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.

This file has been produced by Matthias Koenig.

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:

  1. Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
  2. 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: 2018-10-23 17:51
Modified: 2018-10-23 17:51

id toy_wholecell_top meta_toy_wholecell_top
nametoy_wholecell (TOP)
times
substanceitem
extentitem
volumem3
aream2
lengthm
Access SBML model  L3V1 comp-V1

ModelDefinitions [3] name type sbo cvterm
toy_wholecell_fba toy_wholecell_fba ExternalModelDefinition (source=toy_wholecell_fba.xml)
toy_wholecell_bounds toy_wholecell_bounds ExternalModelDefinition (source=toy_wholecell_bounds.xml)
toy_wholecell_update toy_wholecell_update ExternalModelDefinition (source=toy_wholecell_update.xml)

Submodels [3] name model ref deletions time conversion extent conversion sbo cvterm
fba toy_wholecell_fba
bounds toy_wholecell_bounds
update toy_wholecell_update

UnitDefinitions [9] name units sbo cvterm
s meta_s
ReplacedElement bounds:unitRef=s
ReplacedElement fba:unitRef=s
ReplacedElement update:unitRef=s
second s
kg meta_kg
ReplacedElement bounds:unitRef=kg
ReplacedElement fba:unitRef=kg
ReplacedElement update:unitRef=kg
kilogram kg
m meta_m
ReplacedElement bounds:unitRef=m
ReplacedElement fba:unitRef=m
ReplacedElement update:unitRef=m
meter m
m2 meta_m2
ReplacedElement bounds:unitRef=m2
ReplacedElement fba:unitRef=m2
ReplacedElement update:unitRef=m2
square meter m 2
m3 meta_m3
ReplacedElement bounds:unitRef=m3
ReplacedElement fba:unitRef=m3
ReplacedElement update:unitRef=m3
cubic meter m 3
mM meta_mM
ReplacedElement bounds:unitRef=mM
ReplacedElement fba:unitRef=mM
ReplacedElement update:unitRef=mM
millimolar mole m 3
per_s
ReplacedElement bounds:unitRef=per_s
ReplacedElement fba:unitRef=per_s
ReplacedElement update:unitRef=per_s
1 s
item_per_s
ReplacedElement bounds:unitRef=item_per_s
ReplacedElement fba:unitRef=item_per_s
ReplacedElement update:unitRef=item_per_s
item s
item_per_m3
ReplacedElement bounds:unitRef=item_per_m3
ReplacedElement fba:unitRef=item_per_m3
ReplacedElement update:unitRef=item_per_m3
item m 3

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
extern meta_extern
ReplacedElement update:portRef=extern_port
ReplacedElement bounds:portRef=extern_port
extern 1.0 3 m3 m 3

Species [4] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
A meta_A
ReplacedElement bounds:portRef=A_port
ReplacedElement update:portRef=A_port
A extern 10.0 item item item
C meta_C
ReplacedElement bounds:portRef=C_port
ReplacedElement update:portRef=C_port
C extern 0.0 item item item
dummy_S dummy_S extern 0.0 item item item
D meta_D extern 0.0 item item item

Parameters [9] name constant value unit derived unit sbo cvterm
dt
ReplacedElement bounds:portRef=dt_port
0.1 s s
lb_EX_A
ReplacedElement bounds:portRef=lb_EX_A_port
ReplacedElement fba:portRef=lb_EX_A_port
-1000.0 item_per_s item s
ub_EX_A
ReplacedElement bounds:portRef=ub_EX_A_port
ReplacedElement fba:portRef=ub_EX_A_port
1000.0 item_per_s item s
lb_EX_C
ReplacedElement bounds:portRef=lb_EX_C_port
ReplacedElement fba:portRef=lb_EX_C_port
-1000.0 item_per_s item s
ub_EX_C
ReplacedElement bounds:portRef=ub_EX_C_port
ReplacedElement fba:portRef=ub_EX_C_port
1000.0 item_per_s item s
pEX_A
ReplacedElement update:portRef=pEX_A_port
1.0 item_per_s item s
pEX_C
ReplacedElement update:portRef=pEX_C_port
1.0 item_per_s item s
k_R4 0.1 per_s 1 s
ub_R1
ReplacedElement bounds:portRef=ub_R1_port
ReplacedElement fba:portRef=ub_R1_port
1.0 item_per_s item s

Rules [2]   assignment name derived units sbo cvterm
pEX_A = EX_A item s
pEX_C = EX_C item s

Reactions [3] name equation modifiers kinetic law derived units sbo cvterm
EX_A
ReplacedBy fba:portRef=EX_A_port

➞ dummy_S 0 item s
EX_C
ReplacedBy fba:portRef=EX_C_port

➞ dummy_S 0 item s
R4 meta_R4 R4: C -> D
C ➞ D k_R4 C item s