Wholecell Toy Model
Model version: 15
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 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_fba
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:51
Modified: 2018-10-23 17:51
id toy_wholecell_fba meta_toy_wholecell_fba
name toy_wholecell (FBA)
time s
substance item
extent item
volume m3
area m2
length m
L3V1 fbc-V2 comp-V1
type
Ports [7]
name
referenced element
port ref
id ref
unit ref
metaid ref
sbo
cvterm
Port
EX_A_port
port EX_A
Reaction: EX_A
EX_A
Port
lb_EX_A_port
port lb_EX_A
Parameter: lb_EX_A
lb_EX_A
Port
ub_EX_A_port
port ub_EX_A
Parameter: ub_EX_A
ub_EX_A
Port
EX_C_port
port EX_C
Reaction: EX_C
EX_C
Port
lb_EX_C_port
port lb_EX_C
Parameter: lb_EX_C
lb_EX_C
Port
ub_EX_C_port
port ub_EX_C
Parameter: ub_EX_C
ub_EX_C
Port
ub_R1_port
port ub_R1
Parameter: ub_R1
ub_R1
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 [3]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
extern meta_extern
external compartment
1.0
T
3
m3
m
3
Compartment
cell meta_cell
cell
1.0
T
3
m3
m
3
Compartment
membrane meta_membrane
membrane
1.0
T
2
m2
m
2
type
Species [4]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
A meta_A
A
extern
T
F
F
0.0
item
item
item
Species
C meta_C
C
extern
T
F
F
0.0
item
item
item
Species
B1 meta_B1
B1
cell
T
F
F
0.0
item
item
item
Species
B2 meta_B2
B2
cell
T
F
F
0.0
item
item
item
type
Parameters [7]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
ub_R1
T
1.0
item_per_s
item
s
Parameter
zero
T
0.0
item_per_s
item
s
Parameter
ub_default
T
1000.0
item_per_s
item
s
Parameter
lb_EX_A
T
-1000.0
item_per_s
item
s
Parameter
ub_EX_A
T
1000.0
item_per_s
item
s
Parameter
lb_EX_C
T
-1000.0
item_per_s
item
s
Parameter
ub_EX_C
T
1000.0
item_per_s
item
s
type
Reactions [5]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
R1 meta_R1
A import (R1)
[0.0 1.0]
⇆
A ⇆ B1
Reaction
R2 meta_R2
B1 <-> B2 (R2)
[0.0 1000.0]
⇆
B1 ⇆ B2
Reaction
R3 meta_R3
B2 export (R3)
[0.0 1000.0]
⇆
B2 ⇆ C
Reaction
EX_A
[-1000.0 1000.0]
⇆
A ⇆
Reaction
EX_C
[-1000.0 1000.0]
⇆
C ⇆
type
Objectives [1]
name
type
flux objectives
sbo
cvterm
Objective
R3_maximize
maximize
+1.0*R3