Ordenação por translocação de genomas sem sinal utilizando algoritmos genéticos

Translocações são usadas para mensurar a distância evolutiva entre espécies. Do ponto de vista biológico dois tipos de genomas tem recebido atenção: genomas com e sem sinal. Ao considerar genomas com sinal, computar a distância mínima de translocações é linear enquanto que o caso sem sinal é NP-difícil. Propõem-se algoritmos genéticos (AGs) para resolver o problema de distância de translocação entre genomas sem sinal. A abordagem, consiste em utilizar uma população composta por indivíduos representando genomas com sinal obtidos de um genoma sem sinal provido como entrada. A solução de cada indivíduo é também uma solução admissível para o genoma dado. A função de aptidão utilizada, que é a distância para genomas com sinal, é computada linearmente com um algoritmo proposto por Bergeron et al. O AG baseado nessa abordagem foi aprimorado com duas técnicas de otimização: memética e aprendizagem baseada em oposição. Além disso, foram propostas paralelizações do AG memético buscando diminuir o tempo de processamento assim como melhorar a precisão. A qualidade dos resultados foi validada utilizando uma implementação de um algoritmo de raio de aproximação 1.5+" recentemente proposto por Cui et al. Experimentos foram realizados tomando como entrada genomas sintéticos e gerados a partir de dados biológicos. Os AGs forneceram melhores resultados que o algoritmo de controle de qualidade. As paralelizações apresentaram melhoras tanto no tempo de execução quanto na precisão dos resultados. Utilizou-se o teste de hipóteses de Wilcoxon a fim de verificar a significância estatística das melhorias fornecidas pelos AGs aprimorados em relação àquelas fornecidas pelo AG básico. Desta análise foi possível identificar que o AG memético provê resultados diferentes (melhores) que o AG básico, e que este último e o AG com aprendizagem baseada em oposição não apresentam nenhuma diferença significativa. O teste foi também aplicado para comparar as soluções das paralelizações confirmando que existem aprimoramentos dos resultados comparados com o AG memético. _______________________________________________________________________________________________ ABSTRACTTranslocations are used to measure the evolutionary distance between species. From a biological point of view two types of genomes have received attention: signed and unsigned genomes. When considering signed genomes, the problem can be solved in linear time, while, in the case of unsigned genomes the problem was shown to be NP-hard. Genetic algorithms (GAs) are proposed to solve the translocation distance problem between unsigned genomes. The approach consists in using a population composed of individuals representing signed genomes obtained from a given unsigned genome provided as input. The solution of each individual is also an admissible solution to the given genome. The fitness function used, which is the distance for signed genome, is computed linearly with an algorithm proposed by Bergeron et al. The GA based on this approach has been enhanced with two optimization techniques: memetic and opposition based learning. Also, parallelizations of the GA embedded with memetic were proposed seeking to improve both running time as the accuracy of results. The quality of the results was verified using an implementation of a 1.5+"-approximation algorithm recently proposed by Cui et al. Experiments were performed taking as input synthetic genomes and genomes generated from biological data. The GAs provided better results than the quality control algorithm. The parallelizations showed improvements both regarding runtime as well as accuracy. A statistical analysis based on the Wilcoxon test was performed to check if the improvements in the solutions provided by enhanced GAs compared to those provided by the basic GA have some significance. This analysis can identify that the GA embedded with the technical memetic provides different (better) results than GA and that the results provided by the GA embedded with opposition based learning presents no significant difference. The test was also performed to compare the solutions of the parallelizations confirming that there are improvements of the results regarding the GA embedded memetic

Dspace CRIS

Introduces the free DSpace version tool for Current Research Information System (CRIS), which extends the functionality of the version pattern. This tool seeks to integrate new functionalities, attending to other elements included in the paper offered by scientific repositories.Apresenta a ferramenta livre DSpace versão para o Current Research Information System (CRIS), que estende as funcionalidades da versão padrão. Essa ferramenta procura integrar novas funcionalidades, atendendo a outros elementos incluídos no papel ofertado pelos repositórios científicos

Reconfigurable Heterogeneous Parallel Island Models

Heterogeneous Parallel Island Models (HePIMs) run different bio-inspired algorithms (BAs) in their islands. From a variety of communication topologies and migration policies fine-tuned for homogeneous PIMs (HoPIMs), which run the same BA in all their islands, previous work introduced HePIMs that provided competitive quality solutions regarding the best-adapted BA in HoPIMs. This work goes a step forward, maintaining the population diversity provided by HePIMs, and increasing their flexibility, allowing BA reconfiguration on islands during execution: according to their performance, islands may substitute their BAs dynamically during the evolutionary process. Experiments with the introduced architectures (RecHePIMs) were applied to the NP-hard problem of sorting permutations by reversals, using four different BAs, namely, simple Genetic Algorithm, Double-point crossover Genetic Algorithm, Differential Evolution, and self-adjusting Particle Swarm Optimization. The results showed that the new reconfigurable heterogeneous models compute better quality solutions than the HePIMs closing the gap with the HoPIM running the best-adapted BA

Guia para a Integração do DSpace com o TemaTres

This guide presents the integration between the Digital Library implemented with DSpace and a Thesaurus implemented with TemaTres, resulting from studies developed within the scope of the project signed between the National Youth Secretariat (SNJ), linked to the Ministry of Women, Family and Human Rights (MMFDH), and the Brazilian Institute of Information on Science and Technology (Ibict). Thus, it seeks to present results of studies applied to the technologies used in the project.Este guia apresenta a integração entre a Biblioteca Digital implementada com o DSpace e um Tesauros implementado com o TemaTres, resultante de estudos desenvolvidos no âmbito do projeto firmado entre a Secretaria Nacional da Juventude (SNJ), vinculado ao Ministério da Mulher, Família e Direitos Humanos (MMFDH), e o Instituto Brasileiro de Informação em Ciência e Tecnologia (Ibict). Com isso, busca apresentar resultados de estudos aplicados às tecnologias utilizadas no projeto

Guia do usuário CKAN

This guide is the result of studies carried out with support in the technical documentation of the Existing CKAN on the Internet. The CKAN, short for Comprehensive Knowledge Archive Network, is a free tool for creating open data repositories, maintained by the Open Knowledge Foundation, a collaborative network non-profit promoting free knowledge.O presente guia é fruto dos estudos efetuados com apoio na documentação técnica do CKAN existente na Internet. O CKAN, sigla para Comprehensive Knowledge Archive Network, é uma ferramenta livre para criação de repositórios de dados abertos, mantida pela Open Knowledge Foundation, uma rede colaborativa sem fins lucrativos promotora do conhecimento livre

VuFind : uma ferramenta para recuperação da informação

In 2018, ENAP and IBICT signed a research project that contemplated, among other points, the implementation of a discovery and delivery system that would create a portal with a unique search, with all the information systems maintained by the library. The scenario consisted of its own and signed bases, resulting in a complex environment. After evaluating the scenario, the VuFind Discovery and Delivery System was chosen. Thus, this guide is part of the result of the research that aimed to solve the problem of integrating the informational ecosystem of the ENAP library, for the implementation of the ENAP knowledge portal. This portal offers a unique search tool to the school's information bases, both own and subscribed. Thus, it aims to disseminate the institution's information to its users.Em 2018, a ENAP e IBICT firmaram um projeto de pesquisa que contemplava, entre outros pontos, a implementação de um sistema de descoberta e entrega que criasse um portal com a busca única, com todos os sistemas de informação mantidos pela biblioteca. O cenário compunha-se de bases próprias e assinadas, resultando em um ambiente complexo. Depois da avaliação do cenário, optou-se pelo Sistema de Descoberta e Entrega VuFind. Assim, este guia faz parte do resultado da pesquisa que visou solucionar o problema de integração do ecossistema informacional da biblioteca da ENAP, para a implementação do portal do conhecimento da ENAP. Esta portal oferta a ferramenta de busca única às bases de informação da escola, tanto as próprias como as assinadas. Com isso, visa à disseminação da informação da instituição aos seus usuários

Estratégias para implementação do Ecossistema para informação do Sistema Nacional de Juventude

Esta obra é um produto do Projeto de Pesquisa sobre o Estudo para Sistematização e Desenvolvimento do Sistema Nacional de Juventude (Sinajuve).As opiniões emitidas nesta publicação são de exclusiva e inteira responsabilidade dos autores, não exprimindo, necessariamente, o ponto de vista do Instituto Brasileiro de Informação em Ciência e Tecnologia ou do Ministério da Ciência, Tecnologia e Inovações.This book represents the final result of the research project signed between the Secretaria Nacional de Juventude (SNJ), then linked to the Secretaria Geral da Presidência da República, and the Instituto Brasileiro de Informação em Ciência e Tecnologia (Ibict). In this way, it brings together the main results obtained in the various studies carried out within the scope of proposing strategies for putting this system into execution, constituting one of the lines of support to the SNJ.O presente livro representa o resultado final do projeto de pesquisa firmado entre a Secretaria Nacional de Juventude (SNJ), então vinculada à Secretaria Geral da Presidência da República, e o Instituto Brasileiro de Informação em Ciência e Tecnologia (Ibict).Dessa forma, reúne os principais resultados obtidos nos diversos estudos efetuados no âmbito da proposição de estratégias para a colocação desse sistema em execução, constituindo uma das linhas de apoio à SNJ

ATLANTIC BIRD TRAITS: a data set of bird morphological traits from the Atlantic forests of South America

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ

ATLANTIC BIRD TRAITS

Scientists have long been trying to understand why the Neotropical region holds the highest diversity of birds on Earth. Recently, there has been increased interest in morphological variation between and within species, and in how climate, topography, and anthropogenic pressures may explain and affect phenotypic variation. Because morphological data are not always available for many species at the local or regional scale, we are limited in our understanding of intra- and interspecies spatial morphological variation. Here, we present the ATLANTIC BIRD TRAITS, a data set that includes measurements of up to 44 morphological traits in 67,197 bird records from 2,790 populations distributed throughout the Atlantic forests of South America. This data set comprises information, compiled over two centuries (1820–2018), for 711 bird species, which represent 80% of all known bird diversity in the Atlantic Forest. Among the most commonly reported traits are sex (n = 65,717), age (n = 63,852), body mass (n = 58,768), flight molt presence (n = 44,941), molt presence (n = 44,847), body molt presence (n = 44,606), tail length (n = 43,005), reproductive stage (n = 42,588), bill length (n = 37,409), body length (n = 28,394), right wing length (n = 21,950), tarsus length (n = 20,342), and wing length (n = 18,071). The most frequently recorded species are Chiroxiphia caudata (n = 1,837), Turdus albicollis (n = 1,658), Trichothraupis melanops (n = 1,468), Turdus leucomelas (n = 1,436), and Basileuterus culicivorus (n = 1,384). The species recorded in the greatest number of sampling localities are Basileuterus culicivorus (n = 243), Trichothraupis melanops (n = 242), Chiroxiphia caudata (n = 210), Platyrinchus mystaceus (n = 208), and Turdus rufiventris (n = 191). ATLANTIC BIRD TRAITS (ABT) is the most comprehensive data set on measurements of bird morphological traits found in a biodiversity hotspot; it provides data for basic and applied research at multiple scales, from individual to community, and from the local to the macroecological perspectives. No copyright or proprietary restrictions are associated with the use of this data set. Please cite this data paper when the data are used in publications or teaching and educational activities. © 2019 The Authors. Ecology © 2019 The Ecological Society of Americ