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

Vorschaubild nicht verfügbar
Dateien
Zu diesem Dokument gibt es keine Dateien.
Datum
2009
Autor:innen
Fester
Strickert, Marc
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
eISSN
item.preview.dc.identifier.isbn
Bibliografische Daten
Verlag
Schriftenreihe
URI (zitierfähiger Link)
DOI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
Link zur Lizenz
oops
EU-Projektnummer
Projekt
Open Access-Veröffentlichung
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Beitrag zu einem Konferenzband
Publikationsstatus
Published
Erschienen in
German conference on bioinformatics 2009 / Grosse, Ivo; Neumann, Steffen; Posch, Stefan; Schreiber, Falk; Stadler, Peter (Hrsg.). - Bonn : Gesellschaft für Informatik, 2009. - (Lecture Notes in Informatics ; P-157). - S. 67-79. - ISSN 1617-5468. - ISBN 978-3-88579-251-2
Zusammenfassung
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.
Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
004 Informatik
Schlagwörter
Konferenz
German conference on bioinformatics 2009, 28. Sep. 2009 - 30. Sep. 2009, Halle-Wittenberg
Rezension
undefined / . - undefined, undefined. - (undefined; undefined)
Zitieren
ISO 690FESTER, , Falk SCHREIBER, Marc STRICKERT, 2009. CUDA-based multi-core implementation of MDS-based bioinformatics algorithms. German conference on bioinformatics 2009. Halle-Wittenberg, 28. Sep. 2009 - 30. Sep. 2009. In: GROSSE, Ivo, ed., Steffen NEUMANN, ed., Stefan POSCH, ed., Falk SCHREIBER, ed., Peter STADLER, ed.. German conference on bioinformatics 2009. Bonn:Gesellschaft für Informatik, pp. 67-79. ISSN 1617-5468. ISBN 978-3-88579-251-2
BibTex
@inproceedings{Fester2009CUDAb-40247,
  year={2009},
  title={CUDA-based multi-core implementation of MDS-based bioinformatics algorithms},
  url={http://subs.emis.de/LNI/Proceedings/Proceedings157/67.pdf},
  number={P-157},
  isbn={978-3-88579-251-2},
  issn={1617-5468},
  publisher={Gesellschaft für Informatik},
  address={Bonn},
  series={Lecture Notes in Informatics},
  booktitle={German conference on bioinformatics 2009},
  pages={67--79},
  editor={Grosse, Ivo and Neumann, Steffen and Posch, Stefan and Schreiber, Falk and Stadler, Peter},
  author={Fester and Schreiber, Falk and Strickert, Marc}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/40247">
    <dcterms:issued>2009</dcterms:issued>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:creator>Schreiber, Falk</dc:creator>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T08:55:10Z</dc:date>
    <dc:language>eng</dc:language>
    <dcterms:title>CUDA-based multi-core implementation of MDS-based bioinformatics algorithms</dcterms:title>
    <dcterms:abstract xml:lang="eng">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.</dcterms:abstract>
    <dc:contributor>Strickert, Marc</dc:contributor>
    <dc:creator>Fester</dc:creator>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dc:contributor>Schreiber, Falk</dc:contributor>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/40247"/>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/36"/>
    <dc:creator>Strickert, Marc</dc:creator>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2017-10-05T08:55:10Z</dcterms:available>
    <dc:contributor>Fester</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
Prüfdatum der URL
2017-10-05
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Nein
Begutachtet