title: High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.
abstract: The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure.The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu.
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA vahan.simonyan@fda.hhs.gov vahansim@gmail.com.
authors.forename: Vahan
authors.initials: V
authors.lastname: Simonyan
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Konstantin
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authors.lastname: Chumakov
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Hayley
authors.initials: H
authors.lastname: Dingerdissen
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: William
authors.initials: W
authors.lastname: Faison
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Goldweber
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Anton
authors.initials: A
authors.lastname: Golikov
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Naila
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authors.lastname: Gulzar
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Karagiannis
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Phuc
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authors.lastname: Vinh Nguyen Lam
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
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authors.lastname: Maudru
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Olesja
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authors.lastname: Muravitskaja
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Osipova
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
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authors.lastname: Pschenichnov
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Alexandre
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authors.lastname: Rostovtsev
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Luis
authors.initials: L
authors.lastname: Santana-Quintero
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Krista
authors.initials: K
authors.lastname: Smith
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Elaine E
authors.initials: EE
authors.lastname: Thompson
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Valery
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authors.lastname: Tkachenko
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: John
authors.initials: J
authors.lastname: Torcivia-Rodriguez
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA vahan.simonyan@fda.hhs.gov vahansim@gmail.com.
authors.forename: Alin
authors.initials: A
authors.lastname: Voskanian
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Quan
authors.initials: Q
authors.lastname: Wan
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Tsung-Jung
authors.initials: TJ
authors.lastname: Wu
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
authors.forename: Carolyn
authors.initials: C
authors.lastname: Wilson
authors.affiliation: Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
authors.forename: Raja
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authors.lastname: Mazumder
mesh_terms: D019295:Computational Biology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009154:Mutation / Q000235:genetics; D017955:Poliovirus / Q000235:genetics; D023321:Poliovirus Vaccines / Q000276:immunology; D040901:Proteomics; D011995:Recombination, Genetic; D016415:Sequence Alignment; D013223:Statistics as Topic; D014584:User-Computer Interface
chemical_list: D023321:Poliovirus Vaccines