ATP Toy Model
Model version: 12
FBA submodel
DFBA fba submodel. Unbalanced metabolites are encoded via exchange fluxes.
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_fba
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:48
Modified: 2018-10-23 17:48
id toy_atp_fba meta_toy_atp_fba
name toy_atp (FBA)
time h
substance mmole
extent mmole
volume litre
area m2
length m
L3V1 fbc-V2 comp-V1
type
Ports [12]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
EX_atp_port
port EX_atp
Reaction: EX_atp
EX_atp
Port
lb_EX_atp_port
port lb_EX_atp
Parameter: lb_EX_atp
lb_EX_atp
Port
ub_EX_atp_port
port ub_EX_atp
Parameter: ub_EX_atp
ub_EX_atp
Port
EX_adp_port
port EX_adp
Reaction: EX_adp
EX_adp
Port
lb_EX_adp_port
port lb_EX_adp
Parameter: lb_EX_adp
lb_EX_adp
Port
ub_EX_adp_port
port ub_EX_adp
Parameter: ub_EX_adp
ub_EX_adp
Port
EX_glc_port
port EX_glc
Reaction: EX_glc
EX_glc
Port
lb_EX_glc_port
port lb_EX_glc
Parameter: lb_EX_glc
lb_EX_glc
Port
ub_EX_glc_port
port ub_EX_glc
Parameter: ub_EX_glc
ub_EX_glc
Port
EX_pyr_port
port EX_pyr
Reaction: EX_pyr
EX_pyr
Port
lb_EX_pyr_port
port lb_EX_pyr
Parameter: lb_EX_pyr
lb_EX_pyr
Port
ub_EX_pyr_port
port ub_EX_pyr
Parameter: ub_EX_pyr
ub_EX_pyr
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 [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
cell meta_cell
cell
1.0
T
3
litre
litre
type
Species [6]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
atp meta_atp
ATPC10H12N5O13P3 (-4)
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
adp meta_adp
ADPC10H12N5O10P2 (-3)
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
glc meta_glc
GlucoseC6H12O6
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
pyr meta_pyr
PyruvateC3H4O3
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
fru16bp meta_fru16bp
Fructose 1,6-bisphospateC6H14O12P2
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
Species
pg2 meta_pg2
2-PhosphoglycerateC3H7O7P
cell
F
F
F
0.0
mmole
mmole
10
3
mole
litre
type
Parameters [11]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
ub_R3
T
1.0
mmole_per_h
10
3
mole
3600
s
Parameter
zero
T
0.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_default
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_atp
T
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_atp
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_adp
T
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_adp
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_glc
T
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_glc
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_pyr
T
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_pyr
T
1000.0
mmole_per_h
10
3
mole
3600
s
type
Reactions [7]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
R1 meta_R1
glu + 2 atp -> fru16bp + 2 adp
[0.0 1000.0]
➞
glc + 2.0 atp ➞ fru16bp + 2.0 adp
Reaction
R2 meta_R2
fru16bp -> 2 pg2
[0.0 1000.0]
➞
fru16bp ➞ 2.0 pg2
Reaction
R3 meta_R3
pg2 + adp -> pyr + atp
[0.0 1.0]
➞
pg2 + 2.0 adp ➞ pyr + 2.0 atp
Reaction
EX_atp
[-1000.0 1000.0]
⇆
atp ⇆
Reaction
EX_adp
[-1000.0 1000.0]
⇆
adp ⇆
Reaction
EX_glc
[-1000.0 1000.0]
⇆
glc ⇆
Reaction
EX_pyr
[-1000.0 1000.0]
⇆
pyr ⇆
type
Objectives [1]
name
type
flux objectives
sbo
cvterm
Objective
RATP_maximize
maximize
+1.0*R3