Large Scale Distributed Computing Group

• SEMPLAR - SRB Enabled MPI-IO Library for Access to Remote Storage : SEMPLAR is a remote, parallel I/O library that combines the standard programming interface of MPI-IO with the remote storage functionality of the SDSC Storage Resource Broker (SRB). SEMPLAR relies on parallel TCP streams to maximize the remote data throughput in a design that preserves the parallelism of the access all the way from the storage to the application.

• Hybrid PSI-BLAST : Sequence alignment has been used as a powerful tool to discover the evolutionary relationships among biological sequences, such as regulatory sites, DNA and proteins. In turn, the connection enables us to infer structural and functional properties of unknown sequences. Smith-Waterman algorithm is probably the most widely used algorithm for sequence alignment and has been implemented in many popular sequence alignment tools, such as BLAST and FASTA. But its theoretical limitation for gapped alignment restricts its adoption of many features, for example, position-specific gap costs, which are expected to enhance the sensitivity of the alignment. A newly proposed algorithm, called hybrid algorithm, has a well charactered alignment score statistics and can be used for arbitrary scoring systems including the position-specific gap costs. This hybrid algorithm is particularly suited for iterative sequence alignment tools such as PSI-BLAST or SAM, which dynamically refine their scoring systems to new sequences found in previous searches. This project implements a hybrid algorithm in the framework of PSI-BLAST with the new features, in order to improve the ability of PSI-BLAST to find remotely related biological sequences in sequence databases.
  

1. N. Ali, M. Lauria. "Improving the Performance of Remote I/O Using Asynchronous Primitives", 15^th IEEE International Symposium on High Performance Distributed Computing, Paris, France, June 2006.
2. D. Cotroneo, G. Paolillo, S. Russo, M. Lauria, "CSAR-2: A Case Study of Parallel File System Dependability", 2005 International Conference on High Performance Computing and Communications (HPCC-05),  Sorrento, Italy, 21-24 September, 2005.
3. N. Ali, M. Lauria. “SEMPLAR: High-Performance Remote Parallel I/O over SRB”, 5^th IEEE/ACM International Symposium on Cluster Computing and the Grid, Cardiff, UK, May 2005.
4. Yuheng Li, M. Lauria, R. Bundschuh, "Using Hybrid Alignment for Iterative Sequence Database Searches", Concurrency and Computation: Practice and Experience, Volume 16, Issue 9, August 2004, pp. 841-853.
   
5. Yuheng Li, M. Lauria, R. Bundschuh, "Using Hybrid Alignment for Iterative Sequence Database Searches", 2nd IEEE International Workshop on High Performance Computational Biology (HiCOMB 2003), April 22, 2003, Nice, France (held in conjunction with IPDPS 2003), p. 152.
   
   
   
   

• SEMPLAR Source Code

• Yuheng Li is a Ph.D. candidate in the Biophysics program at the Ohio State University. He is interested in bioinformatics and computational biology, focusing on sequence alignment, proteomics, protein structure and function prediction and annotation. Currently, he is working on a project involving the development of a new sequence alignment algorithm in PSI-BLAST.
  
  
  

• Abhilash Mohan is a second year graduate student in the Biophysics programme at The Ohio State University. His interests include biological workflow management systems,structure based drug designing. Currently his research involves biological workflow management system on a grid computing architecture.
  
  
  

• Nawab Ali is a second year PhD student at the Ohio State University. His research interests span the broad areas of computer architecture, operating systems and high-performance computing. His current research focuses on mechanisms to increase the available data bandwidth between remote clusters over wide area networks. His other interests include music (Rock, Heavy Metal), swimming and UNIX system administration.

• Generoso Paolillo is a visiting scholar at the Ohio State University. He is a Ph.D. student at the University of Naples Federico II in Italy. Generoso works in the area of  Distributed Systems and Computer Networks. His current research is focused on dependability for high-performance parallel file systems.