DyAux - Dynamic Design and Optimization of Auxotrophic Communities

This algorithm helps build auxotrophic communities and further optimize them for bioproduction

Key Scripts

Masterscripts for auxotrophy design and product optimisation:
- AuxMasterHetero.m
- AuxMasterHomo.m
- FSEOF_dfba_masterscript.m
Initial inputs like models and parameters (environment and kinetic) can be changed by manipulating these files.

All models were obtained from the BiGG Models database. Some annotations were adjusted to ensure consistent formatting across the dataset.

All simulations were conducted using MATLAB R2018a, COBRA Toolbox v3.0, and IBM ILOG CPLEX 12.8.

Please initialise the COBRA Toolbox and the solver before running DyAux We recommend the ibm_cplex solver as DyAux uses fastFVA for efficiency.

Clone the repository:

git clone https://github.com/RamanLab/DyAux.git