Wholecell Toy Model
Model version: 15
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_wholecell_update
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:51
Modified: 2018-10-23 17:51
id toy_wholecell_update meta_toy_wholecell_update
name toy_wholecell (UPDATE)
time s
substance item
extent item
volume m3
area m2
length m
L3V1 comp-V1
type
Ports [5]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
extern_port
port extern
Compartment: extern
extern
Port
A_port
port A
Species: A
A
Port
C_port
port C
Species: C
C
Port
pEX_A_port
port pEX_A
Parameter: pEX_A
pEX_A
Port
pEX_C_port
port pEX_C
Parameter: pEX_C
pEX_C
type
UnitDefinitions [9]
name
units
sbo
cvterm
UnitDefinition
s meta_s
second
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
per_s
1
s
UnitDefinition
item_per_s
item
s
UnitDefinition
item_per_m3
item
m
3
type
Compartments [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
extern meta_extern
extern
1.0
T
3
m3
m
3
type
Species [2]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
A meta_A
A
extern
T
F
F
1.0
item
item
item
Species
C meta_C
C
extern
T
F
F
1.0
item
item
item
type
Parameters [2]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
pEX_A
T
1.0
item_per_s
item
s
Parameter
pEX_C
T
1.0
item_per_s
item
s
type
Reactions [2]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
update_A
⇆
A ⇆
pEX_A
item
s
Reaction
update_C
⇆
C ⇆
pEX_C
item
s