6_4 (id:64) dendrite_4_12 (id:58) dendrite_4_11 (id:57) dendrite_4_9 (id:55) dendrite_4_8 (id:54) dendrite_4_4 (id:50) dendrite_4_3 (id:49) dendrite_3_9 (id:44) dendrite_3_6 (id:41) dendrite_1_6 (id:7) dendrite_1_5 (id:6) dendrite_3_8 (id:43) dendrite_3_7 (id:42) dendrite_1_8 (id:9) dendrite_1_7 (id:8) dendrite_1_14 (id:15) dendrite_1_9 (id:10) dendrite_1_22 (id:23) dendrite_1_15 (id:16) dendrite_1_13 (id:14) dendrite_1_10 (id:11) dendrite_1_28 (id:29) dendrite_1_23 (id:24) dendrite_1_19 (id:20) dendrite_1_16 (id:17) dendrite_1_12 (id:13) dendrite_1_11 (id:12) dendrite_1_30 (id:31) dendrite_1_29 (id:30) dendrite_1_25 (id:26) dendrite_1_24 (id:25) dendrite_1_21 (id:22) dendrite_1_20 (id:21) dendrite_1_18 (id:19) dendrite_1_17 (id:18) dendrite_1_27 (id:28) dendrite_1_26 (id:27)
ModelViewParmSubset_2 contains 2 cables: soma (id:0) dendrite_5_0 (id:59)

Biophysical properties of cell: soma

Unit system of biophysical entities
This can be either SI Units or Physiological Units
Physiological Units
Channel Mechanism: pas
An active membrane conductance
This is a Passive Conductance and so conductance density (gmax) and reversal potential (e) should be sufficient parameters to specify the mechanism fully.

Conductance density (gmax) of 0.1 mS cm-2 on: ModelViewParmSubset_1 

Reversal potential (e) of -65 mV on: ModelViewParmSubset_1 

Channel Mechanism: hh
An active membrane conductance

Parameter gnabar has value 0.12 on: ModelViewParmSubset_2 

Parameter gkbar has value 0.036 on: ModelViewParmSubset_2 

Parameter gl has value 0.0003 on: ModelViewParmSubset_2 

Parameter el has value -54.3 on: ModelViewParmSubset_2 

Specific Capacitance
This is the capacitance per unit area of the membrane

Specific Capacitance of 1 uf/cm2 on: all 

Specific Axial Resistance
This is the specific cytoplasmic resistance along a dendrite/axon

Specific Axial Resistance of 0.1 Kohm cm on: all 






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