Enuh et al., "Genome-scale metabolic modelling of Halomonas elongata 153B explains polyhydroxyalkanoates and ectoine biosynthesis"
This repository contains the genome-scale metabolic network model for H. elongata, provided in XML format. The model can be used to study the metabolic capabilities of this organism and perform various analyses.
The resulting model (iEB1239) includes 1534 metabolites, 2314 reactions, and 1239 genes. Below are instructions on how to use the XML model and run some analyses.
Requirements
To run the XML model, you need a software tool that supports reading and analyzing SBML (Systems Biology Markup Language) files, such as the COBRApy package for Python users, or the COBRA toolbox for Matlab users.
If you do not have the COBRApy package installed, you can run the code below in Python to install it:
pip install cobra
Import the package:
import cobra
Analysis
Load the H.elongata_model11.xml file
model = cobra.io.read_sbml_model("H.elongata_model11.xml")
Run Flux balance analysis
solution = model.optimize()
print(solution)fba_solution = flux_analysis.optimize_minimal_flux(model)
Further specific analyses can be run by following the documentation: https://cobrapy.readthedocs.io/en/latest/simulating.html