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A MapReduce job is modelled as a sequence of two computational phases, the map and the reduce phase.
Using an explicit hydrodynamics proxy application from the U.S. Department of Energy, LULESH, we show how code optimizations impact different computational phases of the simulation.
To overcome the limitations of our Monte Carlo software, we unified the two separate computing modules into a single C language implementation which pass data between the two computational phases in main memory and thereby eliminate the need for intermediate disk files.
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The core computational phase is designed to embarrassingly parallelize the computations, iterating through SNP pairs and efficiently carrying out the tests for epistasis.
LPOD and LDEIM use classification approach to find these regions in the offline computational phase.
Since computational phasing of diploid nuclear loci can be more accurate than cloning in separating alleles from heterozygous individuals [47], gametic phases for atpsβ were inferred using Phase [48], [49] as implemented in DnaSP [50].
Few studies used laboratory procedures in conjunction with computational phasing.
Another 17 individuals, for which haplotypes were more ambiguous when subjected to computational phasing, were phased experimentally using standard cloning techniques.
Unresolved sequences showing double peaks in electropherograms (n = 5) were treated as double infections (sequences represented mitochondrial DNA) and were resolved via computational phasing using the program phase 2.1.1 (Stephens et al. 2001; Stephens and Donnelly 2003).
We show that finding high-multiplexing/high-coverage designs is subject to a computational phase transition, becoming dramatically more difficult when the probability of primer pair interaction exceeds a critical threshold.
We postulate that this unexpected result is due to the failure of our algorithm to accurately distinguish certain meiotic errors from mitotic errors, since the method is dependent on computational phasing, which requires meiotic crossovers to produce highly rearranged chromosomes.
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