| Previous changeset 1:de9f53630349 (2021-12-15) Next changeset 3:e4821c820f7c (2022-03-30) |
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Commit message:
"planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty" |
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modified:
rpbasicdesign.xml |
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added:
test-data/biolegio_plate_lycopene.csv test-data/biolegio_plate_muconate.csv test-data/constructs_lycopene.csv test-data/constructs_muconate.csv test-data/muconate_example.xml test-data/user_parts_plate_lycopene.csv test-data/user_parts_plate_muconate.csv |
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removed:
test-data/BASIC_construct_A1.xml test-data/BASIC_construct_B1.xml test-data/BASIC_construct_C1.xml test-data/biolegio_plate.csv test-data/constructs.csv test-data/user_parts_plate.csv |
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| diff -r de9f53630349 -r 8a087d7546b8 rpbasicdesign.xml --- a/rpbasicdesign.xml Wed Dec 15 15:10:43 2021 +0000 +++ b/rpbasicdesign.xml Mon Mar 28 14:16:59 2022 +0000 |
| [ |
| b'@@ -1,7 +1,10 @@\n-<tool id="rpbasicdesign" name="BasicDesign" version="0.3.4">\n+<tool id="rpbasicdesign" name="BasicDesign" version="@TOOL_VERSION@" profile="19.09">\n <description>Build DNA-BOT input files from rpSBML</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.0.1</token>\n+ </macros>\n <requirements>\n- <requirement type="package" version="0.3.4">rpbasicdesign</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">rpbasicdesign</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n python -m rpbasicdesign.cli\n@@ -14,46 +17,112 @@\n --lmp_id \'$adv.lmp_id\'\n --backbone_id \'$backbone_id\'\n --sample_size \'$sample_size\'\n- #if str($adv.cds_permutation) == "true"\n- --cds_permutation true\n- #else\n- --cds_permutation false\n- #end if\n+ $adv.cds_permutation\n --o_dnabot_dir \'out/dnabot_in\'\n- --o_sbol_dir \'out/sbol_export\'\n+ $adv.sbol_output\n+ --max_enz_per_rxn $adv.max_enz_per_rxn\n ]]></command>\n <inputs>\n- <param name="rpsbml_file" type="data" format="xml" label="rpSBML file"/>\n- <param name="backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" />\n- <param name="sample_size" type="integer" value="88" label="Number of constructs to generate" />\n+ <param name="rpsbml_file" type="data" format="xml" label="rpSBML file" help="SBML file from which enzymes UniProt IDs will be collected."/>\n+ <param argument="--backbone_id" type="text" value="BASIC_SEVA_37_CmR-p15A.1" label="Backbone part ID" help="Part ID to be used as the backbone.">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits">\n+ <add value=":" />\n+ <add value="." />\n+ <add value="-" />\n+ <add value="_" />\n+ </valid>\n+ </sanitizer>\n+ <validator type="empty_field" message="Backbone ID is required"/>\n+ <validator type="regex">[0-9a-zA-Z_:-]+</validator>\n+ </param>\n+ <param argument="--sample_size" type="integer" value="88" min="1" max="88" label="Number of constructs to generate" help="Number of construct to generate."/>\n <section name="adv" title="Advanced Options" expanded="false">\n- <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" />\n- <param name="lms_id" type="text" value="LMS" label="LMS part ID" />\n- <param name="lmp_id" type="text" value="LMP" label="LMP part ID" />\n- <param name="cds_permutation" type="boolean" label="Perform CDS permutation?" checked="true" />\n+ <param name="parts_files" type="data" format="csv" optional="true" multiple="true" label="Linkers and user parts" help="List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: Standard Biolegio Parts" />\n+ <param argument="--lms_id" type="text" value="LMS" label="LMS part ID" help="Part ID to be used as the LMS methylated linker." >\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits">\n+ <add value=":" />\n+ <add value="-" />\n+ <add value="_" />\n+ <add value="." />\n+ </valid>\n+ </sanitizer>\n+ <validator type="empty_field" message="LMS ID is required"/>\n+ </param>\n+ <param argument="--lmp_id" type="text" value="LMP" label="LMP part ID" help="Part ID to be used as the LMP methylated linker.">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits">\n+ <add value=":" />\n+ '..b'"BASIC_construct_B1">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_text text="BASIC_construct_B1" />\n+ <has_n_lines n="339" />\n+ </assert_contents>\n+ </element>\n+ <element name="BASIC_construct_C1">\n+ <assert_contents>\n+ <is_valid_xml />\n+ <has_text text="BASIC_construct_C1" />\n+ <has_n_lines n="339" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <!-- test 2: check if identical outputs are produced (Muconate input)-->\n+ <param name="rpsbml_file" value="muconate_example.xml" />\n+ <param name="sample_size" value="88" />\n+ <output name="Constructs" file="constructs_muconate.csv" ftype="csv" compare="diff">\n+ <assert_contents>\n+ <has_n_lines n="89"/>\n+ </assert_contents>\n+ </output>\n+ <output name="User parts plate" file="user_parts_plate_muconate.csv" ftype="csv" compare="diff"/>\n+ <output name="Biolegio plate" file="biolegio_plate_muconate.csv" ftype="csv" compare="diff"/>\n </test>\n </tests>\n <help><![CDATA[\n@@ -76,18 +145,19 @@\n \n Advanced options:\n \n-* **parts_files**\\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, user_parts.csv]\n+* **parts_files**\\ : (string) List of files providing available linkers and user parts (backbone, promoters, ...) for constructs. Default: [data/biolegio_parts.csv, data/user_parts.csv]\n * **lms_id**\\ : (string) part ID to be used as the LMS methylated linker. Default: LMS.\n * **lmp_id**\\ : (string) part ID to be used as the LMP methylated linker. Default: LMP.\n * **backbone_id**\\ : (string) part ID to be used as the backbone. Default: BASIC_SEVA_37_CmR-p15A.1.\n-* **sample_size**\\ : (int) Number of construct to generate.Default: 3.\n+* **sample_size**\\ : (int) Number of construct to generate. Default: 88.\n * **cds_permutation**\\ : (boolean) Whether all combinations of CDS permutation should be built Default: true.\n+* **max_enz_per_rxn**\\ : (integer) Maximum number of enyzme to consider per reaction. If more enzymes are available for a given reaction, then only the last one listed in the MIRIAM annotation section will be kept. (Default: 1). \n \n Output\n ------\n \n * **o_dnabot_dir**\\ : (string) Output folder to write construct and plate files. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/dnabot_in.\n-* **o_sbol_dir**\\ : (string) Output folder to write SBOL depictions of constructs. It will be created if it does not exist yet. Existing files will be overwritten. Default: out/sbol_export.\n+* **o_sbol_dir**\\ : (string) Output folder to write SBOL depictions of constructs. Existing files will be overwritten. Default: not output.\n \n Project Links\n ------------------\n@@ -101,21 +171,6 @@\n \n ]]></help>\n <citations>\n- <citation type="bibtex">\n- @article{10.1093/synbio/ysaa010,\n- author = {Storch, Marko and Haines, Matthew C and Baldwin, Geoff S},\n- title = {DNA-BOT: a low-cost, automated DNA assembly platform for synthetic biology},\n- journal = {Synthetic Biology},\n- volume = {5},\n- number = {1},\n- year = {2020},\n- month = {07},\n- issn = {2397-7000},\n- doi = {10.1093/synbio/ysaa010},\n- url = {https://doi.org/10.1093/synbio/ysaa010},\n- note = {ysaa010},\n- eprint = {https://academic.oup.com/synbio/article-pdf/5/1/ysaa010/33722340/ysaa010.pdf},\n- }\n- </citation>\n+ <citation type="doi">10.1093/synbio/ysaa010</citation>\n </citations>\n </tool>\n\\ No newline at end of file\n' |
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| diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_A1.xml --- a/test-data/BASIC_construct_A1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,339 +0,0 @@\n-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23119_BASIC/1">\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23119_BASIC"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:displayId>PJ23119_BASIC</sbol:displayId>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23119_BASIC/1"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- <sbol:displayId>U1_RBS1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">\n- <sbol:displayId>U2_RBS1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>\n- </sbol:ComponentDefinition>\n- <sbol:C'..b'ion/BASIC_construct_A1/P21684_0/1"/>\n- <sbol:displayId>constraint_4</sbol:displayId>\n- </sbol:SequenceConstraint>\n- </sbol:sequenceConstraint>\n- </sbol:ComponentDefinition>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements></sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23119_BASIC/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23119_BASIC"/>\n- <sbol:elements></sbol:elements>\n- <sbol:displayId>PJ23119_BASIC</sbol:displayId>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">\n- <sbol:elements></sbol:elements>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:displayId>U1_RBS1</sbol:displayId>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">\n- <sbol:displayId>U2_RBS1</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements></sbol:elements>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:displayId>P21683</sbol:displayId>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n- <sbol:displayId>U3_RBS2</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>P21685</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- </sbol:Sequence>\n-</rdf:RDF>\n' |
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| diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_B1.xml --- a/test-data/BASIC_construct_B1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,339 +0,0 @@\n-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS3/1">\n- <sbol:displayId>U1_RBS3</sbol:displayId>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:version>1</sbol:version>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS3/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS3"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U2_RBS1/1">\n- <sbol:displayId>U2_RBS1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U2_RBS1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U2_RBS1/1"/>\n- </sbol:ComponentDefinition>\n- <sbol:C'..b'tity rdf:resource="https://localhost/ComponentDefinition/BASIC_construct_B1/constraint_2"/>\n- </sbol:SequenceConstraint>\n- </sbol:sequenceConstraint>\n- </sbol:ComponentDefinition>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements></sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>\n- <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS3/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS3"/>\n- <sbol:elements></sbol:elements>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>U1_RBS3</sbol:displayId>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS1/1">\n- <sbol:displayId>U2_RBS1</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements></sbol:elements>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS1"/>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:displayId>P21683</sbol:displayId>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n- <sbol:displayId>U3_RBS2</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>P21685</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- </sbol:Sequence>\n-</rdf:RDF>\n' |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/BASIC_construct_C1.xml --- a/test-data/BASIC_construct_C1.xml Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,339 +0,0 @@\n-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:sbol="http://sbols.org/v2#">\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMS/1">\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMS/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMS"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000988"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/LMP/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000001"/>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/LMP/1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/LMP"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/PJ23101_BASIC/1">\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000167"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/PJ23101_BASIC/1"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/PJ23101_BASIC"/>\n- <sbol:version>1</sbol:version>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U1_RBS1/1">\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U1_RBS1/1"/>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- <sbol:displayId>U1_RBS1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U1_RBS1"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/P21684/1">\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000316"/>\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/P21684"/>\n- <sbol:version>1</sbol:version>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/P21684/1"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:ComponentDefinition>\n- <sbol:ComponentDefinition rdf:about="https://localhost/ComponentDefinition/U3_RBS2/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/ComponentDefinition/U3_RBS2"/>\n- <sbol:version>1</sbol:version>\n- <sbol:sequence rdf:resource="https://localhost/Sequence/U3_RBS2/1"/>\n- <sbol:displayId>U3_RBS2</sbol:displayId>\n- <sbol:role rdf:resource="http://identifiers.org/so/SO:0000139"/>\n- <sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>\n- </sbol:ComponentDefinition>\n- <sbol:C'..b'_BASIC_0"/>\n- <sbol:displayId>PJ23101_BASIC_0</sbol:displayId>\n- <sbol:version>1</sbol:version>\n- </sbol:Component>\n- </sbol:component>\n- </sbol:ComponentDefinition>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMS/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMS"/>\n- <sbol:displayId>LMS</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1/1">\n- <sbol:displayId>BASIC_SEVA_37_CmR_p15A_1</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/BASIC_SEVA_37_CmR_p15A_1"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements></sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/LMP/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>LMP</sbol:displayId>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/LMP"/>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/PJ23101_BASIC/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/PJ23101_BASIC"/>\n- <sbol:displayId>PJ23101_BASIC</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U1_RBS1/1">\n- <sbol:elements></sbol:elements>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:displayId>U1_RBS1</sbol:displayId>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U1_RBS1"/>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21684/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21684"/>\n- <sbol:displayId>P21684</sbol:displayId>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U3_RBS2/1">\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U3_RBS2"/>\n- <sbol:displayId>U3_RBS2</sbol:displayId>\n- <sbol:elements></sbol:elements>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21685/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21685"/>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- <sbol:displayId>P21685</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/U2_RBS2/1">\n- <sbol:displayId>U2_RBS2</sbol:displayId>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:version>1</sbol:version>\n- <sbol:elements></sbol:elements>\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/U2_RBS2"/>\n- </sbol:Sequence>\n- <sbol:Sequence rdf:about="https://localhost/Sequence/P21683/1">\n- <sbol:persistentIdentity rdf:resource="https://localhost/Sequence/P21683"/>\n- <sbol:encoding rdf:resource="http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html"/>\n- <sbol:displayId>P21683</sbol:displayId>\n- <sbol:elements>atgc</sbol:elements>\n- <sbol:version>1</sbol:version>\n- </sbol:Sequence>\n-</rdf:RDF>\n' |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate.csv --- a/test-data/biolegio_plate.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,83 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -L1-S,A1, -L1-P,B1, -L2-S,A2, -L2-P,B2, -L3-S,A3, -L3-P,B3, -L4-S,A4, -L4-P,B4, -L5-S,A5, -L5-P,B5, -L6-S,A6, -L6-P,B6, -LMP-S,A7, -LMP-P,B7, -LMS-S,A8, -LMS-P,B8, -U1-S,C1, -U2-S,C2, -U3-S,C3, -U1-RBS1-P,C4, -U1-RBS2-P,C5, -U1-RBS3-P,C6, -U1-A01-P,D1, -U1-A02-P,D2, -U1-A03-P,D3, -U1-A04-P,D4, -U1-A05-P,D5, -U1-A06-P,D6, -U1-A07-P,D7, -U1-A08-P,D8, -U1-A09-P,D9, -U1-A10-P,D10, -U1-A11-P,D11 -U1-A12-P,D12, -U2-RBS1-P,C7, -U2-RBS2-P,C8, -U2-RBS3-P,C9, -U2-A01-P,E1, -U2-A02-P,E2, -U2-A03-P,E3, -U2-A04-P,E4, -U2-A05-P,E5, -U2-A06-P,E6, -U2-A07-P,E7, -U2-A08-P,E8, -U2-A09-P,E9, -U2-A10-P,E10, -U2-A11-P,E11 -U2-A12-P,E12, -U3-RBS1-P,C10, -U3-RBS2-P,C11, -U3-RBS3-P,C12, -U3-A01-P,F1, -U3-A02-P,F2, -U3-A03-P,F3, -U3-A04-P,F4, -U3-A05-P,F5, -U3-A06-P,F6, -U3-A07-P,F7, -U3-A08-P,F8, -U3-A09-P,F9, -U3-A10-P,F10, -U3-A11-P,F11 -U3-A12-P,F12, -U1-AM12-P,A10, -U1-AM24-P,B10, -U2-AM12-P,A11, -U2-AM24-P,B11, -U3-AM12-P,A12, -U3-AM24-P,B12, -LF1-S,A9, -LF1-P,B9, -LF2-S,G1, -LF2-P,H1, -LF3-S,G2, -LF3-P,H2, -LF4-S,G3, -LF4-P,H3, -LF5-S,G4, -LF5-P,H4, -LF6-S,G5, -LF6-P,H5, \ No newline at end of file |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate_lycopene.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/biolegio_plate_muconate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/biolegio_plate_muconate.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| @@ -0,0 +1,83 @@ +Part/linker,Well,Part concentration (ng/uL) +L1-S,A1, +L1-P,B1, +L2-S,A2, +L2-P,B2, +L3-S,A3, +L3-P,B3, +L4-S,A4, +L4-P,B4, +L5-S,A5, +L5-P,B5, +L6-S,A6, +L6-P,B6, +LMP-S,A7, +LMP-P,B7, +LMS-S,A8, +LMS-P,B8, +U1-S,C1, +U2-S,C2, +U3-S,C3, +U1-RBS1-P,C4, +U1-RBS2-P,C5, +U1-RBS3-P,C6, +U1-A01-P,D1, +U1-A02-P,D2, +U1-A03-P,D3, +U1-A04-P,D4, +U1-A05-P,D5, +U1-A06-P,D6, +U1-A07-P,D7, +U1-A08-P,D8, +U1-A09-P,D9, +U1-A10-P,D10, +U1-A11-P,D11 +U1-A12-P,D12, +U2-RBS1-P,C7, +U2-RBS2-P,C8, +U2-RBS3-P,C9, +U2-A01-P,E1, +U2-A02-P,E2, +U2-A03-P,E3, +U2-A04-P,E4, +U2-A05-P,E5, +U2-A06-P,E6, +U2-A07-P,E7, +U2-A08-P,E8, +U2-A09-P,E9, +U2-A10-P,E10, +U2-A11-P,E11 +U2-A12-P,E12, +U3-RBS1-P,C10, +U3-RBS2-P,C11, +U3-RBS3-P,C12, +U3-A01-P,F1, +U3-A02-P,F2, +U3-A03-P,F3, +U3-A04-P,F4, +U3-A05-P,F5, +U3-A06-P,F6, +U3-A07-P,F7, +U3-A08-P,F8, +U3-A09-P,F9, +U3-A10-P,F10, +U3-A11-P,F11 +U3-A12-P,F12, +U1-AM12-P,A10, +U1-AM24-P,B10, +U2-AM12-P,A11, +U2-AM24-P,B11, +U3-AM12-P,A12, +U3-AM24-P,B12, +LF1-S,A9, +LF1-P,B9, +LF2-S,G1, +LF2-P,H1, +LF3-S,G2, +LF3-P,H2, +LF4-S,G3, +LF4-P,H3, +LF5-S,G4, +LF5-P,H4, +LF6-S,G5, +LF6-P,H5, \ No newline at end of file |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs.csv --- a/test-data/constructs.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 -A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, -C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,, |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs_lycopene.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10 +A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,P21684,U2-RBS1,P21683,U3-RBS2,P21685,,,,,,,,,, +C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,P21684,U3-RBS2,P21685,U2-RBS2,P21683,,,,,,,,,, |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/constructs_muconate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/constructs_muconate.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| b'@@ -0,0 +1,89 @@\n+Well,Linker 1,Part 1,Linker 2,Part 2,Linker 3,Part 3,Linker 4,Part 4,Linker 5,Part 5,Linker 6,Part 6,Linker 7,Part 7,Linker 8,Part 8,Linker 9,Part 9,Linker 10,Part 10\r\n+A1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+B1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+C1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+D1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+E1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+F1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+G1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+H1,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+A2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+B2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+C2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+D2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+E2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+F2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+G2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+H2,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+A3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+B3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+C3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+D3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+E3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+F3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+G3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+H3,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+A4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+B4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+C4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS1,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+D4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+E4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+F4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+G4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+H4,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+A5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+B5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+C5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS2,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+D5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS2,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+E5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS3,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+F5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+G5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS2,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+H5,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+A6,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1'..b'O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+G6,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+H6,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS3,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+A7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+B7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+C7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+D7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS3,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+E7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+F7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+G7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS3,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+H7,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS2,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+A8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS3,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+B8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS2,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+C8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS3,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+D8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+E8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+F8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+G8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS3,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+H8,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS1,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+A9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+B9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+C9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+D9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS1,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+E9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+F9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+G9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS1,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+H9,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+A10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS3,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+B10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+C10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS1,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+D10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS3,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+E10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U2-RBS1,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+F10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U2-RBS1,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+G10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS3,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+H10,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U2-RBS2,O33948,U1-RBS2,O85675,,,,,,,,,,,,\r\n+A11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS3,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+B11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS1,O85675,U2-RBS3,O33948,,,,,,,,,,,,\r\n+C11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23104_BASIC,U1-RBS2,O85675,U2-RBS2,O33948,,,,,,,,,,,,\r\n+D11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS2,O33948,U1-RBS3,O85675,,,,,,,,,,,,\r\n+E11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23111_BASIC,U1-RBS3,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+F11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23119_BASIC,U1-RBS1,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n+G11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23101_BASIC,U2-RBS1,O33948,U1-RBS1,O85675,,,,,,,,,,,,\r\n+H11,LMS,BASIC_SEVA_37_CmR-p15A.1,LMP,PJ23108_BASIC,U1-RBS2,O85675,U2-RBS1,O33948,,,,,,,,,,,,\r\n' |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/muconate_example.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/muconate_example.xml Mon Mar 28 14:16:59 2022 +0000 |
| [ |
| b'@@ -0,0 +1,5328 @@\n+<?xml version="1.0" encoding="UTF-8"?>\n+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" level="3" version="1" groups:required="false" fbc:required="false">\n+ <model metaid="a03e1bf0f20b54a66f7b4ce262ea6b0f7579c0a1e47144a649b9e2e711f6b3ed" id="RP_model_001_0001" name="001_0001" substanceUnits="mole" timeUnits="second" extentUnits="mole" fbc:strict="true">\n+ <listOfCompartments>\n+ <compartment metaid="_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6" sboTerm="SBO:0000290" id="c" name="cytosol" size="1" constant="true">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">\n+ <bqbiol:is>\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>\n+ <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>\n+ <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </annotation>\n+ </compartment>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <species metaid="_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995" id="MNXM5" name="MNXM5" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_4a3e4e32a6db24e5ddaa18997f93519c4ef1c0172e96160cd56ad49ecf025995">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:smiles value="N=C(O)c1ccc[n+](C2OC(COP(=O)(O)OP(=O)(O)OCC3OC(n4cnc5c(N)ncnc54)C(OP(=O)(O)O)C3O)C(O)C2O)c1"/>\n+ <brsynth:inchi value="InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/p+1"/>\n+ <brsynth:inchikey value="XJLXINKUBYWONI-UHFFFAOYSA-O"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ </species>\n+ <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <bqbiol:is>\n+ <rdf:Bag/>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">\n+ <brsynth:brs'..b'df:BRSynth rdf:about="#_93eef40c447d295fa61df9270c5fd909ec2ba7ee9883090552c0466873cd4299">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">\n+ <brsynth:global_score value="-1"/>\n+ </brsynth:brsynth>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="rxn_1"/>\n+ <groups:member groups:idRef="rxn_2"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a" groups:id="rp_intermediate_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_613b064337553014ede418c67180137a4561ff11b13f3bfa1a2765ef37ac375a">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="CMPD_0000000003"/>\n+ <groups:member groups:idRef="MNXM4"/>\n+ <groups:member groups:idRef="MNXM188"/>\n+ <groups:member groups:idRef="TARGET_0000000001"/>\n+ <groups:member groups:idRef="MNXM6"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM15"/>\n+ <groups:member groups:idRef="MNXM1"/>\n+ <groups:member groups:idRef="MNXM5"/>\n+ <groups:member groups:idRef="MNXM13"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">\n+ <annotation>\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:BRSynth rdf:about="#_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3">\n+ <brsynth:brsynth xmlns:brsynth="http://brsynth.eu"/>\n+ </rdf:BRSynth>\n+ </rdf:RDF>\n+ </annotation>\n+ <groups:listOfMembers>\n+ <groups:member groups:idRef="MNXM5"/>\n+ <groups:member groups:idRef="MNXM4"/>\n+ <groups:member groups:idRef="MNXM188"/>\n+ <groups:member groups:idRef="MNXM1"/>\n+ <groups:member groups:idRef="MNXM6"/>\n+ <groups:member groups:idRef="MNXM13"/>\n+ <groups:member groups:idRef="MNXM15"/>\n+ </groups:listOfMembers>\n+ </groups:group>\n+ </groups:listOfGroups>\n+ </model>\n+</sbml>\n' |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/user_parts_plate.csv --- a/test-data/user_parts_plate.csv Wed Dec 15 15:10:43 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -Part/linker,Well,Part concentration (ng/uL) -BASIC_SEVA_37_CmR-p15A.1,A1, -P21683,B1, -P21684,C1, -P21685,D1, -PJ23101_BASIC,E1, -PJ23119_BASIC,F1, |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/user_parts_plate_lycopene.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_lycopene.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +P21683,B1, +P21684,C1, +P21685,D1, +PJ23101_BASIC,E1, +PJ23119_BASIC,F1, |
| b |
| diff -r de9f53630349 -r 8a087d7546b8 test-data/user_parts_plate_muconate.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/user_parts_plate_muconate.csv Mon Mar 28 14:16:59 2022 +0000 |
| b |
| @@ -0,0 +1,9 @@ +Part/linker,Well,Part concentration (ng/uL) +BASIC_SEVA_37_CmR-p15A.1,A1, +O33948,B1, +O85675,C1, +PJ23101_BASIC,D1, +PJ23104_BASIC,E1, +PJ23108_BASIC,F1, +PJ23111_BASIC,G1, +PJ23119_BASIC,H1, |