/
NeuroML_v2beta4.xsd
3079 lines (2349 loc) · 127 KB
/
NeuroML_v2beta4.xsd
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<?xml version="1.0" encoding="UTF-8"?>
<xs:schema targetNamespace="http://www.neuroml.org/schema/neuroml2"
xmlns="http://www.neuroml.org/schema/neuroml2"
xmlns:xi="http://www.w3.org/2001/XInclude"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:jxb="http://java.sun.com/xml/ns/jaxb" jxb:version="2.0"
xsi:schemaLocation="http://www.w3.org/2001/XMLSchema http://www.w3.org/2001/XMLSchema.xsd"
elementFormDefault="qualified"
attributeFormDefault="unqualified">
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Core elements -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<xs:simpleType name="NmlId">
<xs:annotation>
<xs:documentation>An id attribute for elements which need to be identified uniquely (normally just within their parent element).</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="[a-zA-Z_][a-zA-Z0-9_]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity">
<xs:annotation>
<xs:documentation>A value for a physical quantity in NeuroML 2, e.g. 20, -60.0mV or 5nA</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*([_a-zA-Z0-9])*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_none">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?"/> <!-- No units string -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_voltage">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(V|mV)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_length">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(m|cm|um)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_resistance">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(ohm|kohm|Mohm)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_conductance">
<xs:restriction base="xs:string">
<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 -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_conductanceDensity">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(S_per_m2|mS_per_cm2|S_per_cm2)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_permeability">
<xs:restriction base="xs:string">
<xs:pattern
value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(m_per_s|
um_per_ms|cm_per_s|cm_per_ms)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_time">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(s|ms)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_pertime">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(per_s|per_ms|Hz)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_capacitance">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(F|uF|nF|pF)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_specificCapacitance">
<xs:restriction base="xs:string">
<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 -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_concentration">
<xs:restriction base="xs:string">
<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 -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_current">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(A|uA|nA|pA)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_currentDensity">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(A_per_m2|uA_per_cm2|mA_per_cm2)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_temperature">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(degC)"/> <!-- Based on set of defined Units in NeuroMLCoreDimensions.xml -->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_rhoFactor">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(mol_per_m_per_A_per_s|mol_per_cm_per_uA_per_ms)"/> <!-- See Cells.xml-->
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="Nml2Quantity_conductancePerVoltage">
<xs:restriction base="xs:string">
<xs:pattern value="-?([0-9]*(\.[0-9]+)?)([eE]-?[0-9]+)?[\s]*(S_per_V|nS_per_mV)"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="MetaId">
<xs:annotation>
<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>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="[a-zA-Z0-9_]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="NeuroLexId">
<xs:annotation>
<xs:documentation>An id string for pointing to an entry in the NeuroLex ontology. Use of this attribute is a shorthand for a full
RDF based reference to the MIRIAM Resource urn:miriam:neurolex, with an bqbiol:is qualifier
</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:string">
<xs:pattern value="[a-zA-Z0-9_:]*"/>
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="NonNegativeInteger">
<xs:annotation>
<xs:documentation>An attribute useful as id of segments, connections, etc: integer >=0 only!</xs:documentation>
<xs:appinfo >
<!-- This tells JAXB to use an int for this attribute instead of BigInteger-->
<jxb:javaType name="int" parseMethod="javax.xml.bind.DatatypeConverter.parseInt" printMethod="javax.xml.bind.DatatypeConverter.printInt" />
</xs:appinfo>
</xs:annotation>
<xs:restriction base="xs:nonNegativeInteger">
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="PositiveInteger">
<xs:annotation>
<xs:documentation>Integer >=1 only!</xs:documentation>
<xs:appinfo >
<!-- This tells JAXB to use an int for this attribute instead of BigInteger-->
<jxb:javaType name="int" parseMethod="javax.xml.bind.DatatypeConverter.parseInt" printMethod="javax.xml.bind.DatatypeConverter.printInt" />
</xs:appinfo>
</xs:annotation>
<xs:restriction base="xs:positiveInteger">
</xs:restriction>
</xs:simpleType>
<xs:simpleType name="DoubleGreaterThanZero">
<xs:annotation>
<xs:documentation>Double >0 only</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:double">
<xs:minExclusive value="0"/>
</xs:restriction>
</xs:simpleType>
<!--NOTE: Base and Standalone definitions moved to end of file, as some XML language binding
generators, e.g. generateDS.py, require superclasses to be defined after the subclasses... -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Metadata elements -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<xs:simpleType name="Notes">
<xs:annotation>
<xs:documentation>Textual human readable notes related to the element in question. It's useful to put these into
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>
</xs:annotation>
<xs:restriction base="xs:string"/>
</xs:simpleType>
<xs:complexType name="Property">
<xs:annotation>
<xs:documentation>Generic property with a tag and value</xs:documentation>
</xs:annotation>
<xs:attribute name="tag" type="xs:string" use="required"/>
<xs:attribute name="value" type="xs:string" use="required"/>
</xs:complexType>
<xs:complexType name="Annotation">
<xs:annotation>
<xs:documentation>Placeholder for MIRIAM related metadata, among others.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! -->
</xs:sequence>
</xs:complexType>
<xs:complexType name="ComponentType">
<xs:annotation>
<xs:documentation>Contains an extension to NeuroML by creating custom LEMS ComponentType.</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="Parameter" type="Parameter" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Constant" type="Constant" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Requirement" type="Requirement" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="Dynamics" type="Dynamics" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="extends" type="xs:string" use="optional"/>
<xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>
<xs:complexType name="Constant">
<xs:annotation>
<xs:documentation>LEMS ComponentType for Constant.</xs:documentation>
</xs:annotation>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="dimension" type="xs:string" use="required"/>
<xs:attribute name="value" type="Nml2Quantity" use="required"/>
<xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>
<!-- for Parameter, StateVariable etc. -->
<xs:complexType name="NamedDimensionalType">
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="dimension" type="xs:string" use="optional" default="none"/>
<xs:attribute name="description" type="xs:string" use="optional"/>
</xs:complexType>
<xs:complexType name="Parameter"> <!-- For language binding generators, so there will be a class of this name... -->
<xs:complexContent>
<xs:extension base="NamedDimensionalType"/>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="Requirement"> <!-- For language binding generators, so there will be a class of this name... -->
<xs:complexContent>
<xs:extension base="NamedDimensionalType"/>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="Dynamics">
<xs:annotation>
<xs:documentation>LEMS ComponentType for Dynamics</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="DerivedVariable" type="DerivedVariable" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="ConditionalDerivedVariable" type="ConditionalDerivedVariable" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="DerivedVariable">
<xs:annotation>
<xs:documentation>LEMS ComponentType for DerivedVariable</xs:documentation>
</xs:annotation>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="dimension" type="xs:string" use="required"/>
<xs:attribute name="value" type="xs:string" use="required"/>
<xs:attribute name="exposure" type="xs:string" use="optional"/>
</xs:complexType>
<xs:complexType name="ConditionalDerivedVariable">
<xs:annotation>
<xs:documentation>LEMS ComponentType for ConditionalDerivedVariable</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="Case" type="Case" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="name" type="xs:string" use="required"/>
<xs:attribute name="dimension" type="xs:string" use="required"/>
<xs:attribute name="exposure" type="xs:string" use="optional"/>
</xs:complexType>
<xs:complexType name="Case">
<xs:attribute name="condition" type="xs:string" use="optional"/>
<xs:attribute name="value" type="xs:string" use="required"/>
</xs:complexType>
<xs:simpleType name="ZeroToOne">
<xs:annotation>
<xs:documentation>Double restricted to between 1 and 0</xs:documentation>
</xs:annotation>
<xs:restriction base="xs:double">
<xs:minInclusive value="0"/>
<xs:maxInclusive value="1"/>
</xs:restriction>
</xs:simpleType>
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Main NeuroML element -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<xs:element name="neuroml" type="NeuroMLDocument">
<xs:annotation>
<xs:documentation>The root NeuroML element.</xs:documentation>
</xs:annotation>
</xs:element>
<xs:complexType name="NeuroMLDocument"> <!-- Making the complexType definition of the root element lowercase, not to confuse language binding generators... -->
<xs:complexContent>
<xs:extension base="Standalone">
<xs:sequence>
<xs:element name="include" type="IncludeType" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="extracellularProperties" type="ExtracellularProperties" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="intracellularProperties" type="IntracellularProperties" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="morphology" type="Morphology" minOccurs="0" maxOccurs="unbounded"/>
<!-- Note: requires type = ionChannelHH -->
<xs:element name="ionChannel" type="IonChannel" minOccurs="0" maxOccurs="unbounded"/>
<!-- Note ionChannel and _ionChannelHH are currently functionally identical. This is needed
since many existing examples use ionChannel, some use ionChannelHH. NeuroML v2beta4 should
remove one of these -->
<xs:element name="ionChannelHH" type="IonChannelHH" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="ionChannelKS" type="IonChannelKS" minOccurs="0" maxOccurs="unbounded"/>
<xs:group ref="ConcentrationModelTypes"/>
<xs:group ref="SynapseTypes"/>
<xs:element name="biophysicalProperties" type="BiophysicalProperties" minOccurs="0" maxOccurs="unbounded"/>
<xs:group ref="CellTypes"/>
<xs:group ref="InputTypes"/>
<xs:group ref="PyNNCellTypes"/>
<xs:group ref="PyNNSynapseTypes"/>
<xs:group ref="PyNNInputTypes"/>
<xs:element name="network" type="Network" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="ComponentType" type="ComponentType" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<!-- A small subset of XLInclude from: http://www.w3.org/2001/XInclude.xsd
Will be sufficient for now... -->
<xs:complexType name="IncludeType" mixed="true">
<xs:attribute name="href" use="optional" type="xs:anyURI"/>
</xs:complexType>
<xs:group name="CellTypes">
<xs:annotation>
<xs:documentation>Various types of cells which are defined in NeuroML 2. This list will be expanded...</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="cell" type="Cell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="cell2CaPools" type="Cell2CaPools" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="baseCell" type="BaseCell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="iafTauCell" type="IafTauCell"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="iafTauRefCell" type="IafTauRefCell"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="iafCell" type="IafCell" minOccurs="0"
maxOccurs="unbounded"/>
<xs:element name="iafRefCell" type="IafRefCell" minOccurs="0"
maxOccurs="unbounded"/>
<xs:element name="izhikevichCell" type="IzhikevichCell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="izhikevich2007Cell" type="Izhikevich2007Cell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="adExIaFCell" type="AdExIaFCell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="fitzHughNagumoCell" type="FitzHughNagumoCell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="fitzHughNagumo1969Cell" type="FitzHughNagumo1969Cell" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="pinskyRinzelCA3Cell" type="PinskyRinzelCA3Cell" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="PyNNCellTypes">
<xs:annotation>
<xs:documentation>Various types of cells which are defined in NeuroML 2 based on PyNN standard cell models. </xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="IF_curr_alpha" type="IF_curr_alpha" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="IF_curr_exp" type="IF_curr_exp" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="IF_cond_alpha" type="IF_cond_alpha" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="IF_cond_exp" type="IF_cond_exp" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="EIF_cond_exp_isfa_ista" type="EIF_cond_exp_isfa_ista" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="EIF_cond_alpha_isfa_ista" type="EIF_cond_alpha_isfa_ista" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="HH_cond_exp" type="HH_cond_exp" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="SynapseTypes">
<xs:annotation>
<xs:documentation>Various types of synapse which are defined in NeuroML 2. This list will be expanded...</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="alphaCurrentSynapse" type="AlphaCurrentSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="alphaSynapse" type="AlphaSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="expOneSynapse" type="ExpOneSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="expTwoSynapse" type="ExpTwoSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="expThreeSynapse" type="ExpThreeSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="blockingPlasticSynapse" type="BlockingPlasticSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gapJunction" type="GapJunction" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="silentSynapse" type="SilentSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="linearGradedSynapse" type="LinearGradedSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gradedSynapse" type="GradedSynapse" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="PyNNSynapseTypes">
<xs:annotation>
<xs:documentation>Various types of synapse which are defined in NeuroML 2 based on PyNN standard cell/synapse models. </xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="expCondSynapse" type="ExpCondSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="alphaCondSynapse" type="AlphaCondSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="expCurrSynapse" type="ExpCurrSynapse" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="alphaCurrSynapse" type="AlphaCurrSynapse" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="InputTypes">
<xs:annotation>
<xs:documentation>Various types of inputs which are defined in NeuroML2. This list will be expanded...</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="pulseGenerator" type="PulseGenerator"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="pulseGeneratorDL" type="PulseGeneratorDL"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sineGenerator" type="SineGenerator"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sineGeneratorDL" type="SineGeneratorDL"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="rampGenerator" type="RampGenerator"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="rampGeneratorDL" type="RampGeneratorDL"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="compoundInput" type="CompoundInput"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="compoundInputDL" type="CompoundInputDL"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="voltageClamp" type="VoltageClamp"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="spikeArray" type="SpikeArray" minOccurs="0"
maxOccurs="unbounded"/>
<xs:element name="timedSynapticInput" type="TimedSynapticInput" minOccurs="0"
maxOccurs="unbounded"/>
<xs:element name="spikeGenerator" type="SpikeGenerator"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="spikeGeneratorRandom" type="SpikeGeneratorRandom"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="spikeGeneratorPoisson" type="SpikeGeneratorPoisson"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="poissonFiringSynapse" type="PoissonFiringSynapse"
minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="transientPoissonFiringSynapse" type="TransientPoissonFiringSynapse"
minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="PyNNInputTypes">
<xs:annotation>
<xs:documentation>Various types of input which are defined in NeuroML 2 based on PyNN standard cell/synapse models. </xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="SpikeSourcePoisson" type="SpikeSourcePoisson" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<xs:group name="ConcentrationModelTypes">
<xs:annotation>
<xs:documentation>Various types of concentration model which are defined in NeuroML 2. This list will be expanded...</xs:documentation>
</xs:annotation>
<xs:sequence>
<xs:element name="decayingPoolConcentrationModel" type="DecayingPoolConcentrationModel" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="fixedFactorConcentrationModel" type="FixedFactorConcentrationModel" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:group>
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- IonChannel element -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<xs:complexType name="IonChannelScalable">
<xs:complexContent>
<xs:extension base="Standalone">
<xs:sequence>
<xs:element name="q10ConductanceScaling" type="Q10ConductanceScaling" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="IonChannelKS">
<xs:annotation>
<xs:documentation>Kinetic scheme based ion channel.</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="Standalone">
<xs:sequence>
<xs:element name="gateKS" type="GateKS" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="species" type="NmlId" use="optional"/>
<xs:attribute name="conductance" type="Nml2Quantity_conductance" use="optional"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="IonChannel">
<xs:annotation>
<xs:documentation>Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH.
NeuroML v2beta4 should remove one of these, probably ionChannelHH.</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="IonChannelScalable">
<xs:choice>
<xs:element name="gate" type="GateHHUndetermined" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHrates" type="GateHHRates" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHratesTau" type="GateHHRatesTau" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHtauInf" type="GateHHTauInf" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHratesInf" type="GateHHRatesInf" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHratesTauInf" type="GateHHRatesTauInf" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateHHInstantaneous" type="GateHHInstantaneous" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="gateFractional" type="GateFractional" minOccurs="0" maxOccurs="unbounded"/>
</xs:choice>
<xs:attribute name="species" type="NmlId" use="optional"/>
<xs:attribute name="type" type="channelTypes" use="optional"/>
<xs:attribute name="conductance" type="Nml2Quantity_conductance" use="optional"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="IonChannelHH">
<xs:annotation>
<xs:documentation>Note ionChannel and ionChannelHH are currently functionally identical. This is needed since many existing examples use ionChannel, some use ionChannelHH.
NeuroML v2beta4 should remove one of these, probably ionChannelHH.</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="IonChannel"/>
</xs:complexContent>
</xs:complexType>
<xs:simpleType name="channelTypes">
<xs:restriction base="xs:string">
<xs:enumeration value="ionChannelPassive"/>
<xs:enumeration value="ionChannelHH"/>
<!--<xs:enumeration value="ionChannelKS"/> use an explicit <ionChannelKS ... > element, not <ionChannel type="ionChannelKS" ..> -->
</xs:restriction>
</xs:simpleType>
<xs:complexType name="Q10ConductanceScaling">
<xs:attribute name="q10Factor" type="Nml2Quantity_none" use="required"/>
<xs:attribute name="experimentalTemp" type="Nml2Quantity_temperature" use="required"/>
</xs:complexType>
<xs:simpleType name="gateTypes">
<xs:restriction base="xs:string">
<xs:enumeration value="gateHHrates"/>
<xs:enumeration value="gateHHratesTau"/>
<xs:enumeration value="gateHHtauInf"/>
<xs:enumeration value="gateHHratesInf"/>
<xs:enumeration value="gateHHratesTauInf"/>
<xs:enumeration value="gateHHInstantaneous"/>
<xs:enumeration value="gateKS"/>
<xs:enumeration value="gateFractional"/>
</xs:restriction>
</xs:simpleType>
<xs:complexType name="ClosedState">
<xs:complexContent>
<xs:extension base="Base">
<!-- Only has id...-->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="OpenState">
<xs:complexContent>
<xs:extension base="Base">
<!-- Only has id...-->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="ForwardTransition">
<xs:complexContent>
<xs:extension base="Base">
<xs:sequence>
<xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! -->
</xs:sequence>
<xs:attribute name="from" type="NmlId" use="required"/>
<xs:attribute name="to" type="NmlId" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="ReverseTransition">
<xs:complexContent>
<xs:extension base="Base">
<xs:sequence>
<xs:any processContents="skip" minOccurs="0" maxOccurs="unbounded"/> <!-- Further elements will be specified!! -->
</xs:sequence>
<xs:attribute name="from" type="NmlId" use="required"/>
<xs:attribute name="to" type="NmlId" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:group name="ForwardReverseTransition">
<xs:sequence>
<xs:element name="forwardTransition" type="ForwardTransition"/>
<xs:element name="reverseTransition" type="ReverseTransition"/>
</xs:sequence>
</xs:group>
<xs:complexType name="TauInfTransition">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="steadyState" type="HHVariable"/>
<xs:element name="timeCourse" type="HHTime"/>
</xs:all>
<xs:attribute name="from" type="NmlId" use="required"/>
<xs:attribute name="to" type="NmlId" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateKS">
<xs:complexContent>
<xs:extension base="Base">
<xs:sequence>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="closedState" type="ClosedState" minOccurs="1" maxOccurs="unbounded"/>
<xs:element name="openState" type="OpenState" minOccurs="1" maxOccurs="unbounded"/>
<xs:choice minOccurs="1" maxOccurs="unbounded">
<xs:group ref="ForwardReverseTransition"/>
<xs:element name ="tauInfTransition" type="TauInfTransition"/>
</xs:choice>
</xs:sequence>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHUndetermined">
<xs:annotation>
<xs:documentation>Note all sub elements for gateHHrates, gateHHratesTau, gateFractional etc. allowed here. Which are valid should be constrained by what type is set</xs:documentation>
</xs:annotation>
<xs:complexContent>
<xs:extension base="Base">
<xs:sequence>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="forwardRate" type="HHRate" minOccurs="0"/>
<xs:element name="reverseRate" type="HHRate" minOccurs="0"/>
<xs:element name="timeCourse" type="HHTime" minOccurs="0"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="0"/>
<xs:element name="subGate" type="GateFractionalSubgate" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<xs:attribute name="type" type="gateTypes" use="required"/> <!-- Required, as it must specify type="gateHHratesTau" etc. -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHRates">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="forwardRate" type="HHRate" minOccurs="1"/>
<xs:element name="reverseRate" type="HHRate" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHTauInf">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="timeCourse" type="HHTime" minOccurs="1"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHRatesTauInf">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="forwardRate" type="HHRate" minOccurs="1"/>
<xs:element name="reverseRate" type="HHRate" minOccurs="1"/>
<xs:element name="timeCourse" type="HHTime" minOccurs="1"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHRatesTau">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="forwardRate" type="HHRate" minOccurs="1"/>
<xs:element name="reverseRate" type="HHRate" minOccurs="1"/>
<xs:element name="timeCourse" type="HHTime" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHRatesInf">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="forwardRate" type="HHRate" minOccurs="1"/>
<xs:element name="reverseRate" type="HHRate" minOccurs="1"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateHHInstantaneous">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="1"/>
</xs:all>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
<!-- <xs:attribute name="type" type="gateTypes" use="optional"/> No longer allowed as it could conflict with the element definition -->
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateFractional">
<xs:complexContent>
<xs:extension base="Base">
<xs:sequence>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="subGate" type="GateFractionalSubgate" minOccurs="1" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="instances" type="PositiveInteger" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="GateFractionalSubgate">
<xs:complexContent>
<xs:extension base="Base">
<xs:all>
<xs:element name="notes" type="Notes" minOccurs="0"/>
<xs:element name="q10Settings" type="Q10Settings" minOccurs="0"/>
<xs:element name="steadyState" type="HHVariable" minOccurs="1"/>
<xs:element name="timeCourse" type="HHTime" minOccurs="1"/>
</xs:all>
<xs:attribute name="fractionalConductance" type="Nml2Quantity_none" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="Q10Settings">
<xs:attribute name="type" type="NmlId" use="required"/>
<xs:attribute name="fixedQ10" type="Nml2Quantity_none" use="optional"/> <!-- TODO: make this and follwing 2 attrs either/or-->
<xs:attribute name="q10Factor" type="Nml2Quantity_none" use="optional"/>
<xs:attribute name="experimentalTemp" type="Nml2Quantity_temperature" use="optional"/>
</xs:complexType>
<xs:complexType name="HHRate">
<xs:attribute name="type" type="NmlId" use="required"/>
<xs:attribute name="rate" type="Nml2Quantity_pertime" use="optional"/>
<xs:attribute name="midpoint" type="Nml2Quantity_voltage" use="optional"/>
<xs:attribute name="scale" type="Nml2Quantity_voltage" use="optional"/>
</xs:complexType>
<xs:complexType name="HHVariable">
<xs:attribute name="type" type="NmlId" use="required"/>
<xs:attribute name="rate" type="xs:float" use="optional"/>
<xs:attribute name="midpoint" type="Nml2Quantity_voltage" use="optional"/>
<xs:attribute name="scale" type="Nml2Quantity_voltage" use="optional"/>
</xs:complexType>
<xs:complexType name="HHTime">
<xs:attribute name="type" type="NmlId" use="required"/>
<xs:attribute name="rate" type="Nml2Quantity_time" use="optional"/>
<xs:attribute name="midpoint" type="Nml2Quantity_voltage" use="optional"/>
<xs:attribute name="scale" type="Nml2Quantity_voltage" use="optional"/>
<xs:attribute name="tau" type="Nml2Quantity_time" use="optional"/> <!-- TODO: make this and prev 3 attrs either/or-->
</xs:complexType>
<!--<xs:complexType name="FixedTimeCourse">
<xs:attribute name="tau" type="Nml2Quantity_time" use="required"/>
</xs:complexType>-->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<!-- Concentration Model types -->
<!--+++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
<xs:complexType name="DecayingPoolConcentrationModel">
<xs:complexContent>
<xs:extension base="Standalone">
<xs:attribute name="ion" type="NmlId" use="required">
<xs:annotation>
<xs:documentation>Should not be required, as it's present on the species element!</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="restingConc" type="Nml2Quantity_concentration" use="required"/>
<xs:attribute name="decayConstant" type="Nml2Quantity_time" use="required"/>
<xs:attribute name="shellThickness" type="Nml2Quantity_length" use="required"/>
</xs:extension>
</xs:complexContent>
</xs:complexType>
<xs:complexType name="FixedFactorConcentrationModel">
<xs:complexContent>
<xs:extension base="Standalone">
<xs:attribute name="ion" type="NmlId" use="required">
<xs:annotation>
<xs:documentation>Should not be required, as it's present on the species element!</xs:documentation>
</xs:annotation>
</xs:attribute>
<xs:attribute name="restingConc" type="Nml2Quantity_concentration" use="required"/>
<xs:attribute name="decayConstant" type="Nml2Quantity_time" use="required"/>