Title: Implementing computational biology pipelines using VisFlow

Authors: Xin Mou; Hasan M. Jamil; Robert Rinker

Addresses: Department of Computer Science, University of Idaho, Moscow, ID 83844, USA ' Department of Computer Science, University of Idaho, Moscow, ID 83844, USA ' Department of Computer Science, University of Idaho, Moscow, ID 83844, USA

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.

Keywords: graphical user interface languages; query languages for non-relational engines; workflow and data management systems.

DOI: 10.1504/IJDMB.2017.084262

International Journal of Data Mining and Bioinformatics, 2017 Vol.17 No.2, pp.115 - 131

Received: 27 Feb 2017
Accepted: 28 Feb 2017
Published online: 22 May 2017 *

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