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MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters
(Springer, 2022)
[Abstract] Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related ...
SparkEC: speeding up alignment-based DNA error correction tools
(BioMed Central (Springer), 2022)
[Abstract]: In recent years, huge improvements have been made in the context of sequencing genomic data under what is called Next Generation Sequencing (NGS). However, the DNA reads generated by current NGS platforms are ...
CUDA-JMI: Acceleration of feature selection on heterogeneous systems
(Elsevier, 2020-01)
[Abstract]: Feature selection is a crucial step nowadays in machine learning and data analytics to remove irrelevant and redundant characteristics and thus to provide fast and reliable analyses. Many research works have ...
SMusket: Spark-based DNA error correction on distributed-memory systems
(Elsevier B.V., 2020)
[Abstract]: Next-Generation Sequencing (NGS) technologies have revolutionized genomics research over the last decade, bringing new opportunities for scientists to perform groundbreaking biological studies. Error correction ...
Real-time resource scaling platform for Big Data workloads on serverless environments
(2020)
The serverless execution paradigm is becoming an increasingly popular option when workloads are to be deployed in an abstracted way, more specifically, without specifying any infrastructure requirements. Currently, such ...
SeQual-Stream: approaching stream processing to quality control of NGS datasets
(BMC, 2023-10)
[Abstract]: Background
Quality control of DNA sequences is an important data preprocessing step in many genomic analyses. However, all existing parallel tools for this purpose are based on a batch processing model, ...
FastMPJ: a scalable and efficient Java message-passing library
(Springer New York LLC, 2014)
[Abstract] The performance and scalability of communications are key for high performance computing (HPC) applications in the current multi-core era. Despite the significant benefits (e.g., productivity, portability, ...
Enhancing in-memory Efficiency for MapReduce-based Data Processing
(Academic Press, 2018-10)
[Abstract] As the memory capacity of computational systems increases, the in-memory data management of Big Data processing frameworks becomes more crucial for performance. This paper analyzes and improves the memory ...
Design of scalable Java message-passing communications over InfiniBand
(Springer New York LLC, 2012-07)
[Abstract] This paper presents ibvdev a scalable and efficient low-level Java message-passing communication device over InfiniBand. The continuous increase in the number of cores per processor underscores the need for ...
General‐purpose computation on GPUs for high performance cloud computing
(John Wiley & Sons Ltd., 2013-08)
[Abstract] Cloud computing is offering new approaches for High Performance Computing (HPC) as it provides dynamically scalable resources as a service over the Internet. In addition, General‐Purpose computation on Graphical ...