4. Test case

We covered a test case to showcase how CobraMod can be implemented in a workflow:

• 4.1. Analysing shikimate production using an E. coli coremodel
  • 4.1.1. Introduction
  • 4.1.2. Loading CobraMod, the E.coli model and setting the growth medium for the simulations
  • 4.1.3. Adding the shikimate pathways
  • 4.1.4. Creating biomass reactions for the two E. coli strains
  • 4.1.5. Simulating shikimate production in the two E.coli strains
  • 4.1.6. Visualization with Escher
  • 4.1.7. Supplementary Information: Approximation of biomass compositions
  • 4.1.8. References

For suggestions or contributions, please contact the maintainers.