Wholecell Toy Model

Model version: 11

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_wholecell_top_flat

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53

id toy_wholecell_top_flat meta_toy_wholecell_top
nametoy_wholecell (TOP)_flat
times
substanceitem
extentitem
volumem3
aream2
lengthm
Access SBML model  L3V1 fbc-V2

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 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 [4] name size constant spatial dimensions units derived units sbo cvterm
extern meta_extern extern 1.0 3 m3 m 3
fba__extern fba__meta_extern external compartment 1.0 3 m3 m 3
fba__cell fba__meta_cell cell 1.0 3 m3 m 3
fba__membrane fba__meta_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
A meta_A A extern 10.0 item item
C meta_C C extern 0.0 item item
dummy_S dummy_S extern 0.0 item item
D meta_D extern 0.0 item item
fba__A fba__meta_A A fba__extern 0.0 item item
fba__C fba__meta_C C fba__extern 0.0 item item
fba__B1 fba__meta_B1 B1 fba__cell 0.0 item item
fba__B2 fba__meta_B2 B2 fba__cell 0.0 item item

Parameters [13] name constant value unit derived unit 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
pEX_A 1.0 item_per_s item s
pEX_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
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 name derived units sbo cvterm
pEX_A = EX_A item s
pEX_C = EX_C 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 kinetic law derived units sbo cvterm
R4 meta_R4 C -> D
C ➞ D k_R4 C item s
fba__R1 fba__meta_R1 A import (R1)
[0.0 1.0]
fba__A ⇆ fba__B1
fba__R2 fba__meta_R2 B1 <-> B2 (R2)
[0.0 1000.0]
fba__B1 ⇆ fba__B2
fba__R3 fba__meta_R3 B2 export (R3)
[0.0 1000.0]
fba__B2 ⇆ fba__C
EX_A
[-1000.0 1000.0]
fba__A ⇆
EX_C
[-1000.0 1000.0]
fba__C ⇆
update__update_A
A ⇆ pEX_A item s
update__update_C
C ⇆ pEX_C item s

Objectives [1] name type flux objectives sbo cvterm
fba__R3_maximize maximize +1.0*fba__R3