Scripts and data for reproducing the analysis in "An experimental demonstration of ensemble epistasis in the lac repressor"

bioRxiv: https://doi.org/10.1101/2022.10.14.512271.

Morrison and Harms

Instructions

1. Install the lacmwc library that implements the lacmwc model described in the paper.
2. Run extract.sh in this directory to unzip all of the MCMC samples into for the lacmwc model against the experimental data .csv files.
3. Run the main-analysis.ipynb notebook to reproduce the figures from the paper.
4. If you want to re-generate the MCMC samples, see the generate-mcmc-samples directory. This has the scripts and directories we used to generate the samples. (We ran this in a high-performance computing environment as the runtime to convergence can be several days).