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2019 | OriginalPaper | Chapter

Distributed Genomic Compression in MapReduce Paradigm

Authors : Pasquale De Luca, Stefano Fiscale, Luca Landolfi, Annabella Di Mauro

Published in: Internet and Distributed Computing Systems

Publisher: Springer International Publishing

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Abstract

In recent years the biological data, represented for computational analysis, has increased in size terms. Despite the representation of the latter is demanded to specific file format, the analysis and managing overcame always more difficult due to high dimension of data. For these reasons, in recent years, a new computational framework, called Hadoop for manage and compute this data have been introduced. Hadoop is based on MapReduce paradigm to manage data in distributed systems. Despite the gain of performance obtained from this framework, our aim is to introduce a new compression method DSRC by decreasing the size of output file and make easy its processing from ad-hoc software. Performance analysis will show the reliability and efficiency achieved by our implementation.

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Literature
1.
go back to reference Cuomo, S., De Michele, P., Galletti, A., Marcellino, L.: A GPU parallel implementation of the local principal component analysis overcomplete method for DW image denoising. In: IEEE Symposium on Computers and Communication (ISCC), Messina 2016, pp. 26–31 (2016). https://doi.org/10.1109/ISCC.2016.7543709 Cuomo, S., De Michele, P., Galletti, A., Marcellino, L.: A GPU parallel implementation of the local principal component analysis overcomplete method for DW image denoising. In: IEEE Symposium on Computers and Communication (ISCC), Messina 2016, pp. 26–31 (2016). https://​doi.​org/​10.​1109/​ISCC.​2016.​7543709
2.
go back to reference Cuomo, S., Galletti, A., Marcellino, L.: A GPU algorithm in a distributed computing system for 3D MRI denoising. In: 2015 10th International Conference on P2P, Parallel, Grid, Cloud and Internet Computing (3PGCIC), Krakow, 2015, pp. 557–562 (2015). https://doi.org/10.1109/3PGCIC.2015.77 Cuomo, S., Galletti, A., Marcellino, L.: A GPU algorithm in a distributed computing system for 3D MRI denoising. In: 2015 10th International Conference on P2P, Parallel, Grid, Cloud and Internet Computing (3PGCIC), Krakow, 2015, pp. 557–562 (2015). https://​doi.​org/​10.​1109/​3PGCIC.​2015.​77
3.
go back to reference De Luca, P., Galletti, A., Giunta G., Marcellino, L., Raei, M.: Performance analysis of a multicore implementation for solving a two-dimensional inverse anomalous diffusion problem. In: Proceedings of the 3rd International Conference and Summer School, NUMTA2019. LNCS (2019) De Luca, P., Galletti, A., Giunta G., Marcellino, L., Raei, M.: Performance analysis of a multicore implementation for solving a two-dimensional inverse anomalous diffusion problem. In: Proceedings of the 3rd International Conference and Summer School, NUMTA2019. LNCS (2019)
4.
go back to reference Montella, R., et al.: Accelerating Linux and Android applications on low-power devices through remote GPGPU offloading. Concurr. Comput. Pract. Exp. 29(24), e4286 (2017)CrossRef Montella, R., et al.: Accelerating Linux and Android applications on low-power devices through remote GPGPU offloading. Concurr. Comput. Pract. Exp. 29(24), e4286 (2017)CrossRef
5.
go back to reference Marcellino, L., et al.: Using GPGPU accelerated interpolation algorithms for Marine Bathymetry processing with on-premises and cloud based computational resources. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds.) PPAM 2017. LNCS, vol. 10778, pp. 14–24. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-78054-2_2CrossRef Marcellino, L., et al.: Using GPGPU accelerated interpolation algorithms for Marine Bathymetry processing with on-premises and cloud based computational resources. In: Wyrzykowski, R., Dongarra, J., Deelman, E., Karczewski, K. (eds.) PPAM 2017. LNCS, vol. 10778, pp. 14–24. Springer, Cham (2018). https://​doi.​org/​10.​1007/​978-3-319-78054-2_​2CrossRef
6.
go back to reference Montella, R., Di Luccio, D., Kosta, S., Giunta, G., Foster, I.: Performance, resilience, and security in moving data from the fog to the cloud: the DYNAMO transfer framework approach. In: Xiang, Y., Sun, J., Fortino, G., Guerrieri, A., Jung, J.J. (eds.) IDCS 2018. LNCS, vol. 11226, pp. 197–208. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-02738-4_17 CrossRef Montella, R., Di Luccio, D., Kosta, S., Giunta, G., Foster, I.: Performance, resilience, and security in moving data from the fog to the cloud: the DYNAMO transfer framework approach. In: Xiang, Y., Sun, J., Fortino, G., Guerrieri, A., Jung, J.J. (eds.) IDCS 2018. LNCS, vol. 11226, pp. 197–208. Springer, Cham (2018). https://​doi.​org/​10.​1007/​978-3-030-02738-4_​17 CrossRef
8.
go back to reference Roguski, Ł., Deorowicz, S.: DSRC 2-industry-oriented compression of FASTQ files. Bioinformatics 30(15), 2213–2215 (2014)CrossRef Roguski, Ł., Deorowicz, S.: DSRC 2-industry-oriented compression of FASTQ files. Bioinformatics 30(15), 2213–2215 (2014)CrossRef
9.
go back to reference Oliveira Jr., W., Justino, E., Oliveira, L.S.: Comparing compression models for authorship attribution. Forensic Sci. Int. 228(1–3), 100–104 (2013)CrossRef Oliveira Jr., W., Justino, E., Oliveira, L.S.: Comparing compression models for authorship attribution. Forensic Sci. Int. 228(1–3), 100–104 (2013)CrossRef
10.
go back to reference Deorowicz, S., Grabowski, S.: Compression of genomic sequences in FASTQ format. Bioinformatics 27(6), 860–862 (2011)CrossRef Deorowicz, S., Grabowski, S.: Compression of genomic sequences in FASTQ format. Bioinformatics 27(6), 860–862 (2011)CrossRef
Metadata
Title
Distributed Genomic Compression in MapReduce Paradigm
Authors
Pasquale De Luca
Stefano Fiscale
Luca Landolfi
Annabella Di Mauro
Copyright Year
2019
DOI
https://doi.org/10.1007/978-3-030-34914-1_35

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