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Parallel algorithms and implementations for genetic analysis of quantitative traits
Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. (Software Aspects of High-Performance Computing)
2007 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be regulated by multiple genetic loci. Standard computational tools for analysis of quantitative traits use linear regression models for relating the observed phenotypes to the genetic composition of individuals in a population. However, using these tools to simultaneously search for multiple genetic loci is very computationally demanding. The main reason for this is the complex nature of the optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms and implementation techniques for such optimization problems. The new computational tools will eventually enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics.

We first describe how the algorithm used for global optimization in the standard, serial software is parallelized and implemented on a grid system. Then, we also describe a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be deployed on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithms such as DIRECT. Finally, a pilot implementation of a grid portal providing a graphical front-end for our code is implemented. After some further development, this portal can be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.

Place, publisher, year, edition, pages
Uppsala University, 2007.
Series
Information technology licentiate theses: Licentiate theses from the Department of Information Technology, ISSN 1404-5117 ; 2007-005
National Category
Software Engineering Computational Mathematics
Research subject
Scientific Computing
Identifiers
URN: urn:nbn:se:uu:diva-85815OAI: oai:DiVA.org:uu-85815DiVA, id: diva2:116624
Supervisors
Available from: 2007-09-28 Created: 2007-09-11 Last updated: 2018-01-13Bibliographically approved

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Jayawardena, Mahen

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CiteExportLink to record
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Citation style
  • apa
  • ieee
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  • nn-NB
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More languages
Output format
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