Title |
cudaMap: a GPU accelerated program for gene expression connectivity mapping
|
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Published in |
BMC Bioinformatics, October 2013
|
DOI | 10.1186/1471-2105-14-305 |
Pubmed ID | |
Authors |
Darragh G McArt, Peter Bankhead, Philip D Dunne, Manuel Salto-Tellez, Peter Hamilton, Shu-Dong Zhang |
Abstract |
Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping. |
X Demographics
Geographical breakdown
Country | Count | As % |
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Germany | 2 | 100% |
Demographic breakdown
Type | Count | As % |
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Science communicators (journalists, bloggers, editors) | 1 | 50% |
Members of the public | 1 | 50% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Spain | 2 | 3% |
Germany | 1 | 2% |
Netherlands | 1 | 2% |
Brazil | 1 | 2% |
France | 1 | 2% |
United States | 1 | 2% |
Luxembourg | 1 | 2% |
Unknown | 56 | 88% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 21 | 33% |
Student > Master | 10 | 16% |
Student > Ph. D. Student | 9 | 14% |
Other | 5 | 8% |
Student > Bachelor | 4 | 6% |
Other | 7 | 11% |
Unknown | 8 | 13% |
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Biochemistry, Genetics and Molecular Biology | 9 | 14% |
Computer Science | 9 | 14% |
Medicine and Dentistry | 7 | 11% |
Engineering | 4 | 6% |
Other | 4 | 6% |
Unknown | 11 | 17% |