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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 ...
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 ...
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, ...
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 ...
The HPS3 Service: Reduction of Cost and Transfer Time for Storing Data on Clouds
(IEEE Computer Society, 2015-03-12)
[Abstract] In the past several years, organizations have been changing their storage methods as the volume of data they managed has increased. The cloud computing paradigm offers new ways of storing data based on scalability ...
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
(Elsevier BV, 2015)
[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of ...
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 ...
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 ...