In [ ]:
# DFBA Simulation Diauxic Growth
Simulation of the diauxic growth model.
In [1]:
from __future__ import print_function, division
import os
import timeit
import pandas as pd
from pprint import pprint
from matplotlib import pylab as plt
from sbmlutils.dfba.simulator import Simulator
# global settings for plots
plt.rcParams.update({
'axes.labelsize': 'large',
'axes.labelweight': 'bold',
'axes.titlesize': 'large',
'axes.titleweight': 'bold',
'legend.fontsize': 'small',
'xtick.labelsize': 'large',
'ytick.labelsize': 'large',
})
out_dir = './results/'
print(os.getcwd())
/home/mkoenig/git/sbmlutils/sbmlutils/dfba/diauxic_growth
In [4]:
from sbmlutils.dfba.diauxic_growth.model_factory import version
sbml_path = os.path.join(os.getcwd(), 'results/v{}/diauxic_top.xml'.format(version))
print(sbml_path)
sim = Simulator(sbml_top_path=sbml_path)
* _process_top
* _process_models
--------------------------------------------------------------------------------
<Model diauxic_top "Top level model"> [ode]
--------------------------------------------------------------------------------
fba : [<Submodel fba>]
ode : [<Submodel bounds>, <Submodel update>]
stochastic : []
logical : []
fba rules :
dummy_vAc <-> vAc
dummy_vGlcxt <-> vGlcxt
dummy_vO2 <-> vO2
dummy_vX <-> vX
<Submodel fba> diauxic_fba.xml
FBA rules : {}
ub parameters : defaultdict(<type 'list'>, {'ub_vO2': ['vO2'], 'ub_vAc': ['vAc'], 'ub': ['vX', 'v1', 'v2', 'v3', 'v4'], 'ub_vGlcxt': ['vGlcxt']})
lb parameters : defaultdict(<type 'list'>, {'lb_vO2': ['vO2'], 'lb_vAc': ['vAc'], 'lb_vGlcxt': ['vGlcxt'], 'lb_irrev': ['vX', 'v1', 'v2', 'v3', 'v4']})
ub replacements : ['ub_vAc', 'ub_vGlcxt', 'ub_vO2']
lb replacements : ['lb_vAc', 'lb_vGlcxt', 'lb_vO2']
flat mapping : {'vGlcxt': 'vGlcxt', 'vAc': 'vAc', 'v1': 'fba__v1', 'v2': 'fba__v2', 'v3': 'fba__v3', 'v4': 'fba__v4', 'vO2': 'vO2', 'vX': 'vX'}
--------------------------------------------------------------------------------
/home/mkoenig/git/sbmlutils/sbmlutils/dfba/diauxic_growth/results/v3/diauxic_top.xml
In [5]:
import logging
logging.getLogger().setLevel(logging.DEBUG)
tend = 100
steps = 100
# reset the model
sim.rr_comp.reset()
start_time = timeit.default_timer()
df = sim.simulate(tstart=0.0, tend=tend, steps=steps)
elapsed = timeit.default_timer() - start_time
print("Simulation time: {}".format(elapsed))
# Create outputs
sim.plot_reactions(filepath=None, df=df, rr_comp=sim.rr_comp)
sim.plot_species(filepath=None, df=df, rr_comp=sim.rr_comp)
print(df)
###########################
# Start Simulation
###########################
--------------------------------------------------------------------------------
Time: 0.0
* FBA set bounds
upper: ub_vAc = vAc = 4.0
upper: ub_vGlcxt = vGlcxt = 14.9791955617
upper: ub_vO2 = vO2 = 2.1
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -2.1
* FBA optimize
status: optimal
v1 : 0.06
v2 : 0.0
v3 : 0.0
v4 : 0.195198019802
vAc : 0.0
vGlcxt : 3.75365792079
vO2 : 2.1
vX : 0.255198019802
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 0.000000
[Ac] 0.400000
[Glcxt] 10.800000
[O2] 0.210000
[X] 0.001000
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.060000
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.195198
update__update_Ac 0.000952
update__update_Glcxt 0.000998
update__update_O2 0.000913
update__update_X 0.001000
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.979196
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -2.100000
lb_vX 0.000000
ub_vAc 4.000000
ub_vGlcxt 14.979196
ub_vO2 2.100000
ub_vX 0.010000
update__Km_vFBA 0.020000
update__Y 0.001000
vAc 0.000000
vGlcxt 3.753658
vO2 2.100000
vX 0.255198
dtype: float64
--------------------------------------------------------------------------------
Time: 1.0
* FBA set bounds
upper: ub_vAc = vAc = 4.0
upper: ub_vGlcxt = vGlcxt = 14.9791955617
upper: ub_vO2 = vO2 = 2.1
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -2.1
* FBA optimize
status: optimal
v1 : 0.06
v2 : 0.0
v3 : 0.0
v4 : 0.195198019802
vAc : 0.0
vGlcxt : 3.75365792079
vO2 : 2.1
vX : 0.255198019802
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.398363
[Glcxt] 10.798284
[O2] 0.208431
[X] 0.002719
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.060000
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.195198
update__update_Ac 0.002589
update__update_Glcxt 0.002714
update__update_O2 0.002481
update__update_X 0.002719
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.979192
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -2.084313
lb_vX 0.000000
ub_vAc 3.983633
ub_vGlcxt 14.979192
ub_vO2 2.084313
ub_vX 0.027187
update__Km_vFBA 0.020000
update__Y 0.002719
vAc 0.000000
vGlcxt 3.753658
vO2 2.100000
vX 0.255198
dtype: float64
--------------------------------------------------------------------------------
Time: 2.0
* FBA set bounds
upper: ub_vAc = vAc = 3.98363293001
upper: ub_vGlcxt = vGlcxt = 14.9791922611
upper: ub_vO2 = vO2 = 2.08431255249
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -2.08431255249
* FBA optimize
status: optimal
v1 : 0.059551787214
v2 : 0.0
v3 : 0.0
v4 : 0.193739848997
vAc : 0.0
vGlcxt : 3.72561729622
vO2 : 2.08431255249
vX : 0.253291636211
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.393915
[Glcxt] 10.793620
[O2] 0.204172
[X] 0.007391
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.059552
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.193740
update__update_Ac 0.007034
update__update_Glcxt 0.007378
update__update_O2 0.006732
update__update_X 0.007391
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.979183
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -2.041716
lb_vX 0.000000
ub_vAc 3.939152
ub_vGlcxt 14.979183
ub_vO2 2.041716
ub_vX 0.073914
update__Km_vFBA 0.020000
update__Y 0.007391
vAc 0.000000
vGlcxt 3.725617
vO2 2.084313
vX 0.253292
dtype: float64
--------------------------------------------------------------------------------
Time: 3.0
* FBA set bounds
upper: ub_vAc = vAc = 3.93915211325
upper: ub_vGlcxt = vGlcxt = 14.9791832824
upper: ub_vO2 = vO2 = 2.04171574243
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -2.04171574243
* FBA optimize
status: optimal
v1 : 0.0583347354981
v2 : 0.0
v3 : 0.0
v4 : 0.189780414248
vAc : 0.0
vGlcxt : 3.64947736599
vO2 : 2.04171574243
vX : 0.248115149746
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.381835
[Glcxt] 10.780940
[O2] 0.192632
[X] 0.020095
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.058335
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.189780
update__update_Ac 0.019095
update__update_Glcxt 0.020058
update__update_O2 0.018205
update__update_X 0.020095
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.979159
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -1.926317
lb_vX 0.000000
ub_vAc 3.818346
ub_vGlcxt 14.979159
ub_vO2 1.926317
ub_vX 0.200949
update__Km_vFBA 0.020000
update__Y 0.020095
vAc 0.000000
vGlcxt 3.649477
vO2 2.041716
vX 0.248115
dtype: float64
--------------------------------------------------------------------------------
Time: 4.0
* FBA set bounds
upper: ub_vAc = vAc = 3.8183463819
upper: ub_vGlcxt = vGlcxt = 14.9791588327
upper: ub_vO2 = vO2 = 1.92631679495
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -1.92631679495
* FBA optimize
status: optimal
v1 : 0.055037622713
v2 : 0.0
v3 : 0.0
v4 : 0.179053916136
vAc : 0.0
vGlcxt : 3.4432068073
vO2 : 1.92631679495
vX : 0.234091538849
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.349091
[Glcxt] 10.746467
[O2] 0.161607
[X] 0.054632
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.055038
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.179054
update__update_Ac 0.051672
update__update_Glcxt 0.054530
update__update_O2 0.048615
update__update_X 0.054632
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.979092
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -1.616073
lb_vX 0.000000
ub_vAc 3.490909
ub_vGlcxt 14.979092
ub_vO2 1.616073
ub_vX 0.546319
update__Km_vFBA 0.020000
update__Y 0.054632
vAc 0.000000
vGlcxt 3.443207
vO2 1.926317
vX 0.234092
dtype: float64
--------------------------------------------------------------------------------
Time: 5.0
* FBA set bounds
upper: ub_vAc = vAc = 3.49090860851
upper: ub_vGlcxt = vGlcxt = 14.9790920709
upper: ub_vO2 = vO2 = 1.6160729249
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -1.6160729249
* FBA optimize
status: optimal
v1 : 0.04617351214
v2 : 0.0
v3 : 0.0
v4 : 0.150216302284
vAc : 0.0
vGlcxt : 2.88865949292
vO2 : 1.6160729249
vX : 0.196389814424
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.261016
[Glcxt] 10.652751
[O2] 0.081438
[X] 0.148523
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.046174
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.150216
update__update_Ac 0.137953
update__update_Glcxt 0.148245
update__update_O2 0.119240
update__update_X 0.148523
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.978908
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -0.814376
lb_vX 0.000000
ub_vAc 2.610163
ub_vGlcxt 14.978908
ub_vO2 0.814376
ub_vX 1.485231
update__Km_vFBA 0.020000
update__Y 0.148523
vAc 0.000000
vGlcxt 2.888659
vO2 1.616073
vX 0.196390
dtype: float64
--------------------------------------------------------------------------------
Time: 6.0
* FBA set bounds
upper: ub_vAc = vAc = 2.61016266873
upper: ub_vGlcxt = vGlcxt = 14.9789083949
upper: ub_vO2 = vO2 = 0.814376313162
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -0.814376313162
* FBA optimize
status: optimal
v1 : 0.0232678946618
v2 : 0.0
v3 : 0.0
v4 : 0.0756974493823
vAc : 0.0
vGlcxt : 1.45566195162
vO2 : 0.814376313162
vX : 0.098965344044
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000
[Ac] 0.042223
[Glcxt] 10.398007
[O2] 0.000014
[X] 0.403751
[dummy_S] 0.000000
dummy_vAc 0.000000
dummy_vGlcxt 0.000000
dummy_vO2 0.000000
dummy_vX 0.000000
fba__v1 0.023268
fba__v2 0.000000
fba__v3 0.000000
fba__v4 0.075697
update__update_Ac 0.273975
update__update_Glcxt 0.402976
update__update_O2 0.000277
update__update_X 0.403751
bounds__Km_vGlcxt 0.015000
bounds__Vmax_vGlcxt 15.000000
bounds__dt 0.100000
bounds__lb_def_vAc 0.000000
bounds__lb_def_vGlcxt 0.000000
bounds__lb_def_vO2 -1000.000000
bounds__lb_def_vX 0.000000
bounds__ub_def_vAc 1000.000000
bounds__ub_def_vGlcxt 10.000000
bounds__ub_def_vO2 15.000000
bounds__ub_def_vX 1000.000000
bounds__ub_kin_vGlcxt 14.978392
dt 0.100000
fba__lb -1000.000000
fba__lb_irrev 0.000000
fba__ub 1000.000000
lb_vAc 0.000000
lb_vGlcxt 0.000000
lb_vO2 -0.000137
lb_vX 0.000000
ub_vAc 0.422226
ub_vGlcxt 14.978392
ub_vO2 0.000137
ub_vX 4.037514
update__Km_vFBA 0.020000
update__Y 0.403751
vAc 0.000000
vGlcxt 1.455662
vO2 0.814376
vX 0.098965
dtype: float64
--------------------------------------------------------------------------------
Time: 7.0
* FBA set bounds
upper: ub_vAc = vAc = 0.422225575993
upper: ub_vGlcxt = vGlcxt = 14.9783924092
upper: ub_vO2 = vO2 = 0.000137106421929
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = -0.000137106421929
* FBA optimize
status: optimal
v1 : 3.91732634083e-06
v2 : 0.0
v3 : 0.0
v4 : 1.27442390775e-05
vAc : 0.0
vGlcxt : 0.00024507171746
vO2 : 0.000137106421929
vX : 1.66615654183e-05
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 1.317395e-11
[Glcxt] 9.705627e+00
[O2] 4.915177e-16
[X] 1.097510e+00
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 3.917326e-06
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 1.274424e-05
update__update_Ac 7.229274e-10
update__update_Glcxt 1.095253e+00
update__update_O2 2.697229e-14
update__update_X 1.097510e+00
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 1.497685e+01
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -4.915177e-15
lb_vX 0.000000e+00
ub_vAc 1.317395e-10
ub_vGlcxt 1.497685e+01
ub_vO2 4.915177e-15
ub_vX 1.097510e+01
update__Km_vFBA 2.000000e-02
update__Y 1.097510e+00
vAc 0.000000e+00
vGlcxt 2.450717e-04
vO2 1.371064e-04
vX 1.666157e-05
dtype: float64
--------------------------------------------------------------------------------
Time: 8.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 14.9768533439
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] -1.331995e-11
[Glcxt] 7.823671e+00
[O2] -4.969649e-16
[X] 2.983777e+00
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac -1.987189e-09
update__update_Glcxt 2.976169e+00
update__update_O2 -7.414162e-14
update__update_X 2.983777e+00
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 1.497130e+01
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 1.331995e-10
lb_vGlcxt 0.000000e+00
lb_vO2 4.969649e-15
lb_vX 0.000000e+00
ub_vAc -1.331995e-10
ub_vGlcxt 1.497130e+01
ub_vO2 -4.969649e-15
ub_vX 2.983777e+01
update__Km_vFBA 2.000000e-02
update__Y 2.983777e+00
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 9.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 14.9712961557
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] -1.466415e-11
[Glcxt] 2.716940e+00
[O2] -5.471159e-16
[X] 8.111719e+00
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac -5.947572e-09
update__update_Glcxt 8.052443e+00
update__update_O2 -2.219025e-13
update__update_X 8.111719e+00
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 1.491764e+01
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 1.466415e-10
lb_vGlcxt 0.000000e+00
lb_vO2 5.471159e-15
lb_vX 0.000000e+00
ub_vAc -1.466415e-10
ub_vGlcxt 1.491764e+01
ub_vO2 -5.471159e-15
ub_vX 8.111719e+01
update__Km_vFBA 2.000000e-02
update__Y 8.111719e+00
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 10.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 14.9176409368
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 7.955788e-32
[Glcxt] 2.476808e-11
[O2] 2.968286e-36
[X] 2.205149e+01
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 8.771848e-29
update__update_Glcxt 2.730865e-08
update__update_O2 3.272756e-33
update__update_X 2.205149e+01
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 2.476808e-08
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -2.968286e-35
lb_vX 0.000000e+00
ub_vAc 7.955788e-31
ub_vGlcxt 2.476808e-10
ub_vO2 2.968286e-35
ub_vX 2.205149e+02
update__Km_vFBA 2.000000e-02
update__Y 2.205149e+01
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 11.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 4.138210e-31
[Glcxt] 1.288318e-10
[O2] 1.543956e-35
[X] 5.994969e+01
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 1.240422e-27
update__update_Glcxt 3.861714e-07
update__update_O2 4.627985e-32
update__update_X 5.994969e+01
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 1.288318e-07
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -1.543956e-34
lb_vX 0.000000e+00
ub_vAc 4.138210e-30
ub_vGlcxt 1.288318e-09
ub_vO2 1.543956e-34
ub_vX 5.994969e+02
update__Km_vFBA 2.000000e-02
update__Y 5.994969e+01
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 12.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 1.759600e-32
[Glcxt] 5.478054e-12
[O2] 6.565025e-37
[X] 1.629685e+02
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 1.433796e-28
update__update_Glcxt 4.463750e-08
update__update_O2 5.349460e-33
update__update_X 1.629685e+02
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 5.478054e-09
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -6.565025e-36
lb_vX 0.000000e+00
ub_vAc 1.759600e-31
ub_vGlcxt 5.478054e-11
ub_vO2 6.565025e-36
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 1.629685e+02
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 13.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] -2.616018e-32
[Glcxt] -8.144279e-12
[O2] -9.760300e-37
[X] 4.430545e+02
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac -5.795192e-28
update__update_Glcxt -1.804180e-07
update__update_O2 -2.162172e-32
update__update_X 4.430545e+02
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt -8.144279e-09
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 2.616018e-31
lb_vGlcxt 8.144279e-11
lb_vO2 9.760300e-36
lb_vX 0.000000e+00
ub_vAc -2.616018e-31
ub_vGlcxt -8.144279e-09
ub_vO2 -9.760300e-36
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 4.430545e+02
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 14.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 7.979234e-32
[Glcxt] 2.484124e-11
[O2] 2.977033e-36
[X] 1.204531e+03
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 4.805617e-27
update__update_Glcxt 1.496102e-06
update__update_O2 1.792964e-31
update__update_X 1.204531e+03
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 2.484124e-08
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -2.977033e-35
lb_vX 0.000000e+00
ub_vAc 7.979234e-31
ub_vGlcxt 2.484124e-10
ub_vO2 2.977033e-35
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 1.204531e+03
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 15.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 9.675694e-32
[Glcxt] 3.012272e-11
[O2] 3.609979e-36
[X] 3.274748e+03
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 1.584273e-26
update__update_Glcxt 4.932216e-06
update__update_O2 5.910885e-31
update__update_X 3.274748e+03
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 3.012272e-08
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -3.609979e-35
lb_vX 0.000000e+00
ub_vAc 9.675694e-31
ub_vGlcxt 3.012272e-10
ub_vO2 3.609979e-35
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 3.274748e+03
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 16.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] 2.274030e-32
[Glcxt] 7.079591e-12
[O2] 8.484351e-37
[X] 8.903726e+03
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac 1.012367e-26
update__update_Glcxt 3.151737e-06
update__update_O2 3.777117e-31
update__update_X 8.903726e+03
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt 7.079591e-09
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 0.000000e+00
lb_vGlcxt 0.000000e+00
lb_vO2 -8.484351e-36
lb_vX 0.000000e+00
ub_vAc 2.274030e-31
ub_vGlcxt 7.079591e-11
ub_vO2 8.484351e-36
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 8.903726e+03
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 17.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = 0.0
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
status: optimal
v1 : 0.0
v2 : 0.0
v3 : 0.0
v4 : 0.0
vAc : 0.0
vGlcxt : 0.0
vO2 : 0.0
vX : 0.0
* ODE set FBA fluxes
No flux replacements
* ODE integration
* Copy fluxes in ODE solution
time 1.000000e+00
[Ac] -7.596239e-32
[Glcxt] -2.364888e-11
[O2] -2.834139e-36
[X] 2.420644e+04
[dummy_S] 0.000000e+00
dummy_vAc 0.000000e+00
dummy_vGlcxt 0.000000e+00
dummy_vO2 0.000000e+00
dummy_vX 0.000000e+00
fba__v1 0.000000e+00
fba__v2 0.000000e+00
fba__v3 0.000000e+00
fba__v4 0.000000e+00
update__update_Ac -9.193895e-26
update__update_Glcxt -2.862276e-05
update__update_O2 -3.430221e-30
update__update_X 2.420644e+04
bounds__Km_vGlcxt 1.500000e-02
bounds__Vmax_vGlcxt 1.500000e+01
bounds__dt 1.000000e-01
bounds__lb_def_vAc 0.000000e+00
bounds__lb_def_vGlcxt 0.000000e+00
bounds__lb_def_vO2 -1.000000e+03
bounds__lb_def_vX 0.000000e+00
bounds__ub_def_vAc 1.000000e+03
bounds__ub_def_vGlcxt 1.000000e+01
bounds__ub_def_vO2 1.500000e+01
bounds__ub_def_vX 1.000000e+03
bounds__ub_kin_vGlcxt -2.364888e-08
dt 1.000000e-01
fba__lb -1.000000e+03
fba__lb_irrev 0.000000e+00
fba__ub 1.000000e+03
lb_vAc 7.596239e-31
lb_vGlcxt 2.364888e-10
lb_vO2 2.834139e-35
lb_vX 0.000000e+00
ub_vAc -7.596239e-31
ub_vGlcxt -2.364888e-08
ub_vO2 -2.834139e-35
ub_vX 1.000000e+03
update__Km_vFBA 2.000000e-02
update__Y 2.420644e+04
vAc 0.000000e+00
vGlcxt 0.000000e+00
vO2 0.000000e+00
vX 0.000000e+00
dtype: float64
--------------------------------------------------------------------------------
Time: 18.0
* FBA set bounds
upper: ub_vAc = vAc = 0.0
upper: ub_vGlcxt = vGlcxt = -2.3648875781e-08
upper: ub_vO2 = vO2 = 0.0
lower: lb_vAc = vAc = 0.0
lower: lb_vGlcxt = vGlcxt = 0.0
lower: lb_vO2 = vO2 = 0.0
* FBA optimize
Traceback (most recent call last):
File "/home/mkoenig/git/sbmlutils/sbmlutils/dfba/simulator.py", line 320, in simulate
# --------------------------------------
File "/home/mkoenig/git/sbmlutils/sbmlutils/dfba/simulator.py", line 573, in optimize
File "/home/mkoenig/git/cobrapy/cobra/core/Model.py", line 272, in optimize
solution = optimize(self, objective_sense=objective_sense, **kwargs)
File "/home/mkoenig/git/cobrapy/cobra/solvers/__init__.py", line 124, in optimize
return solver_dict[solver].solve(cobra_model, **kwargs)
File "cobra/solvers/cglpk.pyx", line 344, in cobra.solvers.cglpk.GLP.solve (cobra/solvers/cglpk.c:5210)
problem.solve_problem(**kwargs)
File "cobra/solvers/cglpk.pyx", line 322, in cobra.solvers.cglpk.GLP.solve_problem (cobra/solvers/cglpk.c:4838)
check_error(glp_simplex(glp, &self.parameters))
File "cobra/solvers/cglpk.pyx", line 134, in cobra.solvers.cglpk.check_error (cobra/solvers/cglpk.c:2339)
raise RuntimeError("glp_simplex failed with error code %s: %s" %
RuntimeError: glp_simplex failed with error code GLP_EBOUND: invalid bounds
Simulation time: 0.368553161621
time [Ac] [Glcxt] [O2] [X] [dummy_S] \
0 0.0 4.000000e-01 1.080000e+01 2.100000e-01 0.001000 0.0
1 1.0 3.983633e-01 1.079828e+01 2.084313e-01 0.002719 0.0
2 2.0 3.939152e-01 1.079362e+01 2.041716e-01 0.007391 0.0
3 3.0 3.818346e-01 1.078094e+01 1.926317e-01 0.020095 0.0
4 4.0 3.490909e-01 1.074647e+01 1.616073e-01 0.054632 0.0
5 5.0 2.610163e-01 1.065275e+01 8.143763e-02 0.148523 0.0
6 6.0 4.222256e-02 1.039801e+01 1.371064e-05 0.403751 0.0
7 7.0 1.317395e-11 9.705627e+00 4.915177e-16 1.097510 0.0
8 8.0 -1.331995e-11 7.823671e+00 -4.969649e-16 2.983777 0.0
9 9.0 -1.466415e-11 2.716940e+00 -5.471159e-16 8.111719 0.0
10 10.0 7.955788e-32 2.476808e-11 2.968286e-36 22.051487 0.0
11 11.0 4.138210e-31 1.288318e-10 1.543956e-35 59.949692 0.0
12 12.0 1.759600e-32 5.478054e-12 6.565025e-37 162.968479 0.0
13 13.0 -2.616018e-32 -8.144279e-12 -9.760300e-37 443.054516 0.0
14 14.0 7.979234e-32 2.484124e-11 2.977033e-36 1204.530859 0.0
15 15.0 9.675694e-32 3.012272e-11 3.609979e-36 3274.747955 0.0
16 16.0 2.274030e-32 7.079591e-12 8.484351e-37 8903.725684 0.0
17 17.0 -7.596239e-32 -2.364888e-11 -2.834139e-36 24206.441281 0.0
dummy_vAc dummy_vGlcxt dummy_vO2 dummy_vX ... ub_vAc \
0 0.0 0.0 0.0 0.0 ... 4.000000e+00
1 0.0 0.0 0.0 0.0 ... 3.983633e+00
2 0.0 0.0 0.0 0.0 ... 3.939152e+00
3 0.0 0.0 0.0 0.0 ... 3.818346e+00
4 0.0 0.0 0.0 0.0 ... 3.490909e+00
5 0.0 0.0 0.0 0.0 ... 2.610163e+00
6 0.0 0.0 0.0 0.0 ... 4.222256e-01
7 0.0 0.0 0.0 0.0 ... 1.317395e-10
8 0.0 0.0 0.0 0.0 ... -1.331995e-10
9 0.0 0.0 0.0 0.0 ... -1.466415e-10
10 0.0 0.0 0.0 0.0 ... 7.955788e-31
11 0.0 0.0 0.0 0.0 ... 4.138210e-30
12 0.0 0.0 0.0 0.0 ... 1.759600e-31
13 0.0 0.0 0.0 0.0 ... -2.616018e-31
14 0.0 0.0 0.0 0.0 ... 7.979234e-31
15 0.0 0.0 0.0 0.0 ... 9.675694e-31
16 0.0 0.0 0.0 0.0 ... 2.274030e-31
17 0.0 0.0 0.0 0.0 ... -7.596239e-31
ub_vGlcxt ub_vO2 ub_vX update__Km_vFBA update__Y \
0 1.497920e+01 2.100000e+00 0.010000 0.02 0.001000
1 1.497919e+01 2.084313e+00 0.027187 0.02 0.002719
2 1.497918e+01 2.041716e+00 0.073914 0.02 0.007391
3 1.497916e+01 1.926317e+00 0.200949 0.02 0.020095
4 1.497909e+01 1.616073e+00 0.546319 0.02 0.054632
5 1.497891e+01 8.143763e-01 1.485231 0.02 0.148523
6 1.497839e+01 1.371064e-04 4.037514 0.02 0.403751
7 1.497685e+01 4.915177e-15 10.975102 0.02 1.097510
8 1.497130e+01 -4.969649e-15 29.837772 0.02 2.983777
9 1.491764e+01 -5.471159e-15 81.117191 0.02 8.111719
10 2.476808e-10 2.968286e-35 220.514868 0.02 22.051487
11 1.288318e-09 1.543956e-34 599.496924 0.02 59.949692
12 5.478054e-11 6.565025e-36 1000.000000 0.02 162.968479
13 -8.144279e-09 -9.760300e-36 1000.000000 0.02 443.054516
14 2.484124e-10 2.977033e-35 1000.000000 0.02 1204.530859
15 3.012272e-10 3.609979e-35 1000.000000 0.02 3274.747955
16 7.079591e-11 8.484351e-36 1000.000000 0.02 8903.725684
17 -2.364888e-08 -2.834139e-35 1000.000000 0.02 24206.441281
vAc vGlcxt vO2 vX
0 0.0 3.753658 2.100000 0.255198
1 0.0 3.753658 2.100000 0.255198
2 0.0 3.725617 2.084313 0.253292
3 0.0 3.649477 2.041716 0.248115
4 0.0 3.443207 1.926317 0.234092
5 0.0 2.888659 1.616073 0.196390
6 0.0 1.455662 0.814376 0.098965
7 0.0 0.000245 0.000137 0.000017
8 0.0 0.000000 0.000000 0.000000
9 0.0 0.000000 0.000000 0.000000
10 0.0 0.000000 0.000000 0.000000
11 0.0 0.000000 0.000000 0.000000
12 0.0 0.000000 0.000000 0.000000
13 0.0 0.000000 0.000000 0.000000
14 0.0 0.000000 0.000000 0.000000
15 0.0 0.000000 0.000000 0.000000
16 0.0 0.000000 0.000000 0.000000
17 0.0 0.000000 0.000000 0.000000
[18 rows x 48 columns]
In [ ]:
Content source: matthiaskoenig/sbmlutils
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