straindesign
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Improve support for non-DNF GPR rules
Some models, e.g., iCHOv1 from Bigg, do not have GPR rules in DNF form. Improve the handling of such models.
import logging
logging.basicConfig(level=logging.INFO)
import straindesign as sd
import cobra
model = cobra.io.load_model('iCHOv1')
module_suppress = sd.SDModule(model,sd.names.SUPPRESS,constraints='BIOMASS_cho >= 0.001')
# Compute strain designs
sols = sd.compute_strain_designs(model,
sd_modules = module_suppress,
time_limit = 300,
max_solutions = 1,
max_cost = 1,
solution_approach = sd.names.ANY,
gene_kos = True,
solver='cplex')