6. Test cases

In the following, we showcase CobraMod’s functionalities in two test cases:

• 6.1. Analysing shikimate production using an E. coli core model
  • 6.1.1. Introduction
  • 6.1.2. Loading CobraMod, the E. coli model and setting the growth medium for the simulations
  • 6.1.3. Adding the shikimate pathways
  • 6.1.4. Creating biomass reactions for the two E. coli strains
  • 6.1.5. Simulating shikimate production in the two E. coli strains
  • 6.1.6. Visualization with Escher
  • 6.1.7. Supplementary Information: Approximation of biomass compositions
  • 6.1.8. References
• 6.2. Adding a synthetic homoserine cycle to a genome-scale model of E.coli to reproduce in silico experiments
  • 6.2.1. Introduction
  • 6.2.2. Loading CobraMod, the E. coli model and setting the growth medium
  • 6.2.3. Adding the homoserine cycle
  • 6.2.4. Adding cross-references
  • 6.2.5. Saving and reloading the model
  • 6.2.6. Using Memote
  • 6.2.7. Reading the debug file
  • 6.2.8. References

For suggestions or contributions, please contact the maintainers.