Model : annotation_example_8

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 annotation_example_8 meta_annotation_example_8
nameannotation_example_8
times
substancemole
extentmole
volumem3
aream2
lengthm
L3V1 comp-V1

Model with inline annotations

Description

Test model demonstrating inline annotations.

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 © 2020 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 [7] name referenced element port ref id ref unit ref metaid ref sbo cvterm
kg_port kg_port kg_port UnitDefinition: kg kg
s_port s_port s_port UnitDefinition: s s
m_port m_port m_port UnitDefinition: m m
m2_port m2_port m2_port UnitDefinition: m2 m2
m3_port m3_port m3_port UnitDefinition: m3 m3
mM_port mM_port mM_port UnitDefinition: mM mM
mole_per_s_port mole_per_s_port mole_per_s_port UnitDefinition: mole_per_s mole_per_s

UnitDefinitions [7] name units sbo cvterm
kg kg
s s
m m
m2 m 2
m3 m 3
mM 10 3 mole litre
mole_per_s mole s

Compartments [3] name size constant spatial dimensions units derived units sbo cvterm
ext meta_ext external Vol_e 3 m3 m 3
cyto meta_cyto cytosol Vol_c 3 m3 m 3
pm meta_pm membrane A_m 2 m2 m 2

Species [2] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
e__gal meta_e__gal D-galactose ext 3.0 mole mole mole m 3
c__gal D-galactose cyto 0.00012 mole mole mole m 3

Parameters [7] name constant value unit derived unit sbo cvterm
x_cell cell diameter 2.5e-05 m m
Vol_e external volume 1e-12 m3 m 3
A_m membrane area 1.0 m2 m 2
Vol_c x_cell x_cell x_cell m3 m 3
GLUT2_Vmax 1e-13 mole_per_s mole s
GLUT2_k_gal 1.0 mM 10 3 mole litre
GLUT2_keq 1.0 dimensionless None

InitialAssignments [3] name assignment derived units sbo cvterm
ext = Vol_e m 3
pm = A_m m 2
Vol_c = x_cell x_cell x_cell m 3

Rules [1]   assignment name derived units sbo cvterm
cyto = Vol_c m 3

Reactions [1] name equation modifiers kinetic law derived units sbo cvterm
e__GLUT2_GAL meta_e__GLUT2_GAL galactose transport [e__]
e__gal ⇆ c__gal GLUT2_Vmax GLUT2_k_gal e__gal c__gal GLUT2_keq 1 c__gal GLUT2_k_gal e__gal GLUT2_k_gal litre mole m 3 0.001 s