A visual interface for on-the-fly biological database integration and workflow design using vizBuilder

Abstract

Data integration plays a major role in modern Life Sciences research primarily because required resources are geographically distributed across continents and experts depend upon leveraging these digitally archived resources. The ever changing and exponentially growing digital archives pose a significant challenge for traditional data integration efforts and efficient development of data processing pipelines for scientific investigations. Thus a forceful argument can be made that in Life Sciences fast and ad hoc application design requiring data integration and workflow processing is urgently warranted. In this paper, we present a new visual application design toolkit, called VizBuilder, that can be used to design ad hoc applications at throw away costs by naive users in the Life Sciences to integrate remote databases and to design application pipelines. We leverage the recent development of BioFlow query language and LifeDB database management system that allows for such application design. We show that VizBuilder can be used as a front end query interface for LifeDB, with which robust and a wide range of applications can be developed at a very abstract and conceptual level without having to learn BioFlow. Users are able to express their application by drawing it using VizBuilder icons and connecting them in a meaningful way. Once completed, VizBuilder can compile and transform the visual application into an error-free BioFlow program to be executed in LifeDB. We present the functionality of VizBuilder using a real life application that our Life Sciences researchers have implemented and executed in LifeDB as part of their investigation. © 2009 Springer Berlin Heidelberg.