Speaker
Mr
Gergely Windisch
(Obuda University - Hungary)
Description
Mapping short fragments to open access eukaryotic genomes at a very large scale presents a data processing challenge to the scientific world. The large volume of data processing requires an immense amount of computing power for the tools to provide feasible response time, which is essential for the researchers. The main tool used for such an application is BLAST which is the one we use in our portlets developed at Obuda University. There are ways for the scientists to use the BLAST algorithm either executing it locally or using a web based BLAST tool. Usually the scope of usability of these solutions is limited because of the lack of computing power available. The portlets developed at Obuda University are served by a web server but computation takes place in a massively parallel supercomputing environment. The type of the algorithm and the data it has to process make it an ideal candidate for a highly parallel execution on the HPSEE infrastructure. The portlets are available to the scientist community on the Bioinformatics eScience Gateway hosted at OU and powered by gUSE/WS-PGRADE technology, while the backend is being served by the Hungarian HPSEE Infrastructure by NIIF.
Lately most of our work has been focused on evaluating the performance and scalability of our applications by profiling, analyzing the results of the tests and improving the performance of both the portlets and the server-side massively parallel algorithm by environment optimization using the data collected during the testing phase.
In this paper we will describe the two portlets (Deep Aligner and Disease Gene Mapper), discuss the issues and challenges during the development and the performance analysis and present our results on the performance and scalability of the applications.
Primary author
Mr
Gergely Windisch
(Obuda University - Hungary)
Co-authors
Dr
Miklos Kozlovszky
(Obuda University - Hungary)
Mr
Ákos Balasko
(Lab. of Parallel & Distrib. Comput., MTA SZTAKI, Budapest, Hungary)
