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This technical note describes the ontology-based meta-analysis framework developed by Illumina, which enables analysis of global high-throughput geneand sequence-centric data sets. Queries enabled within this meta-analysis framework include the user’s own sets of data, as well as genes, single-nucleotide variants (SNVs), sequence regions, or biogroups (i.e., pathways) of interest. This meta-ana...

High Throughput Computing systems (HTC) enable otherwise idles cycles to be available to computations that involve many independent tasks. In a Distributed Computing environment, distributed ownership of computing resources is the major obstacle HTC has to overcome to take advantage of under-utilized systems in the network. This paper addresses HTC and how it fits in current parallel and distri...

Article history: Received 23 May 2012 Received in revised form 17 September 2012 Accepted 2 November 2012 Available online xxxx

The biologists now face with the masses of high dimensional datasets generated from various high-throughput technologies, which are outputs of complex inter-connected biological networks at different levels driven by a number of hidden regulatory signals. So far, many computational and statistical methods such as PCA and ICA have been employed for computing low-dimensional or hidden represe...

Plan-do compilation technique is a new, advanced compilation framework for eager data transfer on distributed-memory parallel architectures. The technique is especially eective for a recent breed of low-latency architectures by realizing a high-throughput low-latency communication scheme, pipelined sends. The compilation of high-level, plan-do style code into low-level, eager data transfer code...

The current high-throughput sequencing technologies produce gigabytes of data even when prokaryotic genomes are processed. In a subsequent assembly phase, the generated overlapping reads are merged, ideally into one contiguous sequence. Often, however, the assembly results in a set of contigs which need to be stitched together with additional lab work. One of the reasons why the assembly produc...

Genome-wide association studies are likely to be conducted in large scale in the near future. In such studies, searching over hundreds of thousands of markers for the few ones that are associated with disease brings out the multiple-hypothesis testing problem in its severe form. We explore, in a two-stage design, how the use of false discovery rate (FDR) can alleviate the burden of a prohibitiv...