E.coli core DFBA model
Model version: 1
UPDATE submodel
Submodel for dynamically updating the metabolite count. This updates the ode model based on the FBA fluxes.
Description
This is a metabolism model of Homo sapiens in SBML format.
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.
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 : rbc_update
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-31 17:30
Modified: 2017-03-31 17:30
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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 | blood | blood | 1.0 | T | 3 | l |
type | Species [76] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | ins_e | Inosine |
blood | F | F | 1.0 | mmol | ||||
Species | gln__L_e | L-Glutamine |
blood | F | F | 1.0 | mmol | ||||
Species | lnlc_e | Lnlc c |
blood | F | F | 1.0 | mmol | ||||
Species | thm_e | Thiamin |
blood | F | F | 1.0 | mmol | ||||
Species | ncam_e | Nicotinamide |
blood | F | F | 1.0 | mmol | ||||
Species | nac_e | Nicotinate |
blood | F | F | 1.0 | mmol | ||||
Species | urea_e | Urea |
blood | F | F | 1.0 | mmol | ||||
Species | hco3_e | Bicarbonate |
blood | F | F | 1.0 | mmol | ||||
Species | fum_e | Fumarate |
blood | F | F | 1.0 | mmol | ||||
Species | pydxn_e | Pyridoxine |
blood | F | F | 1.0 | mmol | ||||
Species | M_4pyrdx_e | 4pyrdx c |
blood | F | F | 1.0 | mmol | ||||
Species | normete__L_e | Normete L c |
blood | F | F | 1.0 | mmol | ||||
Species | bilglcur_e | Bilglcur c |
blood | F | F | 1.0 | mmol | ||||
Species | glyc_e | Glycerol |
blood | F | F | 1.0 | mmol | ||||
Species | h2o_e | H2O |
blood | F | F | 1.0 | mmol | ||||
Species | h_e | H+ |
blood | F | F | 1.0 | mmol | ||||
Species | lac__L_e | L-Lactate |
blood | F | F | 1.0 | mmol | ||||
Species | sprm_e | Spermine C10H30N4 |
blood | F | F | 1.0 | mmol | ||||
Species | M_3moxtyr_e | 3moxtyr c |
blood | F | F | 1.0 | mmol | ||||
Species | nrpphr_e | Nrpphr c |
blood | F | F | 1.0 | mmol | ||||
Species | acnam_e | N-Acetylneuraminate |
blood | F | F | 1.0 | mmol | ||||
Species | thmmp_e | Thiamin monophosphate |
blood | F | F | 1.0 | mmol | ||||
Species | co2_e | CO2 |
blood | F | F | 1.0 | mmol | ||||
Species | lac__D_e | D-Lactate |
blood | F | F | 1.0 | mmol | ||||
Species | mal__L_e | L-Malate |
blood | F | F | 1.0 | mmol | ||||
Species | ocdcea_e | Octadecenoate (n-C18:1) |
blood | F | F | 1.0 | mmol | ||||
Species | k_e | Potassium |
blood | F | F | 1.0 | mmol | ||||
Species | na1_e | Sodium |
blood | F | F | 1.0 | mmol | ||||
Species | dhdascb_e | Dhdascb c |
blood | F | F | 1.0 | mmol | ||||
Species | cl_e | Chloride |
blood | F | F | 1.0 | mmol | ||||
Species | arg__L_e | L-Arginine |
blood | F | F | 1.0 | mmol | ||||
Species | nh4_e | Ammonium |
blood | F | F | 1.0 | mmol | ||||
Species | adrnl_e | Adrnl c |
blood | F | F | 1.0 | mmol | ||||
Species | ala__L_e | L-Alanine |
blood | F | F | 1.0 | mmol | ||||
Species | ptrc_e | Putrescine |
blood | F | F | 1.0 | mmol | ||||
Species | gal_e | D-Galactose |
blood | F | F | 1.0 | mmol | ||||
Species | ascb__L_e | L-Ascorbate |
blood | F | F | 1.0 | mmol | ||||
Species | h2o2_e | Hydrogen peroxide |
blood | F | F | 1.0 | mmol | ||||
Species | mepi_e | Mepi c |
blood | F | F | 1.0 | mmol | ||||
Species | acald_e | Acetaldehyde |
blood | F | F | 1.0 | mmol | ||||
Species | leuktrB4_e | LeuktrB4 c |
blood | F | F | 1.0 | mmol | ||||
Species | adn_e | Adenosine |
blood | F | F | 1.0 | mmol | ||||
Species | pi_e | Phosphate |
blood | F | F | 1.0 | mmol | ||||
Species | orot_e | Orotate |
blood | F | F | 1.0 | mmol | ||||
Species | M_5aop_e | 5-Amino-4-oxopentanoate |
blood | F | F | 1.0 | mmol | ||||
Species | phe__L_e | L-Phenylalanine |
blood | F | F | 1.0 | mmol | ||||
Species | etha_e | Ethanolamine |
blood | F | F | 1.0 | mmol | ||||
Species | co_e | Carbon monoxide |
blood | F | F | 1.0 | mmol | ||||
Species | dopa_e | Dopamine |
blood | F | F | 1.0 | mmol | ||||
Species | man_e | D-Mannose |
blood | F | F | 1.0 | mmol | ||||
Species | gam_e | D-Glucosamine |
blood | F | F | 1.0 | mmol | ||||
Species | pydx_e | Pyridoxal |
blood | F | F | 1.0 | mmol | ||||
Species | ac_e | Acetate |
blood | F | F | 1.0 | mmol | ||||
Species | hxan_e | Hypoxanthine |
blood | F | F | 1.0 | mmol | ||||
Species | glc__D_e | D-Glucose |
blood | F | F | 1.0 | mmol | ||||
Species | uri_e | Uridine |
blood | F | F | 1.0 | mmol | ||||
Species | ade_e | Adenine |
blood | F | F | 1.0 | mmol | ||||
Species | camp_e | CAMP |
blood | F | F | 1.0 | mmol | ||||
Species | hcys__L_e | L-Homocysteine |
blood | F | F | 1.0 | mmol | ||||
Species | o2_e | O2 |
blood | F | F | 1.0 | mmol | ||||
Species | hdca_e | Hexadecanoate (n-C16:0) |
blood | F | F | 1.0 | mmol | ||||
Species | pydam_e | Pyridoxamine |
blood | F | F | 1.0 | mmol | ||||
Species | M_35cgmp_e | 3',5'-Cyclic GMP |
blood | F | F | 1.0 | mmol | ||||
Species | met__L_e | L-Methionine |
blood | F | F | 1.0 | mmol | ||||
Species | gly_e | Glycine |
blood | F | F | 1.0 | mmol | ||||
Species | cys__L_e | L-Cysteine |
blood | F | F | 1.0 | mmol | ||||
Species | chol_e | Choline |
blood | F | F | 1.0 | mmol | ||||
Species | ca2_e | Calcium |
blood | F | F | 1.0 | mmol | ||||
Species | gluala_e | 5 L Glutamyl L alanine C8H13N2O5 |
blood | F | F | 1.0 | mmol | ||||
Species | ribflv_e | Riboflavin |
blood | F | F | 1.0 | mmol | ||||
Species | fru_e | D-Fructose |
blood | F | F | 1.0 | mmol | ||||
Species | spmd_e | Spermidine |
blood | F | F | 1.0 | mmol | ||||
Species | fe2_e | Fe2+ |
blood | F | F | 1.0 | mmol | ||||
Species | leuktrA4_e | LeuktrA4 c |
blood | F | F | 1.0 | mmol | ||||
Species | pyr_e | Pyruvate |
blood | F | F | 1.0 | mmol | ||||
Species | gthox_e | Oxidized glutathione |
blood | F | F | 1.0 | mmol |
type | Parameters [76] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | EX_ins_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gln__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_lnlc_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_thm_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ncam_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_nac_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_urea_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_hco3_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_fum_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_pydxn_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_M_4pyrdx_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_normete__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_bilglcur_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_glyc_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_h2o_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_h_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_lac__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_sprm_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_M_3moxtyr_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_nrpphr_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_acnam_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_thmmp_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_co2_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_lac__D_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_mal__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ocdcea_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_k_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_na1_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_dhdascb_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_cl_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_arg__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_nh4_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_adrnl_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ala__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ptrc_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gal_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ascb__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_h2o2_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_mepi_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_acald_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_leuktrB4_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_adn_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_pi_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_orot_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_M_5aop_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_phe__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_etha_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_co_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_dopa_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_man_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gam_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_pydx_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ac_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_hxan_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_glc__D_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_uri_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ade_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_camp_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_hcys__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_o2_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_hdca_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_pydam_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_M_35cgmp_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_met__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gly_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_cys__L_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_chol_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ca2_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gluala_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_ribflv_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_fru_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_spmd_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_fe2_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_leuktrA4_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_pyr_e | 1.0 | mmol_per_h | T | ||||
Parameter | EX_gthox_e | 1.0 | mmol_per_h | T |
type | Reactions [76] | name | equation | modifiers | formula | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | update_ins_e | ⇆ | ins_e ⇆ | ||||||
Reaction | update_gln__L_e | ⇆ | gln__L_e ⇆ | ||||||
Reaction | update_lnlc_e | ⇆ | lnlc_e ⇆ | ||||||
Reaction | update_thm_e | ⇆ | thm_e ⇆ | ||||||
Reaction | update_ncam_e | ⇆ | ncam_e ⇆ | ||||||
Reaction | update_nac_e | ⇆ | nac_e ⇆ | ||||||
Reaction | update_urea_e | ⇆ | urea_e ⇆ | ||||||
Reaction | update_hco3_e | ⇆ | hco3_e ⇆ | ||||||
Reaction | update_fum_e | ⇆ | fum_e ⇆ | ||||||
Reaction | update_pydxn_e | ⇆ | pydxn_e ⇆ | ||||||
Reaction | update_M_4pyrdx_e | ⇆ | M_4pyrdx_e ⇆ | ||||||
Reaction | update_normete__L_e | ⇆ | normete__L_e ⇆ | ||||||
Reaction | update_bilglcur_e | ⇆ | bilglcur_e ⇆ | ||||||
Reaction | update_glyc_e | ⇆ | glyc_e ⇆ | ||||||
Reaction | update_h2o_e | ⇆ | h2o_e ⇆ | ||||||
Reaction | update_h_e | ⇆ | h_e ⇆ | ||||||
Reaction | update_lac__L_e | ⇆ | lac__L_e ⇆ | ||||||
Reaction | update_sprm_e | ⇆ | sprm_e ⇆ | ||||||
Reaction | update_M_3moxtyr_e | ⇆ | M_3moxtyr_e ⇆ | ||||||
Reaction | update_nrpphr_e | ⇆ | nrpphr_e ⇆ | ||||||
Reaction | update_acnam_e | ⇆ | acnam_e ⇆ | ||||||
Reaction | update_thmmp_e | ⇆ | thmmp_e ⇆ | ||||||
Reaction | update_co2_e | ⇆ | co2_e ⇆ | ||||||
Reaction | update_lac__D_e | ⇆ | lac__D_e ⇆ | ||||||
Reaction | update_mal__L_e | ⇆ | mal__L_e ⇆ | ||||||
Reaction | update_ocdcea_e | ⇆ | ocdcea_e ⇆ | ||||||
Reaction | update_k_e | ⇆ | k_e ⇆ | ||||||
Reaction | update_na1_e | ⇆ | na1_e ⇆ | ||||||
Reaction | update_dhdascb_e | ⇆ | dhdascb_e ⇆ | ||||||
Reaction | update_cl_e | ⇆ | cl_e ⇆ | ||||||
Reaction | update_arg__L_e | ⇆ | arg__L_e ⇆ | ||||||
Reaction | update_nh4_e | ⇆ | nh4_e ⇆ | ||||||
Reaction | update_adrnl_e | ⇆ | adrnl_e ⇆ | ||||||
Reaction | update_ala__L_e | ⇆ | ala__L_e ⇆ | ||||||
Reaction | update_ptrc_e | ⇆ | ptrc_e ⇆ | ||||||
Reaction | update_gal_e | ⇆ | gal_e ⇆ | ||||||
Reaction | update_ascb__L_e | ⇆ | ascb__L_e ⇆ | ||||||
Reaction | update_h2o2_e | ⇆ | h2o2_e ⇆ | ||||||
Reaction | update_mepi_e | ⇆ | mepi_e ⇆ | ||||||
Reaction | update_acald_e | ⇆ | acald_e ⇆ | ||||||
Reaction | update_leuktrB4_e | ⇆ | leuktrB4_e ⇆ | ||||||
Reaction | update_adn_e | ⇆ | adn_e ⇆ | ||||||
Reaction | update_pi_e | ⇆ | pi_e ⇆ | ||||||
Reaction | update_orot_e | ⇆ | orot_e ⇆ | ||||||
Reaction | update_M_5aop_e | ⇆ | M_5aop_e ⇆ | ||||||
Reaction | update_phe__L_e | ⇆ | phe__L_e ⇆ | ||||||
Reaction | update_etha_e | ⇆ | etha_e ⇆ | ||||||
Reaction | update_co_e | ⇆ | co_e ⇆ | ||||||
Reaction | update_dopa_e | ⇆ | dopa_e ⇆ | ||||||
Reaction | update_man_e | ⇆ | man_e ⇆ | ||||||
Reaction | update_gam_e | ⇆ | gam_e ⇆ | ||||||
Reaction | update_pydx_e | ⇆ | pydx_e ⇆ | ||||||
Reaction | update_ac_e | ⇆ | ac_e ⇆ | ||||||
Reaction | update_hxan_e | ⇆ | hxan_e ⇆ | ||||||
Reaction | update_glc__D_e | ⇆ | glc__D_e ⇆ | ||||||
Reaction | update_uri_e | ⇆ | uri_e ⇆ | ||||||
Reaction | update_ade_e | ⇆ | ade_e ⇆ | ||||||
Reaction | update_camp_e | ⇆ | camp_e ⇆ | ||||||
Reaction | update_hcys__L_e | ⇆ | hcys__L_e ⇆ | ||||||
Reaction | update_o2_e | ⇆ | o2_e ⇆ | ||||||
Reaction | update_hdca_e | ⇆ | hdca_e ⇆ | ||||||
Reaction | update_pydam_e | ⇆ | pydam_e ⇆ | ||||||
Reaction | update_M_35cgmp_e | ⇆ | M_35cgmp_e ⇆ | ||||||
Reaction | update_met__L_e | ⇆ | met__L_e ⇆ | ||||||
Reaction | update_gly_e | ⇆ | gly_e ⇆ | ||||||
Reaction | update_cys__L_e | ⇆ | cys__L_e ⇆ | ||||||
Reaction | update_chol_e | ⇆ | chol_e ⇆ | ||||||
Reaction | update_ca2_e | ⇆ | ca2_e ⇆ | ||||||
Reaction | update_gluala_e | ⇆ | gluala_e ⇆ | ||||||
Reaction | update_ribflv_e | ⇆ | ribflv_e ⇆ | ||||||
Reaction | update_fru_e | ⇆ | fru_e ⇆ | ||||||
Reaction | update_spmd_e | ⇆ | spmd_e ⇆ | ||||||
Reaction | update_fe2_e | ⇆ | fe2_e ⇆ | ||||||
Reaction | update_leuktrA4_e | ⇆ | leuktrA4_e ⇆ | ||||||
Reaction | update_pyr_e | ⇆ | pyr_e ⇆ | ||||||
Reaction | update_gthox_e | ⇆ | gthox_e ⇆ |