VIP Barcoding: Composition vector-based software for rapid species identification based on DNA barcoding

Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/.

NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

VisArchive: a time and relevance based visual interface for searching, browsing, and exploring project archives

Background Project archives are becoming increasingly large and complex. On construction projects in particular, the increasing amount of information and the increasing complexity of its structure make searching and exploring information in the project archive challenging and time-consuming. Methods This research investigates a query-driven approach that represents new forms of contextual information to help users understand the set of documents resulting from queries of construction project archives. Specifically, this research extends query-driven interface research by representing three types of contextual information: (1) the temporal context is represented in the form of a timeline to show when each document was created; (2) the search-relevance context shows exactly which of the entered keywords matched each document; and (3) the usage context shows which project participants have accessed or modified a file. Results We implemented and tested these ideas within a prototype query-driven interface we call VisArchive. VisArchive employs a combination of multi-scale and multi-dimensional timelines, color-coded stacked bar charts, additional supporting visual cues and filters to support searching and exploring historical project archives. The timeline-based interface integrates three interactive timelines as focus + context visualizations. Conclusions The feasibility of using these visual design principles is tested in two types of project archives: searching construction project archives of an educational building project and tracking of software defects in the Mozilla Thunderbird project. These case studies demonstrate the applicability, usefulness and generality of the design principles implemented.

Setting up Multilingual Information Repository: A case Study with EPrints.org Software

Today 80 % of the content on the Web is in English, which is spoken by only 8% of the World population and 5% of Indian population. There is wealth of useful content in the various languages of the world other than English, which can be made available on the Internet. But, to date, for various reasons most of it is not yet available on the Internet. India itself has 18 officially recognized languages and scores of dialects. Although the medium of instruction for most of the higher education and research in India is English, substantial amount of literature by way of novels, textbooks, scholarly information are being generated in the other languages in the country. Many of the e-governance initiatives are in the respective state languages. In the past, support for different languages by the operating systems and the software packages were not very encouraging. However, with the advent of Unicode technology, operating systems and software packages are supporting almost all the major languages of the world that have scripts. In the work reported in this paper, we have explained the configuration changes that are needed for Eprints.org software to store multilingual content and to create a multilingual user interface.

Dasher - A data entry interface using continuous gestures and language models

Existing devices for communicating information to computers are bulky, slow to use, or unreliable. Dasher is a new interface incorporating language modelling and driven by continuous two-dimensional gestures, e.g. a mouse, touchscreen, or eye-tracker. Tests have shown that this device can be used to enter text at a rate of up to 34 words per minute, compared with typical ten-finger keyboard typing of 40-60 words per minute. Although the interface is slower than a conventional keyboard, it is small and simple, and could be used on personal data assistants and by motion-impaired computer users.

Desarrollo de software para la realización de ensayos dinámicos de mecanismos de cinemática paralela

[ES]El presente Trabajo de Fin de Grado tiene como objetivo contribuir al desarrollo de un proyecto de investigación mediante la programación y control del movimiento de mecanismos de cinemática paralela para la realización de ensayos dinámicos. Dicho proyecto está enmarcado dentro de una línea de investigación del grupo de investigación CompMech de la UPV-­‐EHU que gira en torno al desarrollo y estudio de este tipo de mecanismos. Esto es; este trabajo, más allá de la utilidad que pudiera tener por sí mismo, está pensado para formar parte de un proyecto de mayor envergadura, para cuyo éxito será imprescindible la colaboración con otros investigadores y la integración de este trabajo con los realizados por ellos. Consiste en la creación de un software para el control y movimiento de mecanismos, generando vibraciones para la realización de ensayos dinámicos. Para ello, se programarán sobre la plataforma LabVIEW la interfaz de usuario y el motor de cálculo. Una vez se compruebe que el programa funciona correctamente, se integrará dentro de un programa principal, un control articular que será el encargado de comunicarse con la máquina. Posteriormente, se procederá a la realización de ensayos experimentales sobre los propios robots, en taller. Se tomarán medidas mediante acelerómetros y otros dispositivos, determinando las medidas más adecuadas para su correcta validación. Finalmente, se generalizará el trabajo realizado para posibilitar su empleo futuro en diferentes mecanismos

SAQUA - sistema baseado em software livre para análise do comportamento da qualidade das águas fluviais: aplicado à bacia do rio Paraíba do Sul.

Nesta dissertação foi desenvolvido o sistema SAQUA (Sistema para Análise da Qualidade das Águas Fluviais), que permite o acompanhamento dos dados de séries históricas de parâmetros físico-químicos para análise da qualidade de águas fluviais. A alimentação do sistema SAQUA se dá a partir do arquivo tipo texto gerado no Hidroweb, sistema de banco de dados hidrológicos da ANA (Agência Nacional de Águas), disponibilizado na internet. O SAQUA constitui uma interface que permite a análise espaço-temporal de parâmetros de qualidade da água específicos definidos pelo usuário. A interface foi construída utilizando o servidor de mapas Mapserver, as linguagens HTML e PHP, além de consultas SQL e o uso do servidor Web Apache. A utilização de uma linguagem dinâmica como o PHP permitiu usar recursos internos do Mapserver por meio de funções que interagem de forma mais flexível com códigos presentes e futuros, além de interagir com o código HTML. O Sistema apresenta como resultado a representação gráfica da série histórica por parâmetro e, em mapa, a localização das estações em análise também definidas pelo usuário, geralmente associadas a uma determinada região hidrográfica. Tanto na representação gráfica da série temporal quanto em mapa, são destacados a partir de código de cores a estação de monitoramento e a observação em que os limites estabelecidos na resolução CONAMA 357/05 não foi atendido. A classe de uso da resolução CONAMA que será usada na análise também pode ser definida pelo usuário. Como caso de estudo e demonstração das funções do SAQUA foi escolhida a bacia hidrográfica do rio Paraíba do Sul, localizada na região hidrográfica Atlântico Sudeste do Brasil. A aplicação do sistema demonstrou ótimos resultados e o potencial da ferramenta computacional como apoio ao planejamento e à gestão dos recursos hídricos. Ressalta-se ainda, que todo o sistema foi desenvolvido a partir de softwares disponibilizados segundo a licença GPL de software livre, ou seja, sem custo na aquisição de licenças, demonstrando o potencial da aplicação destas ferramentas no campo dos recursos hídricos.

Avaliação de sistemas de informações geográficas na internet através de teste de software.

A utilização de sistemas de informações geográficas via Web (Sigweb) tem crescido nos últimos anos pela facilidade na manipulação e visualização de informações de diferentes lugares através da Internet. O objetivo deste estudo é realizar testes de sistemas de informações geográficas na Internet com ênfase na técnica funcional para avaliar a funcionalidade, usabilidade, a navegabilidade dos programas conhecidos como Sigweb prontos para usar. Para tanto, foi necessária a identificação dos casos de uso dos programas propostos para o estudo. Como resultado se pode conferir o comportamento dos sistemas durante os testes, além de distinguir as características de cada SigWeb e as dificuldades encontradas.

La txalaparta digital: Un análisis de la txalaparta a través del desarrollo de software

239 p. + anexos

Política Carioca Rindo a Toa e o Programa Saúde e Cidadania Dentescola: análise da política de saúde bucal no município do Rio de Janeiro e sua trajetória rumo à implementação considerando a interface com o Brasil Sorridente

A presente dissertação constituiu um estudo da política na Área de Saúde Bucal em um município de grande porte através dos seus processos - de formulação e implementação - seus atores e sua interface com a Política Nacional Brasil Sorridente. Tomando como referência a experiência do Rio de Janeiro no período de 2001 a 2006, optou-se por um estudo de caso por tratar-se de descrever a unidade a política - em profundidade e em detalhe. A condução de listas livres possibilitou um maior discernimento das mudanças político-organizacionais e principalmente de dois momentos consecutivos: a suposta centralidade da Saúde Bucal na agenda municipal com o decreto do Programa Saúde e Cidadania Dentescola e a oportunidade de se estabelecer uma política de Saúde Bucal contextualizada no acolhimento, no acesso e na universalidade da atenção. O processo de implementação da Política Carioca Rindo à Toa e do Programa Saúde e Cidadania Dentescola dependeu principalmente do aumento de recursos humanos e da aproximação desses com as propostas de Integralidade e Transversalidade.

A computationally efficient software application for calculating vibration from underground railways

The PiP model is a software application with a user-friendly interface for calculating vibration from underground railways. This paper reports about the software with a focus on its latest version and the plans for future developments. The software calculates the Power Spectral Density of vibration due to a moving train on floating-slab track with track irregularity described by typical values of spectra for tracks with good, average and bad conditions. The latest version accounts for a tunnel embedded in a half space by employing a toolbox developed at K.U. Leuven which calculates Green's functions for a multi-layered half-space. © 2009 IOP Publishing Ltd.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a neces- sity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the chal- lenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabil- ities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry manage- ment in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design sys- tem, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heav- ily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. © 2012 by the authors. Published by the American Institute of Aeronautics and Astronautics, Inc.

Enhancing and developing the practical optimisation capabilities and intelligence of automatic design software

In the modern engineering design cycle the use of computational tools becomes a necessity. The complexity of the engineering systems under consideration for design increases dramatically as the demands for advanced and innovative design concepts and engineering products is expanding. At the same time the advancements in the available technology in terms of computational resources and power, as well as the intelligence of the design software, accommodate these demands and make them a viable approach towards the challenge of real-world engineering problems. This class of design optimisation problems is by nature multi-disciplinary. In the present work we establish enhanced optimisation capabilities within the Nimrod/O tool for massively distributed execution of computational tasks through cluster and computational grid resources, and develop the potential to combine and benefit from all the possible available technological advancements, both software and hardware. We develop the interface between a Free Form Deformation geometry management in-house code with the 2D airfoil aerodynamic efficiency evaluation tool XFoil, and the well established multi-objective heuristic optimisation algorithm NSGA-II. A simple airfoil design problem has been defined to demonstrate the functionality of the design system, but also to accommodate a framework for future developments and testing with other state-of-the-art optimisation algorithms such as the Multi-Objective Genetic Algorithm (MOGA) and the Multi-Objective Tabu Search (MOTS) techniques. Ultimately, heavily computationally expensive industrial design cases can be realised within the presented framework that could not be investigated before. ©2012 AIAA.

Teste de fluxo de dados de programas com ponteiros e registros.

Dois modelos mais precisos de análise de fluxo de dados voltados para o teste de programas que utilizaram ponteiros e campos de registros são apresentados. Os modelos propostos são baseados em uma abordagem conservadora e foram implementados na ferramenta POKE-TOOL. A conjectura é que a análise de fluxo de dados mais precisa aumenta a eficácia do teste a um custo razoável .Para investigar essa conjectura, um estudo de caso foi realizado para avaliar a eficácia eo custo da utilização dos dois modelos no teste com duas famílias diferentes de critérios de teste baseados em análise de fluxo de dados. Os resultados obtidos indicam que a eficácia dos modelos dependem do programa e dos defeitos que ele contém. A segunda observação em especial indica que existem defeitos cuja detecção é facilitada quando os modelos propostos são utilizados. Para uma das famílias de critérios de teste, foi observado que o custo adicional causado pela análise mais precisa de fluxo de dados é razoável.