Wholecell Toy Model

Model version: 7

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_flat

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-04-05 13:28
Modified: 2017-04-05 13:28

SBML model


idtoy_top_flat
nametoy (TOP)_flat
versionL3V1
times
substanceitem
extentitem
volumem3
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
bounds__max min x y x x y y
bounds__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 [4] name size constant spatial dimensions unit derived unit sbo cvterm
extern extern 1.0 3 m3 m 3
fba__extern external compartment 1.0 3 m3 m 3
fba__cell cell 1.0 3 m3 m 3
fba__membrane membrane 1.0 2 m2 m 2

Species [8] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
C C
extern 0.0 item item m 3
A A
extern 10.0 item item m 3
dummy_S dummy_S
extern 0.0 item item m 3
D
extern 0.0 item item
fba__A A
fba__extern 0.0 item item
fba__C C
fba__extern 0.0 item item
fba__B1 B1
fba__cell 0.0 item item
fba__B2 B2
fba__cell 0.0 item item

Parameters [13] name value unit derived unit constant sbo cvterm
dt 0.1 s s
lb_EX_C -1000.0 item_per_s item s
ub_EX_C 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
pEX_C 1.0 item_per_s item s
pEX_A 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
fba__zero 0.0 item_per_s item s
fba__ub_default 1000.0 item_per_s item s
bounds__lb_default -1000.0 item_per_s item s
bounds__k1 k1 -0.2 per_s 1 s

Rules [5]   assignment derived units sbo cvterm
pEX_C = EX_C item s
pEX_A = EX_A item s
d ub_R1/dt = bounds__k1 ub_R1 item s 2
lb_EX_A = bounds__max bounds__lb_default A dt item s
lb_EX_C = bounds__max bounds__lb_default C dt item s

Reactions [8] name equation modifiers formula derived units sbo cvterm
R4 C -> D C ➞ D k_R4 C item m 3 s
fba__R1 A import (R1) fba__A ⇆ fba__B1
fba__R2 B1 <-> B2 (R2) fba__B1 ⇆ fba__B2
fba__R3 B2 export (R3) fba__B2 ⇆ fba__C
EX_A fba__A ⇆
EX_C fba__C ⇆
update__update_C C ⇆ EX_C item s
update__update_A A ⇆ EX_A item s