Version 1

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 design is evaluated by its D-efficiency, defined as:

Deff = (1)/(n)\absXTX(1)/(p)

Where n is the number of experimental runs or library size, p is the number of independent variables, and X is the model matrix, i.e., a row for each experimental run and a column for each term in the model. The library size n can be selected and should be above a minimal threshold depending on the number of combinatorial complexity of the library. The experimental design can be evaluated through the provided diagnostics for D-efficiency, power analysis, and relative prediction variance, allowing the optimal selection of library size.

The resulting design is provided as an SBOL collection containing the definition of each DNA component and the combinatorial library of constructs.

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Created: 28th Jun 2020 at 14:26

Last used: 13th Jul 2020 at 21:54

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