By   March 29, 2015

Thesis Proposal “The relational way to dam the flood of genome data” accepted for publication at SIGMOD/PODS PhD Workshop

Authors

Sebastian Dorok (Bayer Pharma AG, University of Magdeburg)

Abstract

Mutations in genomes can indicate a predisposition for diseases such as cancer or cardiovascular disorder. Genome analysis is an established procedure to determine mutations and deduce their impact on living organisms. The first step in genome analysis is DNA sequencing that makes the biochemically stored hereditary information in DNA digitally readable. The cost and time to sequence a whole genome decreases rapidly and leads to an increase of available raw genome data that must be stored and integrated to be analyzed. Damming this flood of genome data requires efficient and effective analysis as well as data management solutions. State-of-the-art in genome analysis are flat-file-based storage and analysis solutions. Consequently, every analysis application is responsible to manage data on its own, which leads to implementation and process overhead.

Database systems have already shown their ability to reduce data management overhead for analysis applications in various domains. However, current approaches using relational database systems for genome-data management lack scalable performance on increasing amounts of genome data. In this thesis, we investigate the capabilities of relational main-memory database systems to store and query genome data efficiently, while enabling flexible data access.