gempipe.interface.medium

Module Contents

Functions

reset_growth_env(model)

Set all the EX_change reactions to (0, 1000).

set_bounded_uptakes(model, uptakes)

Set uptake of nutrients.

set_bounded_secretions(model, secretions)

Set secretion of metabolites.

set_unbounded_exchanges(model, exrs)

Define which melecules require a free exchange (-1000, 1000).
gempipe.interface.medium.reset_growth_env(model)[source]

Set all the EX_change reactions to (0, 1000).

Parameters:

model (cobra.Model) – target model.

gempipe.interface.medium.set_bounded_uptakes(model, uptakes)[source]

Set uptake of nutrients.

Can be expressed as either concentrations [mmol/L] or fluxes [mmol/(h*gDW)], depending on your aims.

Parameters:

  • model (cobra.Model) – target model.

  • secretions (dict) – dictionary keyed by EX_change reaction ID. Expressing values as tuples, the user can provide the standard deviation.

gempipe.interface.medium.set_bounded_secretions(model, secretions)[source]

Set secretion of metabolites.

Can be expressed as either concentrations [mmol/L] or fluxes [mmol/(h*gDW)], depending on your aims.

Parameters:

  • model (cobra.Model) – target model.

  • secretions (dict) – dictionary keyed by EX_change reaction ID. Expressing values as tuples, the user can provide the standard deviation.

gempipe.interface.medium.set_unbounded_exchanges(model, exrs)[source]

Define which melecules require a free exchange (-1000, 1000).

Parameters:

  • model (cobra.Model) – target model.

  • exrs (list) – IDs of EX_change reactions to unbound.