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Detalhes

Detalhes

  • Nome

    Miguel Gonçalves Areias
  • Cluster

    Informática
  • Cargo

    Investigador Sénior
  • Desde

    16 maio 2011
Publicações

2022

Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers

Autores
Alves, F; Martins, FMS; Areias, M; Munoz Merida, A;

Publicação
SCIENTIFIC REPORTS

Abstract
Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species’ genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies. © 2022, The Author(s).

2021

On the correctness and efficiency of a novel lock-free hash trie map design

Autores
Areias, M; Rocha, R;

Publicação
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Abstract
Hash tries are a trie-based data structure with nearly ideal characteristics for the implementation of hash maps. In this paper, we present a novel, simple and scalable hash trie map design that fully supports the concurrent search, insert and remove operations on hash maps. To the best of our knowledge, our proposal is the first that puts together the following characteristics: (i) be lock-free; (ii) use fixed size data structures; and (iii) maintain the access to all internal data structures as persistent memory references. Our design is modular enough to allow different types of configurations aimed for different performances in memory usage and execution time and can be easily implemented in any type of language, library or within other complex data structures. We discuss in detail the key algorithms required to easily reproduce our implementation by others and we present a proof of correctness showing that our proposal is linearizable and lock-free for the search, insert and remove operations. Experimental results show that our proposal is quite competitive when compared against other state-of-the-art proposals implemented in Java. © 2021 Elsevier Inc.

2021

On the Implementation of Memory Reclamation Methods in a Lock-Free Hash Trie Design

Autores
Moreno, P; Areias, M; Rocha, R;

Publicação
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Abstract

2021

Towards an Elastic Lock-Free Hash Trie Design

Autores
Areias, M; Rocha, R;

Publicação
2021 20TH INTERNATIONAL SYMPOSIUM ON PARALLEL AND DISTRIBUTED COMPUTING (ISPDC)

Abstract

2020

A compression-based design for higher throughput in a lock-free hash map

Autores
Moreno, P; Areias, M; Rocha, R;

Publicação
Euro-Par 2020: Parallel Processing - 26th International Conference on Parallel and Distributed Computing, Warsaw, Poland, August 24-28, 2020, Proceedings

Abstract
Lock-free implementation techniques are known to improve the overall throughput of concurrent data structures. A hash map is an important data structure used to organize information that must be accessed frequently. A key role of a hash map is the ability to balance workloads by dynamically adjusting its internal data structures in order to provide the fastest possible access to the information. This work extends a previous lock-free hash map design to also support lock-free compression. The main goal is to significantly reduce the depth of the internal hash levels within the hash map, in order to minimize cache misses and increase the overall throughput. To materialize our design, we redesigned the existent search, insert, remove and expand operations in order to maintain the lock-freedom property of the whole design. Experimental results show that lock-free compression effectively improves the search operation and, in doing so, it outperforms the previous design, which was already quite competitive when compared against the concurrent hash map design supported by Intel. © Springer Nature Switzerland AG 2020.