# Models

**86**Models visible to you, out of a total of

**96**

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG upon sequential adition of purified enzymes. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the progress curves will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn, but no NAD rec, will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 12 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with no added Mn, but with NAD rec, will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Steady state model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with NAD recycling. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 13 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 10 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, using old enzymes, with optimal protein distribution. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for cascade 16 will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG in cell free extract. If the Mathematica notebook is downloaded and the data file is downloaded in the same directory, then the notebook can be evaluated, and the figure in the manuscript for the cell free extract with added Mn and NAD rec will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG. Protein levels need to be adapted to CFE levels, see SED-ML scripts

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

Model for the Caulobacter crescentus Î±-ketoglutarate semialdehyde dehydrogenase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KGSADH will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus Weimberg pathway, describing the conversion of Xyl to KG, with sequential addition of purified enzymes.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

Model for the Caulobacter crescentus xylose dehydrogenase, describing the initial rate kinetics including substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XDH kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XDH will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus xylonolactonase, describing the initial rate kinetics and substrate dependence. If the Mathematica notebook is downloaded and the data file for the XLA kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XLA will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus xylonate dehydratase, describing the initial rate kinetics for substrate dependence. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for XAD will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

Model for the Caulobacter crescentus 2-keto-3-deoxy-D-xylonate dehydratase, describing the initial rate kinetics for substrate dependence and product inhibition. If the Mathematica notebook is downloaded and the data file for the XAD kinetics is downloaded in the same directory, then the notebook can be evaluated. The model in the notebook will then be parameterised and the figures in the manuscript for KDXD will be reproduced.

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

BPG stability notebook

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Environment**: Mathematica

PGK model for S. solfataricus

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Algebraic equations

**Model format**: Mathematica

**Environment**: Mathematica

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Creators: **Dawie van Niekerk, Jacky Snoep

**Submitter**: Dawie van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: Not specified

**Creators: **Dawie van Niekerk, Jacky Snoep

**Submitter**: Dawie van Niekerk

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

PGK-GAPDH model Sulfolobus kouril8

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

PGK-GAPDH model yeast kouril7

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript

**Creator: **Jacky Snoep

**Submitter**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: Mathematica

**Environment**: Mathematica