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

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

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
UBioLab: a web-LABoratory for Ubiquitous in-silico experiments. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516), 9(1), 2012

Online-Journal: http://journal.imbio.de/article.php?aid=192
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2012/5207



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