ATP Toy Model

Model version: 12

FBA submodel

DFBA fba submodel. Unbalanced metabolites are encoded via exchange fluxes.

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_fba

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

id toy_atp_fba meta_toy_atp_fba
nametoy_atp (FBA)
timeh
substancemmole
extentmmole
volumelitre
aream2
lengthm
Access SBML model  L3V1 fbc-V2 comp-V1

Ports [12] name referenced element port ref id ref unit ref metaid ref sbo cvterm
EX_atp_port port EX_atp Reaction: EX_atp EX_atp
lb_EX_atp_port port lb_EX_atp Parameter: lb_EX_atp lb_EX_atp
ub_EX_atp_port port ub_EX_atp Parameter: ub_EX_atp ub_EX_atp
EX_adp_port port EX_adp Reaction: EX_adp EX_adp
lb_EX_adp_port port lb_EX_adp Parameter: lb_EX_adp lb_EX_adp
ub_EX_adp_port port ub_EX_adp Parameter: ub_EX_adp ub_EX_adp
EX_glc_port port EX_glc Reaction: EX_glc EX_glc
lb_EX_glc_port port lb_EX_glc Parameter: lb_EX_glc lb_EX_glc
ub_EX_glc_port port ub_EX_glc Parameter: ub_EX_glc ub_EX_glc
EX_pyr_port port EX_pyr Reaction: EX_pyr EX_pyr
lb_EX_pyr_port port lb_EX_pyr Parameter: lb_EX_pyr lb_EX_pyr
ub_EX_pyr_port port ub_EX_pyr Parameter: ub_EX_pyr ub_EX_pyr

UnitDefinitions [8] name units sbo cvterm
h meta_h hour 3600 s
kg meta_kg kilogram kg
m meta_m meter m
m2 meta_m2 square meter m 2
m3 meta_m3 cubic meter m 3
mmole 10 3 mole
mM meta_mM millimolar 10 3 mole litre
mmole_per_h 10 3 mole 3600 s

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
cell meta_cell cell 1.0 3 litre litre

Species [6] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
atp meta_atp ATP
C10H12N5O13P3 (-4)
cell 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002
adp meta_adp ADP
C10H12N5O10P2 (-3)
cell 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
glc meta_glc Glucose
C6H12O6
cell 0.0 mmole mmole 10 3 mole litre
pyr meta_pyr Pyruvate
C3H4O3
cell 0.0 mmole mmole 10 3 mole litre
fru16bp meta_fru16bp Fructose 1,6-bisphospate
C6H14O12P2
cell 0.0 mmole mmole 10 3 mole litre
pg2 meta_pg2 2-Phosphoglycerate
C3H7O7P
cell 0.0 mmole mmole 10 3 mole litre

Parameters [11] name constant value unit derived unit sbo cvterm
ub_R3 1.0 mmole_per_h 10 3 mole 3600 s
zero 0.0 mmole_per_h 10 3 mole 3600 s
ub_default 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_atp -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_atp 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_adp -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_adp 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_glc -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_glc 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_pyr -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_pyr 1000.0 mmole_per_h 10 3 mole 3600 s

Reactions [7] name equation modifiers kinetic law derived units sbo cvterm
R1 meta_R1 glu + 2 atp -> fru16bp + 2 adp
[0.0 1000.0]
glc + 2.0 atp ➞ fru16bp + 2.0 adp
R2 meta_R2 fru16bp -> 2 pg2
[0.0 1000.0]
fru16bp ➞ 2.0 pg2
R3 meta_R3 pg2 + adp -> pyr + atp
[0.0 1.0]
pg2 + 2.0 adp ➞ pyr + 2.0 atp
EX_atp
[-1000.0 1000.0]
atp ⇆
EX_adp
[-1000.0 1000.0]
adp ⇆
EX_glc
[-1000.0 1000.0]
glc ⇆
EX_pyr
[-1000.0 1000.0]
pyr ⇆

Objectives [1] name type flux objectives sbo cvterm
RATP_maximize maximize +1.0*R3