Int. J. of Data Mining and Bioinformatics   »   2017 Vol.17, No.2

 

 

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.2017.10005210

 

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

 

Submission date: 24 Feb 2017
Date of acceptance: 28 Feb 2017
Available online: 20 May 2017

 

 

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