| 1 | <?xml version="1.0" encoding="UTF-8"?> |
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| 2 | |
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| 3 | <xs:schema targetNamespace="http://www.neuroml.org/schema/neuroml2" |
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| 4 | xmlns="http://www.neuroml.org/schema/neuroml2" |
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| 5 | xmlns:xi="http://www.w3.org/2001/XInclude" |
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| 6 | xmlns:xs="http://www.w3.org/2001/XMLSchema" |
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| 7 | elementFormDefault="qualified" |
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| 8 | attributeFormDefault="unqualified"> |
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| 9 | |
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| 10 | |
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| 11 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 12 | <!-- Core elements --> |
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| 13 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 14 | |
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| 15 | <xs:simpleType name="NmlId"> |
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| 16 | <xs:annotation> |
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| 17 | <xs:documentation>An id attribute for elements which need to be identified uniquely (normally just within their parent element).</xs:documentation> |
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| 18 | </xs:annotation> |
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| 19 | |
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| 20 | <xs:restriction base="xs:string"> |
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| 21 | <xs:pattern value="[a-zA-Z0-9_]*"/> |
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| 22 | </xs:restriction> |
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| 23 | |
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| 24 | </xs:simpleType> |
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| 25 | |
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| 26 | <xs:simpleType name="Nml2Quantity"> |
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| 27 | <xs:annotation> |
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| 28 | <xs:documentation>A value for a physical quantity in NeuroML 2, e.g. 20, -60.0mV or 5nA</xs:documentation> |
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| 29 | </xs:annotation> |
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| 30 | |
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| 31 | <xs:restriction base="xs:string"> |
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| 32 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*([_a-zA-Z0-9])*"/> |
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| 33 | </xs:restriction> |
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| 34 | |
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| 35 | </xs:simpleType> |
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| 36 | |
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| 37 | <xs:simpleType name="Nml2Quantity_none"> |
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| 38 | |
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| 39 | <xs:restriction base="xs:string"> |
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| 40 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?"/> <!-- No units string --> |
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| 41 | </xs:restriction> |
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| 42 | |
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| 43 | </xs:simpleType> |
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| 44 | |
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| 45 | <xs:simpleType name="Nml2Quantity_voltage"> |
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| 46 | |
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| 47 | <xs:restriction base="xs:string"> |
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| 48 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(V|mV)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 49 | </xs:restriction> |
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| 50 | |
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| 51 | </xs:simpleType> |
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| 52 | |
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| 53 | <xs:simpleType name="Nml2Quantity_length"> |
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| 54 | |
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| 55 | <xs:restriction base="xs:string"> |
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| 56 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(m|cm|um)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 57 | </xs:restriction> |
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| 58 | |
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| 59 | </xs:simpleType> |
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| 60 | |
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| 61 | <xs:simpleType name="Nml2Quantity_conductance"> |
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| 62 | |
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| 63 | <xs:restriction base="xs:string"> |
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| 64 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(S|mS|uS|nS|pS)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 65 | </xs:restriction> |
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| 66 | |
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| 67 | </xs:simpleType> |
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| 68 | |
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| 69 | <xs:simpleType name="Nml2Quantity_conductanceDensity"> |
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| 70 | |
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| 71 | <xs:restriction base="xs:string"> |
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| 72 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(S_per_m2|mS_per_cm2)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 73 | </xs:restriction> |
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| 74 | |
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| 75 | </xs:simpleType> |
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| 76 | |
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| 77 | <xs:simpleType name="Nml2Quantity_time"> |
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| 78 | |
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| 79 | <xs:restriction base="xs:string"> |
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| 80 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(s|ms)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 81 | </xs:restriction> |
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| 82 | |
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| 83 | </xs:simpleType> |
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| 84 | |
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| 85 | <xs:simpleType name="Nml2Quantity_capacitance"> |
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| 86 | |
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| 87 | <xs:restriction base="xs:string"> |
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| 88 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(F|uF|nF|pF)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 89 | </xs:restriction> |
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| 90 | |
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| 91 | </xs:simpleType> |
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| 92 | |
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| 93 | <xs:simpleType name="Nml2Quantity_specificCapacitance"> |
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| 94 | |
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| 95 | <xs:restriction base="xs:string"> |
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| 96 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(F_per_m2|uF_per_cm2)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 97 | </xs:restriction> |
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| 98 | |
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| 99 | </xs:simpleType> |
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| 100 | |
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| 101 | <xs:simpleType name="Nml2Quantity_concentration"> |
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| 102 | |
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| 103 | <xs:restriction base="xs:string"> |
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| 104 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(mol_per_m3|mol_per_cm3|M|mM)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 105 | </xs:restriction> |
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| 106 | |
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| 107 | </xs:simpleType> |
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| 108 | |
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| 109 | <xs:simpleType name="Nml2Quantity_current"> |
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| 110 | |
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| 111 | <xs:restriction base="xs:string"> |
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| 112 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(A|uA|nA|pA)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 113 | </xs:restriction> |
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| 114 | |
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| 115 | </xs:simpleType> |
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| 116 | |
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| 117 | <xs:simpleType name="Nml2Quantity_temperature"> |
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| 118 | |
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| 119 | <xs:restriction base="xs:string"> |
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| 120 | <xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(degC)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml --> |
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| 121 | </xs:restriction> |
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| 122 | |
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| 123 | </xs:simpleType> |
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| 124 | |
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| 125 | |
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| 126 | <xs:simpleType name="MetaId"> |
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| 127 | <xs:annotation> |
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| 128 | <xs:documentation>An id string for pointing to an entry in an annotation element related to a MIRIAM resource. Based on metaid of SBML</xs:documentation> |
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| 129 | </xs:annotation> |
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| 130 | |
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| 131 | <xs:restriction base="xs:string"> |
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| 132 | <xs:pattern value="[a-zA-Z0-9_]*"/> |
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| 133 | </xs:restriction> |
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| 134 | |
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| 135 | </xs:simpleType> |
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| 136 | |
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| 137 | |
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| 138 | <xs:simpleType name="NeuroLexId"> |
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| 139 | <xs:annotation> |
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| 140 | <xs:documentation>An id string for pointing to an entry in the NeuroLex ontology. Use of this attribute is a shorthand for a full |
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| 141 | RDF based reference to the MIRIAM Resource urn:miriam:neurolex, with an bqbiol:is qualifier</xs:documentation> |
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| 142 | </xs:annotation> |
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| 143 | |
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| 144 | <xs:restriction base="xs:string"> |
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| 145 | <xs:pattern value="[a-zA-Z0-9_]*"/> |
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| 146 | </xs:restriction> |
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| 147 | |
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| 148 | </xs:simpleType> |
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| 149 | |
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| 150 | |
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| 151 | <xs:simpleType name="SegmentId"> |
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| 152 | <xs:annotation> |
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| 153 | <xs:documentation>An id attribute for segments: integer >=0 only!</xs:documentation> |
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| 154 | </xs:annotation> |
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| 155 | |
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| 156 | <xs:restriction base="xs:nonNegativeInteger"> |
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| 157 | </xs:restriction> |
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| 158 | |
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| 159 | </xs:simpleType> |
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| 160 | |
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| 161 | <!--NOTE: Base and Standalone definitions moved to end of file, as some XML language binding |
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| 162 | generators, e.g. generateDS.py, require superclasses to be defined after the subclasses... --> |
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| 163 | |
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| 164 | |
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| 165 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 166 | <!-- Metadata elements --> |
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| 167 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 168 | |
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| 169 | <xs:simpleType name="Notes"> |
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| 170 | <xs:annotation> |
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| 171 | <xs:documentation>Textual human readable notes related to the element in question. It's useful to put these into |
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| 172 | the NeuroML files instead of XML comments, as the notes can be extracted and repeated in the files to which the NeuroML is mapped.</xs:documentation> |
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| 173 | </xs:annotation> |
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| 174 | <xs:restriction base="xs:string"/> |
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| 175 | </xs:simpleType> |
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| 176 | |
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| 177 | |
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| 178 | <xs:complexType name="Annotation"> |
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| 179 | <xs:annotation> |
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| 180 | <xs:documentation>Placeholder for MIRIAM related metadata, among others.</xs:documentation> |
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| 181 | </xs:annotation> |
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| 182 | <xs:sequence> |
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| 183 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
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| 184 | </xs:sequence> |
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| 185 | </xs:complexType> |
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| 186 | |
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| 187 | |
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| 188 | |
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| 189 | <xs:simpleType name="ZeroToOne"> |
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| 190 | <xs:annotation> |
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| 191 | <xs:documentation>Double restricted to between 1 and 0</xs:documentation> |
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| 192 | </xs:annotation> |
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| 193 | <xs:restriction base="xs:double"> |
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| 194 | <xs:minInclusive value="0"/> |
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| 195 | <xs:maxInclusive value="1"/> |
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| 196 | </xs:restriction> |
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| 197 | </xs:simpleType> |
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| 198 | |
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| 199 | |
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| 200 | |
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| 201 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 202 | <!-- Main NeuroML element --> |
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| 203 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 204 | |
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| 205 | <xs:element name="neuroml" type="neuroml"> |
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| 206 | <xs:annotation> |
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| 207 | <xs:documentation>The root NeuroML element.</xs:documentation> |
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| 208 | </xs:annotation> |
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| 209 | </xs:element> |
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| 210 | |
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| 211 | <xs:complexType name="neuroml"> <!-- Making the complexType definition of the root element lowercase, not to confuse language binding generators... --> |
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| 212 | |
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| 213 | <xs:complexContent> |
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| 214 | |
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| 215 | <xs:extension base="Standalone"> |
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| 216 | |
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| 217 | <xs:sequence> |
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| 218 | |
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| 219 | <xs:element name="include" type="includeType" minOccurs="0" maxOccurs="unbounded"/> |
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| 220 | |
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| 221 | <xs:element name="extracellularProperties" type="ExtracellularProperties" minOccurs="0" maxOccurs="unbounded"/> |
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| 222 | <xs:element name="intracellularProperties" type="IntracellularProperties" minOccurs="0" maxOccurs="unbounded"/> |
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| 223 | |
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| 224 | <xs:element name="morphology" type="Morphology" minOccurs="0" maxOccurs="unbounded"/> |
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| 225 | |
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| 226 | <xs:element name="ionChannel" type="IonChannel" minOccurs="0" maxOccurs="unbounded"/> |
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| 227 | |
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| 228 | <xs:group ref="synapseTypes"/> |
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| 229 | |
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| 230 | <xs:element name="biophysicalProperties" type="BiophysicalProperties" minOccurs="0" maxOccurs="unbounded"/> |
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| 231 | |
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| 232 | <xs:group ref="cellTypes"/> |
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| 233 | |
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| 234 | <xs:element name="pulseGenerator" type="PulseGenerator" minOccurs="0" maxOccurs="unbounded"/> |
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| 235 | |
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| 236 | <xs:element name="network" type="Network" minOccurs="0" maxOccurs="unbounded"/> |
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| 237 | |
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| 238 | </xs:sequence> |
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| 239 | |
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| 240 | </xs:extension> |
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| 241 | |
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| 242 | </xs:complexContent> |
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| 243 | |
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| 244 | </xs:complexType> |
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| 245 | |
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| 246 | <!-- A small subset of XLInclude from: http://www.w3.org/2001/XInclude.xsd |
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| 247 | Will be sufficient for now... --> |
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| 248 | <xs:complexType name="includeType" mixed="true"> |
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| 249 | <xs:attribute name="href" use="optional" type="xs:anyURI"/> |
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| 250 | </xs:complexType> |
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| 251 | |
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| 252 | <xs:group name="cellTypes"> |
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| 253 | <xs:annotation> |
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| 254 | <xs:documentation>Various types of cells which are defined in NeuroML 2. This list will be expanded...</xs:documentation> |
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| 255 | </xs:annotation> |
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| 256 | <xs:sequence> |
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| 257 | <xs:element name="cell" type="Cell" minOccurs="0" maxOccurs="unbounded"/> |
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| 258 | <xs:element name="abstractCell" type="AbstractCell" minOccurs="0" maxOccurs="unbounded"/> |
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| 259 | <xs:element name="iafTauCell" type="IaFTauCell" minOccurs="0" maxOccurs="unbounded"/> |
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| 260 | <xs:element name="iafCell" type="IaFCell" minOccurs="0" maxOccurs="unbounded"/> |
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| 261 | <xs:element name="izhikevichCell" type="IzhikevichCell" minOccurs="0" maxOccurs="unbounded"/> |
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| 262 | <xs:element name="adExIaFCell" type="AdExIaFCell" minOccurs="0" maxOccurs="unbounded"/> |
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| 263 | </xs:sequence> |
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| 264 | </xs:group> |
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| 265 | |
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| 266 | |
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| 267 | |
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| 268 | <xs:group name="synapseTypes"> |
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| 269 | <xs:annotation> |
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| 270 | <xs:documentation>Various types of synapse which are defined in NeuroML 2. This list will be expanded...</xs:documentation> |
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| 271 | </xs:annotation> |
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| 272 | <xs:sequence> |
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| 273 | <xs:element name="expOneSynapse" type="ExpOneSynapse" minOccurs="0" maxOccurs="unbounded"/> |
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| 274 | <xs:element name="expTwoSynapse" type="ExpTwoSynapse" minOccurs="0" maxOccurs="unbounded"/> |
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| 275 | <xs:element name="nmdaSynapse" type="NmdaSynapse" minOccurs="0" maxOccurs="unbounded"/> |
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| 276 | <xs:element name="stpSynapse" type="StpSynapse" minOccurs="0" maxOccurs="unbounded"/> |
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| 277 | </xs:sequence> |
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| 278 | </xs:group> |
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| 279 | |
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| 280 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 281 | <!-- IonChannel element --> |
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| 282 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 283 | |
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| 284 | <xs:complexType name="IonChannel"> |
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| 285 | |
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| 286 | <xs:complexContent> |
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| 287 | <xs:extension base="Standalone"> |
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| 288 | <xs:choice> |
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| 289 | <xs:element name="gate" type="Gate" minOccurs="0" maxOccurs="unbounded"/> |
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| 290 | <xs:element name="gateHH" type="Gate" minOccurs="0" maxOccurs="unbounded"/> |
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| 291 | </xs:choice> |
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| 292 | |
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| 293 | <xs:attribute name="species" type="NmlId" use="optional"/> |
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| 294 | |
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| 295 | <xs:attribute name="type" type="channelTypes" use="optional"/> |
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| 296 | |
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| 297 | <xs:attribute name="conductance" type="Nml2Quantity_conductance" use="optional"/> |
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| 298 | |
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| 299 | </xs:extension> |
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| 300 | </xs:complexContent> |
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| 301 | </xs:complexType> |
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| 302 | |
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| 303 | <xs:simpleType name="channelTypes"> |
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| 304 | <xs:restriction base="xs:string"> |
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| 305 | <xs:enumeration value="ionChannelPassive"/> |
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| 306 | <xs:enumeration value="ionChannelHH"/> |
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| 307 | <xs:enumeration value="ionChannelKS"/> |
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| 308 | </xs:restriction> |
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| 309 | </xs:simpleType> |
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| 310 | |
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| 311 | <xs:simpleType name="gateTypes"> |
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| 312 | <xs:restriction base="xs:string"> |
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| 313 | <xs:enumeration value="gateHH"/> |
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| 314 | <xs:enumeration value="gateHHQ10"/> |
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| 315 | <xs:enumeration value="gateKS"/> |
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| 316 | </xs:restriction> |
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| 317 | </xs:simpleType> |
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| 318 | |
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| 319 | |
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| 320 | |
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| 321 | <xs:complexType name="Gate"> |
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| 322 | <xs:complexContent> |
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| 323 | <xs:extension base="Base"> |
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| 324 | <xs:sequence> |
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| 325 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
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| 326 | </xs:sequence> |
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| 327 | <xs:attribute name="instances" type="xs:integer" use="optional" default="1"/> |
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| 328 | <xs:attribute name="type" type="gateTypes" use="optional"/> |
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| 329 | </xs:extension> |
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| 330 | </xs:complexContent> |
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| 331 | </xs:complexType> |
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| 332 | |
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| 333 | |
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| 334 | |
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| 335 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 336 | <!-- Synapse types --> |
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| 337 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
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| 338 | |
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| 339 | <xs:complexType name="ConductanceBasedSynapse"> |
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| 340 | |
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| 341 | <xs:complexContent> |
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| 342 | <xs:extension base="Standalone"> |
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| 343 | |
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| 344 | <xs:attribute name="gbase" type="Nml2Quantity_conductance" use="required"/> |
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| 345 | <xs:attribute name="erev" type="Nml2Quantity_voltage" use="required"/> |
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| 346 | |
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| 347 | </xs:extension> |
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| 348 | </xs:complexContent> |
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| 349 | </xs:complexType> |
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| 350 | |
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| 351 | |
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| 352 | <xs:complexType name="ExpOneSynapse"> |
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| 353 | |
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| 354 | <xs:complexContent> |
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| 355 | <xs:extension base="ConductanceBasedSynapse"> |
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| 356 | |
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| 357 | <xs:attribute name="tauDecay" type="Nml2Quantity_time" use="required"/> |
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| 358 | |
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| 359 | </xs:extension> |
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| 360 | </xs:complexContent> |
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| 361 | </xs:complexType> |
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| 362 | |
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| 363 | |
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| 364 | <xs:complexType name="ExpTwoSynapse"> |
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| 365 | |
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| 366 | <xs:complexContent> |
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| 367 | <xs:extension base="ConductanceBasedSynapse"> |
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| 368 | |
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| 369 | <xs:attribute name="tauDecay" type="Nml2Quantity_time" use="required"/> |
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| 370 | <xs:attribute name="tauRise" type="Nml2Quantity_time" use="required"/> |
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| 371 | |
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| 372 | </xs:extension> |
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| 373 | </xs:complexContent> |
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| 374 | </xs:complexType> |
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| 375 | |
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| 376 | |
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| 377 | <xs:complexType name="NmdaSynapse"> |
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| 378 | |
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| 379 | <xs:complexContent> |
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| 380 | <xs:extension base="ExpTwoSynapse"> |
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| 381 | <xs:sequence> |
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| 382 | <xs:element name="voltageConcDepBlock" type="VoltageConcDepBlock"/> |
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| 383 | </xs:sequence> |
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| 384 | |
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| 385 | </xs:extension> |
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| 386 | </xs:complexContent> |
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| 387 | </xs:complexType> |
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| 388 | |
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| 389 | <xs:complexType name="StpSynapse"> |
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| 390 | |
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| 391 | <xs:complexContent> |
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| 392 | <xs:extension base="ExpTwoSynapse"> |
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| 393 | <xs:sequence> |
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| 394 | <xs:element name="stpMechanism" type="StpMechanism"/> |
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| 395 | </xs:sequence> |
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| 396 | |
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| 397 | </xs:extension> |
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| 398 | </xs:complexContent> |
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| 399 | </xs:complexType> |
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| 400 | |
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| 401 | |
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| 402 | |
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| 403 | <xs:complexType name="VoltageConcDepBlock"> |
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| 404 | <xs:attribute name="type" type="xs:string" fixed="voltageConcDepBlock"/> |
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| 405 | <xs:attribute name="species" type="NmlId" use="required"/> |
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| 406 | <xs:attribute name="blockConcentration" type="Nml2Quantity_concentration" use="required"/> |
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| 407 | <xs:attribute name="scalingConc" type="Nml2Quantity_concentration" use="required"/> |
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| 408 | <xs:attribute name="scalingVolt" type="Nml2Quantity_voltage" use="required"/> |
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| 409 | </xs:complexType> |
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| 410 | |
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| 411 | <xs:complexType name="StpMechanism"> |
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| 412 | <xs:attribute name="initReleaseProb" type="ZeroToOne" use="required"/> |
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| 413 | <xs:attribute name="tauFac" type="Nml2Quantity_time" use="required"/> |
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| 414 | <xs:attribute name="tauRec" type="Nml2Quantity_time" use="required"/> |
|---|
| 415 | </xs:complexType> |
|---|
| 416 | |
|---|
| 417 | |
|---|
| 418 | |
|---|
| 419 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 420 | <!-- Cell element --> |
|---|
| 421 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 422 | |
|---|
| 423 | <xs:complexType name="AbstractCell"> |
|---|
| 424 | |
|---|
| 425 | <xs:complexContent> |
|---|
| 426 | <xs:extension base="Standalone"> |
|---|
| 427 | |
|---|
| 428 | </xs:extension> |
|---|
| 429 | </xs:complexContent> |
|---|
| 430 | </xs:complexType> |
|---|
| 431 | |
|---|
| 432 | <xs:complexType name="IaFTauCell"> |
|---|
| 433 | <xs:complexContent> |
|---|
| 434 | <xs:extension base="AbstractCell"> |
|---|
| 435 | <xs:attribute name="leakReversal" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 436 | <xs:attribute name="thresh" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 437 | <xs:attribute name="reset" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 438 | <xs:attribute name="tau" type="Nml2Quantity_time" use="required"/> |
|---|
| 439 | </xs:extension> |
|---|
| 440 | </xs:complexContent> |
|---|
| 441 | </xs:complexType> |
|---|
| 442 | |
|---|
| 443 | <xs:complexType name="IaFCell"> |
|---|
| 444 | <xs:complexContent> |
|---|
| 445 | <xs:extension base="AbstractCell"> |
|---|
| 446 | <xs:attribute name="leakReversal" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 447 | <xs:attribute name="thresh" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 448 | <xs:attribute name="reset" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 449 | <xs:attribute name="C" type="Nml2Quantity_capacitance" use="required"/> |
|---|
| 450 | <xs:attribute name="leakConductance" type="Nml2Quantity_conductance" use="required"/> |
|---|
| 451 | </xs:extension> |
|---|
| 452 | </xs:complexContent> |
|---|
| 453 | </xs:complexType> |
|---|
| 454 | |
|---|
| 455 | <xs:complexType name="IzhikevichCell"> |
|---|
| 456 | <xs:complexContent> |
|---|
| 457 | <xs:extension base="AbstractCell"> |
|---|
| 458 | <xs:attribute name="v0" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 459 | <xs:attribute name="thresh" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 460 | <xs:attribute name="a" type="Nml2Quantity_none" use="required"/> |
|---|
| 461 | <xs:attribute name="b" type="Nml2Quantity_none" use="required"/> |
|---|
| 462 | <xs:attribute name="c" type="Nml2Quantity_none" use="required"/> |
|---|
| 463 | <xs:attribute name="d" type="Nml2Quantity_none" use="required"/> |
|---|
| 464 | <xs:attribute name="Iamp" type="Nml2Quantity_none" use="required"/> |
|---|
| 465 | <xs:attribute name="Idel" type="Nml2Quantity_time" use="required"/> |
|---|
| 466 | <xs:attribute name="Idur" type="Nml2Quantity_time" use="required"/> |
|---|
| 467 | </xs:extension> |
|---|
| 468 | </xs:complexContent> |
|---|
| 469 | </xs:complexType> |
|---|
| 470 | |
|---|
| 471 | <xs:complexType name="AdExIaFCell"> |
|---|
| 472 | <xs:complexContent> |
|---|
| 473 | <xs:extension base="AbstractCell"> |
|---|
| 474 | <xs:attribute name="C" type="Nml2Quantity_capacitance" use="required"/> |
|---|
| 475 | <xs:attribute name="gL" type="Nml2Quantity_conductance" use="required"/> |
|---|
| 476 | <xs:attribute name="EL" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 477 | <xs:attribute name="reset" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 478 | <xs:attribute name="VT" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 479 | <xs:attribute name="thresh" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 480 | <xs:attribute name="delT" type="Nml2Quantity_voltage" use="required"/> |
|---|
| 481 | <xs:attribute name="tauw" type="Nml2Quantity_time" use="required"/> |
|---|
| 482 | <xs:attribute name="a" type="Nml2Quantity_conductance" use="required"/> |
|---|
| 483 | <xs:attribute name="b" type="Nml2Quantity_current" use="required"/> |
|---|
| 484 | <xs:attribute name="Iamp" type="Nml2Quantity_current" use="required"/> |
|---|
| 485 | <xs:attribute name="Idel" type="Nml2Quantity_time" use="required"/> |
|---|
| 486 | <xs:attribute name="Idur" type="Nml2Quantity_time" use="required"/> |
|---|
| 487 | </xs:extension> |
|---|
| 488 | </xs:complexContent> |
|---|
| 489 | </xs:complexType> |
|---|
| 490 | |
|---|
| 491 | |
|---|
| 492 | <xs:complexType name="Cell"> |
|---|
| 493 | |
|---|
| 494 | <xs:complexContent> |
|---|
| 495 | <xs:extension base="AbstractCell"> |
|---|
| 496 | |
|---|
| 497 | <xs:sequence> |
|---|
| 498 | <xs:element name="morphology" type="Morphology" minOccurs="0"/> |
|---|
| 499 | <xs:element name="biophysicalProperties" type="BiophysicalProperties" minOccurs="0"/> |
|---|
| 500 | </xs:sequence> |
|---|
| 501 | |
|---|
| 502 | |
|---|
| 503 | <xs:attribute name="morphology" type="NmlId" use="optional" default="1"> |
|---|
| 504 | <xs:annotation> |
|---|
| 505 | <xs:documentation>Should only be used if morphology element is outside the cell. |
|---|
| 506 | This points to the id of the morphology</xs:documentation> |
|---|
| 507 | </xs:annotation> |
|---|
| 508 | </xs:attribute> |
|---|
| 509 | |
|---|
| 510 | <xs:attribute name="biophysicalProperties" type="NmlId" use="optional" default="1"> |
|---|
| 511 | <xs:annotation> |
|---|
| 512 | <xs:documentation>Should only be used if biophysicalProperties element is outside the cell. |
|---|
| 513 | This points to the id of the biophysicalProperties</xs:documentation> |
|---|
| 514 | </xs:annotation> |
|---|
| 515 | </xs:attribute> |
|---|
| 516 | |
|---|
| 517 | |
|---|
| 518 | </xs:extension> |
|---|
| 519 | </xs:complexContent> |
|---|
| 520 | </xs:complexType> |
|---|
| 521 | |
|---|
| 522 | |
|---|
| 523 | <xs:complexType name="Morphology"> |
|---|
| 524 | <xs:annotation> |
|---|
| 525 | <xs:documentation>Standalone element which is usually inside a single cell, but could be outside and |
|---|
| 526 | referenced by id.</xs:documentation> |
|---|
| 527 | </xs:annotation> |
|---|
| 528 | |
|---|
| 529 | <xs:complexContent> |
|---|
| 530 | |
|---|
| 531 | <xs:extension base="Standalone"> |
|---|
| 532 | |
|---|
| 533 | <xs:sequence> |
|---|
| 534 | <xs:element name="segment" type="Segment" maxOccurs="unbounded"/> |
|---|
| 535 | <xs:element name="segmentGroup" type="SegmentGroup" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 536 | </xs:sequence> |
|---|
| 537 | |
|---|
| 538 | </xs:extension> |
|---|
| 539 | </xs:complexContent> |
|---|
| 540 | </xs:complexType> |
|---|
| 541 | |
|---|
| 542 | <xs:complexType name="Segment"> |
|---|
| 543 | <xs:complexContent> |
|---|
| 544 | <xs:extension base="Base"> |
|---|
| 545 | |
|---|
| 546 | <xs:sequence> |
|---|
| 547 | <xs:element name="parent" type="SegmentParent" minOccurs="0"/> |
|---|
| 548 | <xs:element name="proximal" type="Point3DWithDiam" minOccurs="0"/> |
|---|
| 549 | <xs:element name="distal" type="Point3DWithDiam" minOccurs="1"/> |
|---|
| 550 | </xs:sequence> |
|---|
| 551 | |
|---|
| 552 | <!-- TODO: Do we want to do away with numerical ids and just use unique strings/names in id attribute?? --> |
|---|
| 553 | <!--<xs:attribute name="id" type="SegmentId" use="required"/>--> |
|---|
| 554 | <xs:attribute name="name" type="xs:string" use="required"/> |
|---|
| 555 | |
|---|
| 556 | </xs:extension> |
|---|
| 557 | </xs:complexContent> |
|---|
| 558 | |
|---|
| 559 | </xs:complexType> |
|---|
| 560 | |
|---|
| 561 | <xs:complexType name="SegmentParent"> |
|---|
| 562 | <xs:attribute name="segment" type="SegmentId" use="required"/> |
|---|
| 563 | <xs:attribute name="fractionAlong" type="ZeroToOne" use="optional" default="1"/> |
|---|
| 564 | </xs:complexType> |
|---|
| 565 | |
|---|
| 566 | |
|---|
| 567 | <xs:complexType name="Point3DWithDiam"> |
|---|
| 568 | <xs:annotation> |
|---|
| 569 | <xs:documentation>A 3D point with diameter.</xs:documentation> |
|---|
| 570 | </xs:annotation> |
|---|
| 571 | <xs:attribute name="x" type="xs:double" use="required"/> |
|---|
| 572 | <xs:attribute name="y" type="xs:double" use="required"/> |
|---|
| 573 | <xs:attribute name="z" type="xs:double" use="required"/> |
|---|
| 574 | <xs:attribute name="diameter" type="xs:double" use="required"/> |
|---|
| 575 | </xs:complexType> |
|---|
| 576 | |
|---|
| 577 | |
|---|
| 578 | <xs:complexType name="SegmentGroup"> |
|---|
| 579 | <xs:complexContent> |
|---|
| 580 | <xs:extension base="Base"> |
|---|
| 581 | |
|---|
| 582 | <xs:sequence> |
|---|
| 583 | <xs:element name="member" type="Member" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 584 | <xs:element name="include" type="Include" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 585 | <xs:element name="path" type="Path" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 586 | <xs:element name="subTree" type="SubTree" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 587 | <xs:element name="inhomogeneousParam" type="InhomogeneousParam" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 588 | </xs:sequence> |
|---|
| 589 | |
|---|
| 590 | </xs:extension> |
|---|
| 591 | </xs:complexContent> |
|---|
| 592 | </xs:complexType> |
|---|
| 593 | |
|---|
| 594 | |
|---|
| 595 | <xs:complexType name="InhomogeneousParam"> |
|---|
| 596 | <xs:complexContent> |
|---|
| 597 | <xs:extension base="Base"> |
|---|
| 598 | <xs:sequence> |
|---|
| 599 | <xs:element name="proximal" type="ProximalDetails" minOccurs="0"/> |
|---|
| 600 | <xs:element name="distal" type="DistalDetails" minOccurs="0"/> |
|---|
| 601 | </xs:sequence> |
|---|
| 602 | <xs:attribute name="variable" type="xs:string" use="required"/> |
|---|
| 603 | <xs:attribute name="metric" type="Metric" use="required"/> |
|---|
| 604 | </xs:extension> |
|---|
| 605 | </xs:complexContent> |
|---|
| 606 | </xs:complexType> |
|---|
| 607 | |
|---|
| 608 | |
|---|
| 609 | <xs:simpleType name="Metric"> |
|---|
| 610 | <xs:annotation> |
|---|
| 611 | <xs:documentation>Allowed metrics for InhomogeneousParam</xs:documentation> |
|---|
| 612 | </xs:annotation> |
|---|
| 613 | <xs:restriction base="xs:string"> |
|---|
| 614 | <xs:enumeration value="Path Length from root"/> |
|---|
| 615 | </xs:restriction> |
|---|
| 616 | </xs:simpleType> |
|---|
| 617 | |
|---|
| 618 | |
|---|
| 619 | <xs:complexType name="ProximalDetails"> |
|---|
| 620 | <xs:attribute name="translationStart" type="xs:double" use="required"/> |
|---|
| 621 | </xs:complexType> |
|---|
| 622 | |
|---|
| 623 | <xs:complexType name="DistalDetails"> |
|---|
| 624 | <xs:attribute name="normalizationEnd" type="xs:double" use="required"/> |
|---|
| 625 | </xs:complexType> |
|---|
| 626 | |
|---|
| 627 | <xs:complexType name="Member"> |
|---|
| 628 | <xs:attribute name="segment" type="SegmentId" use="required"/> |
|---|
| 629 | </xs:complexType> |
|---|
| 630 | |
|---|
| 631 | <xs:complexType name="Include"> |
|---|
| 632 | <xs:attribute name="segmentGroup" type="NmlId" use="required"/> |
|---|
| 633 | </xs:complexType> |
|---|
| 634 | |
|---|
| 635 | <xs:complexType name="Path"> |
|---|
| 636 | <xs:sequence> |
|---|
| 637 | <xs:element name="from" type="SegmentEndPoint" minOccurs="0"/> |
|---|
| 638 | <xs:element name="to" type="SegmentEndPoint" minOccurs="0"/> |
|---|
| 639 | </xs:sequence> |
|---|
| 640 | </xs:complexType> |
|---|
| 641 | |
|---|
| 642 | <xs:complexType name="SubTree"> |
|---|
| 643 | <xs:choice> |
|---|
| 644 | <xs:element name="from" type="SegmentEndPoint" minOccurs="0"/> |
|---|
| 645 | <xs:element name="to" type="SegmentEndPoint" minOccurs="0"/> |
|---|
| 646 | </xs:choice> |
|---|
| 647 | </xs:complexType> |
|---|
| 648 | |
|---|
| 649 | <xs:complexType name="SegmentEndPoint"> |
|---|
| 650 | <xs:attribute name="segment" type="SegmentId" use="required"/> |
|---|
| 651 | </xs:complexType> |
|---|
| 652 | |
|---|
| 653 | |
|---|
| 654 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 655 | <!-- Biophysical properties --> |
|---|
| 656 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 657 | |
|---|
| 658 | |
|---|
| 659 | <xs:complexType name="BiophysicalProperties"> |
|---|
| 660 | <xs:annotation> |
|---|
| 661 | <xs:documentation>Standalone element which is usually inside a single cell, but could be outside and |
|---|
| 662 | referenced by id.</xs:documentation> |
|---|
| 663 | </xs:annotation> |
|---|
| 664 | <xs:complexContent> |
|---|
| 665 | <xs:extension base="Standalone"> |
|---|
| 666 | |
|---|
| 667 | <xs:sequence> |
|---|
| 668 | <xs:element name="membraneProperties" type="MembraneProperties"/> |
|---|
| 669 | <xs:element name="intracellularProperties" type="IntracellularProperties" minOccurs="0"/> |
|---|
| 670 | <xs:element name="extracellularProperties" type="ExtracellularProperties" minOccurs="0"/> |
|---|
| 671 | </xs:sequence> |
|---|
| 672 | |
|---|
| 673 | |
|---|
| 674 | </xs:extension> |
|---|
| 675 | </xs:complexContent> |
|---|
| 676 | </xs:complexType> |
|---|
| 677 | |
|---|
| 678 | |
|---|
| 679 | <xs:complexType name="MembraneProperties"> |
|---|
| 680 | |
|---|
| 681 | <xs:sequence> |
|---|
| 682 | <xs:element name="channelPopulation" type="ChannelPopulation" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 683 | <xs:element name="channelDensity" type="ChannelDensity" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 684 | |
|---|
| 685 | <xs:element name="spikeThresh" type="ValueAcrossSegOrSegGroup" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 686 | <xs:element name="specificCapacitance" type="ValueAcrossSegOrSegGroup" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 687 | |
|---|
| 688 | <xs:element name="initMembPotential" type="ValueAcrossSegOrSegGroup" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 689 | |
|---|
| 690 | <xs:element name="reversalPotential" type="ReversalPotential" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 691 | |
|---|
| 692 | </xs:sequence> |
|---|
| 693 | |
|---|
| 694 | </xs:complexType> |
|---|
| 695 | |
|---|
| 696 | <xs:complexType name="ChannelPopulation"> |
|---|
| 697 | |
|---|
| 698 | <xs:complexContent> |
|---|
| 699 | <xs:extension base="Base"> |
|---|
| 700 | |
|---|
| 701 | <xs:sequence> |
|---|
| 702 | <xs:element name="variableParameter" type="VariableParameter" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 703 | </xs:sequence> |
|---|
| 704 | |
|---|
| 705 | <xs:attribute name="ionChannel" type="NmlId" use="required"/> |
|---|
| 706 | <xs:attribute name="number" type="xs:nonNegativeInteger" use="required"/> |
|---|
| 707 | |
|---|
| 708 | <xs:attribute name="erev" type="Nml2Quantity_voltage" use="optional"/> |
|---|
| 709 | |
|---|
| 710 | <!-- Note: only one of the following should be used!! --> |
|---|
| 711 | <xs:attribute name="segmentGroup" type="NmlId" use="optional" default="all"/> |
|---|
| 712 | <xs:attribute name="segment" type="NmlId" use="optional"/> |
|---|
| 713 | |
|---|
| 714 | </xs:extension> |
|---|
| 715 | </xs:complexContent> |
|---|
| 716 | |
|---|
| 717 | </xs:complexType> |
|---|
| 718 | |
|---|
| 719 | <xs:complexType name="ChannelDensity"> |
|---|
| 720 | |
|---|
| 721 | <xs:complexContent> |
|---|
| 722 | <xs:extension base="Base"> |
|---|
| 723 | |
|---|
| 724 | <xs:sequence> |
|---|
| 725 | <xs:element name="variableParameter" type="VariableParameter" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 726 | </xs:sequence> |
|---|
| 727 | |
|---|
| 728 | <xs:attribute name="ionChannel" type="NmlId" use="required"/> |
|---|
| 729 | <xs:attribute name="condDensity" type="Nml2Quantity_conductanceDensity" use="optional"/> |
|---|
| 730 | |
|---|
| 731 | <xs:attribute name="erev" type="Nml2Quantity_voltage" use="optional"/> |
|---|
| 732 | |
|---|
| 733 | <!-- Note: only one of the following should be used!! --> |
|---|
| 734 | <xs:attribute name="segmentGroup" type="NmlId" use="optional" default="all"/> |
|---|
| 735 | |
|---|
| 736 | <xs:attribute name="segment" type="NmlId" use="optional"/> |
|---|
| 737 | |
|---|
| 738 | <xs:attribute name="ion" type="NmlId" use="optional"> |
|---|
| 739 | <xs:annotation> |
|---|
| 740 | <xs:documentation>Specifying the ion here again is redundant, this will be set in ionChannel. It is added here |
|---|
| 741 | TEMPORARILY as selecting all ca or na conducting channel populations/densities in a cell would be difficult otherwise. |
|---|
| 742 | It should be removed in the longer term, due to possible inconsistencies in this value and that in the ionChannel |
|---|
| 743 | element. TODO: remove.</xs:documentation> |
|---|
| 744 | </xs:annotation> |
|---|
| 745 | </xs:attribute> |
|---|
| 746 | |
|---|
| 747 | </xs:extension> |
|---|
| 748 | </xs:complexContent> |
|---|
| 749 | |
|---|
| 750 | </xs:complexType> |
|---|
| 751 | |
|---|
| 752 | <xs:complexType name="ValueAcrossSegOrSegGroup"> |
|---|
| 753 | |
|---|
| 754 | <xs:attribute name="value" type="Nml2Quantity" use="optional"/> |
|---|
| 755 | |
|---|
| 756 | <!-- Note: only one of the following should be used!! --> |
|---|
| 757 | <xs:attribute name="segmentGroup" type="NmlId" use="optional" default="all"/> |
|---|
| 758 | <xs:attribute name="segment" type="NmlId" use="optional"/> |
|---|
| 759 | |
|---|
| 760 | </xs:complexType> |
|---|
| 761 | |
|---|
| 762 | |
|---|
| 763 | <xs:complexType name="VariableParameter"> |
|---|
| 764 | |
|---|
| 765 | <xs:sequence> |
|---|
| 766 | <xs:element name="inhomogeneousValue" type="InhomogeneousValue" minOccurs="0"/> |
|---|
| 767 | </xs:sequence> |
|---|
| 768 | <xs:attribute name="parameter" type="xs:string" use="required"/> |
|---|
| 769 | <xs:attribute name="segmentGroup" type="xs:string" use="required"/> |
|---|
| 770 | |
|---|
| 771 | </xs:complexType> |
|---|
| 772 | |
|---|
| 773 | <xs:complexType name="InhomogeneousValue"> |
|---|
| 774 | <xs:attribute name="inhomogeneousParam" type="xs:string" use="required"/> |
|---|
| 775 | <xs:attribute name="value" type="xs:string" use="required"/> |
|---|
| 776 | </xs:complexType> |
|---|
| 777 | |
|---|
| 778 | |
|---|
| 779 | <xs:complexType name="ReversalPotential"> |
|---|
| 780 | |
|---|
| 781 | <xs:complexContent> |
|---|
| 782 | <xs:extension base="ValueAcrossSegOrSegGroup"> |
|---|
| 783 | <xs:attribute name="species" type="NmlId" use="optional"/> |
|---|
| 784 | </xs:extension> |
|---|
| 785 | </xs:complexContent> |
|---|
| 786 | |
|---|
| 787 | </xs:complexType> |
|---|
| 788 | |
|---|
| 789 | |
|---|
| 790 | <xs:complexType name="Species"> |
|---|
| 791 | |
|---|
| 792 | <xs:complexContent> |
|---|
| 793 | <xs:extension base="ValueAcrossSegOrSegGroup"> |
|---|
| 794 | <xs:choice> |
|---|
| 795 | <xs:element name="decayingPoolConcentrationModel" type="DecayingPoolConcentrationModel"/> |
|---|
| 796 | <xs:element name="concentrationModel" type="ConcentrationModel_D"/> |
|---|
| 797 | <xs:element name="fixedConcentration" type="FixedConcentration"/> |
|---|
| 798 | </xs:choice> |
|---|
| 799 | <xs:attribute name="id" type="NmlId" use="required"/> |
|---|
| 800 | <xs:attribute name="ion" type="NmlId" use="optional"> |
|---|
| 801 | <xs:annotation> |
|---|
| 802 | <xs:documentation>Specifying the ion here again is redundant, the ion name should be the same as id. Kept for now |
|---|
| 803 | until LEMS implementation can select by id. TODO: remove.</xs:documentation> |
|---|
| 804 | </xs:annotation> |
|---|
| 805 | </xs:attribute> |
|---|
| 806 | </xs:extension> |
|---|
| 807 | </xs:complexContent> |
|---|
| 808 | |
|---|
| 809 | </xs:complexType> |
|---|
| 810 | |
|---|
| 811 | |
|---|
| 812 | |
|---|
| 813 | <xs:complexType name="FixedConcentration"> |
|---|
| 814 | <xs:attribute name="concentration" type="Nml2Quantity_concentration" use="required"/> |
|---|
| 815 | </xs:complexType> |
|---|
| 816 | |
|---|
| 817 | <xs:complexType name="DecayingPoolConcentrationModel"> |
|---|
| 818 | <xs:attribute name="resting_conc" type="Nml2Quantity_concentration" use="required"/> |
|---|
| 819 | <xs:attribute name="decay_constant" type="Nml2Quantity_time" use="required"/> |
|---|
| 820 | <xs:attribute name="shell_thickness" type="Nml2Quantity_length" use="required"/> |
|---|
| 821 | <xs:attribute name="initialConcentration" type="Nml2Quantity_concentration" use="required"/> |
|---|
| 822 | <xs:attribute name="extConcentration" type="Nml2Quantity_concentration" use="optional"/> |
|---|
| 823 | </xs:complexType> |
|---|
| 824 | |
|---|
| 825 | <!-- TODO: remove --> |
|---|
| 826 | <xs:complexType name="ConcentrationModel_D"> |
|---|
| 827 | |
|---|
| 828 | <xs:complexContent> |
|---|
| 829 | <xs:extension base="DecayingPoolConcentrationModel"> |
|---|
| 830 | |
|---|
| 831 | <xs:attribute name="type" use="required" fixed="decayingPoolConcentrationModel"/> |
|---|
| 832 | |
|---|
| 833 | </xs:extension> |
|---|
| 834 | </xs:complexContent> |
|---|
| 835 | </xs:complexType> |
|---|
| 836 | |
|---|
| 837 | <xs:complexType name="IntracellularProperties"> |
|---|
| 838 | |
|---|
| 839 | <xs:sequence> |
|---|
| 840 | <xs:element name="species" type="Species" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 841 | <xs:element name="resistivity" type="ValueAcrossSegOrSegGroup" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 842 | </xs:sequence> |
|---|
| 843 | |
|---|
| 844 | </xs:complexType> |
|---|
| 845 | |
|---|
| 846 | <xs:complexType name="ExtracellularProperties"> |
|---|
| 847 | |
|---|
| 848 | <xs:complexContent> |
|---|
| 849 | <xs:extension base="Base"> <!-- Should be standalone, but need some real elements below or XSD not valid... --> |
|---|
| 850 | <xs:sequence> |
|---|
| 851 | <xs:element name="species" type="Species" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
|---|
| 852 | </xs:sequence> |
|---|
| 853 | |
|---|
| 854 | <xs:attribute name="temperature" type="Nml2Quantity_temperature" use="optional"/> |
|---|
| 855 | |
|---|
| 856 | </xs:extension> |
|---|
| 857 | </xs:complexContent> |
|---|
| 858 | |
|---|
| 859 | |
|---|
| 860 | </xs:complexType> |
|---|
| 861 | |
|---|
| 862 | <xs:complexType name="ReactionScheme"> |
|---|
| 863 | |
|---|
| 864 | <xs:complexContent> |
|---|
| 865 | <xs:extension base="Base"> <!-- Should be standalone, but need some real elements below or XSD not valid... --> |
|---|
| 866 | <xs:sequence> |
|---|
| 867 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
|---|
| 868 | </xs:sequence> |
|---|
| 869 | <xs:attribute name="source" type="xs:string" use="required"/> |
|---|
| 870 | <xs:attribute name="type" type="xs:string" use="required"/> |
|---|
| 871 | </xs:extension> |
|---|
| 872 | </xs:complexContent> |
|---|
| 873 | |
|---|
| 874 | </xs:complexType> |
|---|
| 875 | |
|---|
| 876 | |
|---|
| 877 | |
|---|
| 878 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 879 | <!-- Inputs --> |
|---|
| 880 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 881 | |
|---|
| 882 | |
|---|
| 883 | <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 884 | |
|---|
| 885 | <xs:complexType name="PulseGenerator"> |
|---|
| 886 | |
|---|
| 887 | <xs:complexContent> |
|---|
| 888 | <xs:extension base="Standalone"> |
|---|
| 889 | |
|---|
| 890 | <xs:attribute name="delay" type="Nml2Quantity_time" use="required"/> |
|---|
| 891 | <xs:attribute name="duration" type="Nml2Quantity_time" use="required"/> |
|---|
| 892 | <xs:attribute name="amplitude" type="Nml2Quantity_current" use="required"/> |
|---|
| 893 | |
|---|
| 894 | </xs:extension> |
|---|
| 895 | </xs:complexContent> |
|---|
| 896 | </xs:complexType> |
|---|
| 897 | |
|---|
| 898 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 899 | <!-- Networks --> |
|---|
| 900 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 901 | |
|---|
| 902 | |
|---|
| 903 | <xs:complexType name="Network"> |
|---|
| 904 | |
|---|
| 905 | <xs:complexContent> |
|---|
| 906 | <xs:extension base="Standalone"> |
|---|
| 907 | <xs:sequence> |
|---|
| 908 | <xs:element name="space" type="Space" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 909 | <xs:element name="region" type="Region" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 910 | <xs:element name="population" type="Population" maxOccurs="unbounded"/> |
|---|
| 911 | <xs:element name="cellSet" type="CellSet" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 912 | <xs:element name="projection" type="Projection" minOccurs="0" maxOccurs="unbounded"/> |
|---|
| 913 | <xs:element name="synapticConnection" type="SynapticConnection" minOccurs="0" maxOccurs="unbounded"/> <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 914 | <xs:element name="connection" type="Connection" minOccurs="0" maxOccurs="unbounded"/> <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 915 | <xs:element name="explicitInput" type="ExplicitInput" minOccurs="0" maxOccurs="unbounded"/> <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 916 | </xs:sequence> |
|---|
| 917 | </xs:extension> |
|---|
| 918 | </xs:complexContent> |
|---|
| 919 | |
|---|
| 920 | </xs:complexType> |
|---|
| 921 | |
|---|
| 922 | |
|---|
| 923 | <xs:complexType name="Space"> <!-- Something onto which cells & networks can be laid out, e.g. n dim grid or n dim Euclidean space --> |
|---|
| 924 | |
|---|
| 925 | <xs:complexContent> |
|---|
| 926 | <xs:extension base="Base"> |
|---|
| 927 | <xs:sequence> |
|---|
| 928 | <xs:element name="structure" type="SpaceStructure" minOccurs="0"/> |
|---|
| 929 | </xs:sequence> |
|---|
| 930 | <xs:attribute name="basedOn" type="allowedSpaces" use="optional"/> |
|---|
| 931 | </xs:extension> |
|---|
| 932 | </xs:complexContent> |
|---|
| 933 | |
|---|
| 934 | </xs:complexType> |
|---|
| 935 | |
|---|
| 936 | <xs:complexType name="SpaceStructure"> |
|---|
| 937 | <xs:attribute name="xSpacing" type="xs:float"/> |
|---|
| 938 | <xs:attribute name="ySpacing" type="xs:float" use="optional"/> <!-- only use if >= 2D grid--> |
|---|
| 939 | <xs:attribute name="zSpacing" type="xs:float" use="optional"/> <!-- only use if 3D grid--> |
|---|
| 940 | <xs:attribute name="xStart" type="xs:float" use="optional" default="0"/> |
|---|
| 941 | <xs:attribute name="yStart" type="xs:float" use="optional" default="0"/> <!-- only use if >= 2D grid--> |
|---|
| 942 | <xs:attribute name="zStart" type="xs:float" use="optional" default="0"/> <!-- only use if 3D grid--> |
|---|
| 943 | </xs:complexType> |
|---|
| 944 | |
|---|
| 945 | |
|---|
| 946 | <xs:simpleType name="allowedSpaces"> |
|---|
| 947 | <xs:restriction base="xs:string"> |
|---|
| 948 | <xs:enumeration value="Euclidean_1D"/> |
|---|
| 949 | <xs:enumeration value="Euclidean_2D"/> |
|---|
| 950 | <xs:enumeration value="Euclidean_3D"/> |
|---|
| 951 | <xs:enumeration value="Grid_1D"/> |
|---|
| 952 | <xs:enumeration value="Grid_2D"/> |
|---|
| 953 | <xs:enumeration value="Grid_3D"/> |
|---|
| 954 | </xs:restriction> |
|---|
| 955 | </xs:simpleType> |
|---|
| 956 | |
|---|
| 957 | |
|---|
| 958 | <xs:complexType name="Region"> |
|---|
| 959 | |
|---|
| 960 | <xs:complexContent> |
|---|
| 961 | <xs:extension base="Base"> |
|---|
| 962 | <xs:sequence> |
|---|
| 963 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
|---|
| 964 | </xs:sequence> |
|---|
| 965 | |
|---|
| 966 | <xs:attribute name="space" type="NmlId" use="optional"/> |
|---|
| 967 | </xs:extension> |
|---|
| 968 | </xs:complexContent> |
|---|
| 969 | |
|---|
| 970 | </xs:complexType> |
|---|
| 971 | |
|---|
| 972 | |
|---|
| 973 | <xs:complexType name="Population"> |
|---|
| 974 | |
|---|
| 975 | <xs:complexContent> |
|---|
| 976 | <xs:extension base="Standalone"> |
|---|
| 977 | <xs:choice> |
|---|
| 978 | <xs:element name="layout" type="Layout" minOccurs="0"/> |
|---|
| 979 | <xs:element name="instances" type="Instances"/> |
|---|
| 980 | </xs:choice> |
|---|
| 981 | |
|---|
| 982 | <xs:attribute name="cell" type="NmlId" use="optional"/> <!-- Only one of these should be used!!! --> |
|---|
| 983 | <xs:attribute name="network" type="NmlId" use="optional"/> <!-- Only one of these should be used!!! --> |
|---|
| 984 | <xs:attribute name="component" type="NmlId" use="optional"/> <!-- Only one of these should be used!!! --> |
|---|
| 985 | |
|---|
| 986 | <xs:attribute name="size" type="xs:integer" use="optional"/> <!-- Temp!!! --> |
|---|
| 987 | |
|---|
| 988 | <xs:attribute name="extracellularProperties" type="NmlId" use="optional"/> |
|---|
| 989 | |
|---|
| 990 | </xs:extension> |
|---|
| 991 | </xs:complexContent> |
|---|
| 992 | |
|---|
| 993 | </xs:complexType> |
|---|
| 994 | |
|---|
| 995 | |
|---|
| 996 | <xs:complexType name="Layout"> |
|---|
| 997 | |
|---|
| 998 | <xs:choice> |
|---|
| 999 | <xs:element name="random" type="RandomLayout"/> |
|---|
| 1000 | <xs:element name="grid" type="GridLayout"/> |
|---|
| 1001 | <xs:element name="unstructured" type="UnstructuredLayout"/> |
|---|
| 1002 | </xs:choice> |
|---|
| 1003 | |
|---|
| 1004 | <xs:attribute name="space" type="NmlId"/> |
|---|
| 1005 | |
|---|
| 1006 | </xs:complexType> |
|---|
| 1007 | |
|---|
| 1008 | |
|---|
| 1009 | |
|---|
| 1010 | <xs:complexType name="UnstructuredLayout"> |
|---|
| 1011 | <xs:attribute name="number" type="xs:nonNegativeInteger"/> |
|---|
| 1012 | </xs:complexType> |
|---|
| 1013 | |
|---|
| 1014 | |
|---|
| 1015 | <xs:complexType name="RandomLayout"> |
|---|
| 1016 | <xs:attribute name="number" type="xs:nonNegativeInteger"/> |
|---|
| 1017 | <xs:attribute name="region" type="NmlId"/> |
|---|
| 1018 | </xs:complexType> |
|---|
| 1019 | |
|---|
| 1020 | |
|---|
| 1021 | <xs:complexType name="GridLayout"> |
|---|
| 1022 | <xs:attribute name="xSize" type="xs:nonNegativeInteger"/> |
|---|
| 1023 | <xs:attribute name="ySize" type="xs:nonNegativeInteger" use="optional"/> <!-- only use if >= 2D grid--> |
|---|
| 1024 | <xs:attribute name="zSize" type="xs:nonNegativeInteger" use="optional"/> <!-- only use if 3D grid--> |
|---|
| 1025 | </xs:complexType> |
|---|
| 1026 | |
|---|
| 1027 | |
|---|
| 1028 | <xs:complexType name="Instances"> |
|---|
| 1029 | <xs:sequence> |
|---|
| 1030 | <xs:element name="instance" type="Instance" maxOccurs="unbounded"/> |
|---|
| 1031 | </xs:sequence> |
|---|
| 1032 | <xs:attribute name="size" type="xs:nonNegativeInteger"/> |
|---|
| 1033 | </xs:complexType> |
|---|
| 1034 | |
|---|
| 1035 | <xs:complexType name="Instance"> |
|---|
| 1036 | <xs:sequence> |
|---|
| 1037 | <xs:element name="location" type="Location"/> |
|---|
| 1038 | </xs:sequence> |
|---|
| 1039 | <xs:attribute name="id" type="xs:nonNegativeInteger"/> |
|---|
| 1040 | <xs:attribute name="i" type="xs:nonNegativeInteger"/> <!-- for grid --> |
|---|
| 1041 | <xs:attribute name="j" type="xs:nonNegativeInteger"/> <!-- for grid --> |
|---|
| 1042 | <xs:attribute name="k" type="xs:nonNegativeInteger"/> <!-- for grid --> |
|---|
| 1043 | </xs:complexType> |
|---|
| 1044 | |
|---|
| 1045 | <xs:complexType name="Location"> |
|---|
| 1046 | <xs:attribute name="x" type="xs:float"/> |
|---|
| 1047 | <xs:attribute name="y" type="xs:float"/> |
|---|
| 1048 | <xs:attribute name="z" type="xs:float"/> |
|---|
| 1049 | </xs:complexType> |
|---|
| 1050 | |
|---|
| 1051 | |
|---|
| 1052 | <xs:complexType name="CellSet"> |
|---|
| 1053 | |
|---|
| 1054 | <xs:complexContent> |
|---|
| 1055 | <xs:extension base="Base"> |
|---|
| 1056 | <xs:sequence> |
|---|
| 1057 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
|---|
| 1058 | </xs:sequence> |
|---|
| 1059 | |
|---|
| 1060 | <xs:attribute name="select" type="xs:string" use="required"/> |
|---|
| 1061 | </xs:extension> |
|---|
| 1062 | </xs:complexContent> |
|---|
| 1063 | |
|---|
| 1064 | </xs:complexType> |
|---|
| 1065 | |
|---|
| 1066 | |
|---|
| 1067 | <xs:complexType name="Projection"> |
|---|
| 1068 | |
|---|
| 1069 | <xs:complexContent> |
|---|
| 1070 | <xs:extension base="Base"> |
|---|
| 1071 | <xs:sequence> |
|---|
| 1072 | <xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! --> |
|---|
| 1073 | </xs:sequence> |
|---|
| 1074 | </xs:extension> |
|---|
| 1075 | </xs:complexContent> |
|---|
| 1076 | |
|---|
| 1077 | </xs:complexType> |
|---|
| 1078 | |
|---|
| 1079 | |
|---|
| 1080 | <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 1081 | <xs:complexType name="SynapticConnection"> |
|---|
| 1082 | <xs:attribute name="from" type="xs:string"/> |
|---|
| 1083 | <xs:attribute name="to" type="xs:string"/> |
|---|
| 1084 | <xs:attribute name="synapse" type="xs:string"/> |
|---|
| 1085 | </xs:complexType> |
|---|
| 1086 | |
|---|
| 1087 | <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 1088 | <xs:complexType name="Connection"> |
|---|
| 1089 | <xs:attribute name="from" type="xs:string"/> |
|---|
| 1090 | <xs:attribute name="to" type="xs:string"/> |
|---|
| 1091 | </xs:complexType> |
|---|
| 1092 | |
|---|
| 1093 | <!--Will be updated in line with LEMS ComponentType definitions --> |
|---|
| 1094 | <xs:complexType name="ExplicitInput"> |
|---|
| 1095 | <xs:attribute name="target" type="xs:string"/> |
|---|
| 1096 | <xs:attribute name="input" type="xs:string"/> |
|---|
| 1097 | </xs:complexType> |
|---|
| 1098 | |
|---|
| 1099 | |
|---|
| 1100 | |
|---|
| 1101 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 1102 | <!-- Further Core elements --> |
|---|
| 1103 | <!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++--> |
|---|
| 1104 | |
|---|
| 1105 | <!--NOTE: Base and Standalone definitions moved to end of file, as some XML language binding |
|---|
| 1106 | generators, e.g. generateDS.py, require superclasses to be defined after the subclasses... --> |
|---|
| 1107 | |
|---|
| 1108 | <xs:complexType name="Base"> |
|---|
| 1109 | |
|---|
| 1110 | <xs:annotation> |
|---|
| 1111 | <xs:documentation>Anything which can have a unique id (within its parent) i.e. most elements.</xs:documentation> |
|---|
| 1112 | </xs:annotation> |
|---|
| 1113 | |
|---|
| 1114 | <xs:attribute name="id" type="NmlId" use="required"/> |
|---|
| 1115 | |
|---|
| 1116 | <xs:attribute name="neuroLexId" type="NeuroLexId" use="optional"/> |
|---|
| 1117 | |
|---|
| 1118 | </xs:complexType> |
|---|
| 1119 | |
|---|
| 1120 | |
|---|
| 1121 | <xs:complexType name="Standalone"> |
|---|
| 1122 | |
|---|
| 1123 | <xs:annotation> |
|---|
| 1124 | <xs:documentation>Elements which can stand alone and be referenced by id, e.g. cell, morphology.</xs:documentation> |
|---|
| 1125 | </xs:annotation> |
|---|
| 1126 | |
|---|
| 1127 | <xs:complexContent> |
|---|
| 1128 | <xs:extension base="Base"> |
|---|
| 1129 | <xs:sequence> |
|---|
| 1130 | <xs:element name="notes" type="Notes" minOccurs="0"/> <!-- More metadata needed --> |
|---|
| 1131 | <xs:element name="annotation" type="Annotation" minOccurs="0"/> <!-- More metadata needed --> |
|---|
| 1132 | </xs:sequence> |
|---|
| 1133 | <xs:attribute name="metaid" type="MetaId" use="optional"/> |
|---|
| 1134 | |
|---|
| 1135 | </xs:extension> |
|---|
| 1136 | </xs:complexContent> |
|---|
| 1137 | |
|---|
| 1138 | </xs:complexType> |
|---|
| 1139 | |
|---|
| 1140 | </xs:schema> |
|---|
| 1141 | |
|---|
| 1142 | |
|---|
| 1143 | |
|---|
