E.coli core DFBA model

Model version: 6

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 metabolism model of Escherichia coli str. K-12 substr. MG1655 in SBML format.

The content of this model has been carefully created in a manual research effort. This file has been exported from the software COBRApy and further processed with the JSBML-based ModelPolisher application.

This file has been produced by the Systems Biology Research Group using BiGG Models knowledge-base version of Nov 21, 2016, where it is currently hosted and identified by: e_coli_core.

Terms of use

Redistribution and use of any part of this model from BiGG Models knowledge-base, 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.

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.

For specific licensing terms about this particular model and regulations of commercial use, see this model in BiGG Models knowledge-base.

References

When using content from BiGG Models knowledge-base in your research works, please cite

King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, and Lewis NE. (2015).: BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucl Acids Res. doi:10.1093/nar/gkv1049

Model : ecoli_bounds

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-04-26 19:26
Modified: 2017-04-26 19:26

SBO:0000293

id	ecoli_bounds
name	ecoli (BOUNDS)
version	L3V1
time	h
substance	mmol
extent	mmol
volume	l
area	m2
length	m

type	FunctionDefinitions [2]	name	math	sbo	cvterm
FunctionDefinition	max	min	$x y x x y y$
FunctionDefinition	min	max	$x y x x y y$

type	UnitDefinitions [13]	units
UnitDefinition	h	$3600 s$
UnitDefinition	g	$g$
UnitDefinition	m	$m$
UnitDefinition	m2	$m 2$
UnitDefinition	l	$litre$
UnitDefinition	mmol	$103 mole$
UnitDefinition	per_h	$1 3600 s$
UnitDefinition	mmol_per_h	$103 mole 3600 s$
UnitDefinition	mmol_per_hg	$103 mole g 3600 s$
UnitDefinition	mmol_per_l	$103 mole litre$
UnitDefinition	l_per_mmol	$litre 103 mole$
UnitDefinition	g_per_l	$g litre$
UnitDefinition	g_per_mmol	$g 103 mole$

type	Compartments [1]	name	size	constant	spatial dimensions	unit	derived unit	sbo	cvterm
Compartment	bioreactor	bioreactor	1.0	T	3	l	$litre$

type	Species [21]	name	compartment	boundary condition	constant	initial concentration	substance units	derived units
Species	acald_e	Acetaldehyde	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	succ_e	Succinate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	etoh_e	Ethanol	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	o2_e	O2	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	glc__D_e	D-Glucose	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	fru_e	D-Fructose	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	h2o_e	H2O	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	X	biomass	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	gln__L_e	L-Glutamine	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	glu__L_e	L-Glutamate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	co2_e	CO2	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	h_e	H+	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	mal__L_e	L-Malate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	ac_e	Acetate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	nh4_e	Ammonium	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	pi_e	Phosphate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	fum_e	Fumarate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	pyr_e	Pyruvate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	akg_e	2-Oxoglutarate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	lac__D_e	D-Lactate	bioreactor	F	F	1.0	mmol	$103 mole litre$
Species	for_e	Formate	bioreactor	F	F	1.0	mmol	$103 mole litre$

type	Parameters [64]	value	unit	derived unit	constant	sbo
Parameter	dt	0.1	h	$3600 s$	T	SBO:0000346
Parameter	lb_EX_acald_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_acald_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_succ_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_succ_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_etoh_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_etoh_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_o2_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_o2_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_glc__D_e	-10.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_glc__D_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_fru_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_fru_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_h2o_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_h2o_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_X	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_X	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_gln__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_gln__L_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_glu__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_glu__L_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_co2_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_co2_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_h_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_h_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_mal__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_mal__L_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_ac_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_ac_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_nh4_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_nh4_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_pi_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_pi_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_fum_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_fum_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_pyr_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_pyr_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_akg_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_akg_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_lac__D_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_lac__D_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	lb_EX_for_e	0.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	ub_EX_for_e	1000.0	mmol_per_h	$103 mole 3600 s$	F	SBO:0000625
Parameter	fbalb_EX_acald_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_succ_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_etoh_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_o2_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_glc__D_e	-10.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_fru_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_h2o_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_X	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_gln__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_glu__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_co2_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_h_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_mal__L_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_ac_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_nh4_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_pi_e	-1000.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_fum_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_pyr_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_akg_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_lac__D_e	0.0	mmol_per_h	$103 mole 3600 s$	F
Parameter	fbalb_EX_for_e	0.0	mmol_per_h	$103 mole 3600 s$	F

type	Rules [21]		assignment	derived units
Rule	lb_EX_acald_e	=	$max fbalb_EX_acald_e acald_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_succ_e	=	$max fbalb_EX_succ_e succ_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_etoh_e	=	$max fbalb_EX_etoh_e etoh_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_o2_e	=	$max fbalb_EX_o2_e o2_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_glc__D_e	=	$max fbalb_EX_glc__D_e glc__D_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_fru_e	=	$max fbalb_EX_fru_e fru_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_h2o_e	=	$max fbalb_EX_h2o_e h2o_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_X	=	$max fbalb_EX_X X bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_gln__L_e	=	$max fbalb_EX_gln__L_e gln__L_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_glu__L_e	=	$max fbalb_EX_glu__L_e glu__L_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_co2_e	=	$max fbalb_EX_co2_e co2_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_h_e	=	$max fbalb_EX_h_e h_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_mal__L_e	=	$max fbalb_EX_mal__L_e mal__L_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_ac_e	=	$max fbalb_EX_ac_e ac_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_nh4_e	=	$max fbalb_EX_nh4_e nh4_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_pi_e	=	$max fbalb_EX_pi_e pi_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_fum_e	=	$max fbalb_EX_fum_e fum_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_pyr_e	=	$max fbalb_EX_pyr_e pyr_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_akg_e	=	$max fbalb_EX_akg_e akg_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_lac__D_e	=	$max fbalb_EX_lac__D_e lac__D_e bioreactor dt$	$103 mole 3600 s$
Rule	lb_EX_for_e	=	$max fbalb_EX_for_e for_e bioreactor dt$	$103 mole 3600 s$