In [1]:
from cameo import models
Load the E. coli core model.
In [2]:
model = models.bigg.e_coli_core
In [3]:
from cameo.strain_design.deterministic.flux_variability_based import FSEOF
In [4]:
fseof = FSEOF(model)
In [5]:
fseof.run(target=model.reactions.EX_succ_e)
Out[5]:
In [6]:
from cameo.flux_analysis.analysis import phenotypic_phase_plane
from cameo.strain_design.deterministic import DifferentialFVA
The production envelope looks like this.
In [7]:
production_envelope = phenotypic_phase_plane(model,
variables=[model.reactions.BIOMASS_Ecoli_core_w_GAM],
objective=model.metabolites.succ_e)
production_envelope.plot(height=400)
Set up a model that represents a reference state (in this case a model with a constrained growth rate).
In [8]:
model.reactions.EX_o2_e.lower_bound = 0
reference_model = model.copy()
biomass_rxn = reference_model.reactions.BIOMASS_Ecoli_core_w_GAM
biomass_rxn.lower_bound = 0.
target = reference_model.metabolites.succ_e
Set up the differential flux variability analysis strain design method.
In [9]:
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 [10]:
result = diffFVA.run(surface_only=True)
In [11]:
result.solutions
Out[11]:
In [12]:
result.plot(5, variables=['FBP', 'G6PDH2r', 'PGL', 'PGK'])
In [13]:
result.display_on_map(2, map_name="iJO1366.Central metabolism")
In [ ]: