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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) ...
A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
(Public Library of Science, 2017)
[Abstract]
Background:
We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested ...
Exploratory Data Analysis and Data Envelopment Analysis of Construction and Demolition Waste Management in the European Economic Area
(M D P I AG, 2020-06-18)
[Abstract]
This paper deals with the efficiency and sustainability of Construction and Demolition Waste (CDW) management in 30 Member States of the European Economic Area (EEA) (the 28 European Union countries plus Norway ...
Toxo: A Library for Calculating Penetrance Tables of High-Order Epistasis Models
(BioMed Central Ltd., 2020-04-09)
[Abstract]
Background
Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which ...
Big Data Geospatial Processing for Massive Aerial LiDAR Datasets
(M D P I AG, 2020-02-21)
[Abstract] For years, Light Detection and Ranging (LiDAR) technology has been considered as a challenge when it comes to developing efficient software to handle the extremely large volumes of data this surveying method is ...
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 ...
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
(Oxford University Press, 2019-08-21)
[Abstract] ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two ...
Big Data Geospatial Processing for Massive Aerial LiDAR Datasets
(MDPI AG, 2020-02-21)
[Abstract] For years, Light Detection and Ranging (LiDAR) technology has been considered as a challenge when it comes to developing efficient software to handle the extremely large volumes of data this surveying method is ...
High performance genetic algorithm for land use planning
(Pergamon Press, 2013)
[Abstract] This study uses genetic algorithms to formulate and develop land use plans. The restrictions to be imposed and the variables to be optimized are selected based on current local and national legal rules and ...
Enhanced global optimization methods applied to complex fisheries stock assessment models
(Elsevier BV, 2019-04)
[Abstract]
Statistical fisheries models are frequently used by researchers and agencies to understand the behavior of marine ecosystems or to estimate the maximum acceptable catch of different species of commercial interest. ...