Project Description
The goal of this project is to design and build an adaptive grid computing system that, at runtime, identifies and exploits computer resources across the University of Texas at El Paso (UTEP) campus to predict secondary structures of large numbers of RNA segments using a variety of prediction programs. A global overview of the project is presented in this picture:
Our software tool is built upon the existing open-source Grid middleware APST, or AppLeS Parameter Sweep Template [1]. APST supports Grid environments such as CONDOR [2] and GLOBUS [3] to launch application tasks, move data, and discover resources across network domains. It has been used successfully for other bioinformatics applications such as MCell [4] that studies cellular microphysiology. This project extends APST into APSTe (APSTextended), to support BOINC [5], a Grid environment that allows researchers to deploy desktop and laptop PCs owned by students or administration personnel when their computers are idle.
References
[1] H. Casanova and F. Berman: Parameter Sweeps on the Grid with APST. Chapter 33 in Grid Computing: Making the Global Infrastructure a Reality, Wiley Publisher, Inc., 2002
[2] D. Thain, T. Tannenbaum, and M. Livny: Distributed Computing in Practice: The Condor Experience. Concurrency and Computation: Practice and Experience, 2004
[3] I. Foster and C. Kesselman: Globus: A Metacomputing Infrastructure Toolkit. Intl J. Supercomputer Applications, 11(2):115-128, 1997
[4] MCell: A Monte Carlo Simulator of Cellular Microphysiology. http://www.mcell.cnl.salk.edu
[5] D. P. Anderson: BOINC: A System for Public-Resource Computing and Storage. GRID 2004: 4-10, 2004
