Implementing a Bioinformatics Pipeline (BIP) on a Mediator Platform: Comparing Cost and Quality of Alternate Choices

We address the challenges of supporting scientific workflow design for a bioinformatics pipeline (BIP) to detect alternative splicing of an organism’s genes. Scientific workflows depend significantly on the selection of the resources (data sources and applications) selected for their implementation. In addition, each implementation of a workflow may offer different costs and benefits. We present the details of a hard-coded BIP and then discuss the process of implementing a BIP on a database management system (DBMS) enabled mediator platform. Such a solution supports biologists as they customize the pipeline, choosing relevant resources and implementations for operators and applications. We discuss cost and benefit metrics to compare these alternative BIP choices.