Wholecell Toy Model
Model version: 11
BOUNDS submodel
Submodel for dynamically calculating the flux bounds.
The dynamically changing flux bounds are the input to the
FBA 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_bounds
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53
id toy_wholecell_bounds meta_toy_wholecell_bounds
name toy_wholecell (BOUNDS)
time s
substance item
extent item
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
dt_port
Parameter: dt
dt
Port
extern_port
Compartment: extern
extern
Port
A_port
Species: A
A
Port
C_port
Species: C
C
Port
lb_EX_A_port
Parameter: lb_EX_A
lb_EX_A
Port
ub_EX_A_port
Parameter: ub_EX_A
ub_EX_A
Port
lb_EX_C_port
Parameter: lb_EX_C
lb_EX_C
Port
ub_EX_C_port
Parameter: ub_EX_C
ub_EX_C
Port
ub_R1_port
Parameter: ub_R1
ub_R1
type
FunctionDefinitions [2]
name
math
sbo
cvterm
FunctionDefinition
max
min
x
y
x
x
y
y
FunctionDefinition
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 [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
boundary condition
constant
initial amount
initial concentration
substance units
derived units
sbo
cvterm
Species
A meta_A
A
extern
F
F
1.0
item
item
Species
C meta_C
C
extern
F
F
1.0
item
item
type
Parameters [8]
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
lb_default
T
-1000.0
item_per_s
item
s
Parameter
ub_R1
F
1.0
item_per_s
item
s
Parameter
k1
k1
F
-0.2
per_s
1
s
type
Rules [3]
assignment
name
derived units
sbo
cvterm
Rule
d ub_R1/dt
=
k1
ub_R1
item
s
2
Rule
lb_EX_A
=
max
lb_default
A
dt
item
s
Rule
lb_EX_C
=
max
lb_default
C
dt
item
s