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Model : diauxic_top_flat

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-17 21:17
Modified: 2017-03-17 21:17

SBML model


iddiauxic_top_flat
nameTop level model_flat
versionL3V1
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
bounds__max minimum of arguments x y x x y y
bounds__min maximum of arguments x y x x y y

UnitDefinitions [18] name units sbo cvterm
h 3600 s
g g
m m
m2 m 2
l litre
mmol 10 3 mole
per_h 1 3600 s
mmol_per_h 10 3 mole 3600 s
mmol_per_l 10 3 mole litre
l_per_mmol litre 10 3 mole
g_per_l g litre
g_per_mmol g 10 3 mole
fba__per_h 1 3600 s
fba__l_per_mmol litre 10 3 mole
bounds__per_h 1 3600 s
bounds__l_per_mmol litre 10 3 mole
update__per_h 1 3600 s
update__l_per_mmol litre 10 3 mole

Compartments [2] name size constant spatial dimensions unit derived unit sbo cvterm
bioreactor bioreactor 1.0 3 l litre
fba__bioreactor bioreactor 1.0 3 l litre

Species [9] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
Glcxt glucose
bioreactor 10.8 mmol 10 3 mole litre
Ac acetate
bioreactor 0.4 mmol 10 3 mole litre
O2 oxygen
bioreactor 0.21 mmol 10 3 mole litre
X biomass
bioreactor 0.001 mmol 10 3 mole litre
dummy_S dummy_S
bioreactor 0.0 mmol 10 3 mole litre
fba__Glcxt glucose
fba__bioreactor 10.8 mmol 10 3 mole litre
fba__Ac acetate
fba__bioreactor 0.4 mmol 10 3 mole litre
fba__O2 oxygen
fba__bioreactor 0.21 mmol 10 3 mole litre
fba__X biomass
fba__bioreactor 0.001 mmol 10 3 mole litre

Parameters [27] name value unit derived unit constant sbo cvterm
dt fba timestep 0.01 h 3600 s
Y biomass [g_per_l] 1.0 g_per_l g litre
O2_ref O2 reference 0.21 mmol_per_l 10 3 mole litre
kLa O2 mass transfer 7.5 per_h 1 3600 s
EX_Glcxt 1.0 mmol_per_h 10 3 mole 3600 s
EX_Ac 1.0 mmol_per_h 10 3 mole 3600 s
EX_O2 1.0 mmol_per_h 10 3 mole 3600 s
EX_X 1.0 mmol_per_h 10 3 mole 3600 s
lb_EX_Ac -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Ac 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_Glcxt -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Glcxt 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_O2 -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_O2 1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_X -1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_X 1000.0 mmol_per_h 10 3 mole 3600 s
fba__zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
fba__lb_default default lower bound -1000.0 mmol_per_h 10 3 mole 3600 s
fba__ub_default default upper bound 1000.0 mmol_per_h 10 3 mole 3600 s
bounds__zero zero bound 0.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_default default lower bound -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__ub_default default upper bound 1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_kin_EX_Glcxt -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__lb_kin_EX_O2 -1000.0 mmol_per_h 10 3 mole 3600 s
bounds__Vmax_EX_O2 15.0 mmol_per_h 10 3 mole 3600 s
bounds__Vmax_EX_Glcxt 10.0 mmol_per_h 10 3 mole 3600 s
bounds__Km_EX_Glcxt Km_vGlcxt 0.015 mmol_per_l 10 3 mole litre

Rules [11]   assignment derived units sbo cvterm
EX_Glcxt = dummy_EX_Glcxt 10 3 mole 3600 s
EX_Ac = dummy_EX_Ac 10 3 mole 3600 s
EX_O2 = dummy_EX_O2 10 3 mole 3600 s
EX_X = dummy_EX_X 10 3 mole 3600 s
Y = 1 X g litre
bounds__lb_kin_EX_Glcxt = bounds__Vmax_EX_Glcxt Glcxt bounds__Km_EX_Glcxt Glcxt 0.001 mole 3600 s
bounds__lb_kin_EX_O2 = bounds__Vmax_EX_O2 10 3 mole 3600 s
lb_EX_Ac = bounds__max bounds__lb_default Ac bioreactor dt 10 3 mole 3600 s
lb_EX_Glcxt = bounds__max bounds__lb_kin_EX_Glcxt Glcxt bioreactor dt 10 3 mole 3600 s
lb_EX_O2 = bounds__max bounds__lb_kin_EX_O2 O2 bioreactor dt 10 3 mole 3600 s
lb_EX_X = bounds__max bounds__lb_default X bioreactor dt 10 3 mole 3600 s

Reactions [13] name equation modifiers formula derived units sbo cvterm
vO2_transfer oxygen transfer ⇆ O2 kLa O2_ref O2 bioreactor 10 3 mole 3600 s
dummy_EX_O2 fba__O2 ➞
dummy_EX_Glcxt fba__Glcxt ➞
dummy_EX_Ac fba__Ac ⇆
dummy_EX_X fba__X ➞
fba__v1 v1 (39.43 Ac + 35 O2 -> X) 39.43 fba__Ac + 35.0 fba__O2 ➞ fba__X
fba__v2 v2 (9.46 Glcxt + 12.92 O2 -> X) 9.46 fba__Glcxt + 12.92 fba__O2 ➞ fba__X
fba__v3 v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X) 9.84 fba__Glcxt + 12.73 fba__O2 ➞ fba__X + 1.24 fba__Ac
fba__v4 v4 (19.23 Glcxt -> 12.12 Ac + X) 19.23 fba__Glcxt ➞ fba__X + 12.12 fba__Ac
update__update_Glcxt Glcxt ⇆ X
EX_Glcxt X 1 0.001 mole 3600 s
update__update_Ac Ac ⇆ X
EX_Ac X 1 0.001 mole 3600 s
update__update_O2 O2 ⇆ X
EX_O2 X 1 0.001 mole 3600 s
update__update_X X ⇆ X
EX_X X 1 0.001 mole 3600 s