# Models

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

**625**

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 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

Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).

The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model: Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was ...

**Creators: **Daniel Seaton, Yin Hoon Chew, Andrew Millar

**Submitter**: Daniel Seaton

**Model type**: Not specified

**Model format**: Matlab package

**Environment**: Matlab

From published files, Uriel Urquiza created SBML models with all 8 parameter sets published, and versions of F2014.1 to simulate multiple clock mutants, using SloppyCell

**Creators: **Andrew Millar, Uriel Urquiza Garcia

**Submitter**: Andrew Millar

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

**Model format**: SBML

**Environment**: Not specified

F2014.1.2 SBML file including Stepfunction imported back into Copasi v4.8

**Creators: **Andrew Millar, Karl Fogelmark, Carl Troein

**Submitter**: Andrew Millar

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

**Model format**: Copasi

**Environment**: Copasi

F2014.1.1 becomes the published version, with SBML file originally created from SloppyCell by Uriel Urquiza - see separate file. then Andrew Millar converted into SBML L2V4 in Copasi and added ISSF for light input, using SBSI Stepfunction editor (see Adams et al. 2011 J Biol Rhythms).

**Creators: **Andrew Millar, Karl Fogelmark, Carl Troein

**Submitter**: Andrew Millar

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

**Model format**: SBML

**Environment**: Not specified

Simplified model file for PLaSMo accession ID PLM_71, version 2 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Not specified

Originally submitted model file for PLaSMo accession ID PLM_71, version 2

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Copasi

Simplified model file for PLaSMo accession ID PLM_71, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Not specified

Originally submitted model file for PLaSMo accession ID PLM_71, version 1

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Not specified

Originally submitted model file for PLaSMo accession ID PLM_1041, version 1

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Not specified

Simplified model file for PLaSMo accession ID PLM_1041, version 1 (use simplified if your software cannot read the file, e.g. Sloppy Cell)

**Creators: **BioData SynthSys, Andrew Millar, Andrew Millar

**Submitter**: BioData SynthSys

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

**Model format**: SBML

**Environment**: Not specified

Arabidopsis clock model P2011.6.1 SBML imported into Copasi 4.8 and saved as native Copasi file.

**Creators: **Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC

**Submitter**: Andrew Millar

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

**Model format**: Copasi

**Environment**: Copasi

The P2011.3.1 SBML model imported into Copasi v4.8, saved as native Copasi file

**Creators: **Andrew Millar, Uriel Urquiza Garcia, Kevin Stratford, EPCC

**Submitter**: Andrew Millar

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

**Model format**: Copasi

**Environment**: Copasi