The Microbe browser for comparative genomics.

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/api.

Tietokantakäyttäjän autentikoinnin ja auktorisoinnin hallinnointi Active Directory -ympäristössä

Usean nykypäivän yrityksen tietojärjestelmäinfrastruktuuri on muotoutunut heterogeeniseksi ympäristöksi, jossa eri käyttöjärjestelmä- ja laitealustoilla toimii usean eri valmistajan toimittamia järjestelmiä. Heterogeenisen ympäristön hallitsemiseksi yritykseltä vaaditaan keskitettyä tietovarastoa, johon on tallennettu tietoa käytetystä järjestelmäympäristöstä sekä sen komponenteista. Tähän tarkoitukseen Microsoft toi markkinoille vuonna 1999 Active Directory 2000 -hakemistopalvelun. Heterogeenisessa ympäristössä käyttäjien autentikointi ja auktorisointi on erittäin vaativaa. Pahimmassa tapauksessa käyttäjällä voi olla kymmeniä käyttäjätunnus-salasana-yhdistelmiä yrityksen eri tietojärjestelmiin. Lisäksi jokaisessa tietojärjestelmässäon ylläpidettävä käyttäjäkohtaisia toimintavaltuuksia. Niin käyttäjän kuin ylläpitäjänkin näkökulmasta tällainen skenaario on painajainen. Tässä diplomityössä kartoitetaan mahdollisuuksia Oracle-tietokantojen käyttäjien autentikoinnin sekä auktorisoinnin keskittämiseksi Active Directory -hakemistopalveluun. Työssä tarkastellaan tarkoitukseen soveltuvia valmiita kaupallisia ratkaisuja sekä tutkitaan mahdollisuuksia oman ratkaisumallin toteuttamiseksi umpäristöstä löytyvien ohjelmointirajapintojen avulla.

WWW-pohjaisen kauppapaikan palvelinkomponentin toteutus ja jatkokehitys

Diplomityössä perehdytään Java-teknologiaan yleisesti ja tarkemmin Java 2 -liiketoimintasovellusalustan (Java 2 Platform, Enterprise Edition) määritykseen sisältyviin ohjelmointirajapintoihin. Erityisesti paneudutaan Enterprise JavaBeans -liiketoimintasovellusten komponenttiarkkitehtuuriin, jonka avulla voidaan toteuttaa hajautettuja, skaalautuvia, tapahtumankäsittelyä tukevia ja turvallisia liiketoimintasovelluksia. Käytännön osa liittyy projektiin, jossa suunniteltiin ja toteutettiin WWW- pohjaisen kauppapaikan perustoiminnallisuus. Työhön sisältyivät markkinapaikan määrittelyyn ja suunnitteluun osallistuminen sekä markkinapaikan yhden palvelinkomponentin yksityiskohtainen suunnittelu, toteutus ja jatkokehityksen ideointi. Lopputuloksena saavutettiin asetetut tavoitteet täyttävä järjestelmä, joka otettiin tuotantokäyttöön ja joka on hyvä pohja järjestelmän jatkokehitysprojekteille.

Applications of graph transformation in tools for domain-specific modeling languages

The use of domain-specific languages (DSLs) has been proposed as an approach to cost-e ectively develop families of software systems in a restricted application domain. Domain-specific languages in combination with the accumulated knowledge and experience of previous implementations, can in turn be used to generate new applications with unique sets of requirements. For this reason, DSLs are considered to be an important approach for software reuse. However, the toolset supporting a particular domain-specific language is also domain-specific and is per definition not reusable. Therefore, creating and maintaining a DSL requires additional resources that could be even larger than the savings associated with using them. As a solution, di erent tool frameworks have been proposed to simplify and reduce the cost of developments of DSLs. Developers of tool support for DSLs need to instantiate, customize or configure the framework for a particular DSL. There are di erent approaches for this. An approach is to use an application programming interface (API) and to extend the basic framework using an imperative programming language. An example of a tools which is based on this approach is Eclipse GEF. Another approach is to configure the framework using declarative languages that are independent of the underlying framework implementation. We believe this second approach can bring important benefits as this brings focus to specifying what should the tool be like instead of writing a program specifying how the tool achieves this functionality. In this thesis we explore this second approach. We use graph transformation as the basic approach to customize a domain-specific modeling (DSM) tool framework. The contributions of this thesis includes a comparison of di erent approaches for defining, representing and interchanging software modeling languages and models and a tool architecture for an open domain-specific modeling framework that e ciently integrates several model transformation components and visual editors. We also present several specific algorithms and tool components for DSM framework. These include an approach for graph query based on region operators and the star operator and an approach for reconciling models and diagrams after executing model transformation programs. We exemplify our approach with two case studies MICAS and EFCO. In these studies we show how our experimental modeling tool framework has been used to define tool environments for domain-specific languages.

Opetuskäyttöön suunnatun videoneuvottelteluportaalin prototyypin suunnittelu ja toteuttaminen avoimilla tekniikoilla

Työ tutkii, miten yksinkertaisen opetuskäyttöön suunnatun videoneuvotteluportaalin prototyypin rakentaminen onnistuu avoimilla tekniikoilla. WebRTC mahdollistaa selaimen päällä toimivan videoneuvottelusovelluksen rakentamisen avoimia ohjelmistorajapintoja käyttäen. Prototyypin toteuttamiseen käytetään WebRTC:n lisäksi WebSocket-standardia keskustelun tahojen yhdistämiseen. WebSocket toteutetaan Node.js:ää käyttävällä socket.io-kirjastolla. Sovelluksen avulla on tarkoitus pystyä muodostamaan ääni- ja videoyhteys kahden asiakasohjelman välille. Opetuskäyttöä tukevina ominaisuuksina mukana on myös tekstipohjainen keskustelu ja mahdollisuus opetuskalvojen selaamiseen. Lopputuloksena on laajennettavissa oleva avoin videoneuvottelusovelluksen prototyyppi.

Logiciel de génération de nombres aléatoires dans OpenCL

clRNG et clProbdist sont deux interfaces de programmation (APIs) que nous avons développées pour la génération de nombres aléatoires uniformes et non uniformes sur des dispositifs de calculs parallèles en utilisant l’environnement OpenCL. La première interface permet de créer au niveau d’un ordinateur central (hôte) des objets de type stream considérés comme des générateurs virtuels parallèles qui peuvent être utilisés aussi bien sur l’hôte que sur les dispositifs parallèles (unités de traitement graphique, CPU multinoyaux, etc.) pour la génération de séquences de nombres aléatoires. La seconde interface permet aussi de générer au niveau de ces unités des variables aléatoires selon différentes lois de probabilité continues et discrètes. Dans ce mémoire, nous allons rappeler des notions de base sur les générateurs de nombres aléatoires, décrire les systèmes hétérogènes ainsi que les techniques de génération parallèle de nombres aléatoires. Nous présenterons aussi les différents modèles composant l’architecture de l’environnement OpenCL et détaillerons les structures des APIs développées. Nous distinguons pour clRNG les fonctions qui permettent la création des streams, les fonctions qui génèrent les variables aléatoires uniformes ainsi que celles qui manipulent les états des streams. clProbDist contient les fonctions de génération de variables aléatoires non uniformes selon la technique d’inversion ainsi que les fonctions qui permettent de retourner différentes statistiques des lois de distribution implémentées. Nous évaluerons ces interfaces de programmation avec deux simulations qui implémentent un exemple simplifié d’un modèle d’inventaire et un exemple d’une option financière. Enfin, nous fournirons les résultats d’expérimentation sur les performances des générateurs implémentés.

BSmart: desenvolvimento rigoroso de aplicações Java Card com base no método formal B

Java Card technology allows the development and execution of small applications embedded in smart cards. A Java Card application is composed of an external card client and of an application in the card that implements the services available to the client by means of an Application Programming Interface (API). Usually, these applications manipulate and store important information, such as cash and confidential data of their owners. Thus, it is necessary to adopt rigor on developing a smart card application to improve its quality and trustworthiness. The use of formal methods on the development of these applications is a way to reach these quality requirements. The B method is one of the many formal methods for system specification. The development in B starts with the functional specification of the system, continues with the application of some optional refinements to the specification and, from the last level of refinement, it is possible to generate code for some programming language. The B formalism has a good tool support and its application to Java Card is adequate since the specification and development of APIs is one of the major applications of B. The BSmart method proposed here aims to promote the rigorous development of Java Card applications up to the generation of its code, based on the refinement of its formal specification described in the B notation. This development is supported by the BSmart tool, that is composed of some programs that automate each stage of the method; and by a library of B modules and Java Card classes that model primitive types, essential Java Card API classes and reusable data structures

Gestión de vídeo distribuido

[ES] El principal objetivo de este Trabajo Final de Grado (TFG) fue la creación de un sistema de gestión de vídeo distribuido utilizando cámaras de videovigilancia IP. Esta propuesta surgió a partir de la idea de ofrecer un acceso simultáneo, tanto online como offline, a las secuencias de vídeo generadas por una red de cámaras IP en un entorno dado. El resultado obtenido fue una infraestructura software ampliable  que ofrece al usuario una serie de funcionalidades con cámaras de red, abstrayéndolo de detalles internos. El trabajo está compuesto por tres elementos claramente diferenciados: integración de cámaras IP, almacenamiento en vídeo y creación del sistema de vídeo distribuido. La integración de cámaras IP tiene como objetivo comunicar al equipo con la cámara de red para la obtención del flujo de imágenes que transmite. Dicha comunicación se establece vía HTTP (Hypertext Transfer Protocol) gracias a la interfaz de programación (API) de la que disponen estos dispositivos. El segundo elemento, el almacenamiento en vídeo, tiene como función guardar las imágenes de la cámara IP en archivos de vídeo. De esta manera se ofrece su posterior visualización en diferido. Finalmente, el sistema de vídeo distribuido permite la reproducción simultánea de múltiples vídeos grabados por la red de cámaras IP. Adicionalmente, vídeos grabados por otros dispositivos también son admitidos. El material desarrollado dispone del potencial necesario para convertirse en una herramienta libre de amplio uso en sistemas UNIX para cámaras IP, así como suponer la base de futuros proyectos relacionados con estos dispositivos.

Diseño e implementación de funcionalidades OpenMP, basadas en modelos de concurrencia desarrollados en lenguaje Go

A raíz de la aparición de los procesadores dotados de varios “cores”, la programación paralela, un concepto que, por otra parte no era nada nuevo y se conocía desde hace décadas, sufrió un nuevo impulso, pues se creía que se podía superar el techo tecnológico que había estado limitando el rendimiento de esta programación durante años. Este impulso se ha ido manteniendo hasta la actualidad, movido por la necesidad de sistemas cada vez más potentes y gracias al abaratamiento de los costes de fabricación. Esta tendencia ha motivado la aparición de nuevo software y lenguajes con componentes orientados precisamente al campo de la programación paralela. Este es el caso del lenguaje Go, desarrollado por Google y lanzado en 2009. Este lenguaje se basa en modelos de concurrencia que lo hacen muy adecuados para abordar desarrollos de naturaleza paralela. Sin embargo, la programación paralela es un campo complejo y heterogéneo, y los programadores son reticentes a utilizar herramientas nuevas, en beneficio de aquellas que ya conocen y les son familiares. Un buen ejemplo son aquellas implementaciones de lenguajes conocidos, pero orientadas a programación paralela, y que siguen las directrices de un estándar ampliamente reconocido y aceptado. Este es el caso del estándar OpenMP, un Interfaz de Programación de Aplicaciones (API) flexible, portable y escalable, orientado a la programación paralela multiproceso en arquitecturas multi-core o multinucleo. Dicho estándar posee actualmente implementaciones en los lenguajes C, C++ y Fortran. Este proyecto nace como un intento de aunar ambos conceptos: un lenguaje emergente con interesantes posibilidades en el campo de la programación paralela, y un estándar reputado y ampliamente extendido, con el que los programadores se encuentran familiarizados. El objetivo principal es el desarrollo de un conjunto de librerías del sistema (que engloben directivas de compilación o pragmas, librerías de ejecución y variables de entorno), soportadas por las características y los modelos de concurrencia propios de Go; y que añadan funcionalidades propias del estándar OpenMP. La idea es añadir funcionalidades que permitan programar en lenguaje Go utilizando la sintaxis que OpenMP proporciona para otros lenguajes, como Fortan y C/C++ (concretamente, similar a esta última), y, de esta forma, dotar al usuario de Go de herramientas para programar estructuras de procesamiento paralelo de forma sencilla y transparente, de la misma manera que lo haría utilizando C/C++.---ABSTRACT---As a result of the appearance of processors equipped with multiple "cores ", parallel programming, a concept which, moreover, it was not new and it was known for decades, suffered a new impulse, because it was believed they could overcome the technological ceiling had been limiting the performance of this program for years. This impulse has been maintained until today, driven by the need for ever more powerful systems and thanks to the decrease in manufacturing costs. This trend has led to the emergence of new software and languages with components guided specifically to the field of parallel programming. This is the case of Go language, developed by Google and released in 2009. This language is based on concurrency models that make it well suited to tackle developments in parallel nature. However, parallel programming is a complex and heterogeneous field, and developers are reluctant to use new tools to benefit those who already know and are familiar. A good example are those implementations from well-known languages, but parallel programming oriented, and witch follow the guidelines of a standard widely recognized and accepted. This is the case of the OpenMP standard, an application programming interface (API), flexible, portable and scalable, parallel programming oriented, and designed for multi-core architectures. This standard currently has implementations in C, C ++ and Fortran. This project was born as an attempt to combine two concepts: an emerging language, with interesting possibilities in the field of parallel programming, and a reputed and widespread standard, with which programmers are familiar with. The main objective is to develop a set of system libraries (which includes compiler directives or pragmas, runtime libraries and environment variables), supported by the characteristics and concurrency patterns of Go; and that add custom features from the OpenMP standard. The idea is to add features that allow programming in Go language using the syntax OpenMP provides for other languages, like Fortran and C / C ++ (specifically, similar to the latter ), and, in this way, provide Go users with tools for programming parallel structures easily and, in the same way they would using C / C ++.

Design and Development of Geographical Information System (GIS) Map for Nuclear Waste Streams

A nuclear waste stream is the complete flow of waste material from origin to treatment facility to final disposal. The objective of this study was to design and develop a Geographic Information Systems (GIS) module using Google Application Programming Interface (API) for better visualization of nuclear waste streams that will identify and display various nuclear waste stream parameters. A proper display of parameters would enable managers at Department of Energy waste sites to visualize information for proper planning of waste transport. The study also developed an algorithm using quadratic Bézier curve to make the map more understandable and usable. Microsoft Visual Studio 2012 and Microsoft SQL Server 2012 were used for the implementation of the project. The study has shown that the combination of several technologies can successfully provide dynamic mapping functionality. Future work should explore various Google Maps API functionalities to further enhance the visualization of nuclear waste streams.

Aplicações de telemedicina usando WEBRTC

O uso das tecnologias de informação e comunicação em Portugal na área médica tem tido um grande aumento nas últimas décadas. Tal pode constatar-se a vários níveis, como sejam a implementação crescente e em larga escala de sistemas de informação em hospitais e centros de saúde, o desenvolvimento de aplicações para auxiliar a análise dos principais meios complementares de diagnóstico, a receita eletrónica e o registo de paciente eletrónico, apenas para citar alguns exemplos. A procura crescente de profissionais de saúde de várias especialidades tem tido um aumento considerável nos últimos anos. Por um lado, a população está cada vez mais envelhecida, por via do aumento da esperança média de vida. Por outro lado tem aumentado a preocupação com a saúde e o bem estar próprio dos cidadãos, levando-os a recorrer mais vezes e a mais especialidades do que no passado. O êxodo da população do interior do país para os grandes centros no litoral, complementado pelas políticas orçamentais restritivas na área da saúde, tem acentuado as diferenças de prestação de cuidados de saúde a toda a população do país, de forma equitativa e eficaz. Para tal tem ainda contribuído o emagrecimento dos orçamentos dos hospitais e a pressão para que estes cumpram as metas de produtividade definidas, com custos cada vez mais reduzidos. Um dos contributos das tecnologias de informação para mitigar o afastamento entre o paciente e os profissionais de saúde, consiste na implementação de soluções de consulta "à distância", com a utilização de vídeo e voz, através de aplicações de telemedicina. Ao nível da teleconsulta e da telemedicina têm existido alguns avanços significativos, sendo possível encontrar alguns casos de sucesso na utilização destes meios para facilitar o acesso generalizado de toda a população a cuidados médicos de saúde. Constata-se contudo que as aplicações usadas são geralmente proprietárias, carecem de instalação de software específico, muitas vezes proprietário e por vezes com custos para as entidades que disponibilizam o serviço. Por exemplo, a utilização de uma ligação por Skype para uma teleconsulta obriga a que a aplicação esteja instalada em ambos os computadores (médico e paciente). Nesta dissertação apresenta-se uma solução de telemedicina baseada na Application Programming Interface (API) Web Real-Time Comunication (WebRTC), que permite o envio de voz e imagem entre dois browsers usando os protocolos de comunicação na Web. Além do vídeo e da voz foram integrados na aplicação duas funcionalidades particularmente interessantes numa teleconsulta: envio bidirecional de ficheiros (por exemplo, ficheiro PDF com o resultado das últimas análise que o paciente realizou) e desenho num "quadro branco", permitindo ao paciente ou ao médico ilustrarem de forma livre algum aspeto associado à consulta em causa. A aplicação utiliza exclusivamente componentes de software opensource e apenas necessita que ambos os computadores tenham instalado um browser de acesso à Web que suporte a comunicação por WebRTC, como o Google Chrome ou o Firefox. Pretende-se desta forma facilitar o acesso aos serviços de telemedicina evitando a instalação e configuração de software específico, bem como reduzir os custos através de soluções opensource com licença General Public License (GPL) e isenta de custos. Foram realizados alguns testes de aceitação da solução, em ambiente hospitalar. Genericamente, pretendeu-se validar o funcionamento da API WebRTC, aferir sobre a aceitação das funcionalidades implementadas e identificar obstáculos técnicos à sua implementação na rede de um hospital ou centro de saúde. Embora tenham sido identificados alguns problemas na comunicação, resultantes maioritariamente do tipo de configurações da rede em que os computadores estavam instalados, os resultados globais obtidos são bastante promissores, dando-nos boas perspetivas quanto à sua implementação em ambiente de produção.

Applied web traffic analysis for numerical encoding of SQL Injection attack features.

SQL Injection Attack (SQLIA) remains a technique used by a computer network intruder to pilfer an organisation’s confidential data. This is done by an intruder re-crafting web form’s input and query strings used in web requests with malicious intent to compromise the security of an organisation’s confidential data stored at the back-end database. The database is the most valuable data source, and thus, intruders are unrelenting in constantly evolving new techniques to bypass the signature’s solutions currently provided in Web Application Firewalls (WAF) to mitigate SQLIA. There is therefore a need for an automated scalable methodology in the pre-processing of SQLIA features fit for a supervised learning model. However, obtaining a ready-made scalable dataset that is feature engineered with numerical attributes dataset items to train Artificial Neural Network (ANN) and Machine Leaning (ML) models is a known issue in applying artificial intelligence to effectively address ever evolving novel SQLIA signatures. This proposed approach applies numerical attributes encoding ontology to encode features (both legitimate web requests and SQLIA) to numerical data items as to extract scalable dataset for input to a supervised learning model in moving towards a ML SQLIA detection and prevention model. In numerical attributes encoding of features, the proposed model explores a hybrid of static and dynamic pattern matching by implementing a Non-Deterministic Finite Automaton (NFA). This combined with proxy and SQL parser Application Programming Interface (API) to intercept and parse web requests in transition to the back-end database. In developing a solution to address SQLIA, this model allows processed web requests at the proxy deemed to contain injected query string to be excluded from reaching the target back-end database. This paper is intended for evaluating the performance metrics of a dataset obtained by numerical encoding of features ontology in Microsoft Azure Machine Learning (MAML) studio using Two-Class Support Vector Machines (TCSVM) binary classifier. This methodology then forms the subject of the empirical evaluation.

Uma arquitetura de referência para o processamento distribuído de stream de dados em soluções analíticas de near real-time

Dissertação (mestrado)—Universidade de Brasília, Faculdade de Tecnologia, Departamento de Engenharia Elétrica, 2015.

A Java expression evaluator for nonlinear programming

Finding the optimal value for a problem is usual in many areas of knowledge where in many cases it is needed to solve Nonlinear Optimization Problems. For some of those problems it is not possible to determine the expression for its objective function and/or its constraints, they are the result of experimental procedures, might be non-smooth, among other reasons. To solve such problems it was implemented an API contained methods to solve both constrained and unconstrained problems. This API was developed to be used either locally on the computer where the application is being executed or remotely on a server. To obtain the maximum flexibility both from the programmers’ and users’ points of view, problems can be defined as a Java class (because this API was developed in Java) or as a simple text input that is sent to the API. For this last one to be possible it was also implemented on the API an expression evaluator. One of the drawbacks of this expression evaluator is that it is slower than the Java native code. In this paper it is presented a solution that combines both options: the problem can be expressed at run-time as a string of chars that are converted to Java code, compiled and loaded dynamically. To wide the target audience of the API, this new expression evaluator is also compatible with the AMPL format.

Modelação de concerns voláteis em aplicações geoespaciais: o caso dos concerns geoespa

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia Inform