title: BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
abstract: Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: King
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Lu
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen, Germany.
authors.forename: Andreas
authors.identifier: http://orcid.org/0000-0002-1240-5553
authors.initials: A
authors.lastname: Dräger
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Philip
authors.initials: P
authors.lastname: Miller
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Stephen
authors.initials: S
authors.lastname: Federowicz
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Joshua A
authors.identifier: http://orcid.org/0000-0003-0377-2674
authors.initials: JA
authors.lastname: Lerman
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
authors.forename: Ali
authors.initials: A
authors.lastname: Ebrahim
authors.affiliation: Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.affiliation: Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA 92093, USA nlewisres@ucsd.edu.
authors.forename: Nathan E
authors.initials: NE
authors.lastname: Lewis
mesh_terms: D062126:Databases, Chemical; D016678:Genome; D023281:Genomics / Q000592:standards; D051188:Knowledge Bases; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055432:Metabolomics; D008957:Models, Genetic