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‎.github/workflows/python.yml‎

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name: Python SBOL3 Test
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on:
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# Schedule a nightly build. Times are UTC
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# See https://docs.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events
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schedule:
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# 5:15 am UTC (https://en.wikipedia.org/wiki/5:15)
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- cron: '15 5 * * *'
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push:
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pull_request:
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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# Default builds are on Ubuntu
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os: [macos-latest, ubuntu-latest, windows-latest]
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# Only test on with the latest version of Python 3
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python-version: ['3.x']
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: 'recursive'
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install sbol3
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- name: Test with unittest
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run: |
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python -m unittest discover -s src/test/python

‎.gitignore‎

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/.project
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/.classpath
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/.travis.yml~
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/.idea
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__pycache__

‎README.md‎

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@@ -24,7 +24,7 @@ Submission of new files should follow the workflow below to add new SBOL test fi
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1. [Fork](https://help.github.com/articles/fork-a-repo/) this repository.
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2. Add the test file to the correct directory as described above.
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3. Run the validation scripts found within the 'src/test' directory.
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4. If the files are successfully validated, submit a [pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/).
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4. If the files are successfully validated, submit a [pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/). In the pull request, please be sure to explain what the new files you are adding are intended to test.
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# Running Characterization Profile
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‎SBOL2/BBa_I0462.xml‎

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@@ -36,14 +36,6 @@
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:type rdf:resource="http://identifiers.org/so/SO:0000987"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0000804"/>
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<sbol:component>
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<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015"/>
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<sbol:displayId>BBa_B0015</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
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<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_B0015"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
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<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062"/>
@@ -60,6 +52,31 @@
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<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_B0034"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
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<sbol:Component rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015"/>
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<sbol:displayId>BBa_B0015</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
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<sbol:definition rdf:resource="http://www.async.ece.utah.edu/BBa_B0015"/>
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</sbol:Component>
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</sbol:component>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation"/>
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<sbol:displayId>BBa_B0034_annotation</sbol:displayId>
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<prov:wasDerivedFrom rdf:resource="http://sbols.org/anot#1234567"/>
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<sbol:location>
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<sbol:Range rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range"/>
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<sbol:displayId>range</sbol:displayId>
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<sbol:start>1</sbol:start>
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<sbol:end>12</sbol:end>
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<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
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</sbol:Range>
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</sbol:location>
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<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0015_annotation"/>
@@ -94,23 +111,6 @@
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<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_C0062"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation"/>
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<sbol:displayId>BBa_B0034_annotation</sbol:displayId>
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<prov:wasDerivedFrom rdf:resource="http://sbols.org/anot#1234567"/>
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<sbol:location>
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<sbol:Range rdf:about="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range">
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<sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034_annotation/range"/>
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<sbol:displayId>range</sbol:displayId>
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<sbol:start>1</sbol:start>
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<sbol:end>12</sbol:end>
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<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
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</sbol:Range>
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</sbol:location>
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<sbol:component rdf:resource="http://www.async.ece.utah.edu/BBa_I0462/BBa_B0034"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequence rdf:resource="http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973"/>
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</sbol:ComponentDefinition>
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<sbol:Sequence rdf:about="http://www.async.ece.utah.edu/seq_d23749adb3a7e0e2f09168cb7267a6113b238973">

‎SBOL2/ComponentDefinitionOutput.xml‎

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<?xml version="1.0" ?>
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<rdf:RDF xmlns:pr="http://partsregistry.org/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/">
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0040">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0040"/>
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<sbol:displayId>BBa_R0040</sbol:displayId>
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<dcterms:title>BBa_R0040</dcterms:title>
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<dcterms:description>TetR repressible promoter</dcterms:description>
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
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<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0040"/>
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</sbol:ComponentDefinition>
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0062">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
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<sbol:displayId>BBa_R0062</sbol:displayId>
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<dcterms:title>BBa_R0062</dcterms:title>
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<dcterms:description>LuxR inducible promoter</dcterms:description>
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
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<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0062"/>
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</sbol:ComponentDefinition>
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0034">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
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<sbol:displayId>BBa_B0034</sbol:displayId>
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<dcterms:title>BBa_B0034</dcterms:title>
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<dcterms:description>RBS based on Elowitz repressilator</dcterms:description>
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
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<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0034"/>
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</sbol:ComponentDefinition>
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0015">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
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<sbol:displayId>BBa_B0015</sbol:displayId>
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<dcterms:title>BBa_B0015</dcterms:title>
34+
<dcterms:description>Double terminator</dcterms:description>
35+
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
36+
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
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<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0015"/>
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</sbol:ComponentDefinition>
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_F2620">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620"/>
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<sbol:displayId>BBa_F2620</sbol:displayId>
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0001411"/>
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<sbol:component>
11-
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/ter">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/ter"/>
13-
<sbol:displayId>ter</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
19-
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/pLuxR">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
21-
<sbol:displayId>pLuxR</sbol:displayId>
47+
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/luxR">
48+
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/luxR"/>
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<sbol:displayId>luxR</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
23-
<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_R0040"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
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<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/ter">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/ter"/>
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<sbol:displayId>ter</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
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<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/rbs">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/rbs"/>
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</sbol:Component>
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</sbol:component>
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<sbol:component>
43-
<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/luxR">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/luxR"/>
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<sbol:displayId>luxR</sbol:displayId>
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<sbol:Component rdf:about="http://partsregistry.org/cd/BBa_F2620/pLuxR">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
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<sbol:displayId>pLuxR</sbol:displayId>
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<sbol:access rdf:resource="http://sbols.org/v2#public"/>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
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<sbol:definition rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
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</sbol:Component>
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</sbol:component>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5">
52-
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5"/>
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<sbol:displayId>anno5</sbol:displayId>
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<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2"/>
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<sbol:displayId>anno2</sbol:displayId>
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<sbol:location>
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<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5/range">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5/range"/>
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<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2/range">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2/range"/>
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<sbol:displayId>range</sbol:displayId>
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<sbol:start>901</sbol:start>
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<sbol:end>956</sbol:end>
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<sbol:start>56</sbol:start>
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<sbol:end>68</sbol:end>
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<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
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</sbol:Range>
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</sbol:location>
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<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
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<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/rbs"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
@@ -79,22 +115,6 @@
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<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/ter"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2"/>
85-
<sbol:displayId>anno2</sbol:displayId>
86-
<sbol:location>
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<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno2/range">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno2/range"/>
89-
<sbol:displayId>range</sbol:displayId>
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<sbol:start>56</sbol:start>
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<sbol:end>68</sbol:end>
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<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
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</sbol:Range>
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</sbol:location>
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<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/rbs"/>
96-
</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
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<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno1">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno1"/>
@@ -111,6 +131,22 @@
111131
<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/pTetR"/>
112132
</sbol:SequenceAnnotation>
113133
</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
135+
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5"/>
137+
<sbol:displayId>anno5</sbol:displayId>
138+
<sbol:location>
139+
<sbol:Range rdf:about="http://partsregistry.org/cd/BBa_F2620/anno5/range">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno5/range"/>
141+
<sbol:displayId>range</sbol:displayId>
142+
<sbol:start>901</sbol:start>
143+
<sbol:end>956</sbol:end>
144+
<sbol:orientation rdf:resource="http://sbols.org/v2#inline"/>
145+
</sbol:Range>
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</sbol:location>
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<sbol:component rdf:resource="http://partsregistry.org/cd/BBa_F2620/pLuxR"/>
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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<sbol:sequenceAnnotation>
115151
<sbol:SequenceAnnotation rdf:about="http://partsregistry.org/cd/BBa_F2620/anno3">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_F2620/anno3"/>
@@ -128,42 +164,6 @@
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</sbol:SequenceAnnotation>
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</sbol:sequenceAnnotation>
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</sbol:ComponentDefinition>
131-
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0040">
132-
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0040"/>
133-
<sbol:displayId>BBa_R0040</sbol:displayId>
134-
<dcterms:title>BBa_R0040</dcterms:title>
135-
<dcterms:description>TetR repressible promoter</dcterms:description>
136-
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
137-
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
138-
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0040"/>
139-
</sbol:ComponentDefinition>
140-
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_R0062">
141-
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_R0062"/>
142-
<sbol:displayId>BBa_R0062</sbol:displayId>
143-
<dcterms:title>BBa_R0062</dcterms:title>
144-
<dcterms:description>LuxR inducible promoter</dcterms:description>
145-
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
146-
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>
147-
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_R0062"/>
148-
</sbol:ComponentDefinition>
149-
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0034">
150-
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0034"/>
151-
<sbol:displayId>BBa_B0034</sbol:displayId>
152-
<dcterms:title>BBa_B0034</dcterms:title>
153-
<dcterms:description>RBS based on Elowitz repressilator</dcterms:description>
154-
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
155-
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>
156-
<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0034"/>
157-
</sbol:ComponentDefinition>
158-
<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_B0015">
159-
<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_B0015"/>
160-
<sbol:displayId>BBa_B0015</sbol:displayId>
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<dcterms:title>BBa_B0015</dcterms:title>
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<dcterms:description>Double terminator</dcterms:description>
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<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
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<sbol:role rdf:resource="http://identifiers.org/so/SO:0000141"/>
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<sbol:sequence rdf:resource="http://partsregistry.org/seq/BBa_B0015"/>
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</sbol:ComponentDefinition>
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<sbol:ComponentDefinition rdf:about="http://partsregistry.org/cd/BBa_C0062">
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<sbol:persistentIdentity rdf:resource="http://partsregistry.org/cd/BBa_C0062"/>
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<sbol:displayId>BBa_C0062</sbol:displayId>

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