The use of grid computing to drive data-intensive genetic research
2007 (English)In: European Journal of Human Genetics, ISSN 1018-4813, E-ISSN 1476-5438, Vol. 15, no 6, 694-702 p.Article in journal (Refereed) Published
In genetics, with increasing data sizes and more advanced algorithms for mining complex data, a point is reached where increased computational capacity or alternative solutions becomes unavoidable. Most contemporary methods for linkage analysis are based on the Lander-Green hidden Markov model (HMM), which scales exponentially with the number of pedigree members. In whole genome linkage analysis, genotype simulations become prohibitively time consuming to perform on single computers. We have developed 'Grid-Allegro', a Grid aware implementation of the Allegro software, by which several thousands of genotype simulations can be performed in parallel in short time. With temporary installations of the Allegro executable and datasets on remote nodes at submission, the need of predefined Grid run-time environments is circumvented. We evaluated the performance, efficiency and scalability of this implementation in a genome scan on Swedish multiplex Alzheimer's disease families. We demonstrate that 'Grid-Allegro' allows for the full exploitation of the features available in Allegro for genome-wide linkage. The implementation of existing bioinformatics applications on Grids (Distributed Computing) represent a cost-effective alternative for addressing highly resource-demanding and data-intensive bioinformatics task, compared to acquiring and setting up clusters of computational hardware in house (Parallel Computing), a resource not available to most geneticists today.
Place, publisher, year, edition, pages
2007. Vol. 15, no 6, 694-702 p.
grid, bioinformatics, genome-wide, linkage analysis, genotype simulation
Bioinformatics and Systems Biology
IdentifiersURN: urn:nbn:se:kth:diva-7797DOI: 10.1038/sj.ejhg.5201815ISI: 000246792100012ScopusID: 2-s2.0-34249727262OAI: oai:DiVA.org:kth-7797DiVA: diva2:12926
QC 201010042007-12-102007-12-102012-03-20Bibliographically approved