A Mathematical Model of Metabolism and Regulation Provides a Systems-Level View of the Oxygen Response of Escherichia coli
Version 5


The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.

The model is described in
Ederer M, Steinsiek S, Stagge S, Rolfe M, Ter Beek A, Knies D, de Mattos JT, Sauter T, Green J, Poole R, Bettenbrock K and Sawodny O (2014) A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Front. Microbiol. 5:124. doi: 10.3389/fmicb.2014.00124

Instructions: Unpack the tgz file (tar zxvf ecoli.tgz). The file README in the folder "ecoli" contains further instructions. The model is tested with Linux (Ubunutu) and Cygwin under Windows.

SEEK ID: https://fairdomhub.org/models/23?version=5

1 item is associated with this Model:
  • ecoli.tgz (Tar archive (gzip-compressed) - 552 KB) Download

Organism: Escherichia coli

Model type: Ordinary differential equations (ODE)

Model format: Mathematica

Execution or visualisation environment: Not specified

Model image: No image specified

help Creators and Submitter

Views: 4351   Downloads: 225

Created: 26th Oct 2009 at 15:48

Last updated: 18th Mar 2014 at 13:34

Last used: 25th Jan 2021 at 19:15

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