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Nucleic Acids Res. 2020 Jan 8;48(D1):D402-D406. doi: 10.1093/nar/gkz1054.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Author information

1
Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
2
Institute for Systems Biology, Seattle, WA 98109, USA.
3
Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Biomedical Informatics (IBMI), University of Tübingen, 72076 Tübingen, Germany.
4
Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.
5
German Center for Infection Research (DZIF), 72076 Tübingen, Germany.
6
Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
7
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark.

Abstract

The BiGG Models knowledge base (http://bigg.ucsd.edu) is a centralized repository for high-quality genome-scale metabolic models. For the past 12 years, the website has allowed users to browse and search metabolic models. Within this update, we detail new content and features in the repository, continuing the original effort to connect each model to genome annotations and external databases as well as standardization of reactions and metabolites. We describe the addition of 31 new models that expand the portion of the phylogenetic tree covered by BiGG Models. We also describe new functionality for hosting multi-strain models, which have proven to be insightful in a variety of studies centered on comparisons of related strains. Finally, the models in the knowledge base have been benchmarked using Memote, a new community-developed validator for genome-scale models to demonstrate the improving quality and transparency of model content in BiGG Models.

PMID:
31696234
DOI:
10.1093/nar/gkz1054

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