220.127.116.11.1.6.1. Module Contents¶
pfba(model, fraction_of_optimum=1.0, objective=None, reactions=None)¶
Perform basic pFBA (parsimonious Enzyme Usage Flux Balance Analysis) to minimize total flux.
pFBA  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.
- 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.
The solution object to the optimized model with pFBA constraints added.
 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
add_pfba(model, objective=None, fraction_of_optimum=1.0)¶
Add pFBA objective
Add objective to minimize the summed flux of all reactions to the current objective.
- 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.