ATP Toy Model
Model version: 8
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 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
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53
id toy_atp_top meta_toy_atp_top
name toy_atp (TOP)
time h
substance mole
extent mole
volume m3
area m2
length m
L3V1 comp-V1
type
ModelDefinitions [3]
name
type
sbo
cvterm
ModelDefinition
toy_atp_fba
toy_atp_fba
ExternalModelDefinition (source=toy_atp_fba.xml
)
ModelDefinition
toy_atp_bounds
toy_atp_bounds
ExternalModelDefinition (source=toy_atp_bounds.xml
)
ModelDefinition
toy_atp_update
toy_atp_update
ExternalModelDefinition (source=toy_atp_update.xml
)
type
Submodels [3]
name
model ref
deletions
time conversion
extent conversion
sbo
cvterm
Submodel
fba
toy_atp_fba
Submodel
bounds
toy_atp_bounds
Submodel
update
toy_atp_update
type
UnitDefinitions [7]
name
units
sbo
cvterm
UnitDefinition
h meta_h
ReplacedElement bounds:unitRef=h
ReplacedElement fba:unitRef=h
ReplacedElement update:unitRef=h
hour
3600
s
UnitDefinition
kg meta_kg
ReplacedElement bounds:unitRef=kg
ReplacedElement fba:unitRef=kg
ReplacedElement update:unitRef=kg
kilogram
kg
UnitDefinition
m meta_m
ReplacedElement bounds:unitRef=m
ReplacedElement fba:unitRef=m
ReplacedElement update:unitRef=m
meter
m
UnitDefinition
m2 meta_m2
ReplacedElement bounds:unitRef=m2
ReplacedElement fba:unitRef=m2
ReplacedElement update:unitRef=m2
square meter
m
2
UnitDefinition
m3 meta_m3
ReplacedElement bounds:unitRef=m3
ReplacedElement fba:unitRef=m3
ReplacedElement update:unitRef=m3
cubic meter
m
3
UnitDefinition
mM meta_mM
ReplacedElement bounds:unitRef=mM
ReplacedElement fba:unitRef=mM
ReplacedElement update:unitRef=mM
millimolar
mole
m
3
UnitDefinition
mole_per_h
ReplacedElement bounds:unitRef=mole_per_h
ReplacedElement fba:unitRef=mole_per_h
ReplacedElement update:unitRef=mole_per_h
mole
3600
s
type
Compartments [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
cell meta_cell
ReplacedElement update:portRef=cell_port
ReplacedElement bounds:portRef=cell_port
cell
1.0
T
3
m3
m
3
type
Species [5]
name
compartment
boundary condition
constant
initial amount
initial concentration
substance units
derived units
sbo
cvterm
Species
adp meta_adp
ReplacedElement update:portRef=adp_port
ReplacedElement bounds:portRef=adp_port
ADP
cell
F
F
1.0
mole
mole
m
3
Species
glc meta_glc
ReplacedElement update:portRef=glc_port
ReplacedElement bounds:portRef=glc_port
Glucose
cell
F
F
5.0
mole
mole
m
3
Species
pyr meta_pyr
ReplacedElement update:portRef=pyr_port
ReplacedElement bounds:portRef=pyr_port
Pyruvate
cell
F
F
0.0
mole
mole
m
3
Species
atp meta_atp
ReplacedElement update:portRef=atp_port
ReplacedElement bounds:portRef=atp_port
ATP
cell
F
F
2.0
mole
mole
m
3
Species
dummy_S
dummy_S
cell
F
F
0.0
mole
mole
m
3
type
Parameters [17]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
ReplacedElement bounds:portRef=dt_port
T
0.1
h
3600
s
Parameter
lb_EX_adp
ReplacedElement bounds:portRef=lb_EX_adp_port
ReplacedElement fba:portRef=lb_EX_adp_port
F
-1000.0
mole_per_h
mole
3600
s
Parameter
ub_EX_adp
ReplacedElement bounds:portRef=ub_EX_adp_port
ReplacedElement fba:portRef=ub_EX_adp_port
F
1000.0
mole_per_h
mole
3600
s
Parameter
lb_EX_glc
ReplacedElement bounds:portRef=lb_EX_glc_port
ReplacedElement fba:portRef=lb_EX_glc_port
F
-1000.0
mole_per_h
mole
3600
s
Parameter
ub_EX_glc
ReplacedElement bounds:portRef=ub_EX_glc_port
ReplacedElement fba:portRef=ub_EX_glc_port
F
1000.0
mole_per_h
mole
3600
s
Parameter
lb_EX_pyr
ReplacedElement bounds:portRef=lb_EX_pyr_port
ReplacedElement fba:portRef=lb_EX_pyr_port
F
-1000.0
mole_per_h
mole
3600
s
Parameter
ub_EX_pyr
ReplacedElement bounds:portRef=ub_EX_pyr_port
ReplacedElement fba:portRef=ub_EX_pyr_port
F
1000.0
mole_per_h
mole
3600
s
Parameter
lb_EX_atp
ReplacedElement bounds:portRef=lb_EX_atp_port
ReplacedElement fba:portRef=lb_EX_atp_port
F
-1000.0
mole_per_h
mole
3600
s
Parameter
ub_EX_atp
ReplacedElement bounds:portRef=ub_EX_atp_port
ReplacedElement fba:portRef=ub_EX_atp_port
F
1000.0
mole_per_h
mole
3600
s
Parameter
pEX_adp
ReplacedElement update:portRef=pEX_adp_port
F
1.0
mole_per_h
mole
3600
s
Parameter
pEX_glc
ReplacedElement update:portRef=pEX_glc_port
F
1.0
mole_per_h
mole
3600
s
Parameter
pEX_pyr
ReplacedElement update:portRef=pEX_pyr_port
F
1.0
mole_per_h
mole
3600
s
Parameter
pEX_atp
ReplacedElement update:portRef=pEX_atp_port
F
1.0
mole_per_h
mole
3600
s
Parameter
Vmax_RATP meta_Vmax_RATP
T
1.0
mole_per_h
mole
3600
s
Parameter
k_RATP meta_k_RATP
T
0.1
mM
mole
m
3
Parameter
atp_tot
F
atp
adp
mM
mole
m
3
Parameter
c3_tot
F
2
glc
pyr
mM
mole
m
3
type
Rules [6]
assignment
name
derived units
sbo
cvterm
Rule
pEX_adp
=
EX_adp
mole
3600
s
Rule
pEX_glc
=
EX_glc
mole
3600
s
Rule
pEX_pyr
=
EX_pyr
mole
3600
s
Rule
pEX_atp
=
EX_atp
mole
3600
s
Rule
atp_tot meta_atp_tot
=
atp
adp
mole
m
3
Rule
c3_tot meta_c3_tot
=
2
glc
pyr
mole
m
3
type
Reactions [5]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
EX_adp
ReplacedBy fba:portRef=EX_adp_port
➞
➞ dummy_S
0
mole
3600
s
Reaction
EX_glc
ReplacedBy fba:portRef=EX_glc_port
➞
➞ dummy_S
0
mole
3600
s
Reaction
EX_pyr
ReplacedBy fba:portRef=EX_pyr_port
➞
➞ dummy_S
0
mole
3600
s
Reaction
EX_atp
ReplacedBy fba:portRef=EX_atp_port
➞
➞ dummy_S
0
mole
3600
s
Reaction
RATP meta_RATP
atp -> adp
➞
atp ➞ adp
Vmax_RATP
atp
k_RATP
atp
mole
3600
s