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The Phylogenetic Likelihood Library
(Oxford University Press, 2015-03-01)
[Abstract] We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements ...
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
(Institute of Electrical and Electronics Engineers, 2015)
[Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide ...
Mobile Robot Positioning with 433-MHz Wireless Motes with Varying Transmission Powers and a Particle Filter
(Multidisciplinary Digital Publishing Institute, 2015)
In wireless positioning systems, the transmitter’s power is usually fixed. In this paper, we explore the use of varying transmission powers to increase the performance of a wireless localization system. To this extent, we ...
Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model
(Sage Publications Ltd., 2015)
[Abstract] Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, ...
Developing adaptive multi-device applications with the Heterogeneous Programming Library
(Springer, 2015)
[Abstract] The usage of heterogeneous devices presents two main problems. One is their complex programming, a problem that grows when multiple devices are used. The second issue is that even if the codes for these devices ...
Low‐latency Java communication devices on RDMA‐enabled networks
(John Wiley & Sons Ltd., 2015)
[Abstract] Providing high‐performance inter‐node communication is a key capability for running high performance computing applications efficiently on parallel architectures. In fact, current systems deployments are aggregating ...
Nonblocking collectives for scalable Java communications
(John Wiley & Sons Ltd., 2015-04-22)
[Abstract] This paper presents a Java implementation of the recently published MPI 3.0 nonblocking message passing collectives in order to analyze and assess the feasibility of taking advantage of these operations in shared ...
Volatile STT-RAM Scratchpad Design and Data Allocation for Low Energy
(Association for Computing Machinery, 2015)
[Abstract] On-chip power consumption is one of the fundamental challenges of current technology scaling. Cache memories consume a sizable part of this power, particularly due to leakage energy. STT-RAM is one of several ...
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
(Elsevier Ltd, 2015)
[Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting ...
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs
(Elsevier B.V., 2015-07)
[Abstract]: Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex ...