This projects provides the raw data, data analysis notebooks as well as figures for the manuscript "Explore or exploit? A model-based screening strategy for PETase secretion by Corynebacterium glutamicum" (2022) by Laura M. Helleckes*, Carolin Müller*, Tim Griesbach, Vera Waffenschmidt, Matthias Moch, Michael Osthege, Wolfgang Wiechert, Marco Oldiges.
*These authors contributed equally.
Raw data can be found in the data folder. Data analysis is conducted in data_analysis.
To load the MCMC traces, please head over to Zenodo, download and unzip the folder structure and merge with the folder data_analysis.
The MCMC files end in .nc.
Plots for the accompanying paper can be found in paper.
The results for individual experiments can be found by a unique idetentifier, their so-called Run ID.
The following runs were conducted:
| Run ID | Enzyme | Purpose |
|---|---|---|
| BWA7DQ | LCC | TS Round 1.0 |
| BWNZ99 | PE-H | TS Round 1.0 |
| BZACW9 | LCC | TS Round 1.1 |
| BZP1XQ | PE-H | TS Round 1.1 |
| C3C1XZ | LCC | TS Round 2 |
| C4PZHQ | PE-H | TS Round 2 |
| CB4MNH | PE-H | Improved Assay Effect |
| Fermentation_LipALipB | LCC | Comparison to liter-scale bioreactor |
| Fermentation_YoaW | LCC | Comparison to liter-scale bioreactor |
In Thompson Sampling (TS), round 1 refers to the combined analysis of runs BWA7DQ & BZACW9 in case of LCC and BWNZ99 & BZP1XQ in case of PE-H. The results for the combined analysis can be found in the subfolders BZACW9 and BZP1XQ for LCC and PE-H respectively.
Run CB4MNH was conducted after experimental improvements with tip wetting to show that the previous bias in the columns of the assay MTP could be eradicated.
This repository and the corresponding Python package for data analysis (cutisplit) is licensed under the GNU Affero General Public License v3.0.
Head over to Zenodo to generate a BibTeX citation for the latest release.