Wholecell Toy Model
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_top_flat
CreatorMatthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.comCreated: 2017-03-20 00:25
Modified: 2017-03-20 00:25
|
id | toy_top_flat |
name | toy (TOP model)_flat |
version | L3V1 |
time | s |
substance | item |
extent | item |
volume | m3 |
area | m2 |
length | m |
|
type |
FunctionDefinitions [2] |
name |
math |
sbo |
cvterm |
FunctionDefinition |
bounds__max |
minimum of arguments |
|
|
|
FunctionDefinition |
bounds__min |
maximum of arguments |
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|
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type |
UnitDefinitions [9] |
name |
units |
sbo |
cvterm |
UnitDefinition |
s |
|
|
|
|
UnitDefinition |
kg |
|
|
|
|
UnitDefinition |
m |
|
|
|
|
UnitDefinition |
m2 |
|
|
|
|
UnitDefinition |
m3 |
|
|
|
|
UnitDefinition |
mM |
|
|
|
|
UnitDefinition |
per_s |
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|
|
|
UnitDefinition |
item_per_s |
|
|
|
|
UnitDefinition |
item_per_m3 |
|
|
|
|
type |
Compartments [4] |
name |
size |
constant |
spatial dimensions |
unit |
derived unit |
sbo |
cvterm |
Compartment |
extern |
external compartment |
1.0
|
T |
3 |
m3 |
|
|
|
Compartment |
fba__extern |
external compartment |
1.0
|
T |
3 |
m3 |
|
|
|
Compartment |
fba__cell |
cell |
1.0
|
T |
3 |
m3 |
|
|
|
Compartment |
fba__membrane |
membrane |
1.0
|
T |
2 |
m2 |
|
|
|
type |
Species [8] |
name |
compartment |
boundary condition |
constant |
initial amount |
initial concentration |
substance units |
derived units |
sbo |
cvterm |
Species |
dummy_S |
|
extern |
F |
F |
0.0
|
|
item |
|
|
|
Species |
A |
|
extern |
F |
F |
10.0
|
|
item |
|
|
|
Species |
C |
|
extern |
F |
F |
0.0
|
|
item |
|
|
|
Species |
D |
|
extern |
F |
F |
0.0
|
|
item |
|
|
|
Species |
fba__A |
A
|
fba__extern |
F |
F |
0.0
|
|
item |
|
|
|
Species |
fba__C |
C
|
fba__extern |
F |
F |
0.0
|
|
item |
|
|
|
Species |
fba__B1 |
B1
|
fba__cell |
F |
F |
0.0
|
|
item |
|
|
|
Species |
fba__B2 |
B2
|
fba__cell |
F |
F |
0.0
|
|
item |
|
|
|
type |
Parameters [13] |
name |
value |
unit |
derived unit |
constant |
sbo |
cvterm |
Parameter |
dt |
|
0.1
|
s |
|
T |
|
|
Parameter |
EX_A |
|
1.0
|
item_per_s |
|
F |
|
|
Parameter |
EX_C |
|
1.0
|
item_per_s |
|
F |
|
|
Parameter |
k_R4 |
k R4 |
0.1
|
per_s |
|
T |
|
|
Parameter |
ub_R1 |
|
1.0
|
item_per_s |
|
F |
|
|
Parameter |
lb_EX_A |
|
-1000.0
|
item_per_s |
|
F |
|
|
Parameter |
ub_EX_A |
|
1000.0
|
item_per_s |
|
F |
|
|
Parameter |
lb_EX_C |
|
-1000.0
|
item_per_s |
|
F |
|
|
Parameter |
ub_EX_C |
|
1000.0
|
item_per_s |
|
F |
|
|
Parameter |
bounds__lb_default |
|
-1000.0
|
item_per_s |
|
T |
|
|
Parameter |
bounds__k1 |
k1 |
-0.2
|
per_s |
|
F |
|
|
Parameter |
fba__zero |
|
0.0
|
item_per_s |
|
T |
|
|
Parameter |
fba__ub_default |
|
1000.0
|
item_per_s |
|
T |
|
|
type |
Rules [5] |
|
assignment |
derived units |
sbo |
cvterm |
Rule |
EX_A |
= |
|
|
|
|
Rule |
EX_C |
= |
|
|
|
|
Rule |
d ub_R1/dt |
= |
|
|
|
|
Rule |
lb_EX_A |
= |
|
|
|
|
Rule |
lb_EX_C |
= |
|
|
|
|
type |
Reactions [8] |
name |
|
equation |
modifiers |
formula |
derived units |
sbo |
cvterm |
Reaction |
R4 |
C -> D |
➞ |
C ➞ D |
|
|
|
|
|
Reaction |
fba__R1 |
A import (R1) |
⇆ |
fba__A ⇆ fba__B1 |
|
|
|
|
|
Reaction |
fba__R2 |
B1 <-> B2 (R2) |
⇆ |
fba__B1 ⇆ fba__B2 |
|
|
|
|
|
Reaction |
fba__R3 |
B2 export (R3) |
⇆ |
fba__B2 ⇆ fba__C |
|
|
|
|
|
Reaction |
dummy_EX_A |
|
⇆ |
fba__A ⇆ |
|
|
|
|
|
Reaction |
dummy_EX_C |
|
⇆ |
fba__C ⇆ |
|
|
|
|
|
Reaction |
update__update_A |
|
⇆ |
A ⇆ |
|
|
|
|
|
Reaction |
update__update_C |
|
⇆ |
C ⇆ |
|
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|