Free tools and strategies for the generation of 3D finite element meshes: Modeling of the cardiac structures

The Finite Element Method is a well-known technique, being extensively applied in different areas. Studies using the Finite Element Method (FEM) are targeted to improve cardiac ablation procedures. For such simulations, the finite element meshes should consider the size and histological features of the target structures. However, it is possible to verify that some methods or tools used to generate meshes of human body structures are still limited, due to nondetailed models, nontrivial preprocessing, or mainly limitation in the use condition. In this paper, alternatives are demonstrated to solid modeling and automatic generation of highly refined tetrahedral meshes, with quality compatible with other studies focused on mesh generation. The innovations presented here are strategies to integrate Open Source Software (OSS). The chosen techniques and strategies are presented and discussed, considering cardiac structures as a first application context. © 2013 E. Pavarino et al.

Proposta de biomodelagem virtual utilizando softwares livres

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Metodologias de avaliação de sêmen e procedimentos de fertilização artificial de surubim-do-paraíba, Steindachneridion parahybae

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Avanços em reconhecimento de fala para português brasileiro e aplicações: ditado no libreoffice e unidade de resposta audível com asterisk

O reconhecimento automático de voz vem sendo cada vez mais útil e possível. Quando se trata de línguas como a Inglesa, encontram-se no mercado excelentes reconhecedores. Porem, a situação não e a mesma para o Português Brasileiro, onde os principais reconhecedores para ditado em sistemas desktop que já existiram foram descontinuados. A presente dissertação alinha-se com os objetivos do Laboratório de Processamento de Sinais da Universidade Federal do Pará, que é o desenvolvimento de um reconhecedor automático de voz para Português Brasileiro. Mais especificamente, as principais contribuições dessa dissertação são: o desenvolvimento de alguns recursos necessários para a construção de um reconhecedor, tais como: bases de áudio transcrito e API para desenvolvimento de aplicações; e o desenvolvimento de duas aplicações: uma para ditado em sistema desktop e outra para atendimento automático em um call center. O Coruja, sistema desenvolvido no LaPS para reconhecimento de voz em Português Brasileiro. Este alem de conter todos os recursos para fornecer reconhecimento de voz em Português Brasileiro possui uma API para desenvolvimento de aplicativos. O aplicativo desenvolvido para ditado e edição de textos em desktop e o SpeechOO, este possibilita o ditado para a ferramenta Writer do pacote LibreOffice, alem de permitir a edição e formatação de texto com comandos de voz. Outra contribuição deste trabalho e a utilização de reconhecimento automático de voz em call centers, o Coruja foi integrado ao software Asterisk e a principal aplicação desenvolvida foi uma unidade de resposta audível com reconhecimento de voz para o atendimento de um call center nacional que atende mais de 3 mil ligações diárias.

Softwares livres e prototipagem rápida aplicados na engenharia

In modern industry we see a growing need for answers cheaper, accurate and quick to deliver solutions and products to be able to remain competitive. In this way the inclusion of open source software and Rapid Prototyping tools have proven very important to obtain the expected results. This work, through information gathering, analysis software and their applicability, search tools commercially available rapid prototyping will demonstrate the importance of these tools and will also present possible configurations for a space for rapid prototyping within the university, as a proposal to implement a rapid prototyping laboratory at the Faculdade de Engenharia de Guaratinguetá

Concepção e Implementação de um Sistema de Controle de Arborização Urbana através da Integração de Softwares Livres e de Código Aberto

Suitable computacional tools allow to build applications that can link information to its physical location, and represent them into visual and interactive schemes, e ectively reaching the power of visual comunication. This leads the user to synthesize information in a simple and e cient way. These applications are linked to the de nition of Geographic Information System (GIS). GIS are comprised by many concepts and tools, which have the main purpose of collecting, storing, viewing and processing spatial data, obtaining the information needed for decision making. Within this context, this paper presents the Conception and Implementation of a Control System for Urban Forestry through Integration of Free and Open Source Software. This conception arose from the need of an Environmental Project developed by the Agriculture's House of the city of Regente Feij o, which has as main objectives cataloging and management of urban a orestation of the municipality. Due to this diversity of concepts, the challenge in building this system is the integration of platforms that are involved in all stages: collecting and storage of data, including maps and other spatial information, operations on the stored information, obtaining results and graphical visualization of the same. After implementation, it was possible to provide for the system users an improvement in the capacity of perception in the information analysis and facilitate the process of decision making

Processamento de fotomicrografias por meio da transformada wavelet starlet

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Modeling architecture and reference models for the ERF5 project

The adoption of ERPs systems by small and middle-sized companies may not be possible due to their cost. At the same time, when adapting ERP to the company's particular needs, the user keeps depending on the system's sellers due to the lack of access and knowledge of the respective code. Free and open-source software may promote advantages to the enterprises, however, for its adoption it is necessary the development of techniques and tools in order to facilitate its deployment and code maintenance. This article emphasizes the importance of defining modeling architectures and reference models for the development and maintenance of open-source ERPs, in special the ERP5 project.

Desarrollo de interfaces de usuario para una herramienta de telecontrol y automatización industrial

[ES] Este proyecto de fin de carrera aborda la actualización y refactorización de la aplicación Hecaton. Esta aplicación permite la monitorización y actuación en instalaciones industriales de manera remota a través de un interfaz web. Para ello hace uso de sensores y actuadores que, conectados a través de un equipo de adquisición de datos a un sistema informático servidor, permiten obtener, manipular y almacenar los datos y eventos recibidos. Hecaton ha sido desarrollado enteramente utilizando software libre. Además, el sistema permite ser personalizado, lo que posibilita su uso en todo tipo de escenarios, siendo el usuario quién define las reglas de funcionamiento. Este trabajo se trata del cuarto ciclo de desarrollo, pues la aplicación ha sido crea y ampliada en otros tres proyectos. En este último desarrollo se han actualizado las tecnologías y herramientas que forman parte de la aplicación. Se ha puesto especial énfasis en el rediseño de la interfaz web, adoptando el uso de las últimas tecnologías web que permiten un funcionamiento dinámico de la misma. Por otro lado se han corregido algunos errores de diseño e introducido el uso de nuevas herramientas para la gestión del proyecto software. Se trata por lo tanto de un ejercicio de refactorización software donde se ha puesto especial atención en conseguir un proyecto actualizado y que utilice metodologías de desarrollo actuales y que posibilite que sea actualizado en un futuro.

Application-oriented Mixed Integer Non-Linear Programming

In the most recent years there is a renovate interest for Mixed Integer Non-Linear Programming (MINLP) problems. This can be explained for different reasons: (i) the performance of solvers handling non-linear constraints was largely improved; (ii) the awareness that most of the applications from the real-world can be modeled as an MINLP problem; (iii) the challenging nature of this very general class of problems. It is well-known that MINLP problems are NP-hard because they are the generalization of MILP problems, which are NP-hard themselves. However, MINLPs are, in general, also hard to solve in practice. We address to non-convex MINLPs, i.e. having non-convex continuous relaxations: the presence of non-convexities in the model makes these problems usually even harder to solve. The aim of this Ph.D. thesis is to give a flavor of different possible approaches that one can study to attack MINLP problems with non-convexities, with a special attention to real-world problems. In Part 1 of the thesis we introduce the problem and present three special cases of general MINLPs and the most common methods used to solve them. These techniques play a fundamental role in the resolution of general MINLP problems. Then we describe algorithms addressing general MINLPs. Parts 2 and 3 contain the main contributions of the Ph.D. thesis. In particular, in Part 2 four different methods aimed at solving different classes of MINLP problems are presented. Part 3 of the thesis is devoted to real-world applications: two different problems and approaches to MINLPs are presented, namely Scheduling and Unit Commitment for Hydro-Plants and Water Network Design problems. The results show that each of these different methods has advantages and disadvantages. Thus, typically the method to be adopted to solve a real-world problem should be tailored on the characteristics, structure and size of the problem. Part 4 of the thesis consists of a brief review on tools commonly used for general MINLP problems, constituted an integral part of the development of this Ph.D. thesis (especially the use and development of open-source software). We present the main characteristics of solvers for each special case of MINLP.

A Web GIS Decision Support System For Coastal Risk Assessment and Mitigation Planning

Coastal flooding poses serious threats to coastal areas around the world, billions of dollars in damage to property and infrastructure, and threatens the lives of millions of people. Therefore, disaster management and risk assessment aims at detecting vulnerability and capacities in order to reduce coastal flood disaster risk. In particular, non-specialized researchers, emergency management personnel, and land use planners require an accurate, inexpensive method to determine and map risk associated with storm surge events and long-term sea level rise associated with climate change. This study contributes to the spatially evaluation and mapping of social-economic-environmental vulnerability and risk at sub-national scale through the development of appropriate tools and methods successfully embedded in a Web-GIS Decision Support System. A new set of raster-based models were studied and developed in order to be easily implemented in the Web-GIS framework with the purpose to quickly assess and map flood hazards characteristics, damage and vulnerability in a Multi-criteria approach. The Web-GIS DSS is developed recurring to open source software and programming language and its main peculiarity is to be available and usable by coastal managers and land use planners without requiring high scientific background in hydraulic engineering. The effectiveness of the system in the coastal risk assessment is evaluated trough its application to a real case study.

Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

Package Patterns for Visual Architecture Recovery

Recovering the architecture is the first step towards reengineering a software system. Many reverse engineering tools use top-down exploration as a way of providing a visual and interactive process for architecture recovery. During the exploration process, the user navigates through various views on the system by choosing from several exploration operations. Although some sequences of these operations lead to views which, from the architectural point of view, are mode relevant than others, current tools do not provide a way of predicting which exploration paths are worth taking and which are not. In this article we propose a set of package patterns which are used for augmenting the exploration process with in formation about the worthiness of the various exploration paths. The patterns are defined based on the internal package structure and on the relationships between the package and the other packages in the system. To validate our approach, we verify the relevance of the proposed patterns for real-world systems by analyzing their frequency of occurrence in six open-source software projects.

Radiation metabolomics. 3. Biomarker discovery in the urine of gamma-irradiated rats using a simplified metabolomics protocol of gas chromatography-mass spectrometry combined with random forests machine learning algorithm

Abstract Radiation metabolomics employing mass spectral technologies represents a plausible means of high-throughput minimally invasive radiation biodosimetry. A simplified metabolomics protocol is described that employs ubiquitous gas chromatography-mass spectrometry and open source software including random forests machine learning algorithm to uncover latent biomarkers of 3 Gy gamma radiation in rats. Urine was collected from six male Wistar rats and six sham-irradiated controls for 7 days, 4 prior to irradiation and 3 after irradiation. Water and food consumption, urine volume, body weight, and sodium, potassium, calcium, chloride, phosphate and urea excretion showed major effects from exposure to gamma radiation. The metabolomics protocol uncovered several urinary metabolites that were significantly up-regulated (glyoxylate, threonate, thymine, uracil, p-cresol) and down-regulated (citrate, 2-oxoglutarate, adipate, pimelate, suberate, azelaate) as a result of radiation exposure. Thymine and uracil were shown to derive largely from thymidine and 2'-deoxyuridine, which are known radiation biomarkers in the mouse. The radiation metabolomic phenotype in rats appeared to derive from oxidative stress and effects on kidney function. Gas chromatography-mass spectrometry is a promising platform on which to develop the field of radiation metabolomics further and to assist in the design of instrumentation for use in detecting biological consequences of environmental radiation release.

Kostenorientiertes Controlling von E-Learning-Plattformen mit dem TCO-Konzept

Zur administrativen Unterstützung von Lehr- und Lernprozessen werden E-Learning-Plattformen eingesetzt, die auf der Grundlage des Internet Funktionen zur Distribution von Lehr- und Lernmaterialien und zur Kommunikation zwischen Lehrenden und Lernenden anbieten. Zahlreiche wissenschaftliche Beiträge und Marktstudien beschäftigen sich mit der multikriteriellen Evaluation dieser Softwareprodukte zur informatorischen Fundierung strategischer Investitionsentscheidungen. Demgegenüber werden Instrumente zum kostenorientierten Controlling von E-Learning-Plattformen allenfalls marginal thematisiert. Dieser Beitrag greift daher das Konzept der Total Cost of Ownership (TCO) auf, das einen methodischen Ansatzpunkt zur Schaffung von Kostentransparenz von E-Learning-Plattformen bildet. Aufbauend auf den konzeptionellen Grundlagen werden Problembereiche und Anwendungspotenziale für das kostenorientierte Controlling von LMS identifiziert. Zur softwaregestützten Konstruktion und Analyse von TCO-Modellen wird das Open Source-Werkzeug TCO-Tool eingeführt und seine Anwendung anhand eines synthetischen Fallbeispiels erörtert. Abschließend erfolgt die Identifikation weiterführender Entwicklungsperspektiven des TCO-Konzepts im Kontext des E-Learning. Die dargestellte Thematik ist nicht nur von theoretischem Interesse, sondern adressiert auch den steigenden Bedarf von Akteuren aus der Bildungspraxis nach Instrumenten zur informatorischen Fundierung von Investitions- und Desinvestitionsentscheidungen im Umfeld des E-Learning.