Implementing computational biology pipelines using VisFlow Online publication date: Mon, 22-May-2017
by Xin Mou; Hasan M. Jamil; Robert Rinker
International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 17, No. 2, 2017
Abstract: Data integration continues to baffle researchers even though substantial progress has been made. Although the emergence of technologies such as XML, web services, semantic web and cloud computing have helped, a system in which biologists are comfortable articulating new applications and developing them without technical assistance from a computing expert is yet to be realised. The distance between a friendly graphical interface that does little, and a 'traditional' system though clunky yet powerful, is deemed too great more often than not. The question that remains unanswered is, if a user can state her query involving a set of complex, heterogeneous and distributed life sciences resources in an easy to use language and execute it without further help from a computer savvy programmer. In this paper, we present a declarative meta-language, called VisFlow, for requirement specification, and a translator for mapping requirements into executable queries in a variant of SQL augmented with integration artefacts.
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