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bioRxiv · 10.1101/064451

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

Thomas Richard Connor·Nicholas James 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·Sam 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.\n\nDATA SUMMARYThe paper describes a new, freely available public resource and therefore no data has been generated. The resource can be accessed at http://www.climb.ac.uk. Source code for software developed for the project can be found at http://github.com/MRC-CLIMB/\n\nI/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.\n\nIMPACT STATEMENTTechnological advances mean that genome sequencing is now relatively simple, quick, and affordable. However, handling large genome datasets remains a significant challenge for many microbiologists, with substantial requirements for computational resources and expertise in data storage and analysis. This has led to fragmentary approaches to software development and data sharing that reduce the reproducibility of research and limits opportunities for bioinformatics training. Here, we describe a nationwide electronic infrastructure that has been designed to support the UK microbiology community, providing simple mechanisms for accessing large, shared, computational resources designed to meet the bioinformatic needs of microbiologists.

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Thomas Richard Connor, Nicholas James 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, Sam K Sheppard, Mark J Pallen. 2016-07-19. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. https://doi.org/10.1101/064451

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