As pesquisas em biologia molecular têm produzido uma grande quantidade de dados, os quais embutem informações sobre diferentes fenômenos biológicos. Neste sentido, a bioinformática se destaca como uma área de pesquisa multidisciplinar que visa, principalmente, o desenvolvimento de ferramentas (sistemas) computacionais para auxiliar na descoberta de conhecimento a partir de dados biológicos. Dentro da bioinformática, a área de genômica funcional procura estudar as funções gênicas através da medição simultânea e em larga escala dos níveis de expressão gênica de um genoma. Diferentes ferramentas são utilizadas no processo de análise de expressão gênica, cada qual provê suporte a uma atividade de análise específica. Embora alguns ambientes de descoberta de conhecimento ofereçam suporte integrado a este processo de análise e exploração de dados, a maior parte das ferramentas de análise é desenvolvida independentemente de outras ferramentas e ambientes de descoberta de conhecimento. Este cenário representa um desafio para biologistas que precisam combinar e integrar diferentes ferramentas, muitas vezes de forma ad hoc, custosa e sujeita a erros. Modelos conceituais, tais como ontologias, têm contribuído para o sucesso do desenvolvimento de sistemas computacionais em diferentes domínios de aplicação. O desenvolvimento de tais modelos tem por objetivo representar corretamente, em alto nível de abstração, conceitos e situações pertinentes a um dado domínio de interesse. Esta representação abstrata facilita não apenas o entendimento de um dado domínio, mas também serve como base para o processo de desenvolvimento do sistema como um todo. O objetivo deste trabalho é investigar o desenvolvimento e o uso de modelos conceituais em geral e ontologias em particular, na integração de ferramentas na área de análise de expressão gênica. De forma específica, este trabalho tem por objetivo propor uma abordagem para a integração semântica de ferramentas de análise de expressão gênica a partir do uso de conectores e de uma ontologia de domínio. Essa abordagem foi aplicada no desenvolvimento de estudos de caso envolvendo a criação de diferentes ambientes integrados para a análise de expressão gênica e mostrou-se eficaz. / Molecular biology researches are increasingly producing large amounts of data regarding underlying biological phenomena. Bioinformatics is a multidisciplinary research field whose main objective is the development of theories and information systems to help the process of knowledge discovery from biological data. Functional genomics is a field of study bioinformatics concerned with the study of gene function through parallel and large scale expression measurements of a genome. A variety of software tools are usually combined and used in a knowledge discovery process, each providing support for a specific data analysis task. Although some tools are already provided as part of an integrated knowledge discovery environment, most of them are developed independently of other software tools and knowledge discovery environments. This scenario poses a problem and a challenge for biologists that need to combine and integrate different tools in an ad hoc, time consuming and error prone process. Conceptual models, such as ontologies, have contributed to the successful development of information systems in different application domains. The development of such models aims at creating a clear and precise description of the elements of a given domain at a high abstraction level. This abstract and high level description not only promotes a shared understanding of the domain, but also serves as basis for the development process of supporting applications in the domain. This work aims at investigating the development and use of conceptual models in general and ontologies in particular to support the integration of gene expression data analysis systems. Specifically, this work proposes an approach for the semantic integration of gene expression analysis tools using connectors and a domain ontology. This approach was applied in the development of a number of case studies aiming at creating integrated environments for gene expression analysis and proved its effectiveness.

There are many attempts to bridge paper digital gap, new artifacts and tools are being delivered continuously. Many of these artifacts work with paper and cooperate with other artifacts. Despite the fact that these artifacts are good enough to perform their work, they tend to be dull in exchanging data and cooperating with other artifacts. This causes a problem especially when artifact cooperation is essential. In order to solve this we need to have a standard to present the data used in the artifacts and facilitate communication among artifacts. Paper Digital Classes is a new standard that aims at providing a standard implementation of the artifacts in matters of data exchange and interoperability. / Med dagens teknik är det möjligt att skicka till exempel e-post direkt från ett papper utan att röra vid datorn. Genom att använda en särskild digital penna överförs texten man skriver på papper direkt till datorn. Jag har undersökt olika system och verktyg som berör läsning och överföring från papper till digitala dokument. Jag har utifrån min studie tagit fram en standard, PDC, Paper Digital Classes, som låter olika verktyg interagera som om de vore ett. PDC kan komma att få stor betydelse för framtida dokumenthantering. Tekniken underlättar att skicka e-post från ett pappersdokument, redigera pappersdokument och överhuvudtaget all interaktion mellan fysiska och digitala dokument. PDC kan också komma till god hjälp när det gäller att utveckla nya, användbara produkter. / Ashraf Habash Gamla Infartsv. 3A, lhg 510 371 41 Karlskrona (mob) +46 734 08 79 67 (work) +46 457 386 300

There are many attempts to bridge paper digital gap, new artifacts and tools are being delivered continuously. Many of these artifacts work with paper and cooperate with other artifacts. Despite the fact that these artifacts are good enough to perform their work, they tend to be dull in exchanging data and cooperating with other artifacts. This causes a problem especially when artifact cooperation is essential. In order to solve this we need to have a standard to present the data used in the artifacts and facilitate communication among artifacts. Paper Digital Classes is a new standard that aims at providing a standard implementation of the artifacts in matters of data exchange and interoperability. PDC has a direct industrial impact, this was noticed by Sparbanksstiftelsen Kronan and they have awarded me a scholarship for the project. / Med dagens teknik är det möjligt att skicka till exempel e-post direkt från ett papper utan att röra vid datorn. Genom att använda en särskild digital penna överförs texten man skriver på papper direkt till datorn. Jag har undersökt olika system och verktyg som berör läsning och överföring från papper till digitala dokument. Jag har utifrån min studie tagit fram en standard, PDC, Paper Digital Classes, som låter olika verktyg interagera som om de vore ett. PDC kan komma att få stor betydelse för framtida dokumenthantering. Tekniken underlättar att skicka e-post från ett pappersdokument, redigera pappersdokument och överhuvudtaget all interaktion mellan fysiska och digitala dokument. PDC kan också komma till god hjälp när det gäller att utveckla nya, användbara produkter. / Ashraf Habash Gamla Infartsv. 3A 371 41 Karlskrona (mob) +46 734 08 79 67 (work) +46 457 386 307 Ashrafhabash@msn.com www.uth.se

In this thesis we will identify which are the desired features and functionalities for implementing a system capable of acting as an information bridge for content available in the “wired” Internet to be delivered to mobile devices. We will also explore how to design and build such a system based on the specifications within parts of the MUSIS project. The MUSIS’ system development is used as a base of the work described in this thesis and the experiences from those efforts are used in order to design a system with more focus on data portability and media migration. During the development of the MUSIS platform, problems related to system upgrading, i.e. adding new ad-hoc functionalities were discovered. Due to the fact that a user-centred design approach was taken, this was essential in the project. To solve some of these issues, we propose a new component-based system with a high level of scalability and re-usability. We name this system Collect, Convert and Send, CCS. The system shall be seen as a base that can be used as a core system for different projects where interoperability of content between different platforms, devices or systems is important. The implementation of the system is based on the use cases and those theoretical aspects and ideas related to component software, interoperability, media migration and metadata in a Web service context. The results of our efforts give some indications that the use of component software gives a foundation for a service-oriented architecture.

Les entreprises dont le cœur de métier est orienté vers la conception et la production de systèmes réputés complexes cherchent en permanence à améliorer leur position sur des marchés généralement mouvants face à la concurrence internationale. Une des solutions possibles consiste à déployer, améliorer et gérer des processus d'Ingénierie Système. Entre autres avantages, les entreprises peuvent par ce biais espérer gagner à la fois en termes de qualité de leurs prestations et de réactivité avec laquelle elles les fournissent.Ce déploiement nécessite cependant de porter une attention particulière aux besoins, capacités et motivations des ressources et organisations, tant internes qu'externes à l'entreprise, devant être impliqués dans le déploiement ou l'exécution de ces processus. De fait, la maîtrise de leur interopérabilité doit être considérée comme un facteur clef de la réussite du déploiement. Par ailleurs, comme le déploiement de processus appelle à structurer le travail, à modifier l'organisation et le fonctionnement même des entreprises, ces dernières doivent être en mesure de mettre en œuvre des efforts importants de compréhension, d'anticipation, d'adaptation voire de gestion du changement. Elles se trouvent alors souvent dépourvues face au peu de solutions pragmatiques disponibles et applicables réellement pour déployer des processus en milieu industriel.Pour répondre à ces besoins, les travaux de recherche développés au cours de cette thèse ont pour objectif de fournir un cadre méthodologique et technique permettant de lever certains des verrous empêchant ou freinant la réussite du déploiement de processus. Ils sont appliqués ici au déploiement de processus d'Ingénierie Système dans un contexte aéronautique. Ils concernent plus particulièrement les processus d'ingénierie de produits de type hélicoptère et des services associés.La contribution globale de ces travaux consiste donc à définir un guide méthodologique outillé pour assister le déploiement de processus dans une entreprise multi-sites et pluridisciplinaire. Ce guide inclut :• Une analyse comparative détaillée des standards de l'Ingénierie Système applicable en aéronautique,• Un méta-modèle permettant d'établir une vision/compréhension partagée des concepts nécessaires au déploiement,• Un modèle de maturité permettant de connaitre le degré de préparation de l'entreprise pour le déploiement,• Une méthodologie de déploiement formalisée (BPMN 2.0 et modèle formel sous-jacent) facilement automatisable et non ambiguë,• Une méthodologie d'évaluation de l'interopérabilité des ressources et des unités d'organisations à impliquer dans un processus à déployer, formalisée mathématiquement et outillée entre autres par des questionnaires types facilitant son application immédiate,• Des modèles de processus et en particulier celui de définition des exigences réalisé pour valider la méthodologie de déploiement,• Un ensemble cohérent et interopérable de solutions informatiques comprenant un moteur de workflow, des outils de modélisation, des outils d'évaluation de la maturité et de l'interopérabilité, une application récupérant la connaissance des modèles et un générateur de documents. / Companies whose primary business is the design and the supply of complex systems try to constantly improve their performances to be ahead of their international competitors. For this, a solution is to deploy, improve and manage Systems Engineering processes. Indeed, among other things, this may enable companies improving the quality of their services but also the reactivity with which they supply them.Nonetheless, this deployment requires paying a special attention to needs, abilities and motivations of resources and organisations, should they be internal or external to the company, likely to be involved in the deployment or execution of these processes. Thus, mastering their interoperability should be considered as an important need and should be considered as a key factor in the deployment.Moreover, since a process deployment implies to structure the work share, to modify the organisation and the functioning of enterprises, the latter must be able to carry out considerable effort to understand, anticipate, adapt and lead the change. However, they often experience difficulties considering the few pragmatic and applicable solutions available to directly deploy processes in industry.To meet these needs, this thesis research aims to supply a methodological and technical guide that enables getting over obstacles preventing or impeding the success of the deployment. It is here applied for the deployment of Systems Engineering processes in an aeronautics context. More precisely, this work focus on processes in charge of the design of helicopters along with services related to them.Consequently, the global contribution of this thesis consists in the definition of an equipped methodological guided to support the deployment of processes in a company that is multi-sites and multi-cultural. This guide includes:• A detailed comparative analysis of international Systems Engineering norms applicable in a aeronautics,• A meta-model that enables sharing a common vision/understanding of concepts required for the deployment,• A maturity model that enables appraising the readiness of a company for the deployment,• A formalised deployment methodology (BPMN 2.0 and an underlying formal model) that is unambiguous and that can be easily automated,• A methodology enabling the assessment of the interoperability of resources and organisation units to involve in a process to deploy, mathematically formalised and equipped with typical questionnaires to facilitate its immediate application,• Processes models and more particularly the one in charge of the stakeholders requirements definition to validate the deployment methodology,• A consistent and interoperable set of computer applications including a workflow engine, modelling tools, applications for the assessment of maturity and interoperability, an application to collect knowledge in models and a document generator.

Due to a rapid increase in aging population, demand for personalized health care increases proportionally. Personalized patient data can be a helpful way of catering the needs and requirements of elderly people staying at home. Indirectly, it can be a manner of providing better eHealth services according to their needs. Another interesting aspect of providing better personalized eHealth services is to make patient information systems interoperable. Interoperability of eHealth systems is an issue of great concern to current research and development but in this study, we focus on patient information systems. Like in some other European countries, introduction of open source platform to achieve interoperability and personalization of patient information system could save money for health care organizations and make the procedure easier in Sweden also. The purpose of this study is to identify what standards are available for interoperability and what are the benefits and challenges of introducing open source systems for achieving personalized interoperable patient information systems (PIPIS). In light of this investigation, author has identified the benefits and challenges of introducing OSS for achieving PIPIS. Author has also made several recommendations regarding the challenges identified. / In the name of ALLAH, the most gracious and merciful. I extend my gratitude to the beautiful creator of this beautiful universe that He made for us to conquer. Without the love of my parents this thesis report could never be possible for me to write. All my love and care is for them which no one else can share. I thank Mr. Hans Kyhlbäck whose supervision is a source of inspiration for doing this study. He is definitely the best supervisor to work with. In the end, I would like to thank my friends and colleagues whose help just kept me going despite of many hurdles that I faced.

This Master’s Thesis examines and documents challenges related to the flexible interchange of web services within a cross-cloud Service Oriented Computing scenario (SOC).Starting with a theoretical approach, hypotheses are defined and processed to create testing scenarios for a practical examination. Both examinations are used to identify possible challenges. Next, encountered challenges are described, discussed and classified. Lastly, solution approaches to identified challenges are presented. The solution approaches concern related topics, such as service standardization, semantic methods, heuristics, and security/trust mechanisms. Several approaches to different challenges are reviewed in this particular context, to present an overview for future research on the subject.It is remarkable that there will be more service standardization in the future, but to achieve full automation it will be, on the long run, necessary to evolve and adopt more sophisticated solution approaches such as semantic methods or heuristics.This work is embedded into the framework of a research co-operation between the Linnaeus University Växjö and the University of Applied Sciences Karlsruhe. Results however are also applicable to other research scenarios.

Le partage entre sources indépendantes hétérogènes et distribuées peut être résolu par la construction d’un système d’information coopératif (SIC). Un SIC est un ensemble de composants plus ou moins autonomes, souvent préexistants qui travaillent de manière synergique en échangeant information, expertise et en coordonnant leurs activités. Cela implique notamment la prise en compte de l’interopérabilité liée aux différences de description des données et de représentation de la sémantique. La gestion des données est alors assurée sans recours à un schéma global complet pour respecter l’autonomie des bases locales.Dans ce contexte, nous avons choisi de traiter le thème de la sécurité d’accès dans le but de garantir la confidentialité et l’intégrité des données de la coopération. La sécurité ajoute de nouveaux problèmes d’hétérogénéité et de résolution de conflits à ceux déjà existants en terme de coopération de données. Nous utilisons deux modèles canoniques proposés par l’équipe MODEME, permettant de représenter de manière unifiée les schémas locaux de données et de sécurité. Nous construisons un système pour la gestion de l’interopération des données et des politiques de sécurité, ainsi que la résolution sécurisée de requêtes globales. Nous avons choisi d’implémenter notre système en suivant le paradigme multi-agents avec une approche par médiation et intégration de schémas. Deux protocoles sont définis au regard des deux fonctionnalités du système : - Un protocole de gestion des connaissances permettant de traiter le problème d’interopérabilité entre les différents modes de représentation des données et des modèles de sécurité, et de générer les appariements entre ces différents modèles. - Un protocole de résolution de requêtes à partir des connaissances globales construites a priori, dont l’objectif est de présenter des résultats sémantiquement cohérents et sécurisés. Les agents sont décrits dans leur buts, leurs interactions, leurs connaissances en définissant leur rôle pour chaque protocole, avec notamment le rôle clé de médiateur de sécurité. Un scénario d’expérimentation permet d’illustrer sur un cas concret la génération des connaissances à partir des schémas locaux ainsi que le développement complexe du protocole pour le contrôle d’accès. / Sharing heterogeneous and distributed independent data sources can be solved by building a Cooperative Information System (CIS). A CIS is a set of components, exchanging information, expertise and coordinating their activities. This must consider interoperability related to differences of data description and semantic. Data management is provided without using a comprehensive global scheme to respect the autonomy of local databases.In this context, we chose to treat access security in order to ensure confidentiality and data integrity in a cooperation. This adds new security issues regarding heterogeneity and conflict resolution, on top of those in terms of data cooperation. We use two canonical models proposed by the MODEME team, to represent the local schemas and security policies in a unified way.We build a system to manage the interoperation of data and security policies, and the resolution of secure global queries. We have chosen to implement our system using the multi-agent paradigm, with an schema integration and mediation approach. Two protocols have been defined related to the features of the system: - A knowledge management protocol to address the problem of interoperability between different modes of data representation and security models, and to generate the matches between these different models. - A query resolution protocol using the global knowledge, which aims to present the results semantically consistent and secure. Agents are described in their goals, their interactions, their knowledge by defining their role for each protocol, including the key role of security mediator. An experimental scenario illustrates the knowledge generation from local schemas and the development of protocol for access control.

Depuis plusieurs années, la mondialisation du marché, l'augmentation des exigences des clients, et la recherche permanente d'une baisse des coûts induisent un accroissement fort de la complexité du monde industriel. Ainsi, la collaboration inter-organisationnelle devient essentielle pour maintenir et renforcer la compétitivité des entreprises. Dans cette optique, le système d'information peut, selon sa flexibilité et sa robustesse, freiner ou faciliter cette collaboration. Cette problématique est le point de départ du projet MISE (Mediation Information System Engineering) qui propose une solution pour la conception et la réalisation d'un système d'information collaboratif. Cette solution se base sur une démarche d'ingénierie dirigée par les modèles, couplée à une approche Business Process Management (BPM) et reposant sur les Architectures Orientées Services (SOA). Cette démarche se déroule en deux étapes : (i) la génération d'une cartographie de processus répondant à une situation collaborative (niveau métier), et (ii) sa transformation en un système exécutable (niveau technique). Les travaux présentés dans ce manuscrit s'inscrivent dans cette démarche. Ils s'intéressent en particulier au passage du niveau métier vers le niveau technique en se focalisant sur les aspects non-fonctionnels. Nous présentons une approche permettant (i) d'annoter les activités métier à l'aide d'exigences non-fonctionnelles lors de la modélisation des processus collaboratifs, (ii) de rationaliser la gestion des services et leurs propriétés non-fonctionnelles au moyen de la Gouvernance SOA, et enfin (iii) de faire une réconciliation non-fonctionnelle entre les activités et les services. Nous avons validé les concepts de notre approche au travers de deux prototypes : Petals BPM-NFR pour la modélisation et l'annotation non-fonctionnelle des processus métier, et EasierGov-NFR pour la gouvernance des services et leurs propriétés non-fonctionnelles ainsi que la réconciliation non-fonctionnelle. Un cas d'étude illustre notre approche pour prouver son applicabilité. Ces travaux s'inscrivent au sein du projet européen FP7 CHOReOS. / Over the last years, the globalization, the increase of customers requirements, and the constant search for lower costs, have induced a steep complexity of organization's management. Therefore, inter-organizational collaboration becomes essential to maintain and enhance the competitiveness of enterprises. In this context, the information system may, depending on its flexibility and its robustness, hamper or facilitate this collaboration. One approach to resolve this problem has been taken by the MISE (Mediation Information System Engineering) project. It aims to provide an effective implementation of a collaborative information system, based on Model-Driven Engineering, coupled with a Business Process Management approach (BPM) and supported by Service-Oriented Architecture (SOA). This solution consists in two steps: (i) the generation of a business processes map from the description of a collaborative situation (business level), and (ii) the transformation of these process models into an executable system (technical level). The works detailed in this PhD take roots in this solution and improve it by adding non-functional aspects management during the transition from the business level to the technical level. We present an approach that: first (i) annotates the business activities with Non-Functional Requirements (NFR) in the processes modelling stage, second (ii) rationalizes the management of services and their non-functional properties through SOA Governance, and third (iii) makes a non-functional reconciliation between activities and services. We validate our approach through two prototypes: Petals BPM-NFR for modelling and non-functional annotation of business process, and EasierGov-NFR for the governance of services and their non- functional properties, and the non-functional reconciliation. A case study illustrates our approach to demonstrate its applicability. This work is supported by the FP7 European project CHOReOS.

Abstract At the heart of the smart space vision is the idea that devices interoperate with each other autonomously to assist people in their everyday activities. In order to make this vision a reality, it is important to achieve semantic-level interoperability between devices. The goal of this dissertation is to enable Semantic Web technology-based interoperability in smart spaces. There are many challenges that need to be solved before this goal can be achieved. In this dissertation, the focus has been on the following four challenges: The first challenge is that the Semantic Web technologies have neither been designed for sharing real-time data nor large packets of data such as video and audio files. This makes it challenging to apply them in smart spaces, where it is typical that devices produce and consume this type of data. The second challenge is the verbose syntax and encoding formats of Semantic Web technologies that make it difficult to utilise them in resource-constrained devices and networks. The third challenge is the heterogeneity of smart space communication technologies that makes it difficult to achieve interoperability even at the connectivity level. The fourth challenge is to provide users with simple means to interact with and configure smart spaces where device interoperability is based on Semantic Web technologies. Even though autonomous operation of devices is a core idea in smart spaces, this is still important in order to achieve successful end-user adoption. The main result of this dissertation is a semantic interoperability framework, which consists of following individual contributions: 1) a semantic-level interoperability architecture for smart spaces, 2) a knowledge sharing protocol for resource-constrained devices and networks, and 3) an approach to configuring Semantic Web-based smart spaces. The architecture, protocol and smart space configuration approach are evaluated with several reference implementations of the framework components and proof-of-concept smart spaces that are also key contributions of this dissertation. / Tiivistelmä Älytilavision ydinajatuksena on, että erilaiset laitteet tuottavat yhteistyössä ihmisten elämää helpottavia palveluita. Vision toteutumisen kannalta on tärkeää saavuttaa semanttisen tason yhteentoimivuus laitteiden välillä. Tämän väitöskirjan tavoitteena on mahdollistaa semanttisen webin teknologioihin pohjautuva yhteentoimivuus älytilan laitteiden välillä. Monenlaisia haasteita täytyy ratkaista, ennen kuin tämä tavoite voidaan saavuttaa. Tässä työssä keskityttiin seuraaviin neljään haasteeseen: Ensimmäinen haaste on, että semanttisen webin teknologioita ei ole suunniteltu reaaliaikaiseen kommunikaatioon, eivätkä ne sovellu isojen tiedostojen jakamiseen. Tämän vuoksi on haasteellista hyödyntää niitä älytiloissa, joissa laitteet tyypillisesti jakavat tällaista tietoa. Toinen haaste on, että semanttisen webin teknologiat perustuvat syntakseihin ja koodausformaatteihin, jotka tuottavat laitteiden kannalta tarpeettoman pitkiä viestejä. Tämä tekee niiden hyödyntämisestä hankalaa resurssirajoittuneissa laitteissa ja verkoissa. Kolmas haaste on, että älytiloissa hyödynnetään hyvin erilaisia kommunikaatioteknologioita, minkä vuoksi jopa tiedonsiirto laitteiden välillä on haasteellista. Neljäs haaste on tarjota loppukäyttäjälle helppoja menetelmiä sekä vuorovaikutukseen semanttiseen webiin pohjautuvien älytilojen kanssa että tällaisen älytilan muokkaamiseen käyttäjän tarpeiden mukaiseksi. Vaikka laitteiden itsenäinen toiminta onkin älytilojen perusajatuksia, tämä on kuitenkin tärkeää teknologian hyväksymisen ja käyttöönoton kannalta. Väitöskirjan päätulos on laitteiden semanttisen yhteentoimivuuden viitekehys, joka koostuu seuraavista itsenäisistä kontribuutioista: 1) semanttisen tason yhteentoimivuusarkkitehtuuri älytiloille, 2) tiedonjakoprotokolla resurssirajoittuneille laitteille ja verkoille sekä 3) menetelmä semanttiseen webiin pohjautuvien älytilojen konfigurointiin. Näiden kontribuutioiden evaluointi suoritettiin erilaisten järjestelmäkomponenttien referenssitoteutuksilla ja prototyyppiälytiloilla, jotka kuuluvat myös väitöskirjan keskeisiin kontribuutioihin.