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stelmo committed Dec 20, 2023
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# # Enzyme constrained models

using COBREXA

# Here we will construct an enzyme constrained variant of the *E. coli* "core"
# model. We will need the model, which we can download if it is not already present.

import Downloads: download

!isfile("e_coli_core.json") &&
download("http://bigg.ucsd.edu/static/models/e_coli_core.json", "e_coli_core.json")

# Additionally to COBREXA and the model format package, we will need a solver
# -- let's use Tulip here:

import JSONFBCModels
import Tulip

model = load_model("e_coli_core.json")

# Enzyme constrained models require parameters that are usually not used by
# conventional constraint based models. These include reaction specific turnover
# numbers, molar masses of enzymes, and capacity bounds.

import AbstractFBCModels as A

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