MATLAB2008 or higher
License: GNU Free Documentation License (GFDL)
Freely available for non-commercial use.

Computer aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
Mol Syst Biol 4:160, 2008
Publication  

Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli
Microbial Cell Factories 15:112, 2016
Matlab version   SBML version

Improved kinetic model of Escherichia coli central carbon metabolism in batch and continuous cultures
J. Biosci. Bioeng. 125:251-257, 2018
Matlab version SBML version

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations
Biotechnology for Biofuels 10:183, 2017
Matlab version   SBML version

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network
npj Systems Biology and Applications 5:14, 2019
Matlab version  

Computer-aided rational design of efficient NADPH production system by Escherichia coli pgi mutant using a mixture of glucose and xylose
Front Biotech Bioeng 2020
Matlab version