computer aided metabolic engineering and optimization
cameo uses and extends the model data structures defined by cobrapy, our favorite COnstraints-Based Reconstruction and Analysis tool for Python. cameo is thus 100% compatible with cobrapy. For efficiency reasons though cameo implements its own analysis methods that take advantage of a more advanced solver interface.
from cameo import load_model
model = load_model("iJO1366")
Flux variability analysis (FVA) enables the computation of lower and upper bounds of reaction fluxes.
from cameo import flux_variability_analysis
flux_variability_analysis(model, reactions=[model.reactions.PGI, model.reactions.EX_glc_lp_e_rp_])
lower_bound | upper_bound | |
---|---|---|
EX_glc_lp_e_rp_ | -10.00 | -0.134043 |
PGI | -254.35 | 241.850000 |
One very useful application of FVA is determining if alternative optimal solution exist.
flux_variability_analysis(model, reactions=[model.reactions.PGI, model.reactions.EX_glc_lp_e_rp_],
fraction_of_optimum=1.)
lower_bound | upper_bound | |
---|---|---|
EX_glc_lp_e_rp_ | -10.000000 | -10.000000 |
PGI | 5.918065 | 5.918065 |
model.reactions.EX_o2_lp_e_rp_.lower_bound = -10
result = analysis.phenotypic_phase_plane(model,
variables=[model.reactions.BiomassEcoli],
objective=model.reactions.EX_succ_lp_e_rp_,
points=10)
result.plot(height=400)
result.data_frame