ATP Toy Model

Model version: 8

UPDATE submodel

Submodel for dynamically updating the metabolite count. This updates the ode model based on the FBA 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 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_update

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53

id toy_atp_update meta_toy_atp_update
nametoy_atp (UPDATE)
timeh
substancemole
extentmole
volumem3
aream2
lengthm
Access SBML model  L3V1 comp-V1

Ports [9] name referenced element port ref id ref unit ref metaid ref sbo cvterm
cell_port Compartment: cell cell
adp_port Species: adp adp
glc_port Species: glc glc
pyr_port Species: pyr pyr
atp_port Species: atp atp
pEX_adp_port Parameter: pEX_adp pEX_adp
pEX_glc_port Parameter: pEX_glc pEX_glc
pEX_pyr_port Parameter: pEX_pyr pEX_pyr
pEX_atp_port Parameter: pEX_atp pEX_atp

UnitDefinitions [7] 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
mM meta_mM millimolar mole m 3
mole_per_h mole 3600 s

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
cell meta_cell cell 1.0 3 m3 m 3

Species [4] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
adp meta_adp ADP cell 1.0 mole mole m 3
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
glc meta_glc Glucose cell 1.0 mole mole m 3
pyr meta_pyr Pyruvate cell 1.0 mole mole m 3
atp meta_atp ATP cell 1.0 mole mole m 3
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002

Parameters [4] name constant value unit derived unit sbo cvterm
pEX_adp 1.0 mole_per_h mole 3600 s
pEX_glc 1.0 mole_per_h mole 3600 s
pEX_pyr 1.0 mole_per_h mole 3600 s
pEX_atp 1.0 mole_per_h mole 3600 s

Reactions [4] name equation modifiers kinetic law derived units sbo cvterm
update_adp
adp ⇆ pEX_adp mole 3600 s
update_glc
glc ⇆ pEX_glc mole 3600 s
update_pyr
pyr ⇆ pEX_pyr mole 3600 s
update_atp
atp ⇆ pEX_atp mole 3600 s