Designing Integrated Computational Biology Pipelines Visually
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 Viz Builder, by leveraging a recent query language called Bio Flow 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 VizBuildericons 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 debign 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.
computational pipelines data integration workflow what if queries systems biology visual programming ad hoc queries