elementuptakepkg

ElementUptakePkg()

This class applies constraints of elemental consumption to the nutrient intake, which can influence cross-feeding interactions within a community:

from modelseedpy.community import ElementUptakePkg
eleup = ElementUptakePkg(model)

• model cobra.core.model.Model: the CobraKBase model that will be constrained. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

build_package()

The uptake constraints are applied to the model:

eleup.build_package(element_limits)

• element_limits dict: a dictionary of the uptake limits (values) for each elemental symbol (keys).

Accessible content

The ElementUptakePkg class contains a couple of accessible content that may be useful for subsequent post-processing or troubleshooting:

• model cobra.core.model.Model: The cobrakbase model, with the corresponding constraints, that is simulated.

• variables & parameters dict: Dictionaries of the linear programming variables and the simulation parameters, respectively.