ATP Toy Model
Model version: 12
BOUNDS submodel
Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA 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_bounds
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:48
Modified: 2018-10-23 17:48
id toy_atp_bounds meta_toy_atp_bounds
name toy_atp (BOUNDS)
time h
substance mmole
extent mmole
volume litre
area m2
length m
L3V1 comp-V1
type
Ports [14]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
dt_port
port dt
Parameter: dt
dt
Port
cell_port
port cell
Compartment: cell
cell
Port
atp_port
port atp
Species: atp
atp
Port
adp_port
port adp
Species: adp
adp
Port
glc_port
port glc
Species: glc
glc
Port
pyr_port
port pyr
Species: pyr
pyr
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
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
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
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
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
max
min
x
y
x
x
y
y
FunctionDefinition
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 [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
cell meta_cell
cell
1.0
T
3
litre
litre
type
Species [4]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
atp meta_atp
ATP
cell
F
F
F
1.0
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
1.0
mmole
mmole
10
3
mole
litre
Species
pyr meta_pyr
Pyruvate
cell
F
F
F
1.0
mmole
mmole
10
3
mole
litre
type
Parameters [17]
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
ub_EX_atp_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_atp_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_adp_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_adp_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_glc_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_glc_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
ub_EX_pyr_fba
T
1000.0
mmole_per_h
10
3
mole
3600
s
Parameter
lb_EX_pyr_fba
F
-1000.0
mmole_per_h
10
3
mole
3600
s
type
Rules [8]
assignment
name
derived units
sbo
cvterm
Rule
ub_EX_atp
=
ub_EX_atp_fba
10
3
mole
3600
s
Rule
lb_EX_atp
=
max
lb_EX_atp_fba
cell
atp
dt
10
3
mole
3600
s
Rule
ub_EX_adp
=
ub_EX_adp_fba
10
3
mole
3600
s
Rule
lb_EX_adp
=
max
lb_EX_adp_fba
cell
adp
dt
10
3
mole
3600
s
Rule
ub_EX_glc
=
ub_EX_glc_fba
10
3
mole
3600
s
Rule
lb_EX_glc
=
max
lb_EX_glc_fba
cell
glc
dt
10
3
mole
3600
s
Rule
ub_EX_pyr
=
ub_EX_pyr_fba
10
3
mole
3600
s
Rule
lb_EX_pyr
=
max
lb_EX_pyr_fba
cell
pyr
dt
10
3
mole
3600
s