Wholecell Toy Model

Model version: 9

BOUNDS submodel

Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA 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_bounds

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-04-28 12:24
Modified: 2017-04-28 12:24

SBML model


idtoy_bounds
nametoy (BOUNDS)
versionL3V1
times
substanceitem
extentitem
volumem3
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
max min x y x x y y
min max x y x x y y

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 extern 1.0 3 m3 m 3

Species [2] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
A A
extern 1.0 item item
C C
extern 1.0 item item

Parameters [8] name value unit derived unit constant sbo cvterm
dt 0.1 s 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
lb_default -1000.0 item_per_s item s
ub_R1 1.0 item_per_s item s
k1 k1 -0.2 per_s 1 s

Rules [3]   assignment derived units sbo cvterm
d ub_R1/dt = k1 ub_R1 item s 2
lb_EX_A = max lb_default A dt item s
lb_EX_C = max lb_default C dt item s