Incremental DNA sequence analysis in the cloud

Authors:
Romeo Kienzler;Rémy Bruggmann;Anand Ranganathan;Nesime Tatbul
Affiliations:
Department of Computer Science, ETH Zurich, Switzerland;Bioinformatics, Department of Biology, University of Bern, Switzerland;IBM T.J. Watson Research Center, NY;Department of Computer Science, ETH Zurich, Switzerland
Venue:
SSDBM'12 Proceedings of the 24th international conference on Scientific and Statistical Database Management
Year:
2012

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Abstract

In this paper, we propose to demonstrate a "stream-as-you-go" approach that minimizes the data transfer time of data- and compute-intensive scientific applications deployed in the cloud, by making them incrementally processable. We describe a system that implements this approach based on the IBM InfoSphere Streams computing platform deployed over Amazon EC2. The functionality, performance, and usability of the system will be demonstrated through two DNA sequence analysis applications.