[HTML][HTML] The RAST Server: rapid annotations using subsystems technology
…, LK McNeil, D Paarmann, T Paczian, B Parrello… - BMC genomics, 2008 - Springer
Background The number of prokaryotic genome sequences becoming available is growing
steadily and is growing faster than our ability to accurately annotate them. Description We …
steadily and is growing faster than our ability to accurately annotate them. Description We …
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
…, T Disz, RA Edwards, S Gerdes, B Parrello… - Nucleic acids …, 2014 - academic.oup.com
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 …
accurate genome annotations across thousands of genomes and as a platform for discovering …
[HTML][HTML] RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
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 …
2008 to annotate bacterial and archaeal genomes. It works by offering a standard software …
[HTML][HTML] KBase: the United States department of energy systems biology knowledgebase
Although similar integrative tools exist (Supplementary Note 2), no other open platform
shares all KBase’s features, which include the following:(i) comprehensive support for data …
shares all KBase’s features, which include the following:(i) comprehensive support for data …
Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR
…, JC Overbeek, B Parrello, V Parrello… - Nucleic acids …, 2023 - academic.oup.com
The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics
Resource Center (BRC) program to assist researchers with analyzing the growing body …
Resource Center (BRC) program to assist researchers with analyzing the growing body …
Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center
…, R Olson, R Overbeek, B Parrello… - Nucleic acids …, 2017 - academic.oup.com
… b Genomes where phenotypes have been determined as being susceptible, intermediate
or resistant (SIR) to a given antibiotic. In these cases, the determination was made by the …
or resistant (SIR) to a given antibiotic. In these cases, the determination was made by the …
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
…, JC Overbeek, R Overbeek, B Parrello… - Nucleic acids …, 2020 - academic.oup.com
… (A) The website interface allows the selection of genomes; (B) visualization of the aligned
genomic regions with any deletions, insertions or rearrangements; (C) zooming in on the …
genomic regions with any deletions, insertions or rearrangements; (C) zooming in on the …
Job-shop scheduling using automated reasoning: A case study of the car-sequencing problem
BD Parrello, WC Kabat, L Wos - Journal of Automated reasoning, 1986 - Springer
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 …
this paper concerns an assembly line designed to produce various cars, each of which …
[HTML][HTML] SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
The remarkable advance in sequencing technology and the rising interest in medical and
environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of …
environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of …
PATRIC as a unique resource for studying antimicrobial resistance
…, R Olson, R Overbeek, B Parrello… - Briefings in …, 2019 - academic.oup.com
The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org ) is designed
to provide researchers with the tools and services that they need to perform genomic and …
to provide researchers with the tools and services that they need to perform genomic and …