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

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doi doi:10.2390/biecoll-jib-2012-192
submission August 10, 2011
published July 09, 2012
NCBI PubMed PubMed ID 22773116

Ezio Bartocci, Diletta Cacciagrano, Maria Rita Di Berardini, Emanuela Merelli and Leonardo Vito

Correspondence should be addressed to:
Ezio Bartocci
School of Science and Technology, University of Camerino, Via Madonna delle Carceri 9, Camerino (MC), Italy & Department of Computer Engineering, Faculty of Informatics, Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria
ta.ca.neiwut@nulliccotrab.oize


Abstract

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.

Reference

Ezio Bartocci, Diletta Cacciagrano, Maria Rita Di Berardini, Emanuela Merelli and Leonardo Vito. UBioLab: a web-LABoratory for Ubiquitous in-silico experiments. Journal of Integrative Bioinformatics, 9(1):192, 2012. Online Journal: http://journal.imbio.de/index.php?paper_id=192
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