Evidence map›Paper›PMID 26989153›Full record

ArticleDatabase : the journal of biological databases and curation2016

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru and 16 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.

0numbers the graph read from it
0cells of the map it votes in
41citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

41 citing papers in PubMed.

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  19. Bioinformatics tools developed to support BioCompute Objects.Database : the journal of biological databases and curation · 2021
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

26 authors.

Vahan SimonyanCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA vahan.simonyan@fda.hhs.gov vahansim@gmail.com.
Konstantin ChumakovCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Hayley DingerdissenCenter 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.
William FaisonDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
Scott GoldweberCenter 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.
Anton GolikovCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Naila GulzarDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
Konstantinos KaragiannisCenter 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.
Phuc Vinh Nguyen LamCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Thomas MaudruCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Olesja MuravitskajaCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Ekaterina OsipovaCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Yang PanDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
Alexey PschenichnovCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Alexandre RostovtsevCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Luis Santana-QuinteroCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Krista SmithCenter 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.
Elaine E ThompsonCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Valery TkachenkoCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
John Torcivia-RodriguezCenter 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.
Alin VoskanianCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA vahan.simonyan@fda.hhs.gov vahansim@gmail.com.
Quan WanDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
Jing WangCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Tsung-Jung WuDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.
Carolyn WilsonCenter for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA.
Raja MazumderDepartment of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC 20037, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

User-Computer InterfaceComputational BiologyHigh-Throughput Nucleotide SequencingMutationPoliovirusPoliovirus VaccinesProteomicsRecombination, GeneticSequence AlignmentStatistics as TopicPoliovirus Vaccines

Identifiers

PMID26989153
PMCPMC4795927

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.