SBOL Parser API

Generating CSVs for DNABot (BASIC Assembly)

Construct and Parts/Linkers CSVs can be generated by calling the generateCsv method of SBOLParser.

The generateCsv method processes the SBOL Document as follows:

1. Extracts Component Definitions and/or Combinatorial Derivations from SBOL Document
2. Enumerates any Combinatorial Derivations
3. Filters designs to remove designs with repeated parts
4. Select a random subset of the design space
5. Inserts backbone plasmid to each design if not present
6. Inserts up to 7 linkers between designs (neutral BASIC linkers L1-L7)
7. Sorts list of parts/linkers used across all designs alphabetically
8. Writes construct and parts/linkers CSVs

generateCSV can take in several different combinations of parameters depending on the requirements of the experimental setup.

Generate a single construct and parts/linkers CSV for a specific Component Definition/Combinatorial Derivation

generateCsv(SBOLDocument doc, String constructType, String constructURI, int maxSize)

Parameters:

• doc SBOL Document containing construct designs
• constructType Accepts COMPONENT_DEFINITION or COMBINATORIAL_DERIVATION as input
• constructURI URI of Combinatorial Derivation or Component Definition to assemble
• maxSize Maximum number of samples in a single plate

Generate several construct and parts/linkers CSVs for a specific Component Definition/Combinatorial Derivation depending on the number of runs

generateCsv(SBOLDocument doc, String constructType, String constructURI, int maxSize, int numberOfRuns)

Parameters:

• doc SBOL Document containing construct designs
• constructType Accepts COMPONENT_DEFINITION or COMBINATORIAL_DERIVATION as input
• constructURI URI of Combinatorial Derivation or Component Definition to assemble
• maxSize Maximum number of samples in a single plate
• numberOfRuns Number of runs (i.e. number of construct and parts/linkers CSVs to be generated)

Generate a single construct and parts/linkers CSV for all Component Definitions/Combinatorial Derivations/Both

generateCsv(SBOLDocument doc, String constructType, int maxSize)

Parameters:

• doc SBOL Document containing construct designs
• constructType Accepts COMPONENT_DEFINITION or COMBINATORIAL_DERIVATION or BOTH as input
• maxSize Maximum number of samples in a single plate

Generate several construct and parts/linkers CSV for all Component Definitions/Combinatorial Derivations/Both depending on the number of runs

generateCsv(SBOLDocument doc, String constructType, int maxSize, int numberOfRuns)

Parameters:

• doc SBOL Document containing construct designs
• constructType Accepts COMPONENT_DEFINITION or COMBINATORIAL_DERIVATION or BOTH as input
• maxSize Maximum number of samples in a single plate
• numberOfRuns Number of runs (i.e. number of construct and parts/linkers CSVs to be generated)

Generating CSVs for MoClo GoldenGate Assembly

Notes

• Default prefix URI needs to be set for SBOL Document
• No option to change Linkers or Backbone currently
• Linkers and Backbone SBOL files are found in examples/sbol_files directory as linker_parts.xml and dummyBackbone.xml respectively
  • linker_parts.xml and dummyBackbone.xml are generated by linkerOutput.java and backboneOutput.java respectively

Example SBOL Files

• examples/sbol_files/iGEM2020 contains SBOL files specifying designs for Imperial iGEM 2020 (outdated)
  • Trp_Optimization.xml describes fully assembled construct for Trp Optimization
• examples/sbol_filess/synbiohub contains SBOL files taken from SynbioHub
• dummy.xml describes a basic gene design of Pro-RBS-CDS-Ter

REST API