15.1.1.2.1.6. cobra.flux_analysis.parsimonious
¶
15.1.1.2.1.6.1. Module Contents¶

cobra.flux_analysis.parsimonious.
pfba
(model, fraction_of_optimum=1.0, objective=None, reactions=None)[source]¶ Perform basic pFBA (parsimonious Enzyme Usage Flux Balance Analysis) to minimize total flux.
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 turnover 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
 fraction_of_optimum (float, optional) – Fraction of optimum which must be maintained. The original objective reaction is constrained to be greater than maximal_value * fraction_of_optimum.
 objective (dict or model.problem.Objective) – 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.
 reactions (iterable) – List of reactions or reaction identifiers. Implies return_frame to be true. Only return fluxes for the given reactions. Faster than fetching all fluxes if only a few are needed.
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 genomescale models. Molecular Systems Biology, 6, 390. doi:10.1038/msb.2010.47

cobra.flux_analysis.parsimonious.
add_pfba
(model, objective=None, fraction_of_optimum=1.0)[source]¶ Add pFBA objective
Add objective to minimize the summed flux of all reactions to the current objective.
See also
Parameters:  model (cobra.Model) – The model to add the objective to
 objective – An objective to set in combination with the pFBA objective.
 fraction_of_optimum (float) – Fraction of optimum which must be maintained. The original objective reaction is constrained to be greater than maximal_value * fraction_of_optimum.