Parallel and distributed algorithms for computational biology
Computational biology research is now faced with the burgeoning number of genome data. The rigorous postprocessing of this data requires an increased role for high performance computing (HPC). Because the development of HPC applications for computational biology problems is much more complex than th...
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| Format: | Thesis |
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2008
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| Online Access: | https://hdl.handle.net/10356/2474 |
| _version_ | 1826121863715094528 |
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| author | Liu, Weiguo |
| author2 | Bertil Schmidt |
| author_facet | Bertil Schmidt Liu, Weiguo |
| author_sort | Liu, Weiguo |
| collection | NTU |
| description | Computational biology research is now faced with the burgeoning number of genome data. The rigorous postprocessing of this data requires an increased role for high performance computing (HPC). Because the development of HPC applications for computational biology problems is much more complex than the corresponding sequential applications, existing traditional programming techniques have demonstrated their inadequacy. Many high level programming techniques, such as skeleton and pattern-based programming, have therefore been designed to provide users new ways to get HPC applications without much effort. However, most of them remain absent from the mainstream practice for computational biology. In this paper, we present a new parallel pattern-based system prototype for computational biology. The underlying programming techniques are based on generic programming, a programming technique suited for the generic representation of abstract concepts. This allows the system to be built in a generic way at application level and, thus, provides good extensibility and flexibility. We show how this system can be used to develop HPC applications for popular computational biology algorithms and lead to significant runtime savings on distributed memory architectures. |
| first_indexed | 2024-10-01T05:39:06Z |
| format | Thesis |
| id | ntu-10356/2474 |
| institution | Nanyang Technological University |
| last_indexed | 2024-10-01T05:39:06Z |
| publishDate | 2008 |
| record_format | dspace |
| spelling | ntu-10356/24742020-11-10T08:45:01Z Parallel and distributed algorithms for computational biology Liu, Weiguo Bertil Schmidt School of Computer Engineering DRNTU::Engineering::Computer science and engineering::Computer systems organization::Special-purpose and application-based systems Computational biology research is now faced with the burgeoning number of genome data. The rigorous postprocessing of this data requires an increased role for high performance computing (HPC). Because the development of HPC applications for computational biology problems is much more complex than the corresponding sequential applications, existing traditional programming techniques have demonstrated their inadequacy. Many high level programming techniques, such as skeleton and pattern-based programming, have therefore been designed to provide users new ways to get HPC applications without much effort. However, most of them remain absent from the mainstream practice for computational biology. In this paper, we present a new parallel pattern-based system prototype for computational biology. The underlying programming techniques are based on generic programming, a programming technique suited for the generic representation of abstract concepts. This allows the system to be built in a generic way at application level and, thus, provides good extensibility and flexibility. We show how this system can be used to develop HPC applications for popular computational biology algorithms and lead to significant runtime savings on distributed memory architectures. DOCTOR OF PHILOSOPHY (SCE) 2008-09-17T09:03:52Z 2008-09-17T09:03:52Z 2006 2006 Thesis Liu, W. G. (2006). Parallel and distributed algorithms for computational biology. Doctoral thesis, Nanyang Technological University, Singapore. https://hdl.handle.net/10356/2474 10.32657/10356/2474 Nanyang Technological University application/pdf |
| spellingShingle | DRNTU::Engineering::Computer science and engineering::Computer systems organization::Special-purpose and application-based systems Liu, Weiguo Parallel and distributed algorithms for computational biology |
| title | Parallel and distributed algorithms for computational biology |
| title_full | Parallel and distributed algorithms for computational biology |
| title_fullStr | Parallel and distributed algorithms for computational biology |
| title_full_unstemmed | Parallel and distributed algorithms for computational biology |
| title_short | Parallel and distributed algorithms for computational biology |
| title_sort | parallel and distributed algorithms for computational biology |
| topic | DRNTU::Engineering::Computer science and engineering::Computer systems organization::Special-purpose and application-based systems |
| url | https://hdl.handle.net/10356/2474 |
| work_keys_str_mv | AT liuweiguo parallelanddistributedalgorithmsforcomputationalbiology |