Given one or a collection of heterolgous pathways in SBML files, generate the SBOL for the constructs and the assembly protocols to build them
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool uses a multi-objective algorithm to predict the best synthesis and assembling strategy for the previously designed plasmid using either Golden gate assembly, or Gibson assembly, or a mix of both. Given a set of designs (one design is a construct name and list of its parts), it finds a valid and efficient assembly plan to build all the designs. The designs and sequences of parts are provided as an SBOL file (see test_input.xml for an example).
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
The ligase chain reaction (LCR) is a method of DNA amplification that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can then be amplified by standard PCR cycling.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool allows for the design and optimization of novel, reusable synthetic biology parts. For each enzyme predicted, it recovers the DNA sequence from the UNIPROT ID, runs a codon optimization protocol, and adds various strength calculated RBS (ribosome binding site) to it.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool takes as input a TAR collection of rpSBML files, that contain for each heterologous reaction a ranked list of UniProt identifiers for the sequences, and the list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters (generated using the tool "OptDoE Parts Reference Generator"). An optimal design of experiments is performed by using OptBioDes based on logistic regression analysis with an assumed linear model for the response. The
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Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
Convert a single or multiple SBML files to SBOL using the UNIPROT id's from Selenzyme. Here the Ribosome Binding Site (RBS) strengths are characterized to be later used by the PartsGenie node.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This tool generates a CSV file that contains a list of links to the DNA registry SynBioHub for the desired vector backbones, resistance cassette, and promoters. Generate the genetic parts reference CSV file compatible with OptDoE.
Creator: Melchior du Lac
Contributor: Melchior du Lac
Investigations: No Investigations
Studies: No Studies
Assays: No Assays