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BiGG Models specifications


Unique identifier OMICS_02533
Name BiGG Models
Restrictions to use Academic or non-commercial use
Database management system PostgreSQL
Community driven No
Data access File download, Browse, Application programming interface
User data submission Allowed
Version 1.5
Maintained Yes


  • person_outline than E. Lewis

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Publications for BiGG Models

BiGG Models citations


Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

Biotechnol Biofuels
PMCID: 5879999
PMID: 29619083
DOI: 10.1186/s13068-018-1078-z

[…] ST set of reactions that must be directly engineered to improve octanoate yield. See Additional file : Text S1 for expanded execution guidelines. The SBML file for iAF1260 model was obtained from the BIGG models repository ( In addition, GAMS compatible files for the iAF1260 model and the OptForce code in GAMS for current simulation have been included in Additi […]


In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host

Front Microbiol
PMCID: 5727896
PMID: 29276507
DOI: 10.3389/fmicb.2017.02440
call_split See protocol

[…] iated with the close neighborhood of mouse cells (the “extracellular” compartment) were moved from “e” to “em.” All metabolite IDs were updated in line with their current corresponding entries in the BiGG Models database ().A new compartment named “OMV” with ID “o” was added to the integrated model. When analysis was done in a specific medium, the reactions corresponding to metabolites that were n […]


Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

PLoS One
PMCID: 5562313
PMID: 28820904
DOI: 10.1371/journal.pone.0182570
call_split See protocol

[…] ally, some strains produce acetate during aerobic glucose growth, while others do not. Models for the E. coli strains (iJO1366, iB21_1397, iEcolC_1368, iWFL_1372 and iY75_1357) were obtained from the BiGG Models database version 1.3 []. All FBA simulations were performed using COBRApy []. For all simulations, the core E. coli biomass reaction [] was used as the primary objective reaction.When used […]


Computational metabolic engineering strategies for growth coupled biofuel production by Synechocystis

Metab Eng Com
PMCID: 5779732
PMID: 29468126
DOI: 10.1016/j.meteno.2016.07.003

[…] he Synechocystis sp. PCC 6803 model iJN678 () was used to perform flux balance analysis using the COBRA toolbox 2.0 () on MATLAB (Mathworks Inc., Natick, MA). The model iJN678 was downloaded from the BiGG Models database ( The reconstruction iJN678 incorporates 678 genes, 863 reactions and 795 metabolites. Several additions were made in accordance with recent literature: the […]


The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection

Nucleic Acids Res
PMCID: 4702933
PMID: 26740669
DOI: 10.1093/nar/gkv1356

[…] ludes updated resources on metabolic pathways, such as KEGG, MetaCyc, Reactome, WikiPathways and the Escherichia coli metabolism database (ECMDB), and databases of metabolic network modeling, such as BiGG Models and MNXref/MetaNetX. A new arrival here is the Metabolomics Workbench (), which strives to be a one-stop repository for all kinds of metabolomics data, including metabolite standards, prot […]

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BiGG Models institution(s)
Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
BiGG Models funding source(s)
Supported by the National Science Foundation Graduate Research Fellowship [DGE-1144086]; the Department of Energy [DE-SC0008701 and DE-SC0004917]; the European Commission as part of a Marie Curie International Outgoing Fellowship within the EU 7th Framework Program for Research and Technological Development [EU project AMBiCon, 332020]; the National Institutes of Health [R21 HD080682]; and the Novo Nordisk Foundation [NNF 132150- 002].

BiGG Models review

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Marouen Ben Guebila's avatar image No country

Marouen Ben Guebila

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A must in genome scale metabolic networks.