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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 8, Issue 2

Issues

Data partitioning enables the use of standard SOAP Web Services in genome-scale workflows

Paweł Sztromwasser
  • Corresponding author
  • Department of Informatics, University of Bergen, http://www.uib.no/ii Norway
  • Computational Biology Unit, Uni Computing, Uni Research, http://www.computing.uni.no/, Norway
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  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Kjell Petersen
  • Computational Biology Unit, Uni Computing, Uni Research, http://www.computing.uni.no/, Norway
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Pál Puntervoll
  • Computational Biology Unit, Uni Computing, Uni Research, http://www.computing.uni.no/, Norway
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2011-163

Summary

Biological databases and computational biology tools are provided by research groups around the world, and made accessible on the Web. Combining these resources is a common practice in bioinformatics, but integration of heterogeneous and often distributed tools and datasets can be challenging. To date, this challenge has been commonly addressed in a pragmatic way, by tedious and error-prone scripting. Recently however a more reliable technique has been identified and proposed as the platform that would tie together bioinformatics resources, namely Web Services. In the last decade the Web Services have spread wide in bioinformatics, and earned the title of recommended technology. However, in the era of high-throughput experimentation, a major concern regarding Web Services is their ability to handle large-scale data traffic. We propose a stream-like communication pattern for standard SOAP Web Services, that enables efficient flow of large data traffic between a workflow orchestrator and Web Services. We evaluated the data-partitioning strategy by comparing it with typical communication patterns on an example pipeline for genomic sequence annotation. The results show that data-partitioning lowers resource demands of services and increases their throughput, which in consequence allows to execute in-silico experiments on genome-scale, using standard SOAP Web Services and workflows. As a proof-of-principle we annotated an RNA-seq dataset using a plain BPEL workflow engine.

About the article

Published Online: 2016-10-18

Published in Print: 2011-06-01


Citation Information: Journal of Integrative Bioinformatics, Volume 8, Issue 2, Pages 95–114, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2011-163.

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© 2011 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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[1]
Sattanathan Subramanian, Paweł Sztromwasser, Pål Puntervoll, and Kjell Petersen
International Journal of Web Information Systems, 2013, Volume 9, Number 3, Page 204
[2]
Hasan M. Jamil
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, Volume 10, Number 3, Page 605

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