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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 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 12, Issue 1

Issues

Shared Bioinformatics Databases within the Unipro UGENE Platform

Ivan V. Protsyuk
  • Corresponding author
  • Unipro Center for Information Technologies, 6/1 Lavrentieva Ave., 630090 Novosibirsk, Russian Federation
  • Department of Physics, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russian Federation
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/ German A. Grekhov
  • Unipro Center for Information Technologies, 6/1 Lavrentieva Ave., 630090 Novosibirsk, Russian Federation
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/ Alexey V. Tiunov
  • Unipro Center for Information Technologies, 6/1 Lavrentieva Ave., 630090 Novosibirsk, Russian Federation
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/ Mikhail Yu. Fursov
  • Unipro Center for Information Technologies, 6/1 Lavrentieva Ave., 630090 Novosibirsk, Russian Federation
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2015-257

Summary

Unipro UGENE is an open-source bioinformatics toolkit that integrates popular tools along with original instruments for molecular biologists within a unified user interface. Nowadays, most bioinformatics desktop applications, including UGENE, make use of a local data model while processing different types of data. Such an approach causes an inconvenience for scientists working cooperatively and relying on the same data. This refers to the need of making multiple copies of certain files for every workplace and maintaining synchronization between them in case of modifications. Therefore, we focused on delivering a collaborative work into the UGENE user experience. Currently, several UGENE installations can be connected to a designated shared database and users can interact with it simultaneously. Such databases can be created by UGENE users and be used at their discretion. Objects of each data type, supported by UGENE such as sequences, annotations, multiple alignments, etc., can now be easily imported from or exported to a remote storage. One of the main advantages of this system, compared to existing ones, is the almost simultaneous access of client applications to shared data regardless of their volume. Moreover, the system is capable of storing millions of objects. The storage itself is a regular database server so even an inexpert user is able to deploy it. Thus, UGENE may provide access to shared data for users located, for example, in the same laboratory or institution. UGENE is available at: http://ugene.net/download.html.

About the article

Published Online: 2016-10-18

Published in Print: 2015-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 12, Issue 1, Pages 24–34, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2015-257.

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© 2015 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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