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examples_serialization.tex
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examples_serialization.tex
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% -----------------------------------------------------------------------------
\section{Examples of Serialization}
\label{ser:examples}
% -----------------------------------------------------------------------------
\subsection{Simple Examples}
\subsubsection{Serializing Sequence Objects}
This example shows the serialization of a \sbol{Sequence}.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23119:Design"/>
<sbol:elements>ttgacagctagctcagtcctaggtataatgctagc</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing ComponentDefinition Objects}
This example shows the serialization of a simple promoter \sbol{ComponentDefinition} and the \sbol{Sequence} to which it refers.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_J23119"/>
<dcterms:title>J23119 promoter</dcterms:title>
<dcterms:description>Constitutive promoter</dcterms:description>
<sbol:type rdf:resource="http://identifiers.org/chebi/CHEBI:4705"/>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000613"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
</sbol:ComponentDefinition>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23119:Design"/>
<sbol:elements>ttgacagctagctcagtcctaggtataatgctagc</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing SequenceConstraint Objects}
This example shows the serialization of \sbol{SequenceConstraint} between two \sbol{Component} objects in a composite promoter \sbol{ComponentDefinition}. In the example, the promoter \sbol{ComponentDefinition} has two sub-\sbol{Component}s that instantiate the \sbol{ComponentDefinition} objects for a core promoter region and and a binding site. The \sbol{SequenceConstraint} specifies that the core promoter region precedes the binding site.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_K174004">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_K174004"/>
<sbol:displayId>BBa_K174004</sbol:displayId>
<dcterms:title>pspac promoter</dcterms:title>
<dcterms:description>LacI repressible promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:sequenceConstraint>
<sbol:SequenceConstraint rdf:about="http://partsregistry.org/cd/BBa_K174004/r1">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_K174004/r1"/>
<sbol:displayId>r1</sbol:displayId>
<sbol:restriction rdf:resource="http://sbols.org/v2#precedes"/>
<sbol:subject rdf:resource="http://partsregistry.org/cd/pspac"/>
<sbol:object rdf:resource="http://partsregistry.org/cd/LacI_operator"/>
</sbol:SequenceConstraint>
</sbol:sequenceConstraint>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/pspac">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/pspac"/>
<sbol:displayId>pspac</sbol:displayId>
<dcterms:title>constitutive promoter</dcterms:title>
<dcterms:description>pspac core promoter region</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/LacI_operator">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/LacI_operator"/>
<sbol:displayId>LacI_operator</sbol:displayId>
<dcterms:title>LacI operator</dcterms:title>
<dcterms:description>LacI binding site</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000057"/>
</sbol:ComponentDefinition>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing Cut Location Objects}
This example shows the serialization of a \sbol{Cut} \sbol{Location}.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://partsregistry.org/Part:BBa_J23119"/>
<dcterms:title>J23119 promoter</dcterms:title>
<dcterms:description>Constitutive promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000613"/>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_J23119/cutat10">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119/cutat10"/>
<sbol:displayId>cutat10</sbol:displayId>
<sbol:location>
<sbol:Cut rdf:about="http://partsregistry.org/cd/BBa_J23119/cutat10/cut1">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119/cutat10/cut1"/>
<sbol:displayId>cut1</sbol:displayId>
<sbol:at>10</sbol:at>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Cut>
</sbol:location>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_J23119/cutat12">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119/cutat12"/>
<sbol:displayId>cutat12</sbol:displayId>
<sbol:location>
<sbol:Cut rdf:about="http://partsregistry.org/cd/BBa_J23119/cutat12/cut2">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119/cutat12/cut2"/>
<sbol:displayId>cut2</sbol:displayId>
<sbol:at>12</sbol:at>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Cut>
</sbol:location>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
</sbol:ComponentDefinition>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://parts.igem.org/Part:BBa_J23119:Design"/>
<sbol:elements>ttgacagctagctcagtcctaggtataatgctagc</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing Model Objects}
This example shows the serialization of a \sbol{Model}. In this example, the \sbol{Model} refers to an ODE model written in SBML that can be accessed the identified source repository.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:Model rdf:about="http://www.sbolstandard.org/examples/pIKE_Toggle_1">
<sbol:persistentIdentity rdf:resource="http://www.sbolstandard.org/examples/pIKE_Toggle_1"/>
<sbol:displayId>pIKE_Toggle_1</sbol:displayId>
<dcterms:title>pIKE_Toggle_1 toggle switch</dcterms:title>
<sbol:source rdf:resource="http://virtualparts.org/part/pIKE_Toggle_1"/>
<sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
<sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
</sbol:Model>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing ModuleDefinition Objects}
This example shows the serialization of a simple \sbol{ModuleDefinition}. This \sbol{ModuleDefinition} includes an \sbol{Interaction} that represents the translation of a protein.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ModuleDefinition rdf:about="http://sbolstandard.org/example/md/GFP_expression">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression"/>
<sbol:displayId>GFP_expression</sbol:displayId>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/md/GFP_expression/Constitutive_GFP">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression/Constitutive_GFP"/>
<sbol:displayId>Constitutive_GFP</sbol:displayId>
<sbol:definition rdf:resource="http://sbolstandard.org/example/GFP_generator"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#in"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/md/GFP_expression/GFP_protein">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression/GFP_protein"/>
<sbol:displayId>GFP_protein</sbol:displayId>
<sbol:definition rdf:resource="http://sbolstandard.org/example/GFP"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#out"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:interaction>
<sbol:Interaction rdf:about="http://sbolstandard.org/example/md/GFP_expression/express_GFP">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression/express_GFP"/>
<sbol:displayId>express_GFP</sbol:displayId>
<sbol:type rdf:resource="Transcription"/>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/md/GFP_expression/express_GFP/Protein">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression/express_GFP/Protein"/>
<sbol:displayId>Protein</sbol:displayId>
<sbol:participant rdf:resource="http://sbolstandard.org/example/md/GFP_expression/GFP_protein"/>
</sbol:Participation>
</sbol:participation>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/md/GFP_expression/express_GFP/CDS">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/md/GFP_expression/express_GFP/CDS"/>
<sbol:displayId>CDS</sbol:displayId>
<sbol:participant rdf:resource="http://sbolstandard.org/example/md/GFP_expression/Constitutive_GFP"/>
</sbol:Participation>
</sbol:participation>
</sbol:Interaction>
</sbol:interaction>
</sbol:ModuleDefinition>
</rdf:RDF>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing Application Specific Data Within SBOL Objects}
This example shows the serialization of application-specific data from \sbol{Annotation} objects. A \sbol{ComponentDefinition} that represents a promoter is annotated with custom data on the promoter's sigma factor and how it is regulated.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:pr="http://partsregistry.org/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<pr:group>iGEM2006_Berkeley</pr:group>
<pr:experience rdf:resource="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119"/>
<pr:information>
<pr:Information rdf:about="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_J23119">
<pr:sigmafactor>//rnap/prokaryote/ecoli/sigma70</pr:sigmafactor>
<pr:regulation>//regulation/constitutive</pr:regulation>
</pr:Information>
</pr:information>
<dcterms:title>J23119</dcterms:title>
<dcterms:description>Constitutive promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
</sbol:ComponentDefinition>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing Application-Specific Data Outside SBOL Objects}
This example shows the serialization of application-specific data from \sbol{GenericTopLevel} objects. Such data can be referenced by other SBOL objects via \sbol{Annotation} objects.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:myapp="http://www.myapp.org/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/cd/BBa_J23119">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/cd/BBa_J23119"/>
<sbol:displayId>BBa_J23119</sbol:displayId>
<prov:wasDerivedFrom rdf:resource="http://www.partsregistry.org/Part:BBa_J23119"/>
<myapp:datasheet rdf:resource="http://www.partsregistry.org/gen/datasheet1"/>
<dcterms:title>J23119</dcterms:title>
<dcterms:description>Constitutive promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
</sbol:ComponentDefinition>
<myapp:Datasheet rdf:about="http://www.partsregistry.org/gen/datasheet1">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/gen/datasheet1"/>
<sbol:displayId>datasheet1</sbol:displayId>
<myapp:characterizationData rdf:resource="http://www.myapp.org/measurement/1"/>
<myapp:transcriptionRate>1</myapp:transcriptionRate>
<dcterms:title>Datasheet 1</dcterms:title>
</myapp:Datasheet>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Serializing Collection Objects}
This example shows the serialization of a \sbol{Collection}. This \sbol{Collection} represents a library of promoters.
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:Collection rdf:about="http://parts.igem.org/Promoters/Catalog/Anderson">
<sbol:persistentIdentity rdf:resource="http://parts.igem.org/Promoters/Catalog/Anderson"/>
<sbol:displayId>Anderson</sbol:displayId>
<dcterms:title>Anderson promoters</dcterms:title>
<dcterms:description>The Anderson promoter collection</dcterms:description>
<sbol:member rdf:resource="http://partsregistry.org/Part:BBa_J23119"/>
<sbol:member rdf:resource="http://partsregistry.org/Part:BBa_J23118"/>
</sbol:Collection>
</rdf:RDF>
\end{lstlisting}
\subsection{Complex Examples}
\subsubsection{PoPS Receiver}
This example shows the serialization of the PoPS Receiver device designed by Canton and co-workers~\cite{canton-natbio-2008}.
In particular, this example includes the serialization of a \sbol{ComponentDefinition} that composes five \sbol{Component} objects to define the structure of a detector for the cell-cell signaling molecule 3OC$_6$HSL.
The five components are arranged in a sequence:
first come four \sbol{Component} objects that together implement constitutive expression of the LuxR protein, which in turn responds to 3OC$_6$HSL: a constitutive promoter, 5'UTR, coding sequence for LuxR, and terminator.
Finally, after these objects comes the \sbol{Component} object for the pLuxR promoter, which is activated in the presence of LuxR and 3OC$_6$HSL.
%
Complete details of the device can be found in the cited paper and also at \url{http://parts.igem.org/Part:BBa_F2620}.
\label{ser:F2620}
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:pr="http://partsregistry.org" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_F2620">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620"/>
<sbol:displayId>BBa_F2620</sbol:displayId>
<dcterms:title>BBa_F2620</dcterms:title>
<dcterms:description>3OC6HSL -> PoPS Receiver</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:00001411"/>
<sbol:component>
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/pLuxR">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
<sbol:displayId>pLuxR</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/luxR">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/luxR"/>
<sbol:displayId>luxR</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_C0062"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/pTetR">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/pTetR"/>
<sbol:displayId>pTetR</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_R0040"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/ter">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/ter"/>
<sbol:displayId>ter</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/rbs">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/rbs"/>
<sbol:displayId>rbs</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
</sbol:Component>
</sbol:component>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno3">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno3"/>
<sbol:displayId>anno3</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno3/location3">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno3/location3"/>
<sbol:displayId>location3</sbol:displayId>
<sbol:start>69</sbol:start>
<sbol:end>770</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/luxR"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5"/>
<sbol:displayId>anno5</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5/location5">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5/location5"/>
<sbol:displayId>location5</sbol:displayId>
<sbol:start>901</sbol:start>
<sbol:end>956</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno1">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno1"/>
<sbol:displayId>anno1</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno1/location1">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno1/location1"/>
<sbol:displayId>location1</sbol:displayId>
<sbol:start>1</sbol:start>
<sbol:end>55</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/pTetR"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno4">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno4"/>
<sbol:displayId>anno4</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno4/location4">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno4/location4"/>
<sbol:displayId>location4</sbol:displayId>
<sbol:start>771</sbol:start>
<sbol:end>900</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/ter"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2"/>
<sbol:displayId>anno2</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2/location2">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2/location2"/>
<sbol:displayId>location2</sbol:displayId>
<sbol:start>56</sbol:start>
<sbol:end>68</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/rbs"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0062">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
<sbol:displayId>BBa_R0062</sbol:displayId>
<dcterms:title>pLuxR</dcterms:title>
<dcterms:description>LuxR inducible promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0062"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0015">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
<sbol:displayId>BBa_B0015</sbol:displayId>
<dcterms:title>BBa_B0015</dcterms:title>
<dcterms:description>Double terminator</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0015"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_C0062">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_C0062"/>
<sbol:displayId>BBa_C0062</sbol:displayId>
<dcterms:title>luxR</dcterms:title>
<dcterms:description>luxR coding sequence</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_C0062"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0040">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<dcterms:title>pTetR</dcterms:title>
<dcterms:description>TetR repressible promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0040"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0034">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
<sbol:displayId>BBa_B0034</sbol:displayId>
<dcterms:title>BBa_B0034</dcterms:title>
<dcterms:description>RBS based on Elowitz repressilator</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0034"/>
</sbol:ComponentDefinition>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_B0034">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_B0034"/>
<sbol:displayId>BBa_B0034</sbol:displayId>
<sbol:elements>aaagaggagaaa</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_R0040">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<sbol:elements>tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_C0062">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_C0062"/>
<sbol:displayId>BBa_C0062</sbol:displayId>
<sbol:elements>atgcttatctgatatgactaaaatggtacattgtgaatattatttactcgcgatcatttatcctcattcta
tggttaaatctgatatttcaatcctagataattaccctaaaaaatggaggcaatattatgatgacgctaatttaataaaatatgat
cctatagtagattattctaactccaatcattcaccaattaattggaatatatttgaaaacaatgctgtaaataaaaaatctccaaa
tgtaattaaagaagcgaaaacatcaggtcttatcactgggtttagtttccctattcatacggctaacaatggcttcggaatgctta
gttttgcacattcagaaaaagacaactatatagatagtttatttttacatgcgtgtatgaacataccattaattgttccttctcta
gttgataattatcgaaaaataaatatagcaaataataaatcaaacaacgatttaaccaaaagagaaaaagaatgtttagcgtgggc
atgcgaaggaaaaagctcttgggatatttcaaaaatattaggttgcagtgagcgtactgtcactttccatttaaccaatgcgcaaa
tgaaactcaatacaacaaaccgctgccaaagtatttctaaagcaattttaacaggagcaattgattgcccatactttaaaaattaa
taacactgatagtgctagtgtagatcac</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_R0062">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_R0062"/>
<sbol:displayId>BBa_R0062</sbol:displayId>
<sbol:elements>acctgtaggatcgtacaggtttacgcaagaaaatggtttgttatagtcgaataaa</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
<sbol:Sequence rdf:about="http://partsregistry.org/seq/BBa_B0015">
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/seq/BBa_B0015"/>
<sbol:displayId>BBa_B0015</sbol:displayId>
<sbol:elements>ccaggcatcaaataaaacgaaaggctcagtcgaaagactgggcctttcgttttatctgttgtttgtcggtg
aacgctctctactagagtcacactggctcaccttcgggtgggcctttctgcgtttata</sbol:elements>
<sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>
</sbol:Sequence>
</rdf:RDF>
\end{lstlisting}
\subsubsection{Toggle Switch}
This example shows the serialization of the \sbol{ComponentDefinition} and \sbol{ModuleDefinition} objects for a LacI/TetR toggle switch similar to those constructed in \cite{Gardner2000}.
This design is essentially similar to the one presented in \ref{sec:examples}, except that it uses some alternate groupings in how the total design is built up out of smaller entities.
\label{ser:toggleswitch}
\lstsetsbol
\begin{lstlisting}
<?xml version="1.0" ?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:sbol="http://sbols.org/v2#">
<sbol:ModuleDefinition rdf:about="http://sbolstandard.org/example/toggle_switch">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch"/>
<sbol:displayId>toggle_switch</sbol:displayId>
<sbol:role rdf:resource="http://sbolstandard.org/example/module_role/toggle_switch"/>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/toggle_switch/TetR">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/TetR"/>
<sbol:displayId>TetR</sbol:displayId>
<sbol:definition rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/toggle_switch/LacI">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/LacI"/>
<sbol:displayId>LacI</sbol:displayId>
<sbol:definition rdf:resource="http://identifiers.org/uniprot/P03023"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:model rdf:resource="http://sbolstandard.org/example/toogleswitch"/>
<sbol:module>
<sbol:Module rdf:about="http://sbolstandard.org/example/toggle_switch/tetr_inverter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter"/>
<sbol:displayId>tetr_inverter</sbol:displayId>
<sbol:definition rdf:resource="http://sbolstandard.org/example/tetr_inverter"/>
<sbol:mapsTo>
<sbol:MapsTo rdf:about="http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/tetr_inverter/TetR_mapping"/>
<sbol:displayId>TetR_mapping</sbol:displayId>
<sbol:refinement rdf:resource="http://sbols.org/v2#useRemote"/>
<sbol:remote rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
<sbol:local rdf:resource="http://sbolstandard.org/example/toggle_switch/TetR"/>
</sbol:MapsTo>
</sbol:mapsTo>
</sbol:Module>
</sbol:module>
<sbol:module>
<sbol:Module rdf:about="http://sbolstandard.org/example/toggle_switch/laci_inverter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter"/>
<sbol:displayId>laci_inverter</sbol:displayId>
<sbol:definition rdf:resource="http://sbolstandard.org/example/laci_inverter"/>
<sbol:mapsTo>
<sbol:MapsTo rdf:about="http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toggle_switch/laci_inverter/LacI_mapping"/>
<sbol:displayId>LacI_mapping</sbol:displayId>
<sbol:refinement rdf:resource="http://sbols.org/v2#useRemote"/>
<sbol:remote rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
<sbol:local rdf:resource="http://sbolstandard.org/example/toggle_switch/LacI"/>
</sbol:MapsTo>
</sbol:mapsTo>
</sbol:Module>
</sbol:module>
</sbol:ModuleDefinition>
<sbol:ModuleDefinition rdf:about="http://sbolstandard.org/example/laci_inverter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter"/>
<sbol:displayId>laci_inverter</sbol:displayId>
<sbol:role rdf:resource="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter"/>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/laci_inverter/TF">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
<sbol:displayId>TF</sbol:displayId>
<sbol:definition rdf:resource="http://identifiers.org/uniprot/P03023"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/laci_inverter/promoter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/promoter"/>
<sbol:displayId>promoter</sbol:displayId>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:interaction>
<sbol:Interaction rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI"/>
<sbol:displayId>LacI_pLacI</sbol:displayId>
<sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000169"/>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/BBa_R0010"/>
<sbol:displayId>BBa_R0010</sbol:displayId>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000598"/>
<sbol:participant rdf:resource="http://sbolstandard.org/example/laci_inverter/promoter"/>
</sbol:Participation>
</sbol:participation>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/laci_inverter/LacI_pLacI/P03023"/>
<sbol:displayId>P03023</sbol:displayId>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
<sbol:participant rdf:resource="http://sbolstandard.org/example/laci_inverter/TF"/>
</sbol:Participation>
</sbol:participation>
</sbol:Interaction>
</sbol:interaction>
</sbol:ModuleDefinition>
<sbol:ModuleDefinition rdf:about="http://sbolstandard.org/example/tetr_inverter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter"/>
<sbol:displayId>tetr_inverter</sbol:displayId>
<sbol:role rdf:resource="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=inverter"/>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/tetr_inverter/TF">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
<sbol:displayId>TF</sbol:displayId>
<sbol:definition rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:functionalComponent>
<sbol:FunctionalComponent rdf:about="http://sbolstandard.org/example/tetr_inverter/promoter">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/promoter"/>
<sbol:displayId>promoter</sbol:displayId>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:direction rdf:resource="http://sbols.org/v2#inout"/>
</sbol:FunctionalComponent>
</sbol:functionalComponent>
<sbol:interaction>
<sbol:Interaction rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI"/>
<sbol:displayId>LacI_pLacI</sbol:displayId>
<sbol:type rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000169"/>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/Q6QR72"/>
<sbol:displayId>Q6QR72</sbol:displayId>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
<sbol:participant rdf:resource="http://sbolstandard.org/example/tetr_inverter/TF"/>
</sbol:Participation>
</sbol:participation>
<sbol:participation>
<sbol:Participation rdf:about="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/tetr_inverter/LacI_pLacI/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000598"/>
<sbol:participant rdf:resource="http://sbolstandard.org/example/tetr_inverter/promoter"/>
</sbol:Participation>
</sbol:participation>
</sbol:Interaction>
</sbol:interaction>
</sbol:ModuleDefinition>
<sbol:Model rdf:about="http://sbolstandard.org/example/toogleswitch">
<sbol:persistentIdentity rdf:resource="http://sbolstandard.org/example/toogleswitch"/>
<sbol:displayId>toogleswitch</sbol:displayId>
<sbol:source rdf:resource="http://virtualparts.org/part/pIKE_Toggle_1"/>
<sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
<sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
</sbol:Model>
<sbol:ComponentDefinition rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1"/>
<sbol:displayId>pIKE_Toggle_1</sbol:displayId>
<dcterms:title>LacI/TetR Toggle Switch</dcterms:title>
<dcterms:description>LacI/TetR Toggle Switch</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1"/>
<sbol:displayId>pIKERightCassette_1</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1"/>
<sbol:displayId>pIKELeftCassette_1</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1"/>
</sbol:Component>
</sbol:component>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2"/>
<sbol:displayId>anno2</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno2/location2"/>
<sbol:displayId>location2</sbol:displayId>
<sbol:start>1286</sbol:start>
<sbol:end>2834</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKERightCassette_1"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1"/>
<sbol:displayId>anno1</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/anno1/location1"/>
<sbol:displayId>location1</sbol:displayId>
<sbol:start>1</sbol:start>
<sbol:end>1285</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKE_Toggle_1/pIKELeftCassette_1"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_J61130">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61130"/>
<sbol:displayId>BBa_J61130</sbol:displayId>
<dcterms:title>BBa_J61101 RBS</dcterms:title>
<dcterms:description>RBS2</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61130"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_C0012">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_C0012"/>
<sbol:displayId>BBa_C0012</sbol:displayId>
<dcterms:title>lacI</dcterms:title>
<dcterms:description>lacI coding sequence</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_C0012"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/ECK120033736">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/ECK120033736"/>
<sbol:displayId>ECK120033736</sbol:displayId>
<dcterms:title>ECK120033736</dcterms:title>
<dcterms:description>Terminator2</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/ECK120033736"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_R0040">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<dcterms:title>pTetR</dcterms:title>
<dcterms:description>pTet promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_R0040"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://identifiers.org/uniprot/Q6QR72">
<sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/Q6QR72"/>
<sbol:displayId>Q6QR72</sbol:displayId>
<dcterms:title>TetR</dcterms:title>
<dcterms:description>TetR protein</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://identifiers.org/uniprot/P03023">
<sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/P03023"/>
<sbol:displayId>P03023</sbol:displayId>
<dcterms:title>LacI</dcterms:title>
<dcterms:description>LacI protein</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000020"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_J61120">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61120"/>
<sbol:displayId>BBa_J61120</sbol:displayId>
<dcterms:title>BBa_J61101 RBS</dcterms:title>
<dcterms:description>RBS2</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61120"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_E0040">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_E0040"/>
<sbol:displayId>BBa_E0040</sbol:displayId>
<dcterms:title>gfp</dcterms:title>
<dcterms:description>gfp coding sequence</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_E0040"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/ECK120029600">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/ECK120029600"/>
<sbol:displayId>ECK120029600</sbol:displayId>
<dcterms:title>ECK120029600</dcterms:title>
<dcterms:description>Terminator1</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/ECK120029600"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1"/>
<sbol:displayId>pIKELeftCassette_1</sbol:displayId>
<dcterms:title>TetR Inverter</dcterms:title>
<dcterms:description>TetR Inverter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600"/>
<sbol:displayId>ECK120029600</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/ECK120029600"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0040"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012"/>
<sbol:displayId>BBa_C0012</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_C0012"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101"/>
<sbol:displayId>BBa_J61101</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_J61101"/>
</sbol:Component>
</sbol:component>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4"/>
<sbol:displayId>anno4</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno4/location4"/>
<sbol:displayId>location4</sbol:displayId>
<sbol:start>1198</sbol:start>
<sbol:end>1288</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/ECK120029600"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2"/>
<sbol:displayId>anno2</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno2/location2"/>
<sbol:displayId>location2</sbol:displayId>
<sbol:start>56</sbol:start>
<sbol:end>68</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_J61101"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1"/>
<sbol:displayId>anno1</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno1/location1"/>
<sbol:displayId>location1</sbol:displayId>
<sbol:start>1</sbol:start>
<sbol:end>55</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_R0040"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
<sbol:sequenceAnnotation>
<sbol:SequenceAnnotation rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3"/>
<sbol:displayId>anno3</sbol:displayId>
<sbol:location>
<sbol:Range rdf:about="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/anno3/location3"/>
<sbol:displayId>location3</sbol:displayId>
<sbol:start>69</sbol:start>
<sbol:end>1197</sbol:end>
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
</sbol:Range>
</sbol:location>
<sbol:component rdf:resource="http://www.virtualparts.org/part/pIKELeftCassette_1/BBa_C0012"/>
</sbol:SequenceAnnotation>
</sbol:sequenceAnnotation>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_J61101">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_J61101"/>
<sbol:displayId>BBa_J61101</sbol:displayId>
<dcterms:title>BBa_J61101 RBS</dcterms:title>
<dcterms:description>RBS1</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_J61101"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.partsregistry.org/BBa_R0010">
<sbol:persistentIdentity rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
<sbol:displayId>BBa_R0010</sbol:displayId>
<dcterms:title>pLacI</dcterms:title>
<dcterms:description>pLacI promoter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
<sbol:sequence rdf:resource="http://www.virtualparts.org/part/BBa_R0010"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://identifiers.org/uniprot/P42212">
<sbol:persistentIdentity rdf:resource="http://identifiers.org/uniprot/P42212"/>
<sbol:displayId>P42212</sbol:displayId>
<dcterms:title>GFP</dcterms:title>
<dcterms:description>GFP protein</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#Protein"/>
<sbol:role rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000011"/>
</sbol:ComponentDefinition>
<sbol:ComponentDefinition rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1"/>
<sbol:displayId>pIKERightCassette_1</sbol:displayId>
<dcterms:title>LacI Inverter</dcterms:title>
<dcterms:description>LacI Inverter</dcterms:description>
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_R0010"/>
<sbol:displayId>BBa_R0010</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_R0010"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_C0040"/>
<sbol:displayId>BBa_C0040</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_C0040"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61130"/>
<sbol:displayId>BBa_J61130</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_J61130"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_E0040"/>
<sbol:displayId>BBa_E0040</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/BBa_E0040"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/ECK120033736"/>
<sbol:displayId>ECK120033736</sbol:displayId>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
<sbol:definition rdf:resource="http://www.partsregistry.org/ECK120033736"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120">
<sbol:persistentIdentity rdf:resource="http://www.virtualparts.org/part/pIKERightCassette_1/BBa_J61120"/>