This repository contains the code used to train the surrogates presented in the paper "Accelerated design of Escherichia coli genomes with reduced size using a whole-cell model and machine learning surrogate", and to design the corresponding reduced genome.

The notebooks folder contains the notebooks used to train the surrogate and analyse the resulted reduced genome.

The MinesweeperEcoli folder contains the code used to run the Minesweeper algorithm using the E. coli whole-cell model published by the Covert Lab and Stanford University. The latest version of the WCM can be found here.