CUE Simulations

This repository holds the files needed to run FBA simulations and calculate/visualize the CUE.

How to Use the Conda Environment

This repository includes an environment file so that you can re-create the environment in which all this code was run.

To build and use the environment, make sure Conda is installed and run

conda env create --prefix ./env --file environment.yml
conda activate ./env

Organisms

The simulations are grouped by organism:

• ecoli_core is the core model that comes with the COBRApy package. It is a subset of the genome-scale metabolic reconstruction iAF1260 (uses BiGG notation or reactions/metabolites).
• ecoli_full is the genome-scale reconstruction of E. coli that comes with the COBRApy package. It is a reconstruction of iJO1366 (uses BiGG notation or reactions/metabolites).
• mit1002_core is the core model that originally came from Edirisinghe et al. (2016), and is now being manually curated (uses KBase notation for reactions/metabolites).
• mit1002_full is the genome-scale reconstruction of A. macleodii MIT1002 that was drafted using CarveMe and is now being manually curated.