title: Ten years of maintaining and expanding a microbial genome and metagenome analysis system.
abstract: Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure.
authors.affiliation: Biosciences Computing, Computing Research Division, Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA. Electronic address: vmmarkowitz@lbl.gov.
authors.forename: Victor M
authors.initials: VM
authors.lastname: Markowitz
authors.affiliation: Biosciences Computing, Computing Research Division, Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: I-Min A
authors.initials: IA
authors.lastname: Chen
authors.affiliation: Biosciences Computing, Computing Research Division, Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA 94720, USA.
authors.forename: Ken
authors.initials: K
authors.lastname: Chu
authors.affiliation: Microbial Genome & Metagenome Program, DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Microbial Genome & Metagenome Program, DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Microbial Genome & Metagenome Program, DOE Joint Genome Institute, Walnut Creek, California, CA 94598, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D019295:Computational Biology; D003628:Database Management Systems; D030541:Databases, Genetic; D064349:Genome, Microbial / Q000235:genetics*; D023281:Genomics / Q000379:methods; D054892:Metagenome / Q000235:genetics*; D008958:Models, Molecular; D012984:Software; D013223:Statistics as Topic
keywords: comparative genome analysis; metagenomics; microbial genomics