CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

Thomas R Connor; Nicholas J Loman; Simon Thompson; Andy Smith; Joel Southgate; Radoslaw Poplawski; Matthew J Bull; Emily Richardson; Matthew Ismail; Simon Elwood- Thompson; Christine Kitchen; Martyn Guest; Marius Bakke; Samuel K Sheppard; Mark J Pallen

doi:10.1099/mgen.0.000086

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

Thomas R Connor, Nicholas J Loman, Simon Thompson, Andy Smith, Joel Southgate, Radoslaw Poplawski, Matthew J Bull, Emily Richardson, Matthew Ismail, Simon Elwood- Thompson, Christine Kitchen, Martyn Guest, Marius Bakke, Samuel K Sheppard, Mark J Pallen

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Abstract

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

Original language	English
Pages (from-to)	e000086
Journal	Microbial Genomics
Volume	2
Issue number	9
DOIs	https://doi.org/10.1099/mgen.0.000086
Publication status	Published - 1 Sept 2016

Keywords

bioinformatics
population genomics
infrastructure
virtual laboratory
metagenomics
cloud computing

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10.1099/mgen.0.000086Licence: Creative Commons: Attribution-NonCommercial (CC BY-NC)

Connor_CLIMB_the_cloud_infastructure_Microbial_Genomics_2016
First Published Online: 01 September 2016, Microbial Genomics , 2016 2, doi: 10.1099/mgen.0.000086
Final published version, 3.22 MBLicence: Creative Commons: Attribution (CC BY)

http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000086#tab1Licence: Creative Commons: Attribution-NonCommercial (CC BY-NC)

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Connor, T. R., Loman, N. J., Thompson, S., Smith, A., Southgate, J., Poplawski, R., Bull, M. J., Richardson, E., Ismail, M., Thompson, S. E., Kitchen, C., Guest, M., Bakke, M., Sheppard, S. K., & Pallen, M. J. (2016). CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics, 2(9), e000086. https://doi.org/10.1099/mgen.0.000086

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abstract = "The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.",

keywords = "bioinformatics, population genomics, infrastructure, virtual laboratory, metagenomics, cloud computing",

author = "Connor, {Thomas R} and Loman, {Nicholas J} and Simon Thompson and Andy Smith and Joel Southgate and Radoslaw Poplawski and Bull, {Matthew J} and Emily Richardson and Matthew Ismail and Thompson, {Simon Elwood-} and Christine Kitchen and Martyn Guest and Marius Bakke and Sheppard, {Samuel K} and Pallen, {Mark J}",

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month = sep,

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doi = "10.1099/mgen.0.000086",

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Connor, TR, Loman, NJ, Thompson, S, Smith, A, Southgate, J, Poplawski, R, Bull, MJ, Richardson, E, Ismail, M, Thompson, SE, Kitchen, C, Guest, M, Bakke, M, Sheppard, SK & Pallen, MJ 2016, 'CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community', Microbial Genomics, vol. 2, no. 9, pp. e000086. https://doi.org/10.1099/mgen.0.000086

TY - JOUR

T1 - CLIMB (the Cloud Infrastructure for Microbial Bioinformatics)

T2 - an online resource for the medical microbiology community

AU - Connor, Thomas R

AU - Loman, Nicholas J

AU - Thompson, Simon

AU - Smith, Andy

AU - Southgate, Joel

AU - Poplawski, Radoslaw

AU - Bull, Matthew J

AU - Richardson, Emily

AU - Ismail, Matthew

AU - Thompson, Simon Elwood-

AU - Kitchen, Christine

AU - Guest, Martyn

AU - Bakke, Marius

AU - Sheppard, Samuel K

AU - Pallen, Mark J

PY - 2016/9/1

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N2 - The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

AB - The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

KW - bioinformatics

KW - population genomics

KW - infrastructure

KW - virtual laboratory

KW - metagenomics

KW - cloud computing

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DO - 10.1099/mgen.0.000086

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VL - 2

SP - e000086

JO - Microbial Genomics

JF - Microbial Genomics

IS - 9

ER -

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

Abstract

Keywords

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