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The application of Hadoop in Structural Bioinformatics

View ORCID ProfileJamie Alnasir, View ORCID ProfileHugh P. Shanahan
doi: https://doi.org/10.1101/376467
Jamie Alnasir
1Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
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Hugh P. Shanahan
2Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, United Kingdom
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Abstract

The paper reviews the use of the Hadoop platform in Structural Bioinformatics applications. Specifically, we review a number of implementations using Hadoop of high-throughput analyses, e.g. ligand-protein docking and structural alignment, and their scalability in comparison with other batch schedulers and MPI. We find that these deployments for the most part use known executables called from MapReduce rather than rewriting the algorithms. The scalability exhibits a variable behaviour in comparison with other batch schedulers, particularly as direct comparisons on the same platform are generally not available. We do note there is some evidence that MPI implementations scale better than Hadoop. A significant barrier to the use of the Hadoop ecosystem is the difficulty of the interface and configuration of a resource to use Hadoop. This will improve over time as interfaces to Hadoop e.g. Spark improve, usage of cloud platforms (e.g. Azure and AWS) increases and approaches such as the Workflow Definition Language are taken up.

Footnotes

  • jamie.alnasir{at}icr.ac.uk, hugh.shanahan{at}rhul.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 25, 2018.
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The application of Hadoop in Structural Bioinformatics
Jamie Alnasir, Hugh P. Shanahan
bioRxiv 376467; doi: https://doi.org/10.1101/376467
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The application of Hadoop in Structural Bioinformatics
Jamie Alnasir, Hugh P. Shanahan
bioRxiv 376467; doi: https://doi.org/10.1101/376467

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