Resource allocation explains lactic acid production in mixed-culture anaerobic fermentations. Matlab codes

This repository contains the Matlab codes of the model developed an described in the paper "Resource allocation explains lactic acid production in mixed-culture anaerobic fermentations". Two versions of the model are available: The base model described in the manuscript and the comprehensive version described in the Supplementary File 2. Both models are executed in the same way.

The model is a Flux Balance Analysis including contraints related with the resource allocation theory.

Two programmes can be executed:

run.m: The FBA model

montecarlo.m: The Monte Carlo simulations for the uncertainty analysis. (only available for the base model).

Both programmes include the generation of the figures presented in the article. The stoichiometric matrix and the enzyme activities values are extracted from a excel file (Data.xlsx). The parameters of the simulation (e.g. precentage of protein located in the membrane, increase of enzyme requirement in prototrohpic anabolism) are set in the lines 10-13 in run.m and in lines 10-14 in montecarlo.m.