ATP Toy Model
Model version: 8
UPDATE submodel
Submodel for dynamically updating the metabolite count.
This updates the ode model based on the FBA fluxes.
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_update
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53
id toy_atp_update meta_toy_atp_update
name toy_atp (UPDATE)
time h
substance mole
extent mole
volume m3
area m2
length m
L3V1 comp-V1
type
Ports [9]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
cell_port
Compartment: cell
cell
Port
adp_port
Species: adp
adp
Port
glc_port
Species: glc
glc
Port
pyr_port
Species: pyr
pyr
Port
atp_port
Species: atp
atp
Port
pEX_adp_port
Parameter: pEX_adp
pEX_adp
Port
pEX_glc_port
Parameter: pEX_glc
pEX_glc
Port
pEX_pyr_port
Parameter: pEX_pyr
pEX_pyr
Port
pEX_atp_port
Parameter: pEX_atp
pEX_atp
type
UnitDefinitions [7]
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
mM meta_mM
millimolar
mole
m
3
UnitDefinition
mole_per_h
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
m3
m
3
type
Species [4]
name
compartment
boundary condition
constant
initial amount
initial concentration
substance units
derived units
sbo
cvterm
Species
adp meta_adp
ADP
cell
F
F
1.0
mole
mole
m
3
Species
glc meta_glc
Glucose
cell
F
F
1.0
mole
mole
m
3
Species
pyr meta_pyr
Pyruvate
cell
F
F
1.0
mole
mole
m
3
Species
atp meta_atp
ATP
cell
F
F
1.0
mole
mole
m
3
type
Parameters [4]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
pEX_adp
T
1.0
mole_per_h
mole
3600
s
Parameter
pEX_glc
T
1.0
mole_per_h
mole
3600
s
Parameter
pEX_pyr
T
1.0
mole_per_h
mole
3600
s
Parameter
pEX_atp
T
1.0
mole_per_h
mole
3600
s
type
Reactions [4]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
update_adp
⇆
adp ⇆
pEX_adp
mole
3600
s
Reaction
update_glc
⇆
glc ⇆
pEX_glc
mole
3600
s
Reaction
update_pyr
⇆
pyr ⇆
pEX_pyr
mole
3600
s
Reaction
update_atp
⇆
atp ⇆
pEX_atp
mole
3600
s