Ethanolamine metabolism in E. coli

This repository contains the models and data used for investigating ethanolamine and glycerol co-metabolism in Escherichia coli:

• genome-scale model used for flux balance analysis
• isotopic model used for ¹³C metabolic flux analysis

Genome-scale model for Flux Balance Analysis

The genome-scale model iDJ1518 is provided in JSON (.json) and SBML (.xml) formats in the folder genome-scale_model/model and is also available in Biomodels database under identifier MODEL2403010003. The model is decribed in the publication, and the code used to perform flux balance analysis and flux variability analysis can be found in the associated Jupyter notebook genome-scale_model/ethanolamine_metabolism.ipynb.

Isotopic model for ¹³C-Fluxomics

The dynamic ¹³C-flux model can be used to simulate the labeling and metabolite dynamics of intracellular and extracellular metabolite concentrations. The model is provided in COPASI (.cps) and SBML (.xml) formats in the folder isotopic_model/model and is also available in Biomodels database under identifier MODEL2403010002. Detailed description of the model can be found in isotopic_model/model_documentation.pdf.

This model can also be used to calculate fluxes by fitting time-course measurements of the concentration of cells and extracellular (unlabeled and labeled) substrates and products, as detailed in the publication. The data used to calculate fluxes in each biological replicate are provided in the folder isotopic_model/data.

How to cite

Publication in preparation.

Authors

Pierre Millard, Denis Jallet

Contact

📧 [email protected] 📧 [email protected]