Diauxic Growth Model

Model version: 13

TOP model

Main comp DFBA model by combining fba, update and bounds model with additional kinetics in the top model.

Description

Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli

The key variables in the mathematical model of the metabolic network are the glucose concentration (Glcxt), the acetate concentration (Ac), the biomass concentration (X), and the oxygen concentration (O2) in the gas phase.

This file has been produced by Matthias Koenig.

Terms of use

Copyright © 2017 Matthias Koenig

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


Model : diauxic_top

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2018-10-23 17:57
Modified: 2018-10-23 17:57

id diauxic_top meta_diauxic_top
namediauxic (TOP)
timeh
substancemmol
extentmmol
volumel
aream2
lengthm
Access SBML model  L3V1 comp-V1

SBO:0000293
BQB_IS_VERSION_OF
GO:0006007
ModelDefinitions [3] name type sbo cvterm
diauxic_fba diauxic_fba ExternalModelDefinition (source=diauxic_fba.xml)
diauxic_bounds diauxic_bounds ExternalModelDefinition (source=diauxic_bounds.xml)
diauxic_update diauxic_update ExternalModelDefinition (source=diauxic_update.xml)

Submodels [3] name model ref deletions time conversion extent conversion sbo cvterm
fba diauxic_fba
bounds diauxic_bounds
update diauxic_update

UnitDefinitions [14] name units sbo cvterm
h meta_h
ReplacedElement bounds:unitRef=h
ReplacedElement fba:unitRef=h
ReplacedElement update:unitRef=h
hour 3600 s
g
ReplacedElement bounds:unitRef=g
ReplacedElement fba:unitRef=g
ReplacedElement update:unitRef=g
gram g
m meta_m
ReplacedElement bounds:unitRef=m
ReplacedElement fba:unitRef=m
ReplacedElement update:unitRef=m
meter m
m2 meta_m2
ReplacedElement bounds:unitRef=m2
ReplacedElement fba:unitRef=m2
ReplacedElement update:unitRef=m2
cubic meter m 2
l
ReplacedElement bounds:unitRef=l
ReplacedElement fba:unitRef=l
ReplacedElement update:unitRef=l
liter litre
mmol
ReplacedElement bounds:unitRef=mmol
ReplacedElement fba:unitRef=mmol
ReplacedElement update:unitRef=mmol
10 3 mole
per_h
ReplacedElement bounds:unitRef=per_h
ReplacedElement fba:unitRef=per_h
ReplacedElement update:unitRef=per_h
1 3600 s
mmol_per_h
ReplacedElement bounds:unitRef=mmol_per_h
ReplacedElement fba:unitRef=mmol_per_h
ReplacedElement update:unitRef=mmol_per_h
10 3 mole 3600 s
mmol_per_hg
ReplacedElement bounds:unitRef=mmol_per_hg
ReplacedElement fba:unitRef=mmol_per_hg
ReplacedElement update:unitRef=mmol_per_hg
10 3 mole g 3600 s
mmol_per_l
ReplacedElement bounds:unitRef=mmol_per_l
ReplacedElement fba:unitRef=mmol_per_l
ReplacedElement update:unitRef=mmol_per_l
10 3 mole litre
mmol_per_lg
ReplacedElement bounds:unitRef=mmol_per_lg
ReplacedElement fba:unitRef=mmol_per_lg
ReplacedElement update:unitRef=mmol_per_lg
10 3 mole g litre
l_per_mmol
ReplacedElement bounds:unitRef=l_per_mmol
ReplacedElement fba:unitRef=l_per_mmol
ReplacedElement update:unitRef=l_per_mmol
litre 10 3 mole
g_per_l
ReplacedElement bounds:unitRef=g_per_l
ReplacedElement fba:unitRef=g_per_l
ReplacedElement update:unitRef=g_per_l
g litre
g_per_mmol
ReplacedElement bounds:unitRef=g_per_mmol
ReplacedElement fba:unitRef=g_per_mmol
ReplacedElement update:unitRef=g_per_mmol
g 10 3 mole

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
bioreactor
ReplacedElement update:portRef=bioreactor_port
ReplacedElement bounds:portRef=bioreactor_port
bioreactor 1.0 3 l litre

Species [5] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
Ac meta_Ac
ReplacedElement bounds:portRef=Ac_port
ReplacedElement update:portRef=Ac_port
acetate bioreactor 0.4 mmol mmol 10 3 mole litre
Glcxt meta_Glcxt
ReplacedElement bounds:portRef=Glcxt_port
ReplacedElement update:portRef=Glcxt_port
glucose bioreactor 10.8 mmol mmol 10 3 mole litre
O2 meta_O2
ReplacedElement bounds:portRef=O2_port
ReplacedElement update:portRef=O2_port
oxygen bioreactor 0.21 mmol mmol 10 3 mole litre
X meta_X
ReplacedElement bounds:portRef=X_port
ReplacedElement update:portRef=X_port
biomass bioreactor 0.001 mmol mmol 10 3 mole litre
dummy_S dummy_S bioreactor 0.0 mmol mmol 10 3 mole litre

Parameters [15] name constant value unit derived unit sbo cvterm
dt
ReplacedElement bounds:portRef=dt_port
0.1 h 3600 s
lb_EX_Ac
ReplacedElement bounds:portRef=lb_EX_Ac_port
ReplacedElement fba:portRef=lb_EX_Ac_port
-1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Ac
ReplacedElement bounds:portRef=ub_EX_Ac_port
ReplacedElement fba:portRef=ub_EX_Ac_port
1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_Glcxt
ReplacedElement bounds:portRef=lb_EX_Glcxt_port
ReplacedElement fba:portRef=lb_EX_Glcxt_port
-10.0 mmol_per_h 10 3 mole 3600 s
ub_EX_Glcxt
ReplacedElement bounds:portRef=ub_EX_Glcxt_port
ReplacedElement fba:portRef=ub_EX_Glcxt_port
1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_O2
ReplacedElement bounds:portRef=lb_EX_O2_port
ReplacedElement fba:portRef=lb_EX_O2_port
-15.0 mmol_per_h 10 3 mole 3600 s
ub_EX_O2
ReplacedElement bounds:portRef=ub_EX_O2_port
ReplacedElement fba:portRef=ub_EX_O2_port
1000.0 mmol_per_h 10 3 mole 3600 s
lb_EX_X
ReplacedElement bounds:portRef=lb_EX_X_port
ReplacedElement fba:portRef=lb_EX_X_port
-1000.0 mmol_per_h 10 3 mole 3600 s
ub_EX_X
ReplacedElement bounds:portRef=ub_EX_X_port
ReplacedElement fba:portRef=ub_EX_X_port
1000.0 mmol_per_h 10 3 mole 3600 s
pEX_Ac
ReplacedElement update:portRef=pEX_Ac_port
1.0 mmol_per_h 10 3 mole 3600 s
pEX_Glcxt
ReplacedElement update:portRef=pEX_Glcxt_port
1.0 mmol_per_h 10 3 mole 3600 s
pEX_O2
ReplacedElement update:portRef=pEX_O2_port
1.0 mmol_per_h 10 3 mole 3600 s
pEX_X
ReplacedElement update:portRef=pEX_X_port
1.0 mmol_per_h 10 3 mole 3600 s
O2_ref O2 reference 0.21 mmol_per_l 10 3 mole litre
kLa O2 mass transfer 7.5 per_h 1 3600 s

Rules [4]   assignment name derived units sbo cvterm
pEX_Ac = EX_Ac 10 3 mole 3600 s
pEX_Glcxt = EX_Glcxt 10 3 mole 3600 s
pEX_O2 = EX_O2 10 3 mole 3600 s
pEX_X = EX_X 10 3 mole 3600 s

Reactions [5] name equation modifiers kinetic law derived units sbo cvterm
EX_Ac
ReplacedBy fba:portRef=EX_Ac_port

➞ dummy_S 0 10 3 mole 3600 s
EX_Glcxt
ReplacedBy fba:portRef=EX_Glcxt_port

➞ dummy_S 0 10 3 mole 3600 s
EX_O2
ReplacedBy fba:portRef=EX_O2_port

➞ dummy_S 0 10 3 mole 3600 s
EX_X
ReplacedBy fba:portRef=EX_X_port

➞ dummy_S 0 10 3 mole 3600 s
vO2_transfer oxygen transfer
⇆ O2 kLa O2_ref O2 bioreactor 10 3 mole 3600 s