Analyzing models with

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

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

Phenotpic Phase Plane

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