Model : Koenig_demo_14

Creator
Matthias, Koenig, Humboldt-University Berlin, Institute for Theoretical Biology, koenigmx@hu-berlin.de
Created: 1900-01-01 00:00
Modified: 1900-01-01 00:00

id Koenig_demo_14 meta_Koenig_demo_14
nameKoenig_demo_14
timesecond
substancemole
extentmole
volumem3
aream2
lengthmetre
L3V1 comp-V1 fbc-V2

Koenig Demo Metabolism

Description

This is a demonstration model in SBML format.

The content of this model has been carefully created in a manual research effort.
This file has been created by Matthias Koenig.

Terms of use

Copyright © 2021 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.


UnitDefinitions [7] name units sbo cvterm
s s
kg kg
m m
m2 m 2
m3 m 3
mM mole m 3
mole_per_s mole s

Compartments [3] name size constant spatial dimensions units derived units sbo cvterm
e meta_e external compartment 1e-06 3 m3 m 3
c meta_c cell compartment 1e-06 3 m3 m 3
m meta_m plasma membrane 1.0 2 m2 m 2

Species [6] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
c__A meta_c__A A
C6H12O6
c 0.0 mole mole mole m 3
c__B meta_c__B B
C6H12O6
c 0.0 mole mole mole m 3
c__C meta_c__C C
C6H12O6
c 0.0 mole mole mole m 3
e__A meta_e__A A
C6H12O6
e 0.0 mole mole mole m 3
e__B meta_e__B B
C6H12O6
e 0.0 mole mole mole m 3
e__C meta_e__C C
C6H12O6
e 0.0 mole mole mole m 3

Parameters [13] name constant value unit derived unit sbo cvterm
scale_f metabolic scaling factor 1e-06 dimensionless None
Vmax_bA meta_Vmax_bA 5.0 mole_per_s mole s
Km_A meta_Km_A 1.0 mM mole m 3
Vmax_bB meta_Vmax_bB 2.0 mole_per_s mole s
Km_B meta_Km_B 0.5 mM mole m 3
Vmax_bC meta_Vmax_bC 2.0 mole_per_s mole s
Km_C meta_Km_C 3.0 mM mole m 3
Vmax_v1 meta_Vmax_v1 1.0 mole_per_s mole s
Keq_v1 meta_Keq_v1 10.0 dimensionless None
Vmax_v2 meta_Vmax_v2 0.5 mole_per_s mole s
Vmax_v3 meta_Vmax_v3 0.5 mole_per_s mole s
Vmax_v4 meta_Vmax_v4 0.5 mole_per_s mole s
Keq_v4 meta_Keq_v4 2.0 dimensionless None

Reactions [7] name equation modifiers kinetic law derived units sbo cvterm
bA meta_bA bA (A import)
e__A ➞ c__A scale_f Vmax_bA Km_A e__A c__A 1 e__A Km_A c__A Km_A mole s
bB meta_bB bB (B export)
c__B ➞ e__B scale_f Vmax_bB Km_B c__B e__B 1 e__B Km_B c__B Km_B mole s
bC meta_bC bC (C export)
c__C ➞ e__C scale_f Vmax_bC Km_C c__C e__C 1 e__C Km_C c__C Km_C mole s
v1 meta_v1 v1 (A -> B)
c__A ➞ c__B scale_f Vmax_v1 Km_A c__A 1 Keq_v1 c__B mole s
v2 meta_v2 v2 (A -> C)
c__A ➞ c__C scale_f Vmax_v2 Km_A c__A mole s
v3 meta_v3 v3 (C -> A)
c__C ➞ c__A scale_f Vmax_v3 Km_A c__C mole s
v4 meta_v4 v4 (C -> B)
c__C ➞ c__B scale_f Vmax_v4 Km_A c__C 1 Keq_v4 c__B mole s