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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

4 Issues per year


CiteScore 2016: 0.93

SCImago Journal Rank (SJR) 2016: 0.416

Open Access
Online
ISSN
1613-4516
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Volume 9, Issue 1

Issues

UBioLab: a web-LABoratory for Ubiquitous in-silico experiments

E. Bartocci
  • Corresponding author
  • School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, Camerino (MC) Austria
  • Department of Computer Engineering, Faculty of Informatics, Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria
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/ M. R. Di Berardini
  • School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, Camerino (MC), Italy
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/ E. Merelli
  • School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, Camerino (MC), Italy
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/ L. Vito
  • School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, Camerino (MC), Italy
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2012-192

Summary

The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists -for what concerns their management and visualization- and for bioinformaticians -for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle -and possibly to handle in a transparent and uniform way- aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features -as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques- give evidence of an effort in such a direction.

The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) “type” of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.

About the article

Published Online: 2016-10-18

Published in Print: 2012-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 9, Issue 1, Pages 12–31, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2012-192.

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© 2012 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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