MFA sampling

Tools were set up to facilitate the analysis of the fluxes calculated in a metabolic flux analysis. Some tools that can help adapting naming conventions if different models were used and identifying exchange fluxes, i.e. fluxes with non-overlapping forward- and reverse reactions, are presented first, followed by methods to add the MFA-calculated fluxes as constraints to a COBRA model and how to deal with infeasible solutions.

Compatibility

If a different model was used for the MFA than for the subsequent analysis (e.g. a reduced model rather than a genome scale model), issues with the naming conventions might arise. Here, some functions that help with consolidating these models are provided.

Functions

model_rxn_overlap(fittedFluxes, model)	Finds the overlapping reactions between a metabolic model that the calculated fluxes should be fit in to and the MFA output.
rxn_coverage(fittedFluxes, model)	Prints the percentage of how many of the reactions in the input fluxes are part of a given metabolic model.
split_lumped_rxns(lumped_rxns, fittedFluxes)	For data containing lumped reactions that are speparated by and underscore.
split_lumped_reverse_rxns(…)	For data containing lumped reverse reactions that are speparated by and underscore.
find_reverse_rxns(fittedFluxes)	Provides an overview over reverse- and their corresponding forward reactions.
combine_split_rxns(fittedFluxes)	Checks the flux bounds of forward and reverse rections.
cobra_add_split_rxns(rxns_to_split, model)	Adds inverse copies of the reactions that need a defined reverse reaction to the input model.
find_biomass_reaction(model[, biomass_string])	Identifies the biomass reaction(s) in a metabolic model.
get_min_solution_val(fittedFluxes[, …])	Finds the value calculated for the biomass function in the MFA simulation.
replace_biomass_rxn_name(fittedFluxes, …)	Replaces the biomass function name in the INCA simulation results with the biomass funciton name in the metabolic model.

Sampling

Methods are provided to apply the MFA-calculated fluxes as constraints to the model that is used for further analyses and to deal with infeasible solutions.

Functions

add_constraints(model_input, fittedFluxes)	Adds all the constraints defined in the input to a metabolic model.
add_feasible_constraints(model_input, …[, …])	Adds contraints to a metabolic model one by one; always checking that is still produces a feasible solution and that the predicted objective does not fall below a predefined value.
bound_relaxation(infeasible_model, fittedFluxes)	Relaxation function for cobra metabolic models.