Dynamic BLAST – a Grid Enabled BLAST

Basic Local Alignment Search Tool (BLAST) is a heavily used bioinformatics application that has gotten significant attention from the high performance computing community. The authors have taken BLAST execution a step further and enabled it to execute on grid resources. Adapting BLAST to execute on the grid brings up concerns regarding grid resource heterogeneity, which inevitably cause difficulty with application availability, fault tolerance, interoperability, and variability in performance of individual segments that are being distributed across grid resources. This paper describes a BLAST-specific metascheduler, named Dynamic BLAST, a multithreaded, master-worker type application that handles all aspects of a BLAST job submission on the grid for the user. The main contribution realized with Dynamic BLAST is minimization of user job turnaround time through understanding and leveraging of resource heterogeneity found across grid computing environments. Experiments with Dynamic BLAST on UABgrid resources show reduction in total execution time of BLAST jobs up to 50% while improving resource utilization by approximately 40%.