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MapReduce in Computational Biology - A Synopsis

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Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry (WIVACE 2016)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 708))

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Abstract

In the past 20 years, the Life Sciences have witnessed a paradigm shift in the way research is performed. Indeed, the computational part of biological and clinical studies has become central or is becoming so. Correspondingly, the amount of data that one needs to process, compare and analyze, has experienced an exponential growth. As a consequence, High Performance Computing (HPC, for short) is being used intensively, in particular in terms of multi-core architectures. However, recently and thanks to the advances in the processing of other scientific and commercial data, Distributed Computing is also being considered for Bioinformatics applications. In particular, the MapReduce paradigm, together with the main middleware supporting it, i.e., Hadoop and Spark, is becoming increasingly popular.

Here we provide a short review in which the state of the art of MapReduce bioinformatics applications is presented, together with a qualitative evaluation of each of the software systems that have been here included. In order to make the paper self-contained, computer architectural and middleware issues are also briefly presented.

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Author information

Authors and Affiliations

  1. Dipartimento di Informatica, Università degli Studi di Salerno, 84084, Fisciano, Salerno, Italy

    Giuseppe Cattaneo & Gianluca Roscigno

  2. Dipartimento di Matematica ed Informatica, Università di Palermo, 90133, Palermo, Palermo, Italy

    Raffaele Giancarlo

  3. Dipartimento di Farmacia, Università degli Studi di Salerno, 84084, Fisciano, Salerno, Italy

    Stefano Piotto & Luigi Di Biasi

  4. Dipartimento di Scienze Statistiche, Università di Roma “La Sapienza”, 00185, Roma, Italy

    Umberto Ferraro Petrillo

Authors
  1. Giuseppe Cattaneo
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  2. Raffaele Giancarlo
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  3. Stefano Piotto
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  4. Umberto Ferraro Petrillo
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  5. Gianluca Roscigno
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  6. Luigi Di Biasi
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Corresponding author

Correspondence to Gianluca Roscigno .

Editor information

Editors and Affiliations

  1. Chemistry and Biology, University of Salerno, Fisciano, Italy

    Federico Rossi

  2. Department of Pharmacy, University of Salerno, Fisciano, Italy

    Stefano Piotto

  3. Department of Industrial Engineering, University of Salerno, Fisciano, Italy

    Simona Concilio

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Cattaneo, G., Giancarlo, R., Piotto, S., Ferraro Petrillo, U., Roscigno, G., Di Biasi, L. (2017). MapReduce in Computational Biology - A Synopsis. In: Rossi, F., Piotto, S., Concilio, S. (eds) Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry. WIVACE 2016. Communications in Computer and Information Science, vol 708. Springer, Cham. https://doi.org/10.1007/978-3-319-57711-1_5

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  • DOI: https://doi.org/10.1007/978-3-319-57711-1_5

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