cobra.flux_analysis.parsimonious
¶
Provide parsimonious FBA implementation.
Module Contents¶
Functions¶
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Perform basic pFBA to minimize total flux. |
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Perform basic pFBA (parsimonious Enzyme Usage Flux Balance Analysis). |
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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
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