The use of distributed data storage and processing systems in bioinformatic data analysis

Michał Bochenek; Kamil Folkert; Roman Jaksik; Michał Krzesiak; Marcin Michalak; Marek Sikora; Tomasz Stȩclik; Łukasz Wróbel

doi:10.1007/978-3-319-99987-6_2

The use of distributed data storage and processing systems in bioinformatic data analysis

Michał Bochenek
, Kamil Folkert
, Roman Jaksik
, Michał Krzesiak
, Marcin Michalak
, Marek Sikora
, Tomasz Stȩclik
, Łukasz Wróbel

3 Soft S.A.
Institute of Innovative Technologies EMAG

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

The cancer and the cancer mortality may seem the sign of the present times. This leads hundreds of scientists to handle the issue of finding significant premises of cancer occurrence. In this paper a set of data mining tasks is defined that joins the observed genes mutation with the specific cancer type observation. Due to the high computational complexity of this kind of data a Hadoop ecosystem cluster was developed to perform the required calculations. The results may be satisfactory in the domains of distributed data storage (processing) and the genes mutation occurrence interpretation.

Original language	English
Title of host publication	Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings
Editors	Stanislaw Kozielski, Dariusz Mrozek, Pawel Kasprowski, Bozena Malysiak-Mrozek, Daniel Kostrzewa
Publisher	Springer Verlag
Pages	18-32
Number of pages	15
ISBN (Print)	9783319999869
DOIs	https://doi.org/10.1007/978-3-319-99987-6_2
Publication status	Published - 2018
Event	14th International Conference on Beyond Databases, Architectures and Structures, BDAS 2018 Held at the 24th IFIP World Computer Congress, WCC 2018 - Poznan, Poland Duration: 18 Sept 2018 → 20 Sept 2018

Publication series

Name	Communications in Computer and Information Science
Volume	928
ISSN (Print)	1865-0929

Conference

Conference	14th International Conference on Beyond Databases, Architectures and Structures, BDAS 2018 Held at the 24th IFIP World Computer Congress, WCC 2018
Country/Territory	Poland
City	Poznan
Period	18/09/18 → 20/09/18

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Biomedical data
Distributed computing
Gene mutations
Hadoop ecosystem
TCGA data analysis

ASJC Scopus subject areas

General Computer Science
General Mathematics

Access to Document

10.1007/978-3-319-99987-6_2

Cite this

Bochenek, M., Folkert, K., Jaksik, R., Krzesiak, M., Michalak, M., Sikora, M., Stȩclik, T., & Wróbel, Ł. (2018). The use of distributed data storage and processing systems in bioinformatic data analysis. In S. Kozielski, D. Mrozek, P. Kasprowski, B. Malysiak-Mrozek, & D. Kostrzewa (Eds.), Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings (pp. 18-32). (Communications in Computer and Information Science; Vol. 928). Springer Verlag. https://doi.org/10.1007/978-3-319-99987-6_2

Bochenek, Michał ; Folkert, Kamil ; Jaksik, Roman et al. / The use of distributed data storage and processing systems in bioinformatic data analysis. Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings. editor / Stanislaw Kozielski ; Dariusz Mrozek ; Pawel Kasprowski ; Bozena Malysiak-Mrozek ; Daniel Kostrzewa. Springer Verlag, 2018. pp. 18-32 (Communications in Computer and Information Science).

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title = "The use of distributed data storage and processing systems in bioinformatic data analysis",

abstract = "The cancer and the cancer mortality may seem the sign of the present times. This leads hundreds of scientists to handle the issue of finding significant premises of cancer occurrence. In this paper a set of data mining tasks is defined that joins the observed genes mutation with the specific cancer type observation. Due to the high computational complexity of this kind of data a Hadoop ecosystem cluster was developed to perform the required calculations. The results may be satisfactory in the domains of distributed data storage (processing) and the genes mutation occurrence interpretation.",

keywords = "Biomedical data, Distributed computing, Gene mutations, Hadoop ecosystem, TCGA data analysis",

author = "Micha{\l} Bochenek and Kamil Folkert and Roman Jaksik and Micha{\l} Krzesiak and Marcin Michalak and Marek Sikora and Tomasz Stȩclik and {\L}ukasz Wr{\'o}bel",

note = "Publisher Copyright: {\textcopyright} Springer Nature Switzerland AG 2018.; 14th International Conference on Beyond Databases, Architectures and Structures, BDAS 2018 Held at the 24th IFIP World Computer Congress, WCC 2018 ; Conference date: 18-09-2018 Through 20-09-2018",

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booktitle = "Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings",

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Bochenek, M, Folkert, K, Jaksik, R, Krzesiak, M, Michalak, M , Sikora, M , Stȩclik, T & Wróbel, Ł 2018, The use of distributed data storage and processing systems in bioinformatic data analysis. in S Kozielski, D Mrozek, P Kasprowski, B Malysiak-Mrozek & D Kostrzewa (eds), Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings. Communications in Computer and Information Science, vol. 928, Springer Verlag, pp. 18-32, 14th International Conference on Beyond Databases, Architectures and Structures, BDAS 2018 Held at the 24th IFIP World Computer Congress, WCC 2018, Poznan, Poland, 18/09/18. https://doi.org/10.1007/978-3-319-99987-6_2

The use of distributed data storage and processing systems in bioinformatic data analysis. / Bochenek, Michał; Folkert, Kamil; Jaksik, Roman et al.
Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings. ed. / Stanislaw Kozielski; Dariusz Mrozek; Pawel Kasprowski; Bozena Malysiak-Mrozek; Daniel Kostrzewa. Springer Verlag, 2018. p. 18-32 (Communications in Computer and Information Science; Vol. 928).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - The use of distributed data storage and processing systems in bioinformatic data analysis

AU - Bochenek, Michał

AU - Folkert, Kamil

AU - Jaksik, Roman

AU - Krzesiak, Michał

AU - Michalak, Marcin

AU - Sikora, Marek

AU - Stȩclik, Tomasz

AU - Wróbel, Łukasz

N1 - Publisher Copyright: © Springer Nature Switzerland AG 2018.

PY - 2018

Y1 - 2018

N2 - The cancer and the cancer mortality may seem the sign of the present times. This leads hundreds of scientists to handle the issue of finding significant premises of cancer occurrence. In this paper a set of data mining tasks is defined that joins the observed genes mutation with the specific cancer type observation. Due to the high computational complexity of this kind of data a Hadoop ecosystem cluster was developed to perform the required calculations. The results may be satisfactory in the domains of distributed data storage (processing) and the genes mutation occurrence interpretation.

AB - The cancer and the cancer mortality may seem the sign of the present times. This leads hundreds of scientists to handle the issue of finding significant premises of cancer occurrence. In this paper a set of data mining tasks is defined that joins the observed genes mutation with the specific cancer type observation. Due to the high computational complexity of this kind of data a Hadoop ecosystem cluster was developed to perform the required calculations. The results may be satisfactory in the domains of distributed data storage (processing) and the genes mutation occurrence interpretation.

KW - Biomedical data

KW - Distributed computing

KW - Gene mutations

KW - Hadoop ecosystem

KW - TCGA data analysis

UR - https://www.scopus.com/pages/publications/85053823325

U2 - 10.1007/978-3-319-99987-6_2

DO - 10.1007/978-3-319-99987-6_2

M3 - Conference contribution

AN - SCOPUS:85053823325

SN - 9783319999869

T3 - Communications in Computer and Information Science

SP - 18

EP - 32

BT - Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings

A2 - Kozielski, Stanislaw

A2 - Mrozek, Dariusz

A2 - Kasprowski, Pawel

A2 - Malysiak-Mrozek, Bozena

A2 - Kostrzewa, Daniel

PB - Springer Verlag

T2 - 14th International Conference on Beyond Databases, Architectures and Structures, BDAS 2018 Held at the 24th IFIP World Computer Congress, WCC 2018

Y2 - 18 September 2018 through 20 September 2018

ER -

Bochenek M, Folkert K, Jaksik R, Krzesiak M, Michalak M , Sikora M et al. The use of distributed data storage and processing systems in bioinformatic data analysis. In Kozielski S, Mrozek D, Kasprowski P, Malysiak-Mrozek B, Kostrzewa D, editors, Beyond Databases, Architectures and Structures. Facing the Challenges of Data Proliferation and Growing Variety - 14th International Conference, BDAS 2018, Held at the 24th IFIP World Computer Congress, WCC 2018, Proceedings. Springer Verlag. 2018. p. 18-32. (Communications in Computer and Information Science). doi: 10.1007/978-3-319-99987-6_2

The use of distributed data storage and processing systems in bioinformatic data analysis

Abstract

Publication series

Conference

UN SDGs

Keywords

ASJC Scopus subject areas

Access to Document

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