Bruce D. Parrello

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The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are(More)
In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many(More)
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to(More)
The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our(More)
The ‘job-shop scheduling problem’ is known to be NP-complete. The version of interest in this paper concerns an assembly line designed to produce various cars, each of which requires a (possibly different) set of options. The combinatorics of the problem preclude seeking a maximal solution. Nevertheless, because of the underlying economic considerations, an(More)
The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence(More)
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows(More)
Understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. An important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. These gene sets, Atomic Regulons(More)
The design of IMS databases is a current topic of major industrial significance. Compared to many other database management systems, IMS offers a wide variety of physical implementation options. One effort to help users choose among these options was 161. Unfortunately, it dealt mainly with descriptions of the options and offered minimal guidance on how to(More)
General ledger systems, though not often discussed in the database literature. are fundamental to the operation of any business and illustrate many of the subtleties of database design. We present here an application of the entity-relationship model design methodology to general ledger systems. Introductions to the terminology of both entity-relationship(More)