1.3 Running OptMet

from bokeh.io import output_notebook
output_notebook()

Loading BokehJS ...

from cameo import models
from marsi.cobra.strain_design import OptMet

model = models.bigg.iJO1366

optimization = OptMet(model=model)

target = model.metabolites.succ_c
biomass = model.reactions.BIOMASS_Ec_iJO1366_core_53p95M
substrate = model.reactions.EX_glc__D_e

# Succinate production needs to be anaerobic to yield growth coupled designs.
model.reactions.EX_o2_e.lower_bound = 0

result = optimization.run(target=target, biomass=biomass, substrate=substrate, max_evaluations=3000)

result