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

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

Authors: Thomas R. Connor^1,† , Nicholas J. Loman^2,† , Simon Thompson^3,† , Andy Smith² , Joel Southgate¹ , Radoslaw Poplawski^2,3 , Matthew J. Bull¹ , Emily Richardson² , Matthew Ismail⁴ , Simon Elwood- Thompson⁵ , Christine Kitchen⁶ , Martyn Guest⁶ , Marius Bakke⁷ , Samuel K. Sheppard^8,† , Mark J. Pallen^7,†
- VIEW AFFILIATIONS
- ¹ 1Cardiff University School of Biosciences, The Sir Martin Evans Building, Cardiff University, Cardiff CF10 2AX, UK ² 2Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK ³ 3IT Services (Research Computing), University of Birmingham, Birmingham B15 2TT, UK ⁴ 4Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK ⁵ 5College of Medicine, Swansea University, Swansea, UK ⁶ 6Advanced Research [email protected] (ARCCA), Cardiff University, UK ⁷ 7Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, UK ⁸ 8The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
Correspondence Thomas R. Connor ([email protected])
First Published Online: 01 September 2016, Microbial Genomics , 2016 2, doi: 10.1099/mgen.0.000086
Subject: Short Paper - Systems Microbiology - Pangenome analysis

Received: 26/07/2016
Accepted: 21/08/2016
Cover date: 20/09/2016

This is an open access article published by the Microbiology Society under the Creative Commons Attribution License

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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.

†
These authors contributed equally to this work.
All supporting data, code and protocols have been provided within the article or through

supplementary data files.

Keyword(s): bioinformatics, population genomics, infrastructure, virtual laboratory, metagenomics, cloud computing

Abbreviation:

HPC high-performance computing

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Abbreviation:

HPC	high-performance computing