Wholecell Toy Model

Model version: 4

TOP model

Main comp DFBA model by combining fba, update and bounds model with additional kinetics in the top model.

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_top

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-24 14:24
Modified: 2017-03-24 14:24

SBML model


idtoy_top
nametoy (TOP model)
versionL3V1
times
substanceitem
extentitem
volumem3
aream2
lengthm
UnitDefinitions [9] name units sbo cvterm
s s
kg kg
m m
m2 m 2
m3 m 3
mM mole m 3
per_s 1 s
item_per_s item s
item_per_m3 item m 3

Compartments [1] name size constant spatial dimensions unit derived unit sbo cvterm
extern external compartment 1.0 3 m3 m 3

Species [4] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
dummy_S
extern 0.0 item item
A
extern 10.0 item item
C
extern 0.0 item item
D
extern 0.0 item item

Parameters [9] name value unit derived unit constant sbo cvterm
dt 0.1 s s
EX_A 1.0 item_per_s item s
EX_C 1.0 item_per_s item s
k_R4 k R4 0.1 per_s 1 s
ub_R1 1.0 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

Rules [2]   assignment derived units sbo cvterm
EX_A = dummy_EX_A item s
EX_C = dummy_EX_C item s

Reactions [3] name equation modifiers formula derived units sbo cvterm
dummy_EX_A ⇆ dummy_S
dummy_EX_C ⇆ dummy_S
R4 C -> D C ➞ D k_R4 C item s