Analyzing models

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 models
model = models.bigg.e_coli_core

Flux Variability Analysis

Flux variability analysis (FVA) enables the computation of lower and upper bounds of reaction fluxes.

from cameo import flux_variability_analysis
fva_result = flux_variability_analysis(model)
fva_result.data_frame
lower_bound upper_bound
ACALD -20.0000 0.00
ACALDt -20.0000 0.00
ACKr -20.0000 0.00
ACONTa 0.0000 20.00
ACONTb 0.0000 20.00
... ... ...
TALA -0.1545 20.00
THD2 0.0000 333.22
TKT1 -0.1545 20.00
TKT2 -0.4664 20.00
TPI -10.0000 10.00

95 rows × 2 columns

fva_result.plot(index=fva_result.data_frame.index[:25])