In [1]:
import logging
In [2]:
logging.basicConfig(level="INFO")
In [3]:
from cobra.test import create_test_model
In [4]:
from cobra.flux_analysis import flux_variability_analysis
In [5]:
model = create_test_model("ecoli")
In [6]:
%time flux_variability_analysis(model, fraction_of_optimum=0.95, processes=1)
CPU times: user 5.71 s, sys: 0 ns, total: 5.71 s
Wall time: 5.71 s
Out[6]:
minimum
maximum
DM_4CRSOL
0.000208
0.000219
DM_5DRIB
0.000210
0.112258
DM_AACALD
0.000000
0.000000
DM_AMOB
0.000002
0.000002
DM_MTHTHF
0.000418
0.515309
DM_OXAM
0.000000
1.010167
Ec_biomass_iJO1366_WT_53p95M
0.000000
0.049326
Ec_biomass_iJO1366_core_53p95M
0.933253
0.982372
EX_12ppd__R_e
0.000000
0.724815
EX_12ppd__S_e
0.000000
0.713997
EX_14glucan_e
0.000000
0.000000
EX_15dap_e
0.000000
0.394750
EX_23camp_e
0.000000
0.000000
EX_23ccmp_e
0.000000
0.000000
EX_23cgmp_e
0.000000
0.000000
EX_23cump_e
0.000000
0.000000
EX_23dappa_e
0.000000
0.000000
EX_26dap__M_e
0.000000
0.000000
EX_2ddglcn_e
0.000000
0.000000
EX_34dhpac_e
0.000000
0.000000
EX_3amp_e
0.000000
0.000000
EX_3cmp_e
0.000000
0.000000
EX_3gmp_e
0.000000
0.000000
EX_3hcinnm_e
0.000000
0.000000
EX_3hpp_e
0.000000
0.631600
EX_3hpppn_e
0.000000
0.000000
EX_3ump_e
0.000000
0.000000
EX_4abut_e
0.000000
0.667183
EX_4hoxpacd_e
0.000000
0.000000
EX_5dglcn_e
0.000000
0.563929
...
...
...
VALTRS
0.000000
0.000000
VALabcpp
0.000000
15.790000
VALt2rpp
-15.790000
0.000000
VALtex
-0.526333
0.000000
VPAMTr
-999.605083
999.457448
WCOS
0.000000
0.000000
X5PL3E
0.000000
0.000000
XAND
0.000000
1.263200
XANt2pp
0.000000
47.370000
XANtex
-0.644490
0.000000
XANtpp
-47.370000
0.000000
XMPtex
0.000000
0.000000
XPPT
0.000000
11.842500
XTSNH
0.000000
11.842500
XTSNt2rpp
-0.302684
0.000000
XTSNtex
-0.302684
0.000000
XYLI1
0.000000
0.000000
XYLI2
-11.842500
19.342500
XYLK
0.000000
0.000000
XYLK2
0.000000
0.000000
XYLUt2pp
0.000000
0.000000
XYLUtex
0.000000
0.000000
XYLabcpp
0.000000
0.000000
XYLt2pp
0.000000
0.000000
XYLtex
0.000000
0.000000
ZN2abcpp
0.000000
11.842500
ZN2t3pp
0.000000
47.370000
ZN2tpp
0.000000
47.370318
ZNabcpp
0.000000
9.474064
Zn2tex
0.000318
0.000335
2583 rows × 2 columns
In [7]:
%time flux_variability_analysis(model, fraction_of_optimum=0.95, processes=4)
CPU times: user 68.9 ms, sys: 60.2 ms, total: 129 ms
Wall time: 2.03 s
Out[7]:
minimum
maximum
DM_4CRSOL
0.000208
0.000219
DM_5DRIB
0.000210
0.112258
DM_AACALD
0.000000
0.000000
DM_AMOB
0.000002
0.000002
DM_MTHTHF
0.000418
0.515309
DM_OXAM
0.000000
1.010167
Ec_biomass_iJO1366_WT_53p95M
0.000000
0.049326
Ec_biomass_iJO1366_core_53p95M
0.933253
0.982372
EX_12ppd__R_e
0.000000
0.724815
EX_12ppd__S_e
0.000000
0.713997
EX_14glucan_e
0.000000
0.000000
EX_15dap_e
0.000000
0.394750
EX_23camp_e
0.000000
0.000000
EX_23ccmp_e
0.000000
0.000000
EX_23cgmp_e
0.000000
0.000000
EX_23cump_e
0.000000
0.000000
EX_23dappa_e
0.000000
0.000000
EX_26dap__M_e
0.000000
0.000000
EX_2ddglcn_e
0.000000
0.000000
EX_34dhpac_e
0.000000
0.000000
EX_3amp_e
0.000000
0.000000
EX_3cmp_e
0.000000
0.000000
EX_3gmp_e
0.000000
0.000000
EX_3hcinnm_e
0.000000
0.000000
EX_3hpp_e
0.000000
0.631600
EX_3hpppn_e
0.000000
0.000000
EX_3ump_e
0.000000
0.000000
EX_4abut_e
0.000000
0.667183
EX_4hoxpacd_e
0.000000
0.000000
EX_5dglcn_e
0.000000
0.563929
...
...
...
VALTRS
0.000000
0.000000
VALabcpp
0.000000
15.790000
VALt2rpp
-15.790000
0.000000
VALtex
-0.526333
0.000000
VPAMTr
-999.605083
999.457448
WCOS
0.000000
0.000000
X5PL3E
0.000000
0.000000
XAND
0.000000
1.263200
XANt2pp
0.000000
47.370000
XANtex
-0.644490
0.000000
XANtpp
-47.370000
0.000000
XMPtex
0.000000
0.000000
XPPT
0.000000
11.842500
XTSNH
0.000000
11.842500
XTSNt2rpp
-0.302684
0.000000
XTSNtex
-0.302684
0.000000
XYLI1
0.000000
0.000000
XYLI2
-11.842500
19.342500
XYLK
0.000000
0.000000
XYLK2
0.000000
0.000000
XYLUt2pp
0.000000
0.000000
XYLUtex
0.000000
0.000000
XYLabcpp
0.000000
0.000000
XYLt2pp
0.000000
0.000000
XYLtex
0.000000
0.000000
ZN2abcpp
0.000000
11.842500
ZN2t3pp
0.000000
47.370000
ZN2tpp
0.000000
47.370318
ZNabcpp
0.000000
9.474064
Zn2tex
0.000318
0.000335
2583 rows × 2 columns
Content source: opencobra/cobrapy
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