Design of the MCAW compute service for food safety bioinformatics

S. B. Edlund, K. L. Beck, N. Haiminen, L. P. Parida, D. B. Storey, Bart C Weimer, J. H. Kaufman, D. D. Chambliss

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation and Analytics Workbench (MCAW), are presented and illustrated with reference to the analysis of metagenomics data. The service is designed to meet the requirements for analyzing metagenomic and metatranscriptomic sequence data to assess microbial hazards and food authentication in the supply chain. Moreover, MCAW provides for reliable storage and management of raw genomic sequences and analysis results, high-volume informatics processing, meticulous tracking of data provenance and processing steps, and function-rich visualization of results.

Original languageEnglish (US)
Article number7580716
JournalIBM Journal of Research and Development
Volume60
Issue number5-6
DOIs
StatePublished - Sep 1 2016

Fingerprint

Food safety
Bioinformatics
Public health
Ecology
Processing
Authentication
Supply chains
Hazards
Visualization
Genes

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Edlund, S. B., Beck, K. L., Haiminen, N., Parida, L. P., Storey, D. B., Weimer, B. C., ... Chambliss, D. D. (2016). Design of the MCAW compute service for food safety bioinformatics. IBM Journal of Research and Development, 60(5-6), [7580716]. https://doi.org/10.1147/JRD.2016.2584798

Design of the MCAW compute service for food safety bioinformatics. / Edlund, S. B.; Beck, K. L.; Haiminen, N.; Parida, L. P.; Storey, D. B.; Weimer, Bart C; Kaufman, J. H.; Chambliss, D. D.

In: IBM Journal of Research and Development, Vol. 60, No. 5-6, 7580716, 01.09.2016.

Research output: Contribution to journalArticle

Edlund, SB, Beck, KL, Haiminen, N, Parida, LP, Storey, DB, Weimer, BC, Kaufman, JH & Chambliss, DD 2016, 'Design of the MCAW compute service for food safety bioinformatics', IBM Journal of Research and Development, vol. 60, no. 5-6, 7580716. https://doi.org/10.1147/JRD.2016.2584798
Edlund, S. B. ; Beck, K. L. ; Haiminen, N. ; Parida, L. P. ; Storey, D. B. ; Weimer, Bart C ; Kaufman, J. H. ; Chambliss, D. D. / Design of the MCAW compute service for food safety bioinformatics. In: IBM Journal of Research and Development. 2016 ; Vol. 60, No. 5-6.
@article{5c93d1cd2f8142c8a8559778e1bc6d07,
title = "Design of the MCAW compute service for food safety bioinformatics",
abstract = "The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation and Analytics Workbench (MCAW), are presented and illustrated with reference to the analysis of metagenomics data. The service is designed to meet the requirements for analyzing metagenomic and metatranscriptomic sequence data to assess microbial hazards and food authentication in the supply chain. Moreover, MCAW provides for reliable storage and management of raw genomic sequences and analysis results, high-volume informatics processing, meticulous tracking of data provenance and processing steps, and function-rich visualization of results.",
author = "Edlund, {S. B.} and Beck, {K. L.} and N. Haiminen and Parida, {L. P.} and Storey, {D. B.} and Weimer, {Bart C} and Kaufman, {J. H.} and Chambliss, {D. D.}",
year = "2016",
month = "9",
day = "1",
doi = "10.1147/JRD.2016.2584798",
language = "English (US)",
volume = "60",
journal = "IBM Journal of Research and Development",
issn = "0018-8646",
publisher = "IBM Corporation",
number = "5-6",

}

TY - JOUR

T1 - Design of the MCAW compute service for food safety bioinformatics

AU - Edlund, S. B.

AU - Beck, K. L.

AU - Haiminen, N.

AU - Parida, L. P.

AU - Storey, D. B.

AU - Weimer, Bart C

AU - Kaufman, J. H.

AU - Chambliss, D. D.

PY - 2016/9/1

Y1 - 2016/9/1

N2 - The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation and Analytics Workbench (MCAW), are presented and illustrated with reference to the analysis of metagenomics data. The service is designed to meet the requirements for analyzing metagenomic and metatranscriptomic sequence data to assess microbial hazards and food authentication in the supply chain. Moreover, MCAW provides for reliable storage and management of raw genomic sequences and analysis results, high-volume informatics processing, meticulous tracking of data provenance and processing steps, and function-rich visualization of results.

AB - The techniques of microbe community genome sequencing as applied to environmental samples - metagenomics - offer powerful insight into microbial community structure and ecology that can affect food safety decisions for public health security. In this paper, the design and characteristics of a new informatics service, the Metagenomics Computation and Analytics Workbench (MCAW), are presented and illustrated with reference to the analysis of metagenomics data. The service is designed to meet the requirements for analyzing metagenomic and metatranscriptomic sequence data to assess microbial hazards and food authentication in the supply chain. Moreover, MCAW provides for reliable storage and management of raw genomic sequences and analysis results, high-volume informatics processing, meticulous tracking of data provenance and processing steps, and function-rich visualization of results.

UR - http://www.scopus.com/inward/record.url?scp=84994493211&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84994493211&partnerID=8YFLogxK

U2 - 10.1147/JRD.2016.2584798

DO - 10.1147/JRD.2016.2584798

M3 - Article

AN - SCOPUS:84994493211

VL - 60

JO - IBM Journal of Research and Development

JF - IBM Journal of Research and Development

SN - 0018-8646

IS - 5-6

M1 - 7580716

ER -