ATP Toy Model
Model version: 12
TOP model
Main comp DFBA model by combining fba, update and bounds
model with additional kinetics in the top model.
Description
This is a toy model for coupling models with different modeling frameworks via comp.
Terms of use
Copyright © 2017-2018 Matthias Koenig
Redistribution and use of any part of this model, with or without modification, are permitted provided that
the following conditions are met:
Redistributions of this SBML file must retain the above copyright notice, this list of conditions
and the following disclaimer.
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 : toy_atp_top_flat
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:48
Modified: 2018-10-23 17:48
id toy_atp_top_flat meta_toy_atp_top
name toy_atp (TOP)_flat
time h
substance mmole
extent mmole
volume litre
area m2
length m
L3V1 fbc-V2
type
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
bounds__max
min
x
y
x
x
y
y
FunctionDefinition
bounds__min
max
x
y
x
x
y
y
type
UnitDefinitions [8]
name
units
sbo
cvterm
UnitDefinition
h meta_h
hour
3600
s
UnitDefinition
kg meta_kg
kilogram
kg
UnitDefinition
m meta_m
meter
m
UnitDefinition
m2 meta_m2
square meter
m
2
UnitDefinition
m3 meta_m3
cubic meter
m
3
UnitDefinition
mmole
10
3
mole
UnitDefinition
mM meta_mM
millimolar
10
3
mole
litre
UnitDefinition
mmole_per_h
10
3
mole
3600
s
type
Compartments [2]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
cell meta_cell
cell
1.0
T
3
litre
litre
Compartment
fba__cell fba__meta_cell
cell
1.0
T
3
litre
litre
type
Species [11]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
atp meta_atp
ATP
cell
F
F
F
2.0
mmole
mmole
10
3
mole
litre
Species
adp meta_adp
ADP
cell
F
F
F
1.0
mmole
mmole
10
3
mole
litre
Species
glc meta_glc
Glucose
cell
F
F
F
5.0
mmole
mmole
10
3
mole
litre
Species
pyr meta_pyr
Pyruvate
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
dummy_S
dummy_S
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__atp fba__meta_atp
ATPC10H12N5O13P3 (-4)
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__adp fba__meta_adp
ADPC10H12N5O10P2 (-3)
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__glc fba__meta_glc
GlucoseC6H12O6
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__pyr fba__meta_pyr
PyruvateC3H4O3
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__fru16bp fba__meta_fru16bp
Fructose 1,6-bisphospateC6H14O12P2
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fba__pg2 fba__meta_pg2
2-PhosphoglycerateC3H7O7P
fba__cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
type
Parameters [28]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
T
0.1
h
3600
s
Parameter
lb_EX_atp
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_atp
F
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_adp
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_adp
F
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_glc
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_glc
F
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_pyr
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_pyr
F
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
pEX_atp
F
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
pEX_adp
F
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
pEX_glc
F
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
pEX_pyr
F
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
Vmax_RATP meta_Vmax_RATP
T
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
k_RATP meta_k_RATP
T
0.1
mM
10
3
mole
litre
Parameter
atp_tot
F
atp
adp
mM
10
3
mole
litre
Parameter
c3_tot
F
2
glc
pyr
mM
10
3
mole
litre
Parameter
fba__ub_R3
T
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
fba__zero
T
0.0
mmole_per_h
10
3
mole
3600
s
Parameter
fba__ub_default
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__ub_EX_atp_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__lb_EX_atp_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__ub_EX_adp_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__lb_EX_adp_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__ub_EX_glc_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__lb_EX_glc_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__ub_EX_pyr_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
bounds__lb_EX_pyr_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
type
Rules [14]
assignment
name
derived units
sbo
cvterm
Rule
pEX_atp
=
EX_atp
10
3
mole
3600
s
Rule
pEX_adp
=
EX_adp
10
3
mole
3600
s
Rule
pEX_glc
=
EX_glc
10
3
mole
3600
s
Rule
pEX_pyr
=
EX_pyr
10
3
mole
3600
s
Rule
atp_tot meta_8dc182e4447343a8a39d1092990fe6a6
=
atp
adp
10
3
mole
litre
Rule
c3_tot meta_007b254d80014a16948c6a65ea62ea2a
=
2
glc
pyr
10
3
mole
litre
Rule
ub_EX_atp
=
bounds__ub_EX_atp_fba
10
3
mole
3600
s
Rule
lb_EX_atp
=
bounds__max
bounds__lb_EX_atp_fba
cell
atp
dt
10
3
mole
3600
s
Rule
ub_EX_adp
=
bounds__ub_EX_adp_fba
10
3
mole
3600
s
Rule
lb_EX_adp
=
bounds__max
bounds__lb_EX_adp_fba
cell
adp
dt
10
3
mole
3600
s
Rule
ub_EX_glc
=
bounds__ub_EX_glc_fba
10
3
mole
3600
s
Rule
lb_EX_glc
=
bounds__max
bounds__lb_EX_glc_fba
cell
glc
dt
10
3
mole
3600
s
Rule
ub_EX_pyr
=
bounds__ub_EX_pyr_fba
10
3
mole
3600
s
Rule
lb_EX_pyr
=
bounds__max
bounds__lb_EX_pyr_fba
cell
pyr
dt
10
3
mole
3600
s
type
Reactions [12]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
RATP meta_RATP
atp -> adp
➞
atp ➞ adp
Vmax_RATP
atp
k_RATP
atp
0.001
mole
3600
s
Reaction
fba__R1 fba__meta_R1
glu + 2 atp -> fru16bp + 2 adp
[0.0 1000.0]
➞
fba__glc + 2.0 fba__atp ➞ fba__fru16bp + 2.0 fba__adp
Reaction
fba__R2 fba__meta_R2
fru16bp -> 2 pg2
[0.0 1000.0]
➞
fba__fru16bp ➞ 2.0 fba__pg2
Reaction
fba__R3 fba__meta_R3
pg2 + adp -> pyr + atp
[0.0 1.0]
➞
fba__pg2 + 2.0 fba__adp ➞ fba__pyr + 2.0 fba__atp
Reaction
EX_atp
[-1000.0 1000.0]
⇆
fba__atp ⇆
Reaction
EX_adp
[-1000.0 1000.0]
⇆
fba__adp ⇆
Reaction
EX_glc
[-1000.0 1000.0]
⇆
fba__glc ⇆
Reaction
EX_pyr
[-1000.0 1000.0]
⇆
fba__pyr ⇆
Reaction
update__update_atp
⇆
atp ⇆
pEX_atp
10
3
mole
3600
s
Reaction
update__update_adp
⇆
adp ⇆
pEX_adp
10
3
mole
3600
s
Reaction
update__update_glc
⇆
glc ⇆
pEX_glc
10
3
mole
3600
s
Reaction
update__update_pyr
⇆
pyr ⇆
pEX_pyr
10
3
mole
3600
s
type
Objectives [1]
name
type
flux objectives
sbo
cvterm
Objective
fba__RATP_maximize
maximize
+1.0*fba__R3