Models

Preliminary metabolic network of S. pyogenes including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors. The model still needs to be validated.

Batch and chemostat model of L lactis. Scope of the model is to provide a mechanistic explanation of the switch between mixed acid and homolactic fermentation.

The principles of Stealthy Engineering (Adamczyk et al.: Biotechnology Journal 2012; 7(7):877-83) are illustrated in this model by emulating a cross engineering intervention between L. lactis and S. cerevisiae.

The case study consists of replacing the native glucose uptake system of L. lactis with that native to the yeast S. cerevisiae. A modified version of Hoefnagel et al.’s model of L. lacrtis’ central metabolism was used as starting point. The total functional replacement of the PTS with the ...

A reconstruction of the cellular metabolism of the opportunistic human pathogen Enterococcus faecalis V583 represented as stoichiometric model and analysed using constraint-based modelling approaches

Glycolytic model for Plasmodium falciparum; open system

Mathematica notebook for the parameterisation of the glucose transport rate equation based on SEEK linked experimental data.

Glycolytic model for Plasmodium falciparum; closed system

Mathematica notebook for the parameterisation of the G3PDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the ALD rate equation based on SEEK linked experimental data.

Mathematica notebook for the ATPase reaction.

Mathematica notebook for the parameterisation of the ENO rate equation based on SEEK linked experimental data.

Mathematica notebook for the lactate transport rate equation, based on literature data.

Mathematica notebook for the glycerol transport rate equation.

Mathematica notebook for the parameterisation of the GAPDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PGI rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the LDH rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the TPI rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PFK rate equation based on SEEK linked experimental data.

Mathematica notebook for the pyruvate transport rate equation, based on literature data.

Mathematica notebook for the parameterisation of the PGK rate equation based on SEEK linked experimental data.

Mathematica notebook for the parameterisation of the PK rate equation based on the experimental SEEK data set

Mathematica notebook for the parameterisation of the PGM rate equation based on SEEK linked experimental data.

Mathematical model for HK kinetics, GLC and ATP saturation, and inhibition with G6P and ADP.