READ ME
This repository provides all the code and notebooks used in this paper, published at the Biophysical Journal.
Available Model Sizes:
- large
- medium
- small
- Write elasticity coefficient and mass_balance_ODE_mex files specific to model size
zz_SET_UP('model_size')
ex:
zz_SET_UP('small')
- Open TEST_SCRIPT and alter to input Model Size, Ensemble Size, and Screening Parameters
Portions of ensemble modeling code was adapted from MATLAB scripts provided by the Liao and Maranas groups:
- Rizk, M. L., and J. C. Liao. 2009. Ensemble modeling and related mathematical modeling of metabolic networks. Journal of the Taiwan Institute of Chemical Engineers 40:595-601.
- Tan, Y., J. G. Rivera, C. A. Contador, J. A. Asenjo, and J. C. Liao. 2011. Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux. Metab. Eng. 13:60-75.
- Khodayari, A., A. R. Zomorrodi, J. C. Liao, and C. D. Maranas. 2014. A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metab. Eng. 25:50-62.