cobra.flux_analysis.parsimonious

Provide parsimonious FBA implementation.

Module Contents

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.

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

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: Union[Dict, optlang.interface.Objective, None] = None, reactions: Optional[List[cobra.Reaction]] = None) cobra.Solution[source]

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: Union[Dict, optlang.interface.Objective, None] = None, fraction_of_optimum: float = 1.0) None[source]

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