Wholecell Toy Model

Model version: 15

FBA submodel

DFBA fba submodel. Unbalanced metabolites are encoded via exchange 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_wholecell_fba

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2018-10-23 17:51
Modified: 2018-10-23 17:51

id toy_wholecell_fba meta_toy_wholecell_fba
nametoy_wholecell (FBA)
times
substanceitem
extentitem
volumem3
aream2
lengthm
Access SBML model  L3V1 fbc-V2 comp-V1

Ports [7] name referenced element port ref id ref unit ref metaid ref sbo cvterm
EX_A_port port EX_A Reaction: EX_A EX_A
lb_EX_A_port port lb_EX_A Parameter: lb_EX_A lb_EX_A
ub_EX_A_port port ub_EX_A Parameter: ub_EX_A ub_EX_A
EX_C_port port EX_C Reaction: EX_C EX_C
lb_EX_C_port port lb_EX_C Parameter: lb_EX_C lb_EX_C
ub_EX_C_port port ub_EX_C Parameter: ub_EX_C ub_EX_C
ub_R1_port port ub_R1 Parameter: ub_R1 ub_R1

UnitDefinitions [9] name units sbo cvterm
s meta_s second 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
per_s 1 s
item_per_s item s
item_per_m3 item m 3

Compartments [3] name size constant spatial dimensions units derived units sbo cvterm
extern meta_extern external compartment 1.0 3 m3 m 3
cell meta_cell cell 1.0 3 m3 m 3
membrane meta_membrane membrane 1.0 2 m2 m 2

Species [4] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
A meta_A A extern 0.0 item item item
C meta_C C extern 0.0 item item item
B1 meta_B1 B1 cell 0.0 item item item
B2 meta_B2 B2 cell 0.0 item item item

Parameters [7] name constant value unit derived unit sbo cvterm
ub_R1 1.0 item_per_s item s
zero 0.0 item_per_s item s
ub_default 1000.0 item_per_s item s
lb_EX_A -1000.0 item_per_s item s
ub_EX_A 1000.0 item_per_s item s
lb_EX_C -1000.0 item_per_s item s
ub_EX_C 1000.0 item_per_s item s

Reactions [5] name equation modifiers kinetic law derived units sbo cvterm
R1 meta_R1 A import (R1)
[0.0 1.0]
A ⇆ B1
R2 meta_R2 B1 <-> B2 (R2)
[0.0 1000.0]
B1 ⇆ B2
R3 meta_R3 B2 export (R3)
[0.0 1000.0]
B2 ⇆ C
EX_A
[-1000.0 1000.0]
A ⇆
EX_C
[-1000.0 1000.0]
C ⇆

Objectives [1] name type flux objectives sbo cvterm
R3_maximize maximize +1.0*R3