Model : toy_atp_top_flat

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2019-04-24 12:32
Modified: 2019-04-24 12:32

id toy_atp_top_flat meta_toy_atp_top
nametoy_atp (TOP)_flat
timeh
substancemmole
extentmmole
volumelitre
aream2
lengthm
L3V1 fbc-V2

ATP Toy Model

Model version: 13

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.


FunctionDefinitions [2] name math sbo cvterm
bounds__max min x y x x y y
bounds__min max x y x x y y

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 [2] name size constant spatial dimensions units derived units sbo cvterm
cell meta_cell cell 1.0 3 litre litre
fba__cell fba__meta_cell cell 1.0 3 litre litre

Species [11] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
atp meta_atp ATP cell 2.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002
adp meta_adp ADP cell 1.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
glc meta_glc Glucose cell 5.0 mmole mmole 10 3 mole litre
pyr meta_pyr Pyruvate cell 0.0 mmole mmole 10 3 mole litre
dummy_S dummy_S cell 0.0 mmole mmole 10 3 mole litre
fba__atp fba__meta_atp ATP
C10H12N5O13P3 (-4)
fba__cell 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002
fba__adp fba__meta_adp ADP
C10H12N5O10P2 (-3)
fba__cell 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
fba__glc fba__meta_glc Glucose
C6H12O6
fba__cell 0.0 mmole mmole 10 3 mole litre
fba__pyr fba__meta_pyr Pyruvate
C3H4O3
fba__cell 0.0 mmole mmole 10 3 mole litre
fba__fru16bp fba__meta_fru16bp Fructose 1,6-bisphospate
C6H14O12P2
fba__cell 0.0 mmole mmole 10 3 mole litre
fba__pg2 fba__meta_pg2 2-Phosphoglycerate
C3H7O7P
fba__cell 0.0 mmole mmole 10 3 mole litre

Parameters [28] name constant value unit derived unit sbo cvterm
dt 0.1 h 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
pEX_atp 1.0 mmole_per_h 10 3 mole 3600 s
pEX_adp 1.0 mmole_per_h 10 3 mole 3600 s
pEX_glc 1.0 mmole_per_h 10 3 mole 3600 s
pEX_pyr 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
fba__ub_R3 1.0 mmole_per_h 10 3 mole 3600 s
fba__zero 0.0 mmole_per_h 10 3 mole 3600 s
fba__ub_default 1000.0 mmole_per_h 10 3 mole 3600 s
bounds__ub_EX_atp_fba 1000.0 mmole_per_h 10 3 mole 3600 s
bounds__lb_EX_atp_fba -1000.0 mmole_per_h 10 3 mole 3600 s
bounds__ub_EX_adp_fba 1000.0 mmole_per_h 10 3 mole 3600 s
bounds__lb_EX_adp_fba -1000.0 mmole_per_h 10 3 mole 3600 s
bounds__ub_EX_glc_fba 1000.0 mmole_per_h 10 3 mole 3600 s
bounds__lb_EX_glc_fba -1000.0 mmole_per_h 10 3 mole 3600 s
bounds__ub_EX_pyr_fba 1000.0 mmole_per_h 10 3 mole 3600 s
bounds__lb_EX_pyr_fba -1000.0 mmole_per_h 10 3 mole 3600 s

Rules [14]   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_b5efc2a5fd764bfb8a5efcfdb67431fb = atp adp 10 3 mole litre
c3_tot meta_a993fc33ff3d4c26907cff899e77edcf = 2 glc pyr 0.001 mole litre
ub_EX_atp = bounds__ub_EX_atp_fba 10 3 mole 3600 s
lb_EX_atp = bounds__max bounds__lb_EX_atp_fba cell atp dt 10 3 mole 3600 s
ub_EX_adp = bounds__ub_EX_adp_fba 10 3 mole 3600 s
lb_EX_adp = bounds__max bounds__lb_EX_adp_fba cell adp dt 10 3 mole 3600 s
ub_EX_glc = bounds__ub_EX_glc_fba 10 3 mole 3600 s
lb_EX_glc = bounds__max bounds__lb_EX_glc_fba cell glc dt 10 3 mole 3600 s
ub_EX_pyr = bounds__ub_EX_pyr_fba 10 3 mole 3600 s
lb_EX_pyr = bounds__max bounds__lb_EX_pyr_fba cell pyr dt 10 3 mole 3600 s

Reactions [12] name equation modifiers kinetic law derived units sbo cvterm
RATP meta_RATP atp -> adp
atp ➞ adp Vmax_RATP atp k_RATP atp 0.001 mole 3600 s
fba__R1 fba__meta_R1 glu + 2 atp -> fru16bp + 2 adp
[0.0 1000.0]
2.0 fba__atp + fba__glc ➞ 2.0 fba__adp + fba__fru16bp
fba__R2 fba__meta_R2 fru16bp -> 2 pg2
[0.0 1000.0]
fba__fru16bp ➞ 2.0 fba__pg2
fba__R3 fba__meta_R3 pg2 + adp -> pyr + atp
[0.0 1.0]
2.0 fba__adp + fba__pg2 ➞ 2.0 fba__atp + fba__pyr
EX_atp
[-1000.0 1000.0]
fba__atp ⇆
EX_adp
[-1000.0 1000.0]
fba__adp ⇆
EX_glc
[-1000.0 1000.0]
fba__glc ⇆
EX_pyr
[-1000.0 1000.0]
fba__pyr ⇆
update__update_atp
atp ⇆ pEX_atp 10 3 mole 3600 s
update__update_adp
adp ⇆ pEX_adp 10 3 mole 3600 s
update__update_glc
glc ⇆ pEX_glc 10 3 mole 3600 s
update__update_pyr
pyr ⇆ pEX_pyr 10 3 mole 3600 s

Objectives [1] name type flux objectives sbo cvterm
fba__RATP_maximize maximize +1.0*fba__R3

Objectives [1] name type flux objectives sbo cvterm
fba__RATP_maximize maximize +1.0*fba__R3