Model : tiny_example_12

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 tiny_example_12 meta_tiny_example_12
nametiny_example_12
timesecond
substancemmole
extentmmole
volumelitre
aream2
lengthmetre
L3V1 comp-V1 fbc-V2 layout-V1

BQM_IS
GO:0008152
BQB_HAS_TAXON
9606

Description

A minimal example in SBML format.

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

Terms of use

Copyright © 2019 SBML team.

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 [5] name referenced element port ref id ref unit ref metaid ref sbo cvterm
c_port c_port c_port Compartment: c c
glc_port glc_port glc_port Species: glc glc
atp_port atp_port atp_port Species: atp atp
adp_port adp_port adp_port Species: adp adp
phos_port phos_port phos_port Species: phos phos

FunctionDefinitions [1] name math sbo cvterm
f_oscillation x x 10

UnitDefinitions [4] name units sbo cvterm
m2 m 2
mmole 10 3 mole
mM 10 3 mole litre
mmole_per_s 10 3 mole s

Compartments [1] name size constant spatial dimensions units derived units sbo cvterm
c meta_c cell compartment 1e-05 3 litre litre

Species [7] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
glc meta_glc glucose
C6H12O6
c 5.0 mmole mmole 10 3 mole litre
g6p meta_g6p glucose-6-phosphate
C6H11O9P(-2)
c 0.1 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:58225
BQB_IS_VERSION_OF
C00668
atp meta_atp ATP
C10H12N5O13P3(-4)
c 3.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:30616
BQB_IS_VERSION_OF
C00002
adp meta_adp ADP
C10H12N5O10P2(-3)
c 0.8 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:456216
BQB_IS_VERSION_OF
C00008
phos meta_phos P
HO4P(-2)
c 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:43474
BQB_IS_VERSION_OF
C00009
hydron meta_hydron H+
H(1)
c 0.0 mmole mmole 10 3 mole litre
h2o meta_h2o H2O
H2O
c 0.0 mmole mmole 10 3 mole litre
BQB_IS
SBO:0000247; CHEBI:15377
BQB_IS_VERSION_OF
C00001

Parameters [10] name constant value unit derived unit sbo cvterm
Vmax_GK meta_Vmax_GK Vmax Glucokinase 1e-06 mmole_per_s 10 3 mole s
Km_glc meta_Km_glc Km glucose 0.5 mM 10 3 mole litre
Km_atp meta_Km_atp Km ATP 0.1 mM 10 3 mole litre
Km_adp meta_Km_adp Km ADP 0.1 mM 10 3 mole litre
Vmax_ATPASE meta_Vmax_ATPASE Vmax ATPase 1e-06 mmole_per_s 10 3 mole s
zero zero bound 0.0 mmole_per_s 10 3 mole s
inf upper bound inf mmole_per_s 10 3 mole s
minus_1000 -1000.0 mmole_per_s 10 3 mole s
plus_1000 1000.0 mmole_per_s 10 3 mole s
a_sum ATP + ADP balance nan mM 10 3 mole litre

InitialAssignments [1] name assignment derived units sbo cvterm
glc = 4.5 10 3 mole litre

Rules [1]   assignment name derived units sbo cvterm
a_sum = atp adp 10 3 mole litre

Reactions [4] name equation modifiers kinetic law derived units sbo cvterm
GK meta_GK Glucokinase
[0.0 inf]
glc + atp ➞ g6p + adp + hydron Vmax_GK glc Km_glc glc atp Km_atp atp 0.001 mole s
BQB_IS
SBO:0000176
BQB_IS_VERSION_OF
2.7.1.2; P35557; R01092; 36495
ATPPROD ATP production
[0.0 inf]
adp + phos + hydron ➞ atp + h2o Vmax_ATPASE adp Km_adp adp f_oscillation time 1 0.001 mole s
EX_glc glucose exchange
[-1000.0 1000.0]
glc ➞ zero 10 3 mole s
EX_g6p glucose-6 phosphate exchange
[-1000.0 1000.0]
g6p ➞ zero 10 3 mole s

Objectives [1] name type flux objectives sbo cvterm
atp_consume_max maximize +1.0*ATPPROD

Constraints [1] constraint sbo cvterm
atp 0

Events [1] name trigger priority delay assignments sbo cvterm
event_1 reset concentrations time 200
initialValue = False
persistent = True
glc = 4.5
atp = 3
adp = 0.8
g6p = 0.1