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Optimization of Real-World MapReduce Applications With Flame-MR: Practical Use Cases
(Institute of Electrical and Electronics Engineers, 2018-11-12)
[Abstract] Apache Hadoop is a widely used MapReduce framework for storing and processing large amounts of data. However, it presents some performance issues that hinder its utilization in many practical use cases. Although ...
Big Data-Oriented PaaS Architecture with Disk-as-a-Resource Capability and Container-Based Virtualization
(Springer Netherlands, 2018-12)
[Abstract] With the increasing adoption of Big Data technologies as basic tools for the ongoing Digital Transformation, there is a high demand for data-intensive applications. In order to efficiently execute such applications, ...
BDEv 3.0: energy efficiency and microarchitectural characterization of Big Data processing frameworks
(Elsevier BV * North-Holland, 2018-09)
[Abstract] As the size of Big Data workloads keeps increasing, the evaluation of distributed frameworks becomes a crucial task in order to identify potential performance bottlenecks that may delay the processing of large ...
BDWatchdog: real-time monitoring and profiling of Big Data applications and frameworks
(Elsevier BV * North-Holland, 2018-10)
[Abstract] Current Big Data applications are characterized by a heavy use of system resources (e.g., CPU, disk) generally distributed across a cluster. To effectively improve their performance there is a critical need for ...
ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems
(PLoS, 2018)
[Abstract]: Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, ...
SeQual: Big Data Tool to Perform Quality Control and Data Preprocessing of Large NGS Datasets
(Institute of Electrical and Electronics Engineers, 2020-08-07)
[Abstract]
This paper presents SeQual, a scalable tool to efficiently perform quality control of large genomic datasets. Our tool currently supports more than 30 different operations (e.g., filtering, trimming, formatting) ...
MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud
(Oxford University Press, 2017)
[Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ...
HSRA: Hadoop-based spliced read aligner for RNA sequencing data
(Public Library of Science, 2018-07-31)
[Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference ...
A pipeline architecture for feature-based unsupervised clustering using multivariate time series from HPC jobs
(Elsevier B.V., 2023-05)
[Abstract]: Time series are key across industrial and research areas for their ability to model behaviour across time, making them ideal for a wide range of use cases such as event monitoring, trend prediction or anomaly ...
Accelerating binary biclustering on platforms with CUDA-enabled GPUs
(Elsevier Ltd, 2018)
[Abstract]: Data mining is nowadays essential in many scientific fields to extract valuable information from large input datasets and transform it into an understandable structure. For instance, biclustering techniques are ...