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Avoids local file paths
eagmon
reviewed
Nov 5, 2024
| kinetic_params=None, | ||
| biomass_reaction="Biomass_Ecoli_core", | ||
| substrate_update_reactions=None, | ||
| biomass_identifier="biomass", # TODO: How do we differentiate between biomass between models? Do we need to change the biomass identifier to be unique for each model? |
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good question. I did not make this compatible with multi-species dFBA yet, so this one assumes one model. so let's put this on the TODOs. Should be pretty easy.
eagmon
reviewed
Nov 5, 2024
| kinetic_params = {"glucose": (0.5, 1), "acetate": (0.5, 2)} | ||
| # TODO: Look for the biomass reaction in the model, so it doesn't have to be specified | ||
| # if biomass_reaction is None: | ||
| # biomass_reaction = get_biomass_reaction(model_file) |
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Good idea. There's plenty of room for more automated extraction of relevant information with different COBRA functions.
eagmon
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Nov 5, 2024
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@hgscott Great comments on the code. Let's go through these when we meet. Many of them point to the lack of multi-species/multi-model dFBA. I plan to follow roughly the same pattern used in the pure Python version: https://github.com/eagmon/notebook_tests/blob/main/comets.ipynb
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Closes #2.
Here I wanted to extend the functions to work with any model and metabolites other than just glucose, acetate, and biomass, to make it easier to extend simulations to multi-species.
I was a little unsure of the best way to do this.
I added the arguments for
dfba_configtoget_single_dfba_specso that a user runningget_single_dfba_speccan change theconfigsection of the dfba config returned byget_single_dfba_spec.I added an example of this to
demo/particle_comets.ipynbthat runs the full genome-scale model of E. coli, and keeps track of Glucose, Acetate, CO2, and Biomass.