In [1]:
from cameo import load_model
from cameo.flux_analysis.analysis import phenotypic_phase_plane
from cameo.strain_design.deterministic import DifferentialFVA
Load the E. coli core model.
In [2]:
model = load_model('iJO1366')
The production envelope looks like this.
In [3]:
production_envelope = phenotypic_phase_plane(model,
variables=[model.reactions.Ec_biomass_iJO1366_core_53p95M],
objective=model.reactions.EX_succ_lp_e_rp_)
production_envelope.plot(height=300)
Set up a model that represents a reference state (in this case a model with a constrained growth rate).
In [4]:
reference_model = model.copy()
biomass_rxn = reference_model.reactions.Ec_biomass_iJO1366_core_53p95M
biomass_rxn.lower_bound = 0.3
target = reference_model.reactions.EX_succ_lp_e_rp_
target.lower_bound = 2
Set up the differential flux variability analysis strain design method.
In [5]:
diffFVA = DifferentialFVA(design_space_model=model,
reference_model=reference_model,
objective=target,
variables=[biomass_rxn],
normalize_ranges_by=biomass_rxn,
points=10)
Run differential flux variability analysis (only on the surface of the production envelope)
In [6]:
result = diffFVA.run(surface_only=True)
result.plot(height=300)
In [7]:
result.display_on_map("iJO1366.Central metabolism")
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