Wholecell Toy Model
Model version: 15
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_wholecell_top_flat
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2018-10-23 17:51
Modified: 2018-10-23 17:51
id toy_wholecell_top_flat meta_toy_wholecell_top
name toy_wholecell (TOP)_flat
time s
substance item
extent item
volume m3
area m2
length m
L3V1 fbc-V2
type
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
bounds__max
min
x
y
x
x
y
y
FunctionDefinition
bounds__min
max
x
y
x
x
y
y
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 [4]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
extern meta_extern
extern
1.0
T
3
m3
m
3
Compartment
fba__extern fba__meta_extern
external compartment
1.0
T
3
m3
m
3
Compartment
fba__cell fba__meta_cell
cell
1.0
T
3
m3
m
3
Compartment
fba__membrane fba__meta_membrane
membrane
1.0
T
2
m2
m
2
type
Species [8]
name
compartment
hasOnlySubstanceUnits
boundaryCondition
constant
initialAmount
initialConcentration
conversionFactor
units
substanceUnits
derivedUnits
sbo
cvterm
Species
A meta_A
A
extern
T
F
F
10.0
item
item
item
Species
C meta_C
C
extern
T
F
F
0.0
item
item
item
Species
dummy_S
dummy_S
extern
T
F
F
0.0
item
item
item
Species
D meta_D
extern
T
F
F
0.0
item
item
item
Species
fba__A fba__meta_A
A
fba__extern
T
F
F
0.0
item
item
item
Species
fba__C fba__meta_C
C
fba__extern
T
F
F
0.0
item
item
item
Species
fba__B1 fba__meta_B1
B1
fba__cell
T
F
F
0.0
item
item
item
Species
fba__B2 fba__meta_B2
B2
fba__cell
T
F
F
0.0
item
item
item
type
Parameters [13]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
T
0.1
s
s
Parameter
lb_EX_A
F
-1000.0
item_per_s
item
s
Parameter
ub_EX_A
F
1000.0
item_per_s
item
s
Parameter
lb_EX_C
F
-1000.0
item_per_s
item
s
Parameter
ub_EX_C
F
1000.0
item_per_s
item
s
Parameter
pEX_A
F
1.0
item_per_s
item
s
Parameter
pEX_C
F
1.0
item_per_s
item
s
Parameter
k_R4
T
0.1
per_s
1
s
Parameter
ub_R1
F
1.0
item_per_s
item
s
Parameter
fba__zero
T
0.0
item_per_s
item
s
Parameter
fba__ub_default
T
1000.0
item_per_s
item
s
Parameter
bounds__lb_default
T
-1000.0
item_per_s
item
s
Parameter
bounds__k1
k1
F
-0.2
per_s
1
s
type
Rules [5]
assignment
name
derived units
sbo
cvterm
Rule
pEX_A
=
EX_A
item
s
Rule
pEX_C
=
EX_C
item
s
Rule
d ub_R1/dt
=
bounds__k1
ub_R1
item
s
2
Rule
lb_EX_A
=
bounds__max
bounds__lb_default
A
dt
item
s
Rule
lb_EX_C
=
bounds__max
bounds__lb_default
C
dt
item
s
type
Reactions [8]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
R4 meta_R4
R4: C -> D
➞
C ➞ D
k_R4
C
item
s
Reaction
fba__R1 fba__meta_R1
A import (R1)
[0.0 1.0]
⇆
fba__A ⇆ fba__B1
Reaction
fba__R2 fba__meta_R2
B1 <-> B2 (R2)
[0.0 1000.0]
⇆
fba__B1 ⇆ fba__B2
Reaction
fba__R3 fba__meta_R3
B2 export (R3)
[0.0 1000.0]
⇆
fba__B2 ⇆ fba__C
Reaction
EX_A
[-1000.0 1000.0]
⇆
fba__A ⇆
Reaction
EX_C
[-1000.0 1000.0]
⇆
fba__C ⇆
Reaction
update__update_A
⇆
A ⇆
pEX_A
item
s
Reaction
update__update_C
⇆
C ⇆
pEX_C
item
s
type
Objectives [1]
name
type
flux objectives
sbo
cvterm
Objective
fba__R3_maximize
maximize
+1.0*fba__R3