Strain optimization¶
Kinetic models optimization¶
optimModels implements some support for working with strain optimization using Kinetic metabolic models.
The optimization use several parameters which are configured in the optimModels.utils.configurations module.
Evaluation Function¶
Before start the strain optimization, it is required the definition of an evaluation function. The evaluation function is responsible for calculate the fitness value for each candidate solution obtained during the optimization process.
At the moment there are two objective functions available:
- targetFlux : the fitness value is the flux of a given target reaction.
- BPCY : the fitness value is the Biomass-Product Coupled Yield. In this case the user must
specify 3 reactions identifiers (biomass, product and uptake).
from optimModels import build_objective_function
objFunc = build_objective_function("targetFlux", ["vsersynth"])
Knockouts¶
The strain optimization using the knockouts can be performed calling the strain_optim function.
from optimModels import strain_optim
results = strain_optim(model, objFunc=objFunc)
for result in results:
result.print()
Under/Over expression¶
To perform a under/over expression optimization the multiplied factors levels should be given as argument.
levels = [0, 2 ** -5, 2 ** -4, 2 ** -3, 2 ** -2, 2 ** -1, 2 ** 1, 2 ** 2, 2 ** 3, 2 ** 4, 2 ** 5]
results = strain_optim(model, objFunc=objFunc, levels = levels)
for result in results:
result.print()