Student Thesis Projects
Below is a short listing of possible thesis subjects available at the Laboratory
of Bioinformatics. For details, contact prof. dr. Jack Leunissen.
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Text Mining
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Sequence Variation / SNPs
- ProRepeat protein tandem repeat database
- QualitySNP-ng: SNP detection in next-gen sequencing data
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Orthology Detection
- Proteome clustering and phylogenetic profiling
- Genome duplication
- The PROGMAP database
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GPU Programming
Computational performance enhancement by implementation of massively parallel algorithms on GPUs
High end graphics cards are normally associated with video games, but the specific architecture of the graphical processing unit (GPU) also makes it very suitable for doing fast computations. GPU-implementations of scientific algorithms have already resulted in a speed-up of several orders of magnitude. Although writing software to be run on a GPU is still not trivial, with the help of the OpenCL framework it is possible to start with adapting small parts of existing programs. As such we are interested in applying OpenCL and GPU computing to enhance the performance of existing C++ code developed for preprocessing and searching mass spectrometry data . This project will be conducted in a joint fashion between RIKILT-Institute of Food Safety and the Wageningen Bioinformatics group.
Contacts: Arjen Lommen (arjen.lommen@wur.nl ; RIKILT), Harm Nijveen (harm.nijveen@wur.nl ; Bioinformatics), Jack Leunissen (jack.leunissen@wur.nl ; Bioinformatics).
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Analysis of -Omics Data
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