Diauxic Growth Model
Model version: 8
BOUNDS submodel
Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.
Description
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
The key variables in the mathematical model of the metabolic network are the glucose concentration (Glcxt), the acetate concentration (Ac), the biomass concentration (X), and the oxygen concentration (O2) in the gas phase.
Terms of use
Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
- 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.
Model : diauxic_bounds
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-22 11:07
Modified: 2017-03-22 11:07
![]() |
|
type | FunctionDefinitions [2] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | max | minimum of arguments | |||
FunctionDefinition | min | maximum of arguments |
type | UnitDefinitions [12] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | h | ||||
UnitDefinition | g | ||||
UnitDefinition | m | ||||
UnitDefinition | m2 | ||||
UnitDefinition | l | ||||
UnitDefinition | mmol | ||||
UnitDefinition | per_h | ||||
UnitDefinition | mmol_per_h | ||||
UnitDefinition | mmol_per_l | ||||
UnitDefinition | l_per_mmol | ||||
UnitDefinition | g_per_l | ||||
UnitDefinition | g_per_mmol |
type | Compartments [1] | name | size | constant | spatial dimensions | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor | bioreactor | 1.0 | T | 3 | l |
type | Species [4] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | Glcxt | glucose |
bioreactor | F | F | 10.8 | mmol | ||||
Species | Ac | acetate |
bioreactor | F | F | 0.4 | mmol | ||||
Species | O2 | oxygen |
bioreactor | F | F | 0.21 | mmol | ||||
Species | X | biomass |
bioreactor | F | F | 0.001 | mmol |
type | Parameters [17] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt | fba timestep | 0.01 | h | T | |||
Parameter | zero | zero bound | 0.0 | mmol_per_h | T | |||
Parameter | lb_default | default lower bound | -1000.0 | mmol_per_h | T | |||
Parameter | ub_default | default upper bound | 1000.0 | mmol_per_h | T | |||
Parameter | lb_EX_Ac | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Ac | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_Glcxt | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Glcxt | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_O2 | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_O2 | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_X | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_X | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_kin_EX_Glcxt | -1000.0 | mmol_per_h | F | ||||
Parameter | lb_kin_EX_O2 | -1000.0 | mmol_per_h | F | ||||
Parameter | Vmax_EX_O2 | 15.0 | mmol_per_h | T | ||||
Parameter | Vmax_EX_Glcxt | 10.0 | mmol_per_h | T | ||||
Parameter | Km_EX_Glcxt | Km_vGlcxt | 0.015 | mmol_per_l | T |
type | Rules [6] | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|
Rule | lb_kin_EX_Glcxt | = | ||||
Rule | lb_kin_EX_O2 | = | ||||
Rule | lb_EX_Ac | = | ||||
Rule | lb_EX_Glcxt | = | ||||
Rule | lb_EX_O2 | = | ||||
Rule | lb_EX_X | = |