In [1]:

import logging

In [2]:

logging.basicConfig(level="DEBUG")

In [3]:

from cobra.io import load_model

In [4]:

from cobra.flux_analysis import geometric_fba

In [5]:

model = load_model("textbook")

INFO:cobra.core.model:The current solver interface glpk doesn't support setting the optimality tolerance.

Scaling...
 A: min|aij| =  1.000e+00  max|aij| =  1.000e+00  ratio =  1.000e+00
Problem data seem to be well scaled

In [6]:

model.solver = "cplex"

In [7]:

logging.getLogger().setLevel(logging.DEBUG)

In [8]:

%time geometric_fba(model)

DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 4e-13; status: optimal.

CPU times: user 481 ms, sys: 0 ns, total: 481 ms
Wall time: 480 ms

Out[8]:

Optimal solution with objective value 0.000

	fluxes	reduced_costs
ACALD	0.000000	0.0
ACALDt	0.000000	0.0
ACKr	0.000000	0.0
ACONTa	6.007250	0.0
ACONTb	6.007250	0.0
...	...	...
TALA	1.496984	0.0
THD2	0.000000	0.0
TKT1	1.496984	0.0
TKT2	1.181498	0.0
TPI	7.477382	0.0

95 rows × 2 columns

In [9]:

model.solver = "gurobi"

In [10]:

%time geometric_fba(model)

DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 6.47e-12; status: optimal.

CPU times: user 504 ms, sys: 2.91 ms, total: 507 ms
Wall time: 505 ms

Out[10]:

Optimal solution with objective value 0.000

	fluxes	reduced_costs
ACALD	0.000000	0.000000e+00
ACALDt	0.000000	0.000000e+00
ACKr	0.000000	0.000000e+00
ACONTa	6.007250	0.000000e+00
ACONTb	6.007250	0.000000e+00
...	...	...
TALA	1.496984	2.220446e-16
THD2	0.000000	2.220446e-16
TKT1	1.496984	0.000000e+00
TKT2	1.181498	-1.110223e-16
TPI	7.477382	0.000000e+00

95 rows × 2 columns

In [11]:

model.solver = "glpk"

In [12]:

%time geometric_fba(model)

DEBUG:optlang.glpk_interface:Status undefined. GLPK status code returned by glp_simplex was 1
DEBUG:cobra.flux_analysis.geometric:Iteration: 1; delta: 2.96e-13; status: optimal.

CPU times: user 263 ms, sys: 3.46 ms, total: 267 ms
Wall time: 263 ms

Out[12]:

Optimal solution with objective value -0.000

	fluxes	reduced_costs
ACALD	1.495879e-14	2.914335e-16
ACALDt	1.495879e-14	0.000000e+00
ACKr	1.554312e-15	1.110223e-16
ACONTa	6.007250e+00	0.000000e+00
ACONTb	6.007250e+00	0.000000e+00
...	...	...
TALA	1.496984e+00	-1.665335e-15
THD2	5.789919e-14	0.000000e+00
TKT1	1.496984e+00	1.665335e-16
TKT2	1.181498e+00	-2.220446e-16
TPI	7.477382e+00	0.000000e+00

95 rows × 2 columns