Model : toy_atp_bounds

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

id toy_atp_bounds meta_toy_atp_bounds
nametoy_atp (BOUNDS)
timeh
substancemmole
extentmmole
volumelitre
aream2
lengthm
L3V1 comp-V1

ATP Toy Model

Model version: 13

BOUNDS submodel

Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA 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.


Ports [14] name referenced element port ref id ref unit ref metaid ref sbo cvterm
dt_port port dt Parameter: dt dt
cell_port port cell Compartment: cell cell
atp_port port atp Species: atp atp
adp_port port adp Species: adp adp
glc_port port glc Species: glc glc
pyr_port port pyr Species: pyr pyr
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
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
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
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

Ports [14] name referenced element port ref id ref unit ref metaid ref sbo cvterm
dt_port port dt Parameter: dt dt
cell_port port cell Compartment: cell cell
atp_port port atp Species: atp atp
adp_port port adp Species: adp adp
glc_port port glc Species: glc glc
pyr_port port pyr Species: pyr pyr
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
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
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
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

FunctionDefinitions [2] name math sbo cvterm
max min x y x x y y
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 [1] name size constant spatial dimensions units derived units sbo cvterm
cell meta_cell cell 1.0 3 litre litre

Species [4] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
atp meta_atp ATP cell 1.0 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 1.0 mmole mmole 10 3 mole litre
pyr meta_pyr Pyruvate cell 1.0 mmole mmole 10 3 mole litre

Parameters [17] 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
ub_EX_atp_fba 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_atp_fba -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_adp_fba 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_adp_fba -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_glc_fba 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_glc_fba -1000.0 mmole_per_h 10 3 mole 3600 s
ub_EX_pyr_fba 1000.0 mmole_per_h 10 3 mole 3600 s
lb_EX_pyr_fba -1000.0 mmole_per_h 10 3 mole 3600 s

Rules [8]   assignment name derived units sbo cvterm
ub_EX_atp = ub_EX_atp_fba 10 3 mole 3600 s
lb_EX_atp = max lb_EX_atp_fba cell atp dt 10 3 mole 3600 s
ub_EX_adp = ub_EX_adp_fba 10 3 mole 3600 s
lb_EX_adp = max lb_EX_adp_fba cell adp dt 10 3 mole 3600 s
ub_EX_glc = ub_EX_glc_fba 10 3 mole 3600 s
lb_EX_glc = max lb_EX_glc_fba cell glc dt 10 3 mole 3600 s
ub_EX_pyr = ub_EX_pyr_fba 10 3 mole 3600 s
lb_EX_pyr = max lb_EX_pyr_fba cell pyr dt 10 3 mole 3600 s