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root/NeuroML2/examples/NML2_SimpleMorphology.nml

Revision 807, 3.2 KB (checked in by pgleeson, 3 years ago)

Restructuring of the example NML2 files. Named all LEMS/NML2 combined files to LEMS_NML2_*.xml.
Moved the example files from DemoVer?2.0/NMLVer2_Test/web/NeuroMLFiles/ to examples folder here, naming them NML2_*.nml.
Updated the Schema document slightly to require explicit naming of synapse elements, e.g. <expOneSynapse ...> instead of <synapse type="expOneSynapse" ..>

Line 
1<?xml version="1.0" encoding="UTF-8"?>
2
3<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5    xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  ../Schemas/NeuroML2/NeuroML_v2alpha.xsd"
6    id="NML2_SimpleMorphology">
7
8<!-- Example of a cell morphology in NeuroML 2 -->
9
10<!-- This is a "pure" NeuroML 2 file. It cannot yet be used a simulation by the LEMS
11     Interpreter as this does not yet support multicompartment cells -->   
12
13    <!-- Note: no <cells> element -->
14
15    <cell id="SimpleCell">
16
17        <morphology id="SimpleCell_Morphology">
18
19            <!-- Note: no <segments> -->
20
21            <segment id ="0" name="Soma">    <!-- name is optional-->
22                <!-- no parent => root segment -->
23                <proximal x="0" y="0" z="0" diameter="10"/>
24                <distal x="10" y="0" z="0" diameter="10"/>
25            </segment>
26
27            <segment id ="1" name="MainDendrite1" >
28                <parent segment="0"/>
29                <!-- Same proximal 3D point as parent but different diameter -->
30                <proximal x="10" y="0" z="0" diameter="3"/>
31                <distal x="20" y="0" z="0" diameter="3"/>
32            </segment>
33
34            <segment id ="2" name="MainDendrite2">
35                <parent segment="1"/>
36                <!-- no proximal => use distal (including diameter) of parent -->
37                <distal x="30" y="0" z="0" diameter="1"/>
38            </segment>
39
40            <segment id ="3" name="Spine" >
41                <!-- Electrically connected to point 0.5 along parent -->
42                <parent segment="2" fractionAlong="0.5"/>
43                <proximal x="25" y="0" z="0" diameter="0.2"/>
44                <distal x="25" y="1" z="0" diameter="0.2"/>
45            </segment>
46
47            <!-- segmentGroups follow -->
48
49            <segmentGroup id="soma_group" neuroLexId="sao1044911821">    <!-- Reserved/special name of a group -->
50                <member segment="0"/>
51            </segmentGroup>
52
53            <segmentGroup id="thick_dendrites">
54                <member segment="1"/>
55                <member segment="2"/>
56            </segmentGroup>
57
58
59            <!-- The NeuroLex reference points to the concept of a spine -->
60            <segmentGroup id="spines" neuroLexId="sao1145756102">
61                <member segment="3"/>
62            </segmentGroup>
63
64
65            <segmentGroup id="dendrite_group" neuroLexId="sao1211023249">     <!-- Reserved/special name of a group -->
66                <include segmentGroup="thick_dendrites"/>
67                <include segmentGroup="spines"/>
68                <!-- <exclude ...> could be present here -->
69            </segmentGroup>
70
71
72            <segmentGroup id="middle">            <!-- group defined between 2 segs -->
73                <path>
74                    <from segment="1"/>
75                    <to segment="2"/>
76                </path>
77            </segmentGroup>
78
79            <segmentGroup id="tip">              <!-- group defined between 2 segs -->
80                <subTree>
81                    <from segment="1"/>
82                </subTree>
83            </segmentGroup>
84
85            <!-- TODO: Allow wildcard on names?-->
86
87        </morphology>
88
89    </cell>
90
91</neuroml>
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