cdanielmachado
commented
5 months ago When initializing the model with a pre-defined growth medium (using -i) all compounds in the medium get a default limit of 10 mmol/gDW/h.
To specify the flux bounds individually for each reaction during simulation, you will need to do that in the respective tool that you use for simulation.
I am not aware of any methods that use metabolite abundances for reconstruction. For simulation, there are a few methods, for instance those using thermodynamic constraints, where you can try to integrate metabolite concentrations.
Best regards, Daniel
I'm in the process of building my own custom media but need some advice on initialisation and the difference with defining a growth environment.
As I understand it, I can ask carveme to gapfill for a specific media and initialise with that media. My understanding is that when I then simulate with the resulting model using cobrapy I will get a growth rate prediction for that media. Is that correct?
The documentation also mentions "You can define the growth environment of the organism for simulation purposes by setting the flux bounds of the exchange reactions yourself to match the respective medium composition." Is this the same thing as initialisation via carveme? How are flux bounds set - are they set to zero for absent media components and kept to defaults for presence components?
Finally, and maybe moving a bit away from carveme, are there methods (or even a need) to incorporate media metabolite abundances into model generation and simulation?
Many thanks for any clarifications and advice.