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Issue No.03 - May-June (2013 vol.10)
pp: 605-618
Hasan M. Jamil , Dept. of Comput. Sci., Univ. of Idaho, Moscow, ID, USA
ABSTRACT
The long-term cost of developing and maintaining a computational pipeline that depends upon data integration and sophisticated workflow logic is too high to even contemplate "what if" or ad hoc type queries. In this paper, we introduce a novel application building interface for computational biology research, called VizBuilder, by leveraging a recent query language called BioFlow for life sciences databases. Using VizBuilder, it is now possible to develop ad hoc complex computational biology applications at throw away costs. The underlying query language supports data integration and workflow construction almost transparently and fully automatically, using a best effort approach. Users express their application by drawing it with VizBuilder icons and connecting them in a meaningful way. Completed applications are compiled and translated as BioFlow queries for execution by the data management system LifeDB, for which VizBuilder serves as a front end. We discuss VizBuilder features and functionalities in the context of a real life application after we briefly introduce BioFlow. The architecture and design principles of VizBuilder are also discussed. Finally, we outline future extensions of VizBuilder. To our knowledge, VizBuilder is a unique system that allows visually designing computational biology pipelines involving distributed and heterogeneous resources in an ad hoc manner.
INDEX TERMS
Pipelines, Data integration, Computational biology, Databases, Visualization, Object recognition, Programming,ad hoc queries, visual programming, ad hoc networks, biological techniques, biology computing, data integration, distributed databases, query languages, heterogeneous resources, integrated computational biology pipeline, data integration, workflow logic, what if queries, ad hoc type queries, computational biology research, query language, life sciences databases, ad hoc complex computational biology applications, workflow construction, VizBuilder icons, BioFlow queries, data management system, LifeDB, front end, real life application, distributed resources, Pipelines, Data integration, Computational biology, Databases, Visualization, Object recognition, Programming, workflow, Data integration, computational pipelines, what if queries, systems biology, visual programming
CITATION
Hasan M. Jamil, "Designing Integrated Computational Biology Pipelines Visually", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 3, pp. 605-618, May-June 2013, doi:10.1109/TCBB.2013.69
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