Search results for "Computer Science Applications"
showing 10 items of 3993 documents
MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study
2019
Abstract Motivation Metagenomes offer a glimpse into the total genomic diversity contained within a sample. Currently, however, there is no straightforward way to obtain a non-redundant list of all putative homologs of a set of reference sequences present in a metagenome. Results To address this problem, we developed a novel clustering approach called ‘metagenomic clustering by reference library’ (MCRL), where a reference library containing a set of reference genes is clustered with respect to an assembled metagenome. According to our proposed approach, reference genes homologous to similar sets of metagenomic sequences, termed ‘signatures’, are iteratively clustered in a greedy fashion, re…
WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees
2021
Trees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL, matK, and trnH-psbA), together with modelled occurrences and a phylogeny for all…
Spanish electoral archive. SEA database
2021
This paper introduces the SEA database (acronym for Spanish Electoral Archive). SEA brings together the most complete public repository available to date on Spanish election outcomes. SEA holds all the results recorded from the electoral processes of General (1979–2019), Regional (1989–2021), Local (1979–2019) and European Parliamentary (1987–2019) elections held in Spain since the restoration of democracy in the late 70 s, in addition to other data sets with electoral content. The data are offered for free and is presented in a homogeneous and friendly format. Most of the databases are available for download with data from various electoral levels, including from the ballot box level. This…
A database for the monitoring of thermal anomalies over the Amazon forest and adjacent intertropical oceans
2015
AbstractAdvances in information technologies and accessibility to climate and satellite data in recent years have favored the development of web-based tools with user-friendly interfaces in order to facilitate the dissemination of geo/biophysical products. These products are useful for the analysis of the impact of global warming over different biomes. In particular, the study of the Amazon forest responses to drought have recently received attention by the scientific community due to the occurrence of two extreme droughts and sustained warming over the last decade. Thermal Amazoni@ is a web-based platform for the visualization and download of surface thermal anomalies products over the Ama…
Galaxy LIMS for next-generation sequencing.
2013
Abstract Summary: We have developed a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation. In addition, the platform provides the researcher with a user-friendly interface to create a request, submit accompanying samples, upload sample quality measurements and access to the sequencing results. As the LIMS is within the Galaxy platform, the …
Textual data compression in computational biology: a synopsis.
2009
Abstract Motivation: Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. Results: The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been use…
Weighted distance-based trees for ranking data
2017
Within the framework of preference rankings, the interest can lie in finding which predictors and which interactions are able to explain the observed preference structures, because preference decisions will usually depend on the characteristics of both the judges and the objects being judged. This work proposes the use of a univariate decision tree for ranking data based on the weighted distances for complete and incomplete rankings, and considers the area under the ROC curve both for pruning and model assessment. Two real and well-known datasets, the SUSHI preference data and the University ranking data, are used to display the performance of the methodology.
Stochastic Learning for SAT- Encoded Graph Coloring Problems
2010
The graph coloring problem (GCP) is a widely studied combinatorial optimization problem due to its numerous applications in many areas, including time tabling, frequency assignment, and register allocation. The need for more efficient algorithms has led to the development of several GC solvers. In this paper, the authors introduce a team of Finite Learning Automata, combined with the random walk algorithm, using Boolean satisfiability encoding for the GCP. The authors present an experimental analysis of the new algorithm’s performance compared to the random walk technique, using a benchmark set containing SAT-encoding graph coloring test sets.
Mean-field games and dynamic demand management in power grids
2013
This paper applies mean-field game theory to dynamic demand management. For a large population of electrical heating or cooling appliances (called agents), we provide a mean-field game that guarantees desynchronization of the agents thus improving the power network resilience. Second, for the game at hand, we exhibit a mean-field equilibrium, where each agent adopts a bang-bang switching control with threshold placed at a nominal temperature. At equilibrium, through an opportune design of the terminal penalty, the switching control regulates the mean temperature (computed over the population) and the mains frequency around the nominal value. To overcome Zeno phenomena we also adjust the ban…