OptDoE
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.

Help
help Contributor and Creators
Activity

Views: 23

Created: 28th Jun 2020 at 14:26

Last used: 13th Jul 2020 at 21:54

help Attributions

None

Related items

Powered by
(v.1.10.pre)
Copyright © 2008 - 2019 The University of Manchester and HITS gGmbH
IBISBA is a pan-European research infrastructure that is currently funded by the EU Horizon 2020 projects
IBISBA 1.0 (grant agreement number 730976) and PREP-IBISBA (grant agreement number 871118).
Registering data or other knowledge assets on this platform is the sole responsibility of Users.
IBISBA cannot be held responsible for misuse or misappropriation of data and assets belonging to a Third Party..