Model : toy_wholecell_bounds

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2019-04-24 12:37
Modified: 2019-04-24 12:37

id toy_wholecell_bounds meta_toy_wholecell_bounds
nametoy_wholecell (BOUNDS)
times
substanceitem
extentitem
volumem3
aream2
lengthm
L3V1 comp-V1

Wholecell Toy Model

Model version: 16

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.


Ports [9] name referenced element port ref id ref unit ref metaid ref sbo cvterm
dt_port port dt Parameter: dt dt
extern_port port extern Compartment: extern extern
C_port port C Species: C C
A_port port A Species: A A
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
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
ub_R1_port port ub_R1 Parameter: ub_R1 ub_R1

Ports [9] name referenced element port ref id ref unit ref metaid ref sbo cvterm
dt_port port dt Parameter: dt dt
extern_port port extern Compartment: extern extern
C_port port C Species: C C
A_port port A Species: A A
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
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
ub_R1_port port ub_R1 Parameter: ub_R1 ub_R1

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 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 [1] name size constant spatial dimensions units derived units sbo cvterm
extern meta_extern extern 1.0 3 m3 m 3

Species [2] name compartment hasOnlySubstanceUnits boundaryCondition constant initialAmount initialConcentration conversionFactor units substanceUnits derivedUnits sbo cvterm
C meta_C C extern 1.0 item item item
A meta_A A extern 1.0 item item item

Parameters [8] name constant value unit derived unit 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
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 name 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