cobra.flux_analysis.parsimonious

Provide parsimonious FBA implementation.

Functions

optimize_minimal_flux(→ Callable[[cobra.Model, float, ...)	Perform basic pFBA to minimize total flux.
pfba(→ cobra.Solution)	Perform basic pFBA (parsimonious Enzyme Usage Flux Balance Analysis).
add_pfba(→ None)	Add pFBA objective to the model.

Module Contents

cobra.flux_analysis.parsimonious.optimize_minimal_flux(*args, **kwargs) → Callable[[cobra.Model, float, Dict | optlang.interface.Objective, List[cobra.Reaction]], cobra.Solution]

Perform basic pFBA to minimize total flux.

Deprecated since version 0.6.0a4: optimize_minimal_flux will be removed in cobrapy 1.0.0, it is replaced by pfba.

Parameters:

• *args (Any) – Non-keyword variable-length arguments.

• **kwargs (Any) – Keyword-only variable-length arguments.

Return type:

A function performing the parsimonious FBA.

cobra.flux_analysis.parsimonious.pfba(model: cobra.Model, fraction_of_optimum: float = 1.0, objective: Dict | optlang.interface.Objective | None = None, reactions: List[cobra.Reaction] | None = None) → cobra.Solution

Perform basic pFBA (parsimonious Enzyme Usage Flux Balance Analysis).

pFBA [1] adds the minimization of all fluxes the the objective of the model. This approach is motivated by the idea that high fluxes have a higher enzyme turn-over and that since producing enzymes is costly, the cell will try to minimize overall flux while still maximizing the original objective function, e.g. the growth rate.

Parameters:

• model (cobra.Model) – The model to perform pFBA on.

• fraction_of_optimum (float, optional) – The fraction of optimum which must be maintained. The original objective reaction is constrained to be greater than maximal value times the fraction_of_optimum (default 1.0).

• objective (dict or cobra.Model.objective, optional) – A desired objective to use during optimization in addition to the pFBA objective. Dictionaries (reaction as key, coefficient as value) can be used for linear objectives (default None).

• reactions (list of cobra.Reaction, optional) – List of cobra.Reaction. Implies return_frame to be true. Only return fluxes for the given reactions. Faster than fetching all fluxes if only a few are needed (default None).

Returns:

The solution object to the optimized model with pFBA constraints added.

Return type:

cobra.Solution

References

[1]

Lewis, N. E., Hixson, K. K., Conrad, T. M., Lerman, J. A., Charusanti, P., Polpitiya, A. D., Palsson, B. O. (2010). Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Molecular Systems Biology, 6, 390. doi:10.1038/msb.2010.47

cobra.flux_analysis.parsimonious.add_pfba(model: cobra.Model, objective: Dict | optlang.interface.Objective | None = None, fraction_of_optimum: float = 1.0) → None

Add pFBA objective to the model.

This adds objective to minimize the summed flux of all reactions to the current objective.

Parameters:

• model (cobra.Model) – The model to add the objective to.

• objective (dict or cobra.Model.objective, optional) – A desired objective to use during optimization in addition to the pFBA objective. Dictionaries (reaction as key, coefficient as value) can be used for linear objectives (default None).

• fraction_of_optimum (float, optional) – Fraction of optimum which must be maintained. The original objective reaction is constrained to be greater than maximal value times the fraction_of_optimum.

See also

pfba