My WorkSphere: Integrative work environment for grid-unaware biomedical researchers and applications

Abstract

In order to deliver cyberinfrastructure to the general scientific and biomedical research community, transparent access and ease of use are of critical importance. Applications in systematic modeling of biological processes across scales of time and length demand more and more sophisticated algorithms and larger and longer simulations. The increased level of sophistication requires that cyberinfrastructure developers either work closely with the applications scientists, or develop middleware that flattens the learning curve for these scientists to use the grid willingly and transparently. Many life sciences researchers prefer to run applications in the grid environment without modifications, and without knowledge of specific computational resources being utilized. Here we report the latest advances in the use of Gfarm-FUSE (Grid Data Farm-Filesystem in UserSpaceE) as a computational data grid, with CSF4 (Community Scheduler Framework 4) as the metascheduler, through a GridSphere portal based environment, termed My WorkSphere. We describe the design and performance of this transparent grid computing environment using bioinformatics and computational biology applications as examples. All the components developed or utilized are open source and available freely.