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Biological Data Management & Technology Center

IMGThe Biological Data Management and Technology Center (BDMTC) is part of the Computational Research Division (CRD) at DOE’s Lawrence Berkeley National Laboratory (LBNL). BDMTC’s mission is to address key data management challenges caused by the massive increase in the amount and range of biological data, the difficulty of quantifying the quality of data generated using inherently imprecise tools and techniques, and the high complexity of integrating data residing in diverse and sometimes poorly correlated repositories. BDMTC’s strategy involves using existing database technologies and analysis methods, adapted as needed to a specific application, in order to address immediate biological data management and bioinformatics requirements. Critical data management and analysis problems that cannot be resolved using existing technologies and methods are pursued as part of longer term R&D activities.

In partnership with scientists of the Microbial Genome and Metagenome Programs at the DOE Joint Genome Institute (JGI), BDMTC engineers and computer scientists have developed and maintained a suite of microbial genome and metagenome data management and analysis systems, called the Integrated Microbial Genomes (IMG) systems. These systems have a large community of scientific users worldwide, and have provided support for the completion of thousands of microbial genome and metagenome studies. BDMTC’s activities are mainly of a production nature, whereby the key challenges regard the regular content and software updates of the IMG systems while coping with a rapid increase in the number and size of new microbial genome and metagenome datasets.

Background

Biological data management, which addresses the problems of collection, storage, organization, management, retrieval, and integration of rapidly expanding, evolving, and heterogeneous biological data, is considered today one of the most critical areas of modern data intensive biology research.[1] The main focus of the past several years has been the development of … Read More »

Results

BDMTC is focused on maintaining and extending the Integrated Microbial Genomes (IMG) systems. The IMG systems enable scientists to study microbial genomes, single cell genomes, and microbial community metagenomes in the integrated context of an expanding universe of genome and metagenome datasets generated by sequencing centers worldwide. The IMG systems consist of a data warehouse, genome and metagenome annotation (data interpretation) pipelines, data integration utilities, and application… Read More »

Publications

Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Ivanova, N., and Kyrpides, N. “The Integrated Microbial Genomes (IMG) System, A Case Study in Biological Data Management”, Proc. of 31st Int. Conf. on Very Large Data Bases, August 2005. Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., et al. ”The Integrated Microbial Genomes (IMG) System”, Nucleic Acids Research 34, Special Database Issue, D344-D348, 2006. Markowitz, V.M., Ivanova, N., Korzeniewski, F.,… Read More »