Ontological representation of tumor-node-metastasis classification and an ontology-driven classifier: a study on colorectal cancer

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Informática Médica)

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.

Integració del Racó de l'estudiant a l'entorn Android

El projecte consisteix en integrar les principals funcionalitats del Racó de l'estudiant als dispositius mòbils Android. Concretament, la consulta d'avisos de les assignatures, el correu, l'ocupació de les aules, l'horari personal i l'agenda. Addicionalment, les notícies de la FIB i la localització.

Integració del Racó de l'estudiant a l'entorn Android

El projecte consisteix en integrar les principals funcionalitats del Racó de l'estudiant als dispositius mòbils Android. Concretament, la consulta d'avisos de les assignatures, el correu, l'ocupació de les aules, l'horari personal i l'agenda. Addicionalment, les notícies de la FIB i la localització.

Sovellus meteorologisen tiedon tuotantojärjestelmän seurantaan

Työssä käsitellään selainkäyttöliittymää käyttävien oliopohjaisten tietokantasovellusten toteuttamista. Erityisesti keskitytään olio- ja relaatiomallien yhteensovittamiseen ja oliopohjaisten selainkäyttöliittymien toteutukseen Java-servlettien ja JSP-sivujen avulla. Myös hajautetut sovellusarkkitehtuurit käydään läpi ja niiden toteuttamista arvioidaan servlet-sovellusten näkökulmasta. Työssä on toteutettu selainkäyttöliittymän avulla hallittava kaksitasoarkkitehtuuria käyttävä oliopohjainen sovellus Ilmatieteen laitoksen tuotantojärjestelmän seurantaan. Sovellus mahdollistaa mm. tuotantoajojen ja laajempien tuotantoketjujen suoritusaikojen tilastollisen seurannan. Työn tuloksena todettiin Java-servlettien ja JSP-sivujen olevan suorituskykyinen ja monipuolinen ratkaisu selainkäyttöliittymien toteuttamiseen. Olio- ja relaatiomallien väliset erot sekä käyttöliittymän eriyttäminen toimintalogiikasta osoittautuivat ongelmakohdiksi.

Matkapuhelinverkon MAP-protokollatoteutus älyverkkopalveluiden ohjauspisteeseen

Työssä esitellään yleiseurooppalaisen GSM-matkapuhelinjärjestelmän verkkoelementtejä ja perehdytään niiden väliseen standardoituun merkinantoprotokollaan. Lisäksi tarkastellaan protokollan lyhytsanomien välitykseen liittyviä operaatioita ja niissä tapahtunutta kehitystä standardoinnin eri vaiheissa. Tavoitteena oli toteuttaa GSM-matkapuhelinverkon merkinantoprotokollaan perustuva ohjelma, jonka tehtävänä on välittää lyhytsanomia matkapuhelin- ja lyhytsanomakeskuksen välillä. Matkapuhelimeen päättyvän lyhytsanoman välitykseen liittyy lisäksi reititystiedon hakeminen vastaanottajan kotirekisteristä. Toteutuksessa on ohjelmointirajapinta, joka helpottaa matkapuhelinverkon uusien palvelusovellusten kehittämistä. Toteutus testattiin standardoituja testitapauksia soveltaen. Yhdenmukaisuustestauksessa käytettiin apuna merkinantoanalysaattoria. Testauksessa tarkastettiin, että protokolla toimii loogisesti oikein. Suorituskykyä ei ole voitu testata todellisessa testiympäristössä, mutta ohjelmallisesti toteutettujen simulaattoreiden avulla on saatu hyviä tuloksia.

Läsnäolotietojen hallinta viestintäsovelluksissa

Läsnäolotietoja on käytetty jo pitkään hyväksi erilaisissa pikaviestintäsovelluksissa. Nämä sovellukset ovat käyttäneet omia tekniikoitaan läsnäolotietojen tarjoamiseksi muille käyttäjille. Viime vuosina erilaisista ryhmistä ja yrityksistä koostuvat standardointiorganisaatiot ovat kuitenkin kehittäneet standardoituja tekniikoita, jotka pyrkivät takaamaan sen, että eri sovellukset ovat mahdollisimman yhteensopivia. Näiden tekniikoiden käyttö nopeuttaa myös palveluiden kehittämistä. Palveluiden kehittämisen nopeuttamiseksi on laadittu myös valmis ohjelmointirajapinta. Läsnäolotietojen käyttö on viime vuosina monipuolistunut. Tietoja voidaankin käyttää useissa sovelluskohteissa. Tämä on johtanut siihen, että esimerkiksi matkapuhelinvalmistajat ovat yhdessä laatineet matkapuhelimille tarkoitetun tekniikan, joka on jo toteutettu Nokian uusimmissa matkapuhelinmalleissa. Muita läsnäolotietojen sovelluskohteita on olemassa suuri määrä; diplomityön lopuksi suunnitellaankin palvelu, jossa läsnäolotiedot haetaan käyttäjän täyttämästä kalenterista ja jaetaan matkapuhelimille.

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.

Construction Plan Image Service for Mobile Devices

The forthcoming media revolution of exchanging paper documents to digital media in construction engineering requires new tools to be developed. The basis of this bachelor’s thesis was to explore the preliminary possibilities of exporting imagery from a Building Information Modelling –software to a mobile phone on a construction yard. This was done by producing a Web Service which uses the design software’s Application Programming Interface to interact with a structures model in order to produce the requested imagery. While mobile phones were found lacking as client devices, because of limited processing power and small displays, the implementation showed that the Tekla Structures API can be used to automatically produce various types of imagery. Web Services can be used to transfer this data to the client. Before further development the needs of the contractor, benefits for the building master and inspector and the full potential of the BIM-software need to be mapped out with surveys.

The Human Communication Science Virtual Lab (HCS vLab): A repository microclimate in a rapidly evolving research-ecosystem

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Embedded Service Bus for Internet of Things Interoperability

Internet of Things (IoT) technologies are developing rapidly, and therefore there exist several standards of interconnection protocols and platforms. The existence of heterogeneous protocols and platforms has become a critical challenge for IoT system developers. To mitigate this challenge, few alliances and organizations have taken the initiative to build a framework that helps to integrate application silos. Some of these frameworks focus only on a specific domain like home automation. However, the resource constraints in the large proportion of connected devices make it difficult to build an interoperable system using such frameworks. Therefore, a general purpose, lightweight interoperability framework that can be used for a range of devices is required. To tackle the heterogeneous nature, this work introduces an embedded, distributed and lightweight service bus, Lightweight IoT Service bus Architecture (LISA), which fits inside the network stack of a small real-time operating system for constrained nodes. LISA provides a uniform application programming interface for an IoT system on a range of devices with variable resource constraints. It hides platform and protocol variations underneath it, thus facilitating interoperability in IoT implementations. LISA is inspired by the Network on Terminal Architecture, a service centric open architecture by Nokia Research Center. Unlike many other interoperability frameworks, LISA is designed specifically for resource constrained nodes and it provides essential features of a service bus for easy service oriented architecture implementation. The presented architecture utilizes an intermediate computing layer, a Fog layer, between the small nodes and the cloud, thereby facilitating the federation of constrained nodes into subnetworks. As a result of a modular and distributed design, the part of LISA running in the Fog layer handles the heavy lifting to assist the lightweight portion of LISA inside the resource constrained nodes. Furthermore, LISA introduces a new networking paradigm, Node Centric Networking, to route messages across protocol boundaries to facilitate interoperability. This thesis presents a concept implementation of the architecture and creates a foundation for future extension towards a comprehensive interoperability framework for IoT.

Dialekter och röstigenkänning : Ett röstigenkännings-API:s förmåga att uppfatta svenska dialekters kännetecken och röstkombinationer

Allt eftersom utvecklingen går framåt inom applikationer och system så förändras också sättet på vilket vi interagerar med systemet på. Hittills har navigering och användning av applikationer och system mestadels skett med händerna och då genom mus och tangentbord. På senare tid så har navigering via touch-skärmar och rösten blivit allt mer vanligt. Då man ska styra en applikation med hjälp av rösten är det viktigt att vem som helst kan styra applikationen, oavsett vilken dialekt man har. För att kunna se hur korrekt ett röstigenkännings-API (Application Programming Interface) uppfattar svenska dialekter så initierades denna studie med dokumentstudier om dialekters kännetecken och ljudkombinationer. Dessa kännetecken och ljudkombinationer låg till grund för de ord vi valt ut till att testa API:et med. Varje dialekt fick alltså ett ord uppbyggt för att vara extra svårt för API:et att uppfatta när det uttalades av just den aktuella dialekten. Därefter utvecklades en prototyp, närmare bestämt en android-applikation som fungerade som ett verktyg i datainsamlingen. Då arbetet innehåller en prototyp och en undersökning så valdes Design and Creation Research som forskningsstrategi med datainsamlingsmetoderna dokumentstudier och observationer för att få önskat resultat. Data samlades in via observationer med prototypen som hjälpmedel och med hjälp av dokumentstudier. Det empiriska data som registrerats via observationerna och med hjälp av applikationen påvisade att vissa dialekter var lättare för API:et att uppfatta korrekt. I vissa fall var resultaten väntade då vissa ord uppbyggda av ljudkombinationer i enlighet med teorin skulle uttalas väldigt speciellt av en viss dialekt. Ibland blev det väldigt låga resultat på just dessa ord men i andra fall förvånansvärt höga. Slutsatsen vi drog av detta var att de ord vi valt ut med en baktanke om att de skulle få låga resultat för den speciella dialekten endast visade sig stämma vid två tillfällen. Det var istället det ord innehållande sje- och tje-ljud som enligt teorin var gemensamma kännetecken för alla dialekter som fick lägst resultat överlag.

Organização e armazenamento de conteúdo instrucional no ambiente AdaptWeb utilizando XML

O uso da Internet como ferramenta de ensino tem se tornado cada vez mais freqüente. A recente popularização da Internet vem permitindo o desenvolvimento de ambientes de ensino-aprendizagem baseados na Web. Os principais recursos explorados para fins educacionais são hipertexto e hipermídia, que proporcionam uma grande gama de elementos para o instrutor que pretende utilizar a WWW. Este trabalho está inserido no desenvolvimento do ambiente AdaptWeb (Ambiente de Ensino e Aprendizagem Adaptativo para a Web), que visa o desenvolvimento de um ambiente de educação a distância. A arquitetura do ambiente é composta por quatro módulos entre eles o módulo de Armazenamento de dados que armazena todos os dados provenientes da fase de Autoria utilizando XML (Extensible Markup Language). Na etapa de Autoria é feita a inserção de todos os dados relativos a disciplina que deseja disponibilizar, estes dados serão armazenados temporariamente em uma representação matricial em memória. A entrada de dados do módulo de Armazenamento de Dados é esta representação matricial que serve então como base para a geração dos arquivos XML, que são utilizados nas demais etapas do ambiente. Para a validação dos arquivos XML foram desenvolvidas DTD (Document Type Definition) e também foi implementado um analisador de documentos XML, utilizando a API (Application Programming Interface) DOM (Document Object Model), para efetuar a validação sintática destes documentos. Para conversão da representação matricial em memória foi especificado e implementado um algoritmo que funciona em conformidade com as DTD especificadas e com a sintaxe da linguagem XML.

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

Agraphs: definição, implementação e suas ferramentas

Programs manipulate information. However, information is abstract in nature and needs to be represented, usually by data structures, making it possible to be manipulated. This work presents the AGraphs, a representation and exchange format of the data that uses typed directed graphs with a simulation of hyperedges and hierarchical graphs. Associated to the AGraphs format there is a manipulation library with a simple programming interface, tailored to the language being represented. The AGraphs format in ad-hoc manner was used as representation format in tools developed at UFRN, and, to make it more usable in other tools, an accurate description and the development of support tools was necessary. These accurate description and tools have been developed and are described in this work. This work compares the AGraphs format with other representation and exchange formats (e.g ATerms, GDL, GraphML, GraX, GXL and XML). The main objective this comparison is to capture important characteristics and where the AGraphs concepts can still evolve