CUDA-based multi-core implementation of MDS-based bioinformatics algorithms

Thilo Fester, Falk Schreiber, Marc Strickert

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

6 Citations (Scopus)


Solving problems in bioinformatics often needs extensive computational power. Current trends in processor architecture, especially massive multi-core processors for graphic cards, combine a large number of cores into a single chip to improve the overall performance. The Compute Unified Device Architecture (CUDA) provides programming interfaces to make full use of the computing power of graphics processing units. We present a way to use CUDA for substantial performance improvement of methods based on multi-dimensional scaling (MDS). The suitability of the CUDA architecture as a high-performance computing platform is studied by adapting a MDS algorithm on specific hardware properties. We show how typical bioinformatics problems related to dimension reduction and network layout benefit from the multi-core implementation of the MDS algorithm. CUDA-based methods are introduced and compared to standard solutions, demonstrating 50-fold acceleration and above.

Original languageEnglish
Title of host publicationGCB 2009 - German Conference on Bioinformatics 2009
PublisherSchloss Dagstuhl
Number of pages13
ISBN (Print)9783885792512
Publication statusPublished - 2009
Externally publishedYes
EventGerman Conference on Bioinformatics 2009, GCB 2009 - Halle-Wittenberg, Germany
Duration: 28 Sept 200930 Sept 2009


ConferenceGerman Conference on Bioinformatics 2009, GCB 2009

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