BiGG Models is a knowledgebase of genome-scale metabolic network
BiGG Models integrates more than 70 published genome-scale metabolic
networks into a single database with a set of stardized identifiers called
BiGG IDs. Genes in the BiGG models are mapped to NCBI genome annotations,
and metabolites are linked to many external databases (KEGG, PubChem, and
many more). For details about updates to the BiGG Models website and
database, see the updates page and the
If you have questions or find any bugs in the database, please sumbit an
issue to our issue tracker
or contact Zachary King (zaking-AT-ucsd-DOT-edu).
How do I use BiGG Models?
BiGG can be browsed on this website or accessed using a web
API. Try searching for a metabolite, reaction, gene, or organism in the
search box to browse the content of genome-scale models. Question marks like
are available throughout the site to
provide more help. Further information is available in the
BiGG Models publication.
How do I add my model to BiGG?
We encourage contributions of models to BiGG. The following are the minimal
requirements for acceptance into the knowledge base:
A genome-scale metabolic network reconstruction that has been
published in a peer-reviewed journal
A COBRApy-compatible file (SBML, MAT, or JSON) representing all
model content, ideally included as a supplementary file to the
The accession ID for a NCBI RefSeq genome annotation. In some
cases we can accept genome annotations in Genbank format, but we
prefer annotations from a well-known genome repository.
Reactions, metabolites, and compartments using the BiGG Models
Gene identifiers that match locus tags from the genome annotation
Please note that loading models into BiGG is time-consuming, so we
cannot make any guarantee regarding the time it will take to load a model.
How do I cite BiGG Models?
When using the BiGG Models knowledgebase in your research, we kindly ask
that you cite the latest publication. Your citation of BiGG Models will help
us to apply for ongoing funding to maintain this resource.
Latest BiGG Models publication:
King ZA, Lu JS, Dräger A, Miller PC, Federowicz S, Lerman JA, Ebrahim A,
Palsson BO, and Lewis NE. BiGG Models: A platform for
integrating, standardizing, and sharing genome-scale models
(2016) Nucleic Acids Research 44(D1):D515-D522.
Permission to use, copy, modify and distribute any part of BiGG Models for
educational, research and non-profit purposes, without fee, and without a
written agreement is hereby granted, provided that the above copyright
notice, this paragraph and the following three paragraphs appear in all
Those desiring to incorporate BiGG Models into commercial products or use
for commercial purposes should contact the Technology Transfer &
Intellectual Property Services, University of California, San Diego, 9500
Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, Ph: (858) 534-5815,
FAX: (858) 534-7345, e-mail: firstname.lastname@example.org.
In no event shall the University of California be liable to any party for
direct, indirect, special, incidental, or consequential damages, including
lost profits, arising out of the use of this bigg database, even if the
University of California has been advised of the possibility of such damage.
The BiGG Models provided herein is on an "as is" basis, and the University
of California has no obligation to provide maintenance, support, updates,
enhancements, or modifications. The University of California makes no
representations and extends no warranties of any kind, either implied or
express, including, but not limited to, the implied warranties of
merchantability or fitness for a particular purpose, or that the use of the
BiGG Models will not infringe any patent, trademark or other rights.