ATP Toy Model

Model version: 12

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 © 2017-2018 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_atp_top

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2018-10-23 17:48
Modified: 2018-10-23 17:48

id toy_atp_top meta_toy_atp_top
nametoy_atp (TOP)
timeh
substancemmole
extentmmole
volumelitre
aream2
lengthm
Access SBML model  L3V1 comp-V1

ModelDefinitions [3] name type sbo cvterm
toy_atp_fba toy_atp_fba ExternalModelDefinition (source=toy_atp_fba.xml)
toy_atp_bounds toy_atp_bounds ExternalModelDefinition (source=toy_atp_bounds.xml)
toy_atp_update toy_atp_update ExternalModelDefinition (source=toy_atp_update.xml)

Submodels [3] name model ref deletions time conversion extent conversion sbo cvterm
fba toy_atp_fba
bounds toy_atp_bounds
update toy_atp_update

UnitDefinitions [8] name units sbo cvterm
h meta_h
ReplacedElement bounds:unitRef=h
ReplacedElement fba:unitRef=h
ReplacedElement update:unitRef=h
hour 3600 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
mmole
ReplacedElement bounds:unitRef=mmole
ReplacedElement fba:unitRef=mmole
ReplacedElement update:unitRef=mmole
10 3 mole
mM meta_mM
ReplacedElement bounds:unitRef=mM
ReplacedElement fba:unitRef=mM
ReplacedElement update:unitRef=mM
millimolar 10 3 mole litre
mmole_per_h
ReplacedElement bounds:unitRef=mmole_per_h
ReplacedElement fba:unitRef=mmole_per_h
ReplacedElement update:unitRef=mmole_per_h
10 3 mole 3600 s

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
cell meta_cell
ReplacedElement update:portRef=cell_port
ReplacedElement bounds:portRef=cell_port
cell 1.0 3 litre litre

Species [5] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
atp meta_atp
ReplacedElement bounds:portRef=atp_port
ReplacedElement update:portRef=atp_port
ATP cell 2.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002
adp meta_adp
ReplacedElement bounds:portRef=adp_port
ReplacedElement update:portRef=adp_port
ADP cell 1.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
glc meta_glc
ReplacedElement bounds:portRef=glc_port
ReplacedElement update:portRef=glc_port
Glucose cell 5.0 mmole mmole 10 3 mole litre
pyr meta_pyr
ReplacedElement bounds:portRef=pyr_port
ReplacedElement update:portRef=pyr_port
Pyruvate cell 0.0 mmole mmole 10 3 mole litre
dummy_S dummy_S cell 0.0 mmole mmole 10 3 mole litre

Parameters [17] name constant value unit derived unit sbo cvterm
dt
ReplacedElement bounds:portRef=dt_port
0.1 h 3600 s
lb_EX_atp
ReplacedElement bounds:portRef=lb_EX_atp_port
ReplacedElement fba:portRef=lb_EX_atp_port
-1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_atp
ReplacedElement bounds:portRef=ub_EX_atp_port
ReplacedElement fba:portRef=ub_EX_atp_port
1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_adp
ReplacedElement bounds:portRef=lb_EX_adp_port
ReplacedElement fba:portRef=lb_EX_adp_port
-1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_adp
ReplacedElement bounds:portRef=ub_EX_adp_port
ReplacedElement fba:portRef=ub_EX_adp_port
1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_glc
ReplacedElement bounds:portRef=lb_EX_glc_port
ReplacedElement fba:portRef=lb_EX_glc_port
-1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_glc
ReplacedElement bounds:portRef=ub_EX_glc_port
ReplacedElement fba:portRef=ub_EX_glc_port
1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_pyr
ReplacedElement bounds:portRef=lb_EX_pyr_port
ReplacedElement fba:portRef=lb_EX_pyr_port
-1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_pyr
ReplacedElement bounds:portRef=ub_EX_pyr_port
ReplacedElement fba:portRef=ub_EX_pyr_port
1000.0 mmole_per_h 10 3 mole 3600 s
pEX_atp
ReplacedElement update:portRef=pEX_atp_port
1.0 mmole_per_h 10 3 mole 3600 s
pEX_adp
ReplacedElement update:portRef=pEX_adp_port
1.0 mmole_per_h 10 3 mole 3600 s
pEX_glc
ReplacedElement update:portRef=pEX_glc_port
1.0 mmole_per_h 10 3 mole 3600 s
pEX_pyr
ReplacedElement update:portRef=pEX_pyr_port
1.0 mmole_per_h 10 3 mole 3600 s
Vmax_RATP meta_Vmax_RATP 1.0 mmole_per_h 10 3 mole 3600 s
k_RATP meta_k_RATP 0.1 mM 10 3 mole litre
atp_tot atp adp mM 10 3 mole litre
c3_tot 2 glc pyr mM 10 3 mole litre

Rules [6]   assignment name derived units sbo cvterm
pEX_atp = EX_atp 10 3 mole 3600 s
pEX_adp = EX_adp 10 3 mole 3600 s
pEX_glc = EX_glc 10 3 mole 3600 s
pEX_pyr = EX_pyr 10 3 mole 3600 s
atp_tot meta_8dc182e4447343a8a39d1092990fe6a6 = atp adp 10 3 mole litre
c3_tot meta_007b254d80014a16948c6a65ea62ea2a = 2 glc pyr 10 3 mole litre

Reactions [5] name equation modifiers kinetic law derived units sbo cvterm
EX_atp
ReplacedBy fba:portRef=EX_atp_port

➞ dummy_S 0 10 3 mole 3600 s
EX_adp
ReplacedBy fba:portRef=EX_adp_port

➞ dummy_S 0 10 3 mole 3600 s
EX_glc
ReplacedBy fba:portRef=EX_glc_port

➞ dummy_S 0 10 3 mole 3600 s
EX_pyr
ReplacedBy fba:portRef=EX_pyr_port

➞ dummy_S 0 10 3 mole 3600 s
RATP meta_RATP atp -> adp
atp ➞ adp Vmax_RATP atp k_RATP atp 0.001 mole 3600 s