Wholecell Toy Model
Model version: 14
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
Creator Matthias, Koenig, Humboldt University Berlin,
konigmatt@googlemail.com Created: 2017-11-11 18:07
Modified: 2017-11-11 18:07
id toy_wholecell_top meta_toy_wholecell_top
name toy_wholecell (TOP)
time s
substance item
extent item
volume m3
area m2
length m
L3V1 comp-V1
type
ModelDefinitions [3]
name
type
sbo
cvterm
ModelDefinition
toy_wholecell_fba
toy_wholecell_fba
ExternalModelDefinition (source=toy_wholecell_fba.xml
)
ModelDefinition
toy_wholecell_bounds
toy_wholecell_bounds
ExternalModelDefinition (source=toy_wholecell_bounds.xml
)
ModelDefinition
toy_wholecell_update
toy_wholecell_update
ExternalModelDefinition (source=toy_wholecell_update.xml
)
type
Submodels [3]
name
model ref
deletions
time conversion
extent conversion
sbo
cvterm
Submodel
fba
toy_wholecell_fba
Submodel
bounds
toy_wholecell_bounds
Submodel
update
toy_wholecell_update
type
UnitDefinitions [9]
name
units
sbo
cvterm
UnitDefinition
s meta_s
ReplacedElement bounds:unitRef=s
ReplacedElement fba:unitRef=s
ReplacedElement update:unitRef=s
second
s
UnitDefinition
kg meta_kg
ReplacedElement bounds:unitRef=kg
ReplacedElement fba:unitRef=kg
ReplacedElement update:unitRef=kg
kilogram
kg
UnitDefinition
m meta_m
ReplacedElement bounds:unitRef=m
ReplacedElement fba:unitRef=m
ReplacedElement update:unitRef=m
meter
m
UnitDefinition
m2 meta_m2
ReplacedElement bounds:unitRef=m2
ReplacedElement fba:unitRef=m2
ReplacedElement update:unitRef=m2
square meter
m
2
UnitDefinition
m3 meta_m3
ReplacedElement bounds:unitRef=m3
ReplacedElement fba:unitRef=m3
ReplacedElement update:unitRef=m3
cubic meter
m
3
UnitDefinition
mM meta_mM
ReplacedElement bounds:unitRef=mM
ReplacedElement fba:unitRef=mM
ReplacedElement update:unitRef=mM
millimolar
mole
m
3
UnitDefinition
per_s
ReplacedElement bounds:unitRef=per_s
ReplacedElement fba:unitRef=per_s
ReplacedElement update:unitRef=per_s
1
s
UnitDefinition
item_per_s
ReplacedElement bounds:unitRef=item_per_s
ReplacedElement fba:unitRef=item_per_s
ReplacedElement update:unitRef=item_per_s
item
s
UnitDefinition
item_per_m3
ReplacedElement bounds:unitRef=item_per_m3
ReplacedElement fba:unitRef=item_per_m3
ReplacedElement update:unitRef=item_per_m3
item
m
3
type
Compartments [1]
name
size
constant
spatial dimensions
units
derived units
sbo
cvterm
Compartment
extern meta_extern
ReplacedElement update:portRef=extern_port
ReplacedElement bounds:portRef=extern_port
extern
1.0
T
3
m3
m
3
type
Species [4]
name
compartment
boundary condition
constant
initial amount
initial concentration
conversion factor
units
substance units
derived units
sbo
cvterm
Species
C meta_C
ReplacedElement update:portRef=C_port
ReplacedElement bounds:portRef=C_port
C
extern
F
F
0.0
item
item
item
Species
A meta_A
ReplacedElement update:portRef=A_port
ReplacedElement bounds:portRef=A_port
A
extern
F
F
10.0
item
item
item
Species
dummy_S
dummy_S
extern
F
F
0.0
item
item
item
Species
D meta_D
extern
F
F
0.0
item
item
item
type
Parameters [9]
name
constant
value
unit
derived unit
sbo
cvterm
Parameter
dt
ReplacedElement bounds:portRef=dt_port
T
0.1
s
s
Parameter
lb_EX_C
ReplacedElement bounds:portRef=lb_EX_C_port
ReplacedElement fba:portRef=lb_EX_C_port
F
-1000.0
item_per_s
item
s
Parameter
ub_EX_C
ReplacedElement bounds:portRef=ub_EX_C_port
ReplacedElement fba:portRef=ub_EX_C_port
F
1000.0
item_per_s
item
s
Parameter
lb_EX_A
ReplacedElement bounds:portRef=lb_EX_A_port
ReplacedElement fba:portRef=lb_EX_A_port
F
-1000.0
item_per_s
item
s
Parameter
ub_EX_A
ReplacedElement bounds:portRef=ub_EX_A_port
ReplacedElement fba:portRef=ub_EX_A_port
F
1000.0
item_per_s
item
s
Parameter
pEX_C
ReplacedElement update:portRef=pEX_C_port
F
1.0
item_per_s
item
s
Parameter
pEX_A
ReplacedElement update:portRef=pEX_A_port
F
1.0
item_per_s
item
s
Parameter
k_R4
T
0.1
per_s
1
s
Parameter
ub_R1
ReplacedElement bounds:portRef=ub_R1_port
ReplacedElement fba:portRef=ub_R1_port
F
1.0
item_per_s
item
s
type
Rules [2]
assignment
name
derived units
sbo
cvterm
Rule
pEX_C
=
EX_C
item
s
Rule
pEX_A
=
EX_A
item
s
type
Reactions [3]
name
equation
modifiers
kinetic law
derived units
sbo
cvterm
Reaction
EX_C
ReplacedBy fba:portRef=EX_C_port
➞
➞ dummy_S
0
item
s
Reaction
EX_A
ReplacedBy fba:portRef=EX_A_port
➞
➞ dummy_S
0
item
s
Reaction
R4 meta_R4
R4: C -> D
➞
C ➞ D
k_R4
C
item
s