Building Cyberinfrastructure for Bioinformatics Using Service Oriented Architecture

Abstract

Cyberinfrastructure makes the development and deployment of bioinformatics applications easier by providing the framework and components that may be loosely coupled using service oriented architecture. Here we describe an end to end prototype environment that allows existing applications to run on the grid, taking advantage of open source software that provides a portal interface using GridSphere, with transparent GSI authentication using GAMA, a Web service wrapper using Opal, a metascheduler using CSF4, a virtual file system using Gfarm, and a grid-enabled cluster environment using Rocks. Solutions to complex problems may be developed using workflow tools such as Kepler that coordinate different interoperable services. The availability of this type of cyberinfrastructure suggests that new applications should be designed with the grid in mind, using service oriented architecture for interoperability and efficiency. This approach may enable bioinformaticians to focus on their problems of interest, and make use of the emerging cyberinfrastructure through virtually "drag and drop" deployment