Main schema CopasiML.xsd
Element schema:COPASI
Namespace
http://www.copasi.org/static/schema
Annotations
This is the only top element of a CopasiML file. It contains the models as
well as the task information.
Diagram
Properties
Model
schema:ListOfFunctions{0,1} ,
schema:Model{0,1} ,
schema:ListOfTasks{0,1} ,
schema:ListOfReports{0,1} ,
schema:ListOfPlots{0,1} ,
schema:GUI{0,1} ,
schema:ListOfLayouts{0,1} ,
schema:SBMLReference{0,1} ,
schema:ListOfUnitDefinitions{0,1} ,
ANY element from ANY namespace OTHER than 'http://www.copasi.org/static/schema'
Children
schema:GUI , schema:ListOfFunctions , schema:ListOfLayouts , schema:ListOfPlots , schema:ListOfReports , schema:ListOfTasks , schema:ListOfUnitDefinitions , schema:Model , schema:SBMLReference
Instance
<schema:COPASI copasiSourcesModified= "" versionDevel= "" versionMajor= "" versionMinor= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:ListOfFunctions > {0,1} </schema:ListOfFunctions>
<schema:Model areaUnit= "" avogadroConstant= "" key= "" lengthUnit= "" name= "" quantityUnit= "" simulationType= "" timeUnit= "" type= "" volumeUnit= "" > {0,1} </schema:Model>
<schema:ListOfTasks > {0,1} </schema:ListOfTasks>
<schema:ListOfReports > {0,1} </schema:ListOfReports>
<schema:ListOfPlots > {0,1} </schema:ListOfPlots>
<schema:GUI > {0,1} </schema:GUI>
<schema:ListOfLayouts > {0,1} </schema:ListOfLayouts>
<schema:SBMLReference file= "" > {0,1} </schema:SBMLReference>
<schema:ListOfUnitDefinitions > {0,1} </schema:ListOfUnitDefinitions>
</schema:COPASI>
Attributes
Wildcard: ANY attribute from ANY namespace OTHER than 'http://www.copasi.org/static/schema'
Source
<xs:element name= "COPASI" >
<xs:annotation >
<xs:documentation > This is the only top element of a CopasiML file. It contains the models as well as the task information. </xs:documentation>
</xs:annotation>
<xs:complexType >
<xs:sequence >
<xs:element minOccurs= "0" ref= "schema:ListOfFunctions" />
<xs:element minOccurs= "0" ref= "schema:Model" />
<xs:element minOccurs= "0" ref= "schema:ListOfTasks" />
<xs:element minOccurs= "0" ref= "schema:ListOfReports" />
<xs:element minOccurs= "0" ref= "schema:ListOfPlots" />
<xs:element minOccurs= "0" ref= "schema:GUI" />
<xs:element minOccurs= "0" ref= "schema:ListOfLayouts" />
<xs:element minOccurs= "0" ref= "schema:SBMLReference" />
<xs:element minOccurs= "0" ref= "schema:ListOfUnitDefinitions" />
<xs:any minOccurs= "0" maxOccurs= "unbounded" namespace= "##other" processContents= "skip" >
<xs:annotation >
<xs:documentation > We explicitedly allow the addition of elements which are not in the CopasiML name space so that this may be expandend by other user to suit their needs. </xs:documentation>
</xs:annotation>
</xs:any>
</xs:sequence>
<xs:attribute name= "versionMajor" use= "required" type= "xs:integer" />
<xs:attribute name= "versionMinor" use= "required" type= "xs:integer" />
<xs:attribute name= "versionDevel" use= "required" type= "xs:integer" />
<xs:attribute name= "copasiSourcesModified" use= "required" type= "xs:boolean" />
<xs:anyAttribute namespace= "##other" processContents= "skip" />
</xs:complexType>
</xs:element>
Element schema:ListOfFunctions
Element schema:Function
Element schema:MiriamAnnotation
Element schema:Comment
Namespace
http://www.copasi.org/static/schema
Diagram
Properties
Used by
Model
Source
Element schema:ListOfUnsupportedAnnotations
Element schema:UnsupportedAnnotation
Element schema:Expression
Element schema:ListOfParameterDescriptions
Element schema:ParameterDescription
Element schema:Model
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:model.datatype
Properties
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:InitialExpression{0,1} ,
schema:ListOfCompartments{0,1} ,
schema:ListOfMetabolites{0,1} ,
schema:ListOfModelValues{0,1} ,
schema:ListOfReactions{0,1} ,
schema:ListOfEvents{0,1} ,
schema:ListOfModelParameterSets{0,1} ,
schema:StateTemplate{0,1} ,
schema:InitialState{0,1}
Children
schema:Comment , schema:InitialExpression , schema:InitialState , schema:ListOfCompartments , schema:ListOfEvents , schema:ListOfMetabolites , schema:ListOfModelParameterSets , schema:ListOfModelValues , schema:ListOfReactions , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:StateTemplate
Instance
<schema:Model areaUnit= "" avogadroConstant= "" key= "" lengthUnit= "" name= "" quantityUnit= "" simulationType= "" timeUnit= "" type= "" volumeUnit= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:MiriamAnnotation > {0,1} </schema:MiriamAnnotation>
<schema:Comment > {0,1} </schema:Comment>
<schema:ListOfUnsupportedAnnotations > {0,1} </schema:ListOfUnsupportedAnnotations>
<schema:InitialExpression > {0,1} </schema:InitialExpression>
<schema:ListOfCompartments > {0,1} </schema:ListOfCompartments>
<schema:ListOfMetabolites > {0,1} </schema:ListOfMetabolites>
<schema:ListOfModelValues > {0,1} </schema:ListOfModelValues>
<schema:ListOfReactions > {0,1} </schema:ListOfReactions>
<schema:ListOfEvents > {0,1} </schema:ListOfEvents>
<schema:ListOfModelParameterSets activeSet= "" > {0,1} </schema:ListOfModelParameterSets>
<schema:StateTemplate > {0,1} </schema:StateTemplate>
<schema:InitialState type= "" > {0,1} </schema:InitialState>
</schema:Model>
Attributes
Source
<xs:element name= "Model" type= "schema:model.datatype" />
Element schema:InitialExpression
Element schema:ListOfCompartments
Element schema:Compartment
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:compartment.datatype
Properties
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:Expression{0,1} ,
schema:InitialExpression{0,1} ,
schema:NoiseExpression{0,1}
Children
schema:Comment , schema:Expression , schema:InitialExpression , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression
Instance
<schema:Compartment addNoise= "" dimensionality= "" key= "" name= "" simulationType= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:MiriamAnnotation > {0,1} </schema:MiriamAnnotation>
<schema:Comment > {0,1} </schema:Comment>
<schema:ListOfUnsupportedAnnotations > {0,1} </schema:ListOfUnsupportedAnnotations>
<schema:Expression > {0,1} </schema:Expression>
<schema:InitialExpression > {0,1} </schema:InitialExpression>
<schema:NoiseExpression > {0,1} </schema:NoiseExpression>
</schema:Compartment>
Attributes
Source
<xs:element name= "Compartment" type= "schema:compartment.datatype" />
Element schema:NoiseExpression
Element schema:ListOfMetabolites
Element schema:Metabolite
Element schema:ListOfModelValues
Element schema:ModelValue
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:modelValue.datatype
Properties
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:Expression{0,1} ,
schema:InitialExpression{0,1} ,
schema:NoiseExpression{0,1} ,
schema:Unit{0,1}
Children
schema:Comment , schema:Expression , schema:InitialExpression , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression , schema:Unit
Instance
<schema:ModelValue addNoise= "" key= "" name= "" simulationType= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:MiriamAnnotation > {0,1} </schema:MiriamAnnotation>
<schema:Comment > {0,1} </schema:Comment>
<schema:ListOfUnsupportedAnnotations > {0,1} </schema:ListOfUnsupportedAnnotations>
<schema:Expression > {0,1} </schema:Expression>
<schema:InitialExpression > {0,1} </schema:InitialExpression>
<schema:NoiseExpression > {0,1} </schema:NoiseExpression>
<schema:Unit > {0,1} </schema:Unit>
</schema:ModelValue>
Attributes
QName
Type
Use
addNoise
xs:boolean
required
key
restriction of xs:ID
required
name
restriction of xs:string
required
simulationType
restriction of xs:string
required
Source
<xs:element name= "ModelValue" type= "schema:modelValue.datatype" />
Element schema:Unit
Element schema:ListOfReactions
Element schema:Reaction
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:reaction.datatype
Properties
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:ListOfSubstrates{0,1} ,
schema:ListOfProducts{0,1} ,
schema:ListOfModifiers{0,1} ,
schema:ListOfConstants{0,1} ,
schema:KineticLaw{0,1} ,
schema:NoiseExpression{0,1}
Children
schema:Comment , schema:KineticLaw , schema:ListOfConstants , schema:ListOfModifiers , schema:ListOfProducts , schema:ListOfSubstrates , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression
Instance
<schema:Reaction addNoise= "" fast= "" key= "" name= "" reversible= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:MiriamAnnotation > {0,1} </schema:MiriamAnnotation>
<schema:Comment > {0,1} </schema:Comment>
<schema:ListOfUnsupportedAnnotations > {0,1} </schema:ListOfUnsupportedAnnotations>
<schema:ListOfSubstrates > {0,1} </schema:ListOfSubstrates>
<schema:ListOfProducts > {0,1} </schema:ListOfProducts>
<schema:ListOfModifiers > {0,1} </schema:ListOfModifiers>
<schema:ListOfConstants > {0,1} </schema:ListOfConstants>
<schema:KineticLaw function= "" scalingCompartment= "" unitType= "" > {0,1} </schema:KineticLaw>
<schema:NoiseExpression > {0,1} </schema:NoiseExpression>
</schema:Reaction>
Attributes
QName
Type
Use
addNoise
xs:boolean
required
fast
xs:boolean
required
key
restriction of xs:ID
required
name
restriction of xs:string
required
reversible
xs:boolean
required
Source
<xs:element name= "Reaction" type= "schema:reaction.datatype" />
Element schema:ListOfSubstrates
Element schema:Substrate
Element schema:ListOfProducts
Element schema:Product
Element schema:ListOfModifiers
Element schema:Modifier
Element schema:ListOfConstants
Element schema:Constant
Element schema:KineticLaw
Element schema:ListOfCallParameters
Element schema:CallParameter
Element schema:SourceParameter
Element schema:ListOfEvents
Element schema:Event
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:event.datatype
Properties
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:TriggerExpression ,
schema:DelayExpression{0,1} ,
schema:PriorityExpression{0,1} ,
schema:ListOfAssignments{0,1}
Children
schema:Comment , schema:DelayExpression , schema:ListOfAssignments , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:PriorityExpression , schema:TriggerExpression
Instance
<schema:Event delayAssignment= "" fireAtInitialTime= "" key= "" name= "" persistentTrigger= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:MiriamAnnotation > {0,1} </schema:MiriamAnnotation>
<schema:Comment > {0,1} </schema:Comment>
<schema:ListOfUnsupportedAnnotations > {0,1} </schema:ListOfUnsupportedAnnotations>
<schema:TriggerExpression > {1,1} </schema:TriggerExpression>
<schema:DelayExpression > {0,1} </schema:DelayExpression>
<schema:PriorityExpression > {0,1} </schema:PriorityExpression>
<schema:ListOfAssignments > {0,1} </schema:ListOfAssignments>
</schema:Event>
Attributes
Source
<xs:element name= "Event" type= "schema:event.datatype" />
Element schema:TriggerExpression
Element schema:DelayExpression
Element schema:PriorityExpression
Element schema:ListOfAssignments
Element schema:Assignment
Element schema:ListOfModelParameterSets
Element schema:ModelParameterSet
Element schema:ModelParameterGroup
Element schema:ModelParameter
Element schema:StateTemplate
Element schema:StateTemplateVariable
Element schema:InitialState
Element schema:ListOfTasks
Element schema:Task
Element schema:Problem
Element schema:ParameterGroup
Element schema:Parameter
Element schema:ParameterText
Element schema:Method
Element schema:ListOfReports
Element schema:Table
Element schema:Object
Element schema:Header
Element schema:Body
Element schema:Footer
Element schema:ListOfPlots
Element schema:PlotSpecification
Element schema:ListOfPlotItems
Element schema:PlotItem
Element schema:ListOfChannels
Element schema:ChannelSpec
Element schema:GUI
Element schema:ListOfSliders
Element schema:Slider
Element schema:ListOfLayouts
Element schema:Layout
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:layout.datatype
Properties
Used by
Model
schema:Dimensions ,
schema:ListOfCompartmentGlyphs{0,1} ,
schema:ListOfMetabGlyphs{0,1} ,
schema:ListOfReactionGlyphs{0,1} ,
schema:ListOfTextGlyphs{0,1} ,
schema:ListOfAdditionalGraphicalObjects{0,1} ,
schema:ListOfRenderInformation{0,1}
Children
schema:Dimensions , schema:ListOfAdditionalGraphicalObjects , schema:ListOfCompartmentGlyphs , schema:ListOfMetabGlyphs , schema:ListOfReactionGlyphs , schema:ListOfRenderInformation , schema:ListOfTextGlyphs
Instance
<schema:Layout key= "" name= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:Dimensions height= "" width= "" > {1,1} </schema:Dimensions>
<schema:ListOfCompartmentGlyphs > {0,1} </schema:ListOfCompartmentGlyphs>
<schema:ListOfMetabGlyphs > {0,1} </schema:ListOfMetabGlyphs>
<schema:ListOfReactionGlyphs > {0,1} </schema:ListOfReactionGlyphs>
<schema:ListOfTextGlyphs > {0,1} </schema:ListOfTextGlyphs>
<schema:ListOfAdditionalGraphicalObjects > {0,1} </schema:ListOfAdditionalGraphicalObjects>
<schema:ListOfRenderInformation > {0,1} </schema:ListOfRenderInformation>
</schema:Layout>
Attributes
QName
Type
Use
key
restriction of xs:ID
required
name
xs:string
optional
Source
<xs:element name= "Layout" type= "schema:layout.datatype" />
Element schema:ListOfCompartmentGlyphs
Element schema:CompartmentGlyph
Element schema:BoundingBox
Element schema:Position
Element schema:ListOfMetabGlyphs
Element schema:MetaboliteGlyph
Element schema:ListOfReactionGlyphs
Element schema:ReactionGlyph
Element schema:ListOfCurveSegments
Element schema:LineSegment
Element schema:Start
Element schema:End
Element schema:CubicBezier
Element schema:BasePoint1
Element schema:BasePoint2
Element schema:ListOfMetaboliteReferenceGlyphs
Element schema:MetaboliteReferenceGlyph
Element schema:ListOfTextGlyphs
Element schema:TextGlyph
Element schema:ListOfAdditionalGraphicalObjects
Element schema:AdditionalGraphicalObject
Element schema:ListOfRenderInformation
Element schema:ListOfColorDefinitions
Element schema:ColorDefinition
Element schema:ListOfGradientDefinitions
Element schema:gradientGroup.datatype
Element schema:ListOfLineEndings
Element schema:LineEnding
Element schema:Group
Namespace
http://www.copasi.org/static/schema
Diagram
Type
schema:group.datatype
Properties
Used by
Model
Children
schema:Curve , schema:Ellipse , schema:Group , schema:Image , schema:Polygon , schema:Rectangle , schema:Text
Instance
<schema:Group endHead= "" fill= "" fill-rule= "" font-family= "" font-size= "" font-style= "" font-weight= "" startHead= "" stroke= "" stroke-dasharray= "" stroke-width= "" text-anchor= "" transform= "" vtext-anchor= "" xmlns:schema= "http://www.copasi.org/static/schema" >
<schema:Group endHead= "" fill= "" fill-rule= "" font-family= "" font-size= "" font-style= "" font-weight= "" startHead= "" stroke= "" stroke-dasharray= "" stroke-width= "" text-anchor= "" transform= "" vtext-anchor= "" > {1,1} </schema:Group>
<schema:Text font-family= "" font-size= "" font-style= "" font-weight= "" stroke= "" stroke-dasharray= "" stroke-width= "" text-anchor= "" transform= "" vtext-anchor= "" x= "" y= "" > {1,1} </schema:Text>
<schema:Rectangle fill= "" fill-rule= "" height= "" rx= "" ry= "" stroke= "" stroke-dasharray= "" stroke-width= "" transform= "" width= "" x= "" y= "" > {1,1} </schema:Rectangle>
<schema:Ellipse cx= "" cy= "" fill= "" fill-rule= "" rx= "" ry= "" stroke= "" stroke-dasharray= "" stroke-width= "" transform= "" > {1,1} </schema:Ellipse>
<schema:Polygon fill= "" fill-rule= "" stroke= "" stroke-dasharray= "" stroke-width= "" transform= "" > {1,1} </schema:Polygon>
<schema:Image height= "" href= "" transform= "" width= "" x= "" y= "" > {1,1} </schema:Image>
<schema:Curve endHead= "" startHead= "" stroke= "" stroke-dasharray= "" stroke-width= "" transform= "" > {1,1} </schema:Curve>
</schema:Group>
Attributes
Source
<xs:element name= "Group" type= "schema:group.datatype" />
Element schema:Text
Element schema:Rectangle
Element schema:Ellipse
Element schema:Polygon
Element schema:ListOfElements
Element schema:renderCurve.element
Element schema:Image
Element schema:ListOfGlobalRenderInformation
Element schema:SBMLReference
Element schema:SBMLMap
Element schema:ListOfUnitDefinitions
Element schema:UnitDefinition
Element schema:Stop
Element schema:RadialGradient
Element schema:LinearGradient
Element schema:RenderPoint
Element schema:RenderCubicBezier
Complex Type schema:listOfFunctions.datatype
Complex Type schema:rdf.datatype
Complex Type schema:listOfUnsupportedAnnotations.datatype
Complex Type schema:UnsupportedAnnotation.datatype
Simple Type schema:expression.simpletype
Complex Type schema:listOfParameterDescriptions.datatype
Complex Type schema:model.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:InitialExpression{0,1} ,
schema:ListOfCompartments{0,1} ,
schema:ListOfMetabolites{0,1} ,
schema:ListOfModelValues{0,1} ,
schema:ListOfReactions{0,1} ,
schema:ListOfEvents{0,1} ,
schema:ListOfModelParameterSets{0,1} ,
schema:StateTemplate{0,1} ,
schema:InitialState{0,1}
Children
schema:Comment , schema:InitialExpression , schema:InitialState , schema:ListOfCompartments , schema:ListOfEvents , schema:ListOfMetabolites , schema:ListOfModelParameterSets , schema:ListOfModelValues , schema:ListOfReactions , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:StateTemplate
Attributes
Source
<xs:complexType name= "model.datatype" >
<xs:sequence >
<xs:group ref= "schema:annotation.datatype" />
<xs:element minOccurs= "0" ref= "schema:InitialExpression" />
<xs:element minOccurs= "0" ref= "schema:ListOfCompartments" />
<xs:element minOccurs= "0" ref= "schema:ListOfMetabolites" />
<xs:element minOccurs= "0" ref= "schema:ListOfModelValues" />
<xs:element minOccurs= "0" ref= "schema:ListOfReactions" />
<xs:element minOccurs= "0" ref= "schema:ListOfEvents" />
<xs:element minOccurs= "0" ref= "schema:ListOfModelParameterSets" />
<xs:element minOccurs= "0" ref= "schema:StateTemplate" />
<xs:element minOccurs= "0" ref= "schema:InitialState" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "Model_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "simulationType" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "time" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "timeUnit" use= "required" type= "xs:string" />
<xs:attribute name= "volumeUnit" use= "required" type= "xs:string" />
<xs:attribute name= "areaUnit" use= "required" type= "xs:string" />
<xs:attribute name= "lengthUnit" use= "required" type= "xs:string" />
<xs:attribute name= "quantityUnit" use= "required" type= "xs:string" />
<xs:attribute name= "type" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "stochastic" />
<xs:enumeration value= "deterministic" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "avogadroConstant" use= "required" type= "xs:double" />
</xs:complexType>
Complex Type schema:listOfCompartments.datatype
Complex Type schema:compartment.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:Expression{0,1} ,
schema:InitialExpression{0,1} ,
schema:NoiseExpression{0,1}
Children
schema:Comment , schema:Expression , schema:InitialExpression , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression
Attributes
Source
<xs:complexType name= "compartment.datatype" >
<xs:sequence >
<xs:group ref= "schema:annotation.datatype" />
<xs:element minOccurs= "0" ref= "schema:Expression" />
<xs:element minOccurs= "0" ref= "schema:InitialExpression" />
<xs:element minOccurs= "0" ref= "schema:NoiseExpression" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "Compartment_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "simulationType" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "ode" />
<xs:enumeration value= "assignment" />
<xs:enumeration value= "fixed" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "dimensionality" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:int" >
<xs:minInclusive value= "0" />
<xs:maxInclusive value= "3" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "addNoise" use= "required" type= "xs:boolean" />
</xs:complexType>
Complex Type schema:listOfMetabolites.datatype
Complex Type schema:metabolite.datatype
Complex Type schema:listOfModelValues.datatype
Complex Type schema:modelValue.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:Expression{0,1} ,
schema:InitialExpression{0,1} ,
schema:NoiseExpression{0,1} ,
schema:Unit{0,1}
Children
schema:Comment , schema:Expression , schema:InitialExpression , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression , schema:Unit
Attributes
QName
Type
Use
addNoise
xs:boolean
required
key
restriction of xs:ID
required
name
restriction of xs:string
required
simulationType
restriction of xs:string
required
Source
<xs:complexType name= "modelValue.datatype" >
<xs:sequence >
<xs:group ref= "schema:annotation.datatype" />
<xs:element minOccurs= "0" ref= "schema:Expression" />
<xs:element minOccurs= "0" ref= "schema:InitialExpression" />
<xs:element minOccurs= "0" ref= "schema:NoiseExpression" />
<xs:element minOccurs= "0" ref= "schema:Unit" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "ModelValue_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "simulationType" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "ode" />
<xs:enumeration value= "assignment" />
<xs:enumeration value= "fixed" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "addNoise" use= "required" type= "xs:boolean" />
</xs:complexType>
Complex Type schema:listOfReactions.datatype
Complex Type schema:reaction.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:ListOfSubstrates{0,1} ,
schema:ListOfProducts{0,1} ,
schema:ListOfModifiers{0,1} ,
schema:ListOfConstants{0,1} ,
schema:KineticLaw{0,1} ,
schema:NoiseExpression{0,1}
Children
schema:Comment , schema:KineticLaw , schema:ListOfConstants , schema:ListOfModifiers , schema:ListOfProducts , schema:ListOfSubstrates , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:NoiseExpression
Attributes
QName
Type
Use
addNoise
xs:boolean
required
fast
xs:boolean
required
key
restriction of xs:ID
required
name
restriction of xs:string
required
reversible
xs:boolean
required
Source
<xs:complexType name= "reaction.datatype" >
<xs:sequence >
<xs:group ref= "schema:annotation.datatype" />
<xs:element minOccurs= "0" ref= "schema:ListOfSubstrates" />
<xs:element minOccurs= "0" ref= "schema:ListOfProducts" />
<xs:element minOccurs= "0" ref= "schema:ListOfModifiers" />
<xs:element minOccurs= "0" ref= "schema:ListOfConstants" />
<xs:element minOccurs= "0" ref= "schema:KineticLaw" />
<xs:element minOccurs= "0" ref= "schema:NoiseExpression" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "Reaction_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "reversible" use= "required" type= "xs:boolean" />
<xs:attribute name= "fast" use= "required" type= "xs:boolean" />
<xs:attribute name= "addNoise" use= "required" type= "xs:boolean" />
</xs:complexType>
Complex Type schema:listOfConstants.datatype
Complex Type schema:kineticLaw.datatype
Complex Type schema:listOfCallParameters.datatype
Complex Type schema:callParameter.datatype
Complex Type schema:listOfEvents.datatype
Complex Type schema:event.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:MiriamAnnotation{0,1} ,
schema:Comment{0,1} ,
schema:ListOfUnsupportedAnnotations{0,1} ,
schema:TriggerExpression ,
schema:DelayExpression{0,1} ,
schema:PriorityExpression{0,1} ,
schema:ListOfAssignments{0,1}
Children
schema:Comment , schema:DelayExpression , schema:ListOfAssignments , schema:ListOfUnsupportedAnnotations , schema:MiriamAnnotation , schema:PriorityExpression , schema:TriggerExpression
Attributes
Source
<xs:complexType name= "event.datatype" >
<xs:sequence >
<xs:group ref= "schema:annotation.datatype" />
<xs:element ref= "schema:TriggerExpression" />
<xs:element minOccurs= "0" ref= "schema:DelayExpression" />
<xs:element minOccurs= "0" ref= "schema:PriorityExpression" />
<xs:element minOccurs= "0" ref= "schema:ListOfAssignments" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "Event_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "fireAtInitialTime" use= "required" type= "xs:boolean" />
<xs:attribute name= "persistentTrigger" use= "required" type= "xs:boolean" />
<xs:attribute name= "delayAssignment" type= "xs:boolean" />
</xs:complexType>
Complex Type schema:listOfEventAssignments.datatype
Complex Type schema:listOfModelParameterSets.datatype
Complex Type schema:modelParameterSet.datatype
Complex Type schema:modelParameter.datatype
Complex Type schema:listOfTasks.datatype
Complex Type schema:task.datatype
Complex Type schema:parameterList.datatype
Simple Type schema:taskTypeEnumeration.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Type
restriction of xs:string
Facets
enumeration
lyapunovExponents
enumeration
parameterFitting
enumeration
timeCourse
enumeration
moieties
enumeration
sensitivities
enumeration
optimization
enumeration
metabolicControlAnalysis
enumeration
timeScaleSeparationAnalysis
enumeration
scan
enumeration
steadyState
enumeration
fluxMode
enumeration
timeScaleSeparation
enumeration
crosssection
enumeration
linearNoiseApproximation
enumeration
unset
Used by
Source
<xs:simpleType name= "taskTypeEnumeration.datatype" >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "lyapunovExponents" />
<xs:enumeration value= "parameterFitting" />
<xs:enumeration value= "timeCourse" />
<xs:enumeration value= "moieties" />
<xs:enumeration value= "sensitivities" />
<xs:enumeration value= "optimization" />
<xs:enumeration value= "metabolicControlAnalysis" />
<xs:enumeration value= "timeScaleSeparationAnalysis" />
<xs:enumeration value= "scan" />
<xs:enumeration value= "steadyState" />
<xs:enumeration value= "fluxMode" />
<xs:enumeration value= "timeScaleSeparation" />
<xs:enumeration value= "crosssection" />
<xs:enumeration value= "linearNoiseApproximation" />
<xs:enumeration value= "unset" />
</xs:restriction>
</xs:simpleType>
Complex Type schema:listOfReportSpecifications.datatype
Complex Type schema:reportSpecification.datatype
Complex Type schema:reportSection.datatype
Complex Type schema:listOfPlotSpecifications.datatype
Complex Type schema:plotSpecification.datatype
Complex Type schema:listOfPlotItems.datatype
Complex Type schema:plotItem.datatype
Complex Type schema:listOfChannels.datatype
Complex Type schema:gui.datatype
Complex Type schema:listOfSliders.datatype
Complex Type schema:listOfLayouts.datatype
Complex Type schema:layout.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Model
schema:Dimensions ,
schema:ListOfCompartmentGlyphs{0,1} ,
schema:ListOfMetabGlyphs{0,1} ,
schema:ListOfReactionGlyphs{0,1} ,
schema:ListOfTextGlyphs{0,1} ,
schema:ListOfAdditionalGraphicalObjects{0,1} ,
schema:ListOfRenderInformation{0,1}
Children
schema:Dimensions , schema:ListOfAdditionalGraphicalObjects , schema:ListOfCompartmentGlyphs , schema:ListOfMetabGlyphs , schema:ListOfReactionGlyphs , schema:ListOfRenderInformation , schema:ListOfTextGlyphs
Attributes
QName
Type
Use
key
restriction of xs:ID
required
name
xs:string
optional
Source
<xs:complexType name= "layout.datatype" >
<xs:sequence >
<xs:element name= "Dimensions" >
<xs:complexType >
<xs:attributeGroup ref= "schema:dimension.datatype" />
</xs:complexType>
</xs:element>
<xs:element minOccurs= "0" ref= "schema:ListOfCompartmentGlyphs" />
<xs:element minOccurs= "0" ref= "schema:ListOfMetabGlyphs" />
<xs:element minOccurs= "0" ref= "schema:ListOfReactionGlyphs" />
<xs:element minOccurs= "0" ref= "schema:ListOfTextGlyphs" />
<xs:element minOccurs= "0" ref= "schema:ListOfAdditionalGraphicalObjects" />
<xs:element minOccurs= "0" ref= "schema:ListOfRenderInformation" />
</xs:sequence>
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "Layout_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "name" type= "xs:string" />
</xs:complexType>
Complex Type schema:listOfCompartmentGlyphs.datatype
Complex Type schema:glyph.datatype
Complex Type schema:boundingBox.datatype
Complex Type schema:listOfMetabGlyphs.datatype
Complex Type schema:listOfReactionGlyphs.datatype
Complex Type schema:layoutCurve.datatype
Complex Type schema:lineSegment.datatype
Complex Type schema:cubicBezier.datatype
Complex Type schema:metaboliteReferenceGlyp.datatype
Complex Type schema:listOfTextGlyphs.datatype
Complex Type schema:listOfAdditionalGraphicalObjects.datatype
Complex Type schema:listOfLocalRenderInformation.datatype
Complex Type schema:localRenderInformation.datatype
Complex Type schema:renderInformationBase.datatype
Simple Type schema:layoutId.datatype
Simple Type schema:colorValue.datatype
Complex Type schema:lineEnding.datatype
Complex Type schema:group.datatype
Simple Type schema:colorValueOrId.datatype
Simple Type schema:relAbsValue.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Type
restriction of xs:string
Facets
pattern
\s*((([+\-]?[0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?)([+\-][0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?%))|([+\-]?[0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?%?))\s*
Used by
Attributes
schema:ellipse.datatype/@cx , schema:ellipse.datatype/@cy , schema:ellipse.datatype/@rx , schema:ellipse.datatype/@ry , schema:gradientStop.datatype/@offset , schema:group.datatype/@font-size , schema:groupElements.datatype/@font-size , schema:image.dataype/@height , schema:image.dataype/@width , schema:image.dataype/@x , schema:image.dataype/@y , schema:linearGradient.datatype/@x1 , schema:linearGradient.datatype/@x2 , schema:linearGradient.datatype/@y1 , schema:linearGradient.datatype/@y2 , schema:linearGradient.datatype/@z1 , schema:linearGradient.datatype/@z2 , schema:radialGradient.datatype/@cx , schema:radialGradient.datatype/@cy , schema:radialGradient.datatype/@fx , schema:radialGradient.datatype/@fy , schema:radialGradient.datatype/@r , schema:rectangle.datatype/@height , schema:rectangle.datatype/@rx , schema:rectangle.datatype/@ry , schema:rectangle.datatype/@width , schema:rectangle.datatype/@x , schema:rectangle.datatype/@y , schema:renderCubicBezier.datatype/@basePoint1_x , schema:renderCubicBezier.datatype/@basePoint1_y , schema:renderCubicBezier.datatype/@basePoint2_x , schema:renderCubicBezier.datatype/@basePoint2_y , schema:renderPoint.datatytpe/@x , schema:renderPoint.datatytpe/@y , schema:text.datatype/@font-size , schema:text.datatype/@x , schema:text.datatype/@y
Source
<xs:simpleType name= "relAbsValue.datatype" >
<xs:restriction base= "xs:string" >
<xs:pattern value= "\s*((([+\-]?[0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?)([+\-][0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?%))|([+\-]?[0-9]*(\.[0-9]*)?([eE][+\-]?[0-9]+)?%?))\s*" />
</xs:restriction>
</xs:simpleType>
Simple Type schema:fontStyle.datatype
Simple Type schema:fontWeight.datatype
Simple Type schema:textAnchor.datatype
Simple Type schema:vtextAnchor.datatype
Complex Type schema:polygon.datatype
Complex Type schema:renderCurveElements.datatype
Complex Type schema:renderCurve.datatype
Simple Type schema:layoutIdRef.datatype
Complex Type schema:localStyle.datatype
Complex Type schema:style.datatype
Simple Type schema:wsSeparatedStringList.datatype
Complex Type schema:listOfGlobalRenderInformation.datatype
Complex Type schema:globalRenderInformation.datatype
Complex Type schema:globalStyle.dataType
Complex Type schema:listOfUnitDefinitions.datatype
Simple Type schema:commaSeparatedStringList.datatype
Complex Type schema:gradientBase.datatype
Complex Type schema:radialGradient.datatype
Complex Type schema:linearGradient.datatype
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
product
enumeration
volume
enumeration
time
enumeration
modifier
enumeration
variable
enumeration
substrate
enumeration
constant
Used by
Source
<xs:attribute name= "role" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "product" />
<xs:enumeration value= "volume" />
<xs:enumeration value= "time" />
<xs:enumeration value= "modifier" />
<xs:enumeration value= "variable" />
<xs:enumeration value= "substrate" />
<xs:enumeration value= "constant" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
MassAction
enumeration
PreDefined
enumeration
UserDefined
enumeration
Function
enumeration
Expression
Used by
Source
<xs:attribute name= "type" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "MassAction" />
<xs:enumeration value= "PreDefined" />
<xs:enumeration value= "UserDefined" />
<xs:enumeration value= "Function" />
<xs:enumeration value= "Expression" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
Model
enumeration
Compartment
enumeration
Species
enumeration
ModelValue
enumeration
ReactionParameter
Used by
Source
<xs:attribute name= "type" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "Model" />
<xs:enumeration value= "Compartment" />
<xs:enumeration value= "Species" />
<xs:enumeration value= "ModelValue" />
<xs:enumeration value= "ReactionParameter" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
time
enumeration
ode
enumeration
assignment
enumeration
reactions
enumeration
fixed
Used by
Source
<xs:attribute name= "simulationType" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "time" />
<xs:enumeration value= "ode" />
<xs:enumeration value= "assignment" />
<xs:enumeration value= "reactions" />
<xs:enumeration value= "fixed" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
float
enumeration
unsignedFloat
enumeration
integer
enumeration
unsignedInteger
enumeration
bool
enumeration
string
enumeration
cn
enumeration
key
enumeration
file
Used by
Source
<xs:attribute name= "type" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "float" />
<xs:enumeration value= "unsignedFloat" />
<xs:enumeration value= "integer" />
<xs:enumeration value= "unsignedInteger" />
<xs:enumeration value= "bool" />
<xs:enumeration value= "string" />
<xs:enumeration value= "cn" />
<xs:enumeration value= "key" />
<xs:enumeration value= "file" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
schema:taskTypeEnumeration.datatype
Properties
Facets
enumeration
lyapunovExponents
enumeration
parameterFitting
enumeration
timeCourse
enumeration
moieties
enumeration
sensitivities
enumeration
optimization
enumeration
metabolicControlAnalysis
enumeration
timeScaleSeparationAnalysis
enumeration
scan
enumeration
steadyState
enumeration
fluxMode
enumeration
timeScaleSeparation
enumeration
crosssection
enumeration
linearNoiseApproximation
enumeration
unset
Used by
Source
<xs:attribute name= "type" use= "required" type= "schema:taskTypeEnumeration.datatype" />
Namespace
No namespace
Type
schema:taskTypeEnumeration.datatype
Properties
Facets
enumeration
lyapunovExponents
enumeration
parameterFitting
enumeration
timeCourse
enumeration
moieties
enumeration
sensitivities
enumeration
optimization
enumeration
metabolicControlAnalysis
enumeration
timeScaleSeparationAnalysis
enumeration
scan
enumeration
steadyState
enumeration
fluxMode
enumeration
timeScaleSeparation
enumeration
crosssection
enumeration
linearNoiseApproximation
enumeration
unset
Used by
Source
<xs:attribute name= "taskType" use= "required" type= "schema:taskTypeEnumeration.datatype" />
Namespace
No namespace
Type
restriction of xs:string
Properties
Facets
enumeration
unsignedInteger
enumeration
unsignedFloat
enumeration
integer
enumeration
float
Used by
Source
<xs:attribute name= "objectType" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "unsignedInteger" />
<xs:enumeration value= "unsignedFloat" />
<xs:enumeration value= "integer" />
<xs:enumeration value= "float" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
Namespace
No namespace
Type
schema:textAnchor.datatype
Properties
Facets
enumeration
start
enumeration
middle
enumeration
end
Source
<xs:attribute name= "text-anchor" type= "schema:textAnchor.datatype" />
Namespace
No namespace
Type
schema:vtextAnchor.datatype
Properties
Facets
enumeration
top
enumeration
middle
enumeration
bottom
Source
<xs:attribute name= "vtext-anchor" type= "schema:vtextAnchor.datatype" />
Element Group schema:annotation.datatype
Element Group schema:xhtml.datatype
Element Group schema:modelParameterGroup.datatype
Element Group schema:curveSegment.element
Element Group schema:groupElements.datatype
Element Group schema:other.datatype
Element Group schema:rdfContent.datatype
Attribute Group schema:parameterDescription.datatype
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Attributes
QName
Type
Use
key
restriction of xs:ID
required
name
restriction of xs:string
required
order
xs:nonNegativeInteger
required
role
restriction of xs:string
required
Source
<xs:attributeGroup name= "parameterDescription.datatype" >
<xs:attributeGroup ref= "schema:name.attribute" />
<xs:attribute name= "key" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:ID" >
<xs:pattern value= "FunctionParameter_\d+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
<xs:attribute name= "order" use= "required" type= "xs:nonNegativeInteger" />
<xs:attribute name= "role" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:enumeration value= "product" />
<xs:enumeration value= "volume" />
<xs:enumeration value= "time" />
<xs:enumeration value= "modifier" />
<xs:enumeration value= "variable" />
<xs:enumeration value= "substrate" />
<xs:enumeration value= "constant" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
</xs:attributeGroup>
Attribute Group schema:name.attribute
Namespace
http://www.copasi.org/static/schema
Diagram
Used by
Attribute Groups
schema:constant.datatype , schema:parameter.datatype , schema:parameterDescription.datatype , schema:parameterText.datatype
Elements
schema:Function , schema:Method , schema:ParameterGroup , schema:UnitDefinition
Complex Types
schema:compartment.datatype , schema:event.datatype , schema:metabolite.datatype , schema:model.datatype , schema:modelParameterSet.datatype , schema:modelValue.datatype , schema:plotItem.datatype , schema:plotSpecification.datatype , schema:reaction.datatype , schema:reportSpecification.datatype , schema:task.datatype
Attributes
QName
Type
Use
name
restriction of xs:string
required
Source
<xs:attributeGroup name= "name.attribute" >
<xs:attribute name= "name" use= "required" >
<xs:simpleType >
<xs:restriction base= "xs:string" >
<xs:pattern value= "[\S ]+" />
</xs:restriction>
</xs:simpleType>
</xs:attribute>
</xs:attributeGroup>
Attribute Group schema:reactionParticipant.datatype
Attribute Group schema:constant.datatype
Attribute Group schema:report.datatype
Attribute Group schema:parameter.datatype
Attribute Group schema:parameterText.datatype
Attribute Group schema:channelSpec.datatype
Attribute Group schema:slider.datatype
Attribute Group schema:dimension.datatype
Attribute Group schema:layoutPoint.datatype
Attribute Group schema:colorDefinition.datatype
Attribute Group schema:text.datatype
Attribute Group schema:graphicalPrimitive1D.datatype
Attribute Group schema:transformation.datatype
Attribute Group schema:rectangle.datatype
Attribute Group schema:graphicalPrimitive2D.datatype
Attribute Group schema:ellipse.datatype
Attribute Group schema:image.dataype
Attribute Group schema:gradientStop.datatype
Attribute Group schema:renderPoint.datatytpe
Attribute Group schema:renderCubicBezier.datatype