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