O surgimento e o uso crescente de novas tecnologias têm levado à produção e armazenamento de grandes volumes de dados biomédicos. Tais dados são provenientes de diferentes técnicas, armazenados em formatos de representação diversos e utilizados por diferentes ferramentas. Esta heterogeneidade representa um empecilho ao maior uso desses dados em abordagens integrativas de pesquisa como, por exemplo, a biologia sistêmica. Neste cenário, artefatos de modelagem conceitual, tais como ontologias, têm sido utilizados para organizar e integrar dados heterogêneos de uma forma coerente. A OBO Foundry representa, atualmente, o maior esforço no desenvolvimento de ontologias biomédicas de forma colaborativa. Dentre as ontologias desenvolvidas pela OBO Foundry, destaca-se Ontologia de Relacionamentos (RO-OBO). A RO-OBO provê definições formais para um conjunto de relacionamentos de propósito geral utilizados nas ontologias biomédicas e busca promover a criação de ontologias mais corretas e integráveis. Um perfil UML foi proposto para representar formalmente o conjunto de conceitos e relacionamentos existentes na RO-OBO. Este perfil permite desenvolver modelos UML utilizando os conceitos presentes nesta ontologia, bem como torna possível o desenvolvimento de suporte à validação sintática dos modelos criados em relação a um conjunto de restrições formalmente definidas. Adicionalmente, percebe-se na literatura que o suporte à integração de modelos UML e ontologias OBO, em particular as ontologias representadas na linguagem OBO File Format, é limitado. Neste sentido, este trabalho teve como objetivo geral investigar o suporte ao desenvolvimento de ontologias biomédicas na linguagem UML. De forma específica, investigou-se o desenvolvimento de um editor gráfico, chamado OBO-RO Editor, para o suporte à construção de ontologias utilizando o perfil UML proposto, bem como a integração de ontologias desenvolvidas utilizando UML e ontologias desenvolvidas na linguagem OBO File Format. De forma a atingir nossos objetivos, uma arquitetura de referência foi definida e um processo de desenvolvimento orientado a modelos foi utilizado. A arquitetura definida é composta por uma série de artefatos inter-relacionados os quais são transformados (semi) automaticamente em código de aplicação, possibilitando a obtenção de ciclos de desenvolvimento mais rápidos e confiáveis. O OBO-RO Editor disponibiliza um conjunto de elementos gráficos de modelagem definidos a partir do perfil UML proposto, bem como provê mecanismos para a validação sintática (semi) automática de uma ontologia desenvolvida segundo as restrições definidas neste perfil. Adicionalmente, o OBO-RO Editor também provê suporte à integração de modelos UML a outras ontologias da OBO Foundry, permitindo o reuso e o desenvolvimento menos propenso a erros de ontologias no domínio biomédico. / The development and increasing use of new technologies has resulted in the production and storage of a huge amount of biomedical data. These data are produced using different techniques, stored in different formats and consumed by different (software) tools. This heterogeneity hinders effective data usage in integrative research approaches, including systems biology. In this scenario, conceptual modeling artifacts, such as ontologies, have been used to organize and integrate heterogeneous data in a coherent manner. Nowadays, the OBO Foundry represents the most important effort for the collaborative development of ontologies in the biomedical domain. The OBO Relation Ontology (OBO-RO) can be considered one of the most relevant ontologies in the domain. This ontology provides formal definitions for a number of general purpose relationships used in biomedical ontologies, thus facilitating the integration of existing ontologies and the development of new ontologies in the domain. An UML profile has been proposed to formally define the different types of concepts and relationships provided by the OBO-RO. This profile enables the creation of UML models using such concepts and allows the development of support for the automatic validation of these models based on formal constraints. Additionally, the support for the integration between UML models and OBO ontologies, particularly ontologies represented using the OBO File Format, is limited. In this sense, this project aimed at investigating the support for the development of biomedical ontologies using UML. In particular, we investigated the development of a graphical editor, named OBO-RO Editor, to support ontology development using the proposed UML profile. Additionally, we also investigated the integration of ontologies developed using UML and ontologies developed using the OBO File Format. In order to achieve our goals, we have defined a reference architecture and a model-driven development process. The reference architecture consists of a number of related artifacts that are transformed to application code (semi) automatically. Such characteristic allowed us to obtain faster and more reliable development cycles. The OBO-RO Editor provides a number of graphical elements defined in the proposed UML profile for the modeling of biomedical ontologies and support the (semi) automatic syntactic validation of such ontologies against the contraints defined in the profile. Additionally, OBO-RO Editor also provides support for the integration of developed UML models and other OBO ontologies, allowing the reuse and the accurate development of biomedical ontologies.

<p>Agentska paradigma predstavlja najprirodniji i najdosledniji&nbsp;postojeći pristup implementaciji distribuiranih sistema. Uz&nbsp;pomoć agenata moguće je u potpunosti realizovati koncept<br />distribuiranih softverskih komponenti, koje će, osim re&scaron;enja&nbsp;zadatka na distribuiranom nivou, pružiti i određenu količinu&nbsp;autonomnosti i inteligencije da bi se zadati cilj ostvario.&nbsp;Agentsko okruženje predstavlja programsko okruženje koje&nbsp;upravlja životnim tokom agenata i obezbeđuje mu sve potrebne&nbsp;mehanizme za realizaciju zadatka. U ovoj doktorskoj disertaciji&nbsp;predložen je model agentskog okruženja baziran na tehnologiji&nbsp;distribuiranih komponenti, koji podržava FIPA specifikaciju i&nbsp;sledeće koncepte: razmenu poruka, mobilnost agenata,&nbsp;sigurnosne mehanizme i direktorijume agenata i servisa. Model&nbsp;agentskog okruženja je implementiran u J2EE tehnologiji.&nbsp;Podržan je sistem plug-in-ova za sve bitne komponente&nbsp;agentskog okruženja (menadžere). Modelovan je i<br />implementiran koncept mobilnih zadataka. Dat je model i&nbsp;implementacija sistema međusobnog uređenja odnosa agentskih&nbsp;centara. Predloženo re&scaron;enje agentskog okruženja verifikovano&nbsp;je na bibliotečkom informacionom sistemu BISIS. Verifikacija&nbsp;je izvr&scaron;ena na sledećim agentskim zadacima: pretraživanje&nbsp;bibliotečke mreže, ocenjivanje kvaliteta zapisa i inteligentna&nbsp;raspodela opterećenja.</p> / <p>Agent technology is one of the most consistent approaches to&nbsp;the distributed computing implementation. Agents can be used&nbsp;to fully implement distributed software component concept.&nbsp;Agents can solve distributed problems utilizing certain degree&nbsp;of autonomy and intelligence. Agent framework represents&nbsp;programming environment that controls agent life cycle and&nbsp;provides all necessary mechanisms for task execution. The&nbsp;subject of the dissertation is formal specification of an agent&nbsp;framework based on distributed component technology. This&nbsp;framework supports FIPA specification and following concepts:&nbsp;message interchange, agent mobility, security and agent and&nbsp;service directory. Agent framework is implemented in J2EE&nbsp;technology. Plug-in system is designed for all key elements of&nbsp;agent framework. Mobile tasks were specified and&nbsp;implemented. Also, inter-facilitator connectivity mechanism is&nbsp;specified and implemented. The framework is verified by a case&nbsp;study on the library information system BISIS. Following agent&nbsp;tasks were performed: library network search, library record&nbsp;quality estimation and intelligent load balansing.&nbsp;</p>

Les CPS intègrent des composants physiques et des composants logiciels. Ils sont particulièrement difficiles à modéliser et à vérifier. En effet, de par la nature hétérogène de leurs composants, leur conception nécessite l’utilisation de différents formalismes de modélisation. Les modèles de ces systèmes combinent à la fois des formalismes à temps continu, et d’autres à événements discrets, pour représenter respectivement leurs composants physiques et logiciels. La vérification de l'ensemble du système nécessite donc la composition de ces composants. La vérification globale peut être réalisée par co-simulation des différents composants. En particulier, la norme FMI offre une interface normative pour coupler plusieurs simulateurs dans un environnement de co-simulation, nommé « Master ». Celui-ci est chargé de fournir un algorithme pour une synchronisation efficace des différents composants du système, nommés FMU. Cependant, FMI est initialement conçu pour la co-simulation des processus physiques, avec un support limité des formalismes à événements discrets qui est modèle de calcul et de communication largement utilisé dans les environnements de modélisation spécifiques au logiciel. En particulier, aucune des solutions actuelles de co-simulation basées sur FMI ne permet de le prendre en considération les modèle UML. La thèse défendue dans ce document est que l'ingénierie système en général bénéficierait de l’intégration des modèles UML dans une approche de co-simulation basée sur la norme FMI. Cela permettra à un grand nombre de concepteurs logiciels d’évaluer le comportement de leurs composants logiciels dans un environnement simulé, et donc de les aider à faire les meilleurs choix de conception le plus tôt possible dans leur processus de développement. Cela pourrait également ouvrir de nouvelles perspectives intéressantes pour les ingénieurs système des CPS, en leur permettant d'envisager l’utilisation d’un langage largement utilisé pour la modélisation des composants logiciels de leurs systèmes. L'objectif de cette thèse est de définir et formaliser un environnement de co-simulation basé sur la norme FMI pour les CPS et intégrant des modèles UML pour la partie logicielle. Nous abordons principalement la question d’adaptation entre la sémantique d’exécution définie dans UML et celle de FMI. Notre contribution intervient à deux niveaux : localement, au niveau des modèles UML, et globalement au niveau du « Master ». Localement, nous mettons en place une approche incrémentale où nous abordons différents types de systèmes à événements discrets caractérisant les composants logiciels. Nous basons nos propositions sur les normes OMG fUML et PSCS qui définissent une sémantique d’exécution précise pour un sous-ensemble de UML. Ces deux normes constitue notre socle de définition nous donne une base intéressante et formelle pour l'intégration des modèles UML dans les approches de co-simulation de CPS. Pour chaque type de système, nous identifions d'abord un ensemble de règles pour le modéliser avec UML et les éventuelles extensions à fUML dans le cas où la sémantique d'exécution des éléments UML requis n’est pas définie dans fUML. Ensuite, au niveau global, nous proposons un algorithme de « Master » pour chaque type de systèmes. Les algorithmes de « Master » reposent sur l'adaptation de la sémantique d’exécution des modèles UML et celle de FMI. Sur cette base, le « Master » est capable de propager les données entre les composants et de les stimuler aux bonnes dates durant la simulation. L'approche est illustrée par des cas d'utilisation du domaine des bâtiments intelligents, où l’objectif est d’évaluer différentes stratégies de gestion d'énergie. Ces stratégies représentent des composants logiciels à différents niveaux de contrôle d’un bâtiment pour des fins d’optimisation de son auto-consommation en électricité. / Cyber Physical Systems (CPS) are integrations of physical and computational components. CPS are difficult to model and verify because the heterogeneous nature of their components requires many different modeling formalisms. The global verification of the system can be achieved by co-simulation. FMI standard offers a standard interface to couple two or more simulators in a co-simulation environment, known as master. This latter is responsible for providing an algorithm with efficient orchestration and synchronization of the involved components, known as FMUs. However, FMI was originally intended for co-simulation of physical processes, with limited support for formalisms such as DE and Dara-Flow, even if this kind of formalisms are commonly used to model the logic of software parts of a system. In particular, while UML is the reference standard for software modeling and is very commonly used in industry, none of the present-day FMI-based co-simulation solutions consider UML models. Our thesis is that system engineering in general would greatly benefit from the consideration of UML in FMI-based co-simulation approach. It would indeed enable a significant number of software designers to evaluate the behavior of their software components in their simulated environment, as soon as possible in their development processes, and therefore make early and better design decisions. It would also open new interesting perspectives for CPS system engineers, by allowing them to consider a widely used modeling language for the software parts of their systems. In this context, the objective of this work is to define an FMI-based co-simulation environment for CPS with integration of UML models for software part. Our contribution is twofold: locally at the level of UML models, and globally at the master level. At the local level, we set up an incremental approach where we address different kinds of discrete event systems characterizing the computational components. We base our proposals on OMG standards fUML and PSCS which define precise execution semantics for a subset of UML. They provide an interesting and formal basis for the integration of UML models in CPSs co-simulation approaches. For each kind of system, we first identify a set of rules to model it with UML and potential extensions to fUML in case where execution semantics of the required UML elements are not defined by fUML. Then, at the global level, we propose a master algorithm for each kind of systems. The proposed masters take into account not only external and internal dependencies between components and their capabilities, but also and especially their models of time. They rely on adaptation of fUML semantics to that of the FMI API. Based on these adaptations, the master algorithm is able both to propagate data between components and to trigger them at the correct points of time. The approach is illustrated with use cases from the energy domain where the purpose is to verify energy management strategies defined as software components at different levels of the control module of an energy system.

Les systèmes informatiques envahissent de plus en plus notre quotidien, en allant de la plus simple application de lecture des fichiers audio, à la plus critique comme les voitures et les avions. Dans les systèmes critiques, la validation par vérification formelle s'impose. Cette thèse s'inscrit dans ce cadre et tend à doter le langage UML, langage de modélisation standard de facto, d'une sémantique formelle pour des finalités de vérification. En premier lieu, nous avons analysé et révisé le fondement théorique des principales approches de formalisation et de vérification issues de la littérature et se focalisant sur le langage UML, ses profils et les concepts des réseaux de Petri (RdPs). En deuxième lieu, nous avons proposé une nouvelle approche hiérarchique de formalisation des diagrammes globaux d'interactions (IOD). En se basant sur ce point, nous avons développé des formalismes temporels et temporisés des diagrammes de Timing UML2 (TD), appliqués par des exemples d'illustration. Ensuite, nous avons conçu une approche de vérification sur les approches développées, s'intéressant aux Systèmes Temps Réel (STRs), utilisant l'extension temporelle du langage des contraintes objets OCL/Temps Réel (OCL TR), le profil UML MARTE et la logique temporelle temporisée (TCTL), exploitée d'une technique de vérification automatique après la transformation du modèle (Model Checking). Enfin, nous avons appliqué les formalismes proposés sur une étude de cas, afin de garantir leurs efficacités logique et temporelle. / The computer systems have increasingly invaded our daily lives from the simplest application as audio files reading to the most critical one as cars and airplanes. For critical systems, the validation by the formal verification is required. This Thesis concerns this area of research and aims to ensure the betterment of UML language, which is the de facto standard, with formal semantics for verification finality. For the first part, we have analyzed and revised the theoretical foundations the existing formal verification methods used UML, their profiles and the basic concepts of the Petri nets (PNs). For the second part, we have created a novel hierarchical approach to formalize the Interaction Overview Diagrams (IOD). Based on this idea, we have developed temporal formalisms based on the UML2 Timing Diagrams (TD), applied by illustration examples. Then, we have proposed a Formal Verification approach based on last formalisms which are interested in Real Time Systems (RTS) and employ the temporal extension of the Object Constraints language (OCL/Real Time) (OCL TR), the UML MARTE profile and the timed computation Tree logic (TCTL), given by the Model Checking technique after the model's transformation. Finally, we have applied all the proposed formalisms through a case study, in order to ensure its logical and temporal efficiency.

Alla människor uppfattar och registrerar data. Hur data visualiseras kommer påverka hur enkelt vi människor förstår informationen. Detta projekt undersöker hur ett system ska utvecklas för att en datavisualisering av betalingnstider enkelt ska presenteras på en webbsida. Olika idéer och designer av webbsidan framställdes och analyserades. Fokuset är på hur data ska visas i olika diagram och tabeller. En utvecklingsmiljö formades med en databas och slumpgenererad data för att testa systemet för applikationen. Resultatet blev en färdig webbapplikation som hämtar data från en databas med SQL-frågor. Därefter mellanlagras den användbara data i JSON-filer och sedan visualiseras statistiken på en webbapplikation med hjälp av JavaScript biblioteket Chart.js. Webbsidan utvärderades med användbarhetstester som visade på att det fanns otydligheter i topp- och bottenlistor samt en sökfunktion. Användbarhetstesterna visade även att webbsidan var mycket strukturerad och att det var enkelt att hitta och extrahera information. / All individuals perceive and register data. How data is visualized will affect how easily we humans understand the information. This project investigates how a system should be developed to present a data visualization of payment deadlines easily on a website. Various ideas and designs for the webpage were created and analyzed. The focus is on how data should be displayed in different charts and tables. A development environment was set up with a database and randomly generated data to test the system for the application. The result was a completed web application that retrieves data from a database using SQL queries. The useful data is then cached in JSON-files and the statistics are visualized on a website using the JavaScript library Chart.js. The usability of the website was evaluated through usability testing, which revealed ambiguities in the top and bottom lists as well as a search function. The usability tests also showed that the website was highly structured and it was easy to find and extract information.

<p>Један од основних постулата друштва знања је доступност знања. Научно-истраживачке институције су један од главних извора верификованих знања. Ова знања су доступна путем интерних информационих система научно-истраживачке делатности. Са друге стране библиотечки информациони системи садрже велику количину структуираног научног садржаја. Интеграција ових система може довести до тога да разноликост и количина доступног научног садржаја буду значајно повећани. Модел података информационог система описаног у овој дисертације је базиран на MARC 21 формату и компатибилан је са CERIF моделом података. Овакав модел података омогућује имплементираном информационом систему да може да размењује податке са другим системима и по CERIF стандарду и по библиотечком стандарду. Другим речима, овај систем је интероперабилан са другим CERIF компатибилним информационим системима научно-истраживачке делатности, али је исто тако и интероперабилан и са библиотечким системима. Такође, модел података система омогућује и вредновање научно-истраживачких резултата. За моделирање описаног система коришћен је UML 2.0. Систем је имплементиран у вишеслојној клијент-сервер архитектури у Јава окружењу.</p> / <p>Jedan od osnovnih postulata društva znanja je dostupnost znanja. Naučno-istraživačke institucije su jedan od glavnih izvora verifikovanih znanja. Ova znanja su dostupna putem internih informacionih sistema naučno-istraživačke delatnosti. Sa druge strane bibliotečki informacioni sistemi sadrže veliku količinu struktuiranog naučnog sadržaja. Integracija ovih sistema može dovesti do toga da raznolikost i količina dostupnog naučnog sadržaja budu značajno povećani. Model podataka informacionog sistema opisanog u ovoj disertacije je baziran na MARC 21 formatu i kompatibilan je sa CERIF modelom podataka. Ovakav model podataka omogućuje implementiranom informacionom sistemu da može da razmenjuje podatke sa drugim sistemima i po CERIF standardu i po bibliotečkom standardu. Drugim rečima, ovaj sistem je interoperabilan sa drugim CERIF kompatibilnim informacionim sistemima naučno-istraživačke delatnosti, ali je isto tako i interoperabilan i sa bibliotečkim sistemima. Takođe, model podataka sistema omogućuje i vrednovanje naučno-istraživačkih rezultata. Za modeliranje opisanog sistema korišćen je UML 2.0. Sistem je implementiran u višeslojnoj klijent-server arhitekturi u Java okruženju.</p> / <p>One of the fundamental postulates of the knowledge society is the availability of&nbsp;knowledge. Scientific-research institutions are a major source of verified knowledge. This knowledge is available through internal information systems of scientific-research activities. On the other hand library information systems contain a large amount of structured scientific content. Integration of these systems can lead to significant increase of variety and quantity of available scientific content.&nbsp;</p><p><span style="font-size: 12px;">Data model of the information system presented in this dissertation is based on the MARC 21 format and model is compliant with CERIF data model. This model enables that implemented system can exchange data with other systems in accordance with CERIF standard and librarian standards. It means this system is interoperable with other CERIF-compliant information systems and interoperable with librarian systems. Also, system data model enables evaluation of scientific-research results. </span></p><p><span style="font-size: 12px;">The modelling of presented system was carried out using UML 2.0. The System was implemented in the multi-tiered client-server architecture on the Java platform.</span></p>

Made available in DSpace on 2015-04-11T14:03:09Z (GMT). No. of bitstreams: 1 Yassue Kashimura.pdf: 1457324 bytes, checksum: 9b71c57d354a148d432e33de69b187fc (MD5) Previous issue date: 2006-09-13 / The communication between portable devices is becoming essential in our life, offering mobility and access to services independent of where are located. The large diversity of members such as agents, routing protocols, topologies changes and measure of services of quality of network involved in this environment become the modeling of the problems in Ad Hoc networking a hard task. The simulation becomes an important task in this context, however there are difficulties as for the process to elaborate models of simulations. Software Engineering can minimize the difficulties found in the use of simulation tools. The purpose of this work is to propose an environment to assist the teaching of simulations of systems from models of networking being represented through of the modeling techniques employed in the Software Engineering. These techniques involve diagrams and extension mechanisms used in modeling tools that let a conversion the models described in UML to XMI pattern, giving a generation of a OTcl script in the syntax of the network simulator. Besides, it expects this work assists in the methodology to describe a scene to simulation of Ad Hoc networks. / A comunicação entre dispositivos portáteis está tornando-se essencial no nosso cotidiano, proporcionando mobilidade e acesso a serviços independentemente de onde estão localizados. A grande diversidade de elementos tais como agentes de conexão, protocolos de roteamento, alterações topológicas e medição da qualidade de serviço da rede envolvidos nesse ambiente tornam a modelagem dos problemas em redes Ad Hoc uma tarefa difícil. A simulação é uma atividade importante, nesse contexto, porém existem dificuldades quanto ao processo de elaborar modelos de simulação. A área da Engenharia de Software pode miminizar as dificuldades encontradas na utilização de ferramentas de simulação. O objetivo deste trabalho é apresentar um método para auxiliar o ensino de simulação de redes de computadores a partir de modelos de cenários representados através das técnicas de modelagem empregadas na Engenharia de Software. Estas técnicas envolvem diagramas e mecanismos de extensões encontrados em ferramentas de modelagem, que permitem a conversão dos modelos descritos em UML no padrão XMI, proporcionando a geração de um script OTcl na sintaxe do Network Simulator. Além disso, espera-se que este trabalho auxilie na metodologia para descrever um cenário para simulação de redes Ad Hoc especificamente.

In model-driven development (MDD), domain-specific modeling languages (DSMLs) act as a communication vehicle for aligning the requirements of domain experts with the needs of software engineers. With the rise of the UML as a de facto standard, UML/MOF-based DSMLs are now widely used for MDD. This paper documents design decisions collected from 90 UML/MOF-based DSML projects. These recurring design decisions were gained, on the one hand, by performing a systematic literature review (SLR) on the development of UML/MOF-based DSMLs. Via the SLR, we retrieved 80 related DSML projects for review. On the other hand, we collected decisions from developing ten DSML projects by ourselves. The design decisions are presented in the form of reusable decision records, with each decision record corresponding to a decision point in DSML development processes. Furthermore, we also report on frequently observed (combinations of) decision options as well as on associations between options which may occur within a single decision point or between two decision points. This collection of decision-record documents targets decision makers in DSML development (e.g., DSML engineers, software architects, domain experts). (authors' abstract) / Series: Technical Reports / Institute for Information Systems and New Media

In model-driven development (MDD), domain-specific modeling languages (DSMLs) act as a communication vehicle for aligning the requirements of domain experts with the needs of software engineers. With the rise of the UML as a de facto standard, UML/MOF-based DSMLs are now widely used for MDD. This paper documents design decisions collected from 90 UML/MOF-based DSML projects. These recurring design decisions were gained, on the one hand, by performing a systematic literature review (SLR) on the development of UML/MOF-based DSMLs. Via the SLR, we retrieved 80 related DSML projects for review. On the other hand, we collected decisions from developing ten DSML projects by ourselves. The design decisions are presented in the form of reusable decision records, with each decision record corresponding to a decision point in DSML development processes. Furthermore, we also report on frequently observed (combinations of) decision options as well as on associations between options which may occur within a single decision point or between two decision points. This collection of decision-record documents targets decision makers in DSML development (e.g., DSML engineers, software architects, domain experts). / Series: Technical Reports / Institute for Information Systems and New Media

ITC/USA 2005 Conference Proceedings / The Forty-First Annual International Telemetering Conference and Technical Exhibition / October 24-27, 2005 / Riviera Hotel & Convention Center, Las Vegas, Nevada / This paper presents an approach to development of generic ground systems to be used for spacecraft testing and operations. This method makes use of a standard modeling method, which enables virtualization of spacecraft. By virtualizing spacecraft, development of generic systems that are applicable to different spacecraft becomes possible even if spacecraft themselves are not standardized. This is because systems can utilize (1) a standard database that can store information on any virtual spacecraft and (2) standard software tools that can be used for any virtual spacecraft. This paper explains the concept of virtualization of spacecraft, introduces the standard model used for virtualization of spacecraft, shows how to manipulate virtual spacecraft with software tools, and presents the core elements of generic ground systems.