Differential flux variability analysis¶

from cameo import load_model
from cameo.flux_analysis.analysis import phenotypic_phase_plane
from cameo.strain_design.deterministic import DifferentialFVA

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E. coli model and succinate production¶

Load the E. coli core model.

model = load_model('iJO1366')

The production envelope looks like this.

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).

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.

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)

result = diffFVA.run(surface_only=True)
result.plot(height=300)

Scanning grid points 0%

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result.display_on_map("iJO1366.Central metabolism")

Ec_biomass_iJO1366_core_53p95M 0.000000
EX_succ_lp_e_rp_ 17.096429

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