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.

Simulink Block Library for LEGO NXT Abstract Dominik Škoda July 30, 2014 The goal of this work is to create a support for the LEGO NXT platform in Simulink development environment. Such support of the target platform already exists, but it suffers from several disadvantages. At first it is provided exclusively for Windows operating systems, and the implementation is closed, therefor neither extensible nor customizable. The main premise of this project is the support of Linux operating systems. The project is also opened to ensure the extensibility and customizability. The model-driven development of systems for the LEGO NXT platform using this project comprises the model testing in a simulation and code generation in Simulink environment by using its standard tools, and deployment of completed programs to target devices. The systems generated with the help of this project are categorized as real-time systems.

Information systems often hold data of considerable value. Their continuing development or maintenance will often necessitate evolution of the system and migration of the data from one version to the next: a process that may be expensive, time-consuming, and prone to error. That such a process remains a source of challenges, is recognized by both academia and industry. In current practice, data migration is often considered only in the later stages of development, leaving critical data to be transformed and loaded by hand-written scripts, long after the design process has been completed. The advent of model-driven engineering offers an opportunity to consider the question of information system evolution and data migration earlier in the development process. A precise account of the proposed changes to an existing system model can be used to predict the consequences for existing data, and to generate the necessary data migration implementation. This dissertation shows how automatic data migration can be achieved by extending the definition of a data modeling language to include model level operations, each of which corresponds to the addition, modification, or deletion of a model component. Using the Unified Modeling Language (UML) notation as an example, we show how the specification of these operations may be translated into an abstract program in the Abstract Machine Notation (AMN), employed in the B-method, and then formally checked for consistency and applicability prior to translation into a concrete programming notation, such as Structured Query Language (SQL).

Test Driven Development (TDD), Model-Driven Development (MDD), and Test Case Generation with their associated practices and tools each in their own right promise to deliver robust higher quality code more economically then other approaches. These process are not mutually exclusive but are not typically used together. This thesis develops a combined approach using complimentary aspects of each of the above three process. Test cases are described, generated, and then injected back into the model, which is then used to produce the test and production code. We have enhanced a model-driven tool to support the approach, adding a test case generator, capable of understanding augmented MDD software model and utilizing the constraints captured in our test-centric language to generate model-level test cases back into the model. Our results show that, with a reduction in overall effort one can produce a tested model-based system in which its test and implementation for multiple platforms such as C and Java, using one of multiple test xUnit frameworks.

Model driven development (MDD) is on the rise in software engineering and no more so than in the realm of real-time and embedded systems. Being able to leverage the code generation and validation techniques made available through MDD is worth exploring, and is the focus of much academic and industrial research. However given the iterative nature of MDD, the natural evolution of models causes test case generation to occur multiple times throughout a software modeling project. Currently, the existing process of regenerating test cases for a modified model of a system can be costly, inefficient, and even redundant. The focus of this research was to achieve an improved understanding of the impact of typical model evolution steps on both the execution of the model and its test cases, and how this impact can be mitigated by reusing previously generated test cases. In this thesis we use existing techniques for symbolic execution and test case generation to perform an analysis on example models and determine how evolution affects model artifacts; these findings were then used to classify evolution steps based on their impact. From these classifications, we were able to determine exactly how to perform updates to existing symbolic execution trees and test suites in order to obtain the resulting test suites using minimal computational resources whenever possible. The approach was implemented in a software plugin, IncreTesCaGen, that is capable of incrementally generating test cases for a subset of UML-RT models by leveraging the existing testing artifacts (symbolic execution trees and test suites), as well as presenting additional analysis results to the user. Finally, we present the results of an initial evaluation of our tool, which provides insight into the tool’s performance, the effects of model evolution on execution and test case generation, as well as design tips to produce optimal models for evolution. / Thesis (Master, Computing) -- Queen's University, 2012-09-26 14:18:50.838

Model Driven Development (MDD) is a paradigm introduced to overcome the complexities of modern software development. In MDD we use models as a primary artifact that is being developed, tested and refined, with code being a result of code generation. Analysis and verification of models is an important aspect of MDD paradigm, because they improve understanding of a developed system and enable discovery of faults early in the development. Even though many analysis methods exist (e.g., model checking, proof systems), they are not directly applicable in the context of industrial MDD tools such as IBM Rational Software Architect Real Time Edition (IBM RSA RTE). One of the main reasons for this inapplicability is the difference between modeling languages used in MDD tools (e.g. UML-RT language in IBM RSA RTE) and languages used in existing tools. These differences require an implementation of a transformation from a modeling language to an input language of a tool. UML-RT as well as other industrial MMD models, cannot be easily translated, if the target languages do not directly support key model features. To address this problem we follow a research direction that deviates from the standard approaches and instead of bringing MDD models to analysis tools, the approach brings analysis "closer" to MDD models. We introduce analysis of UML-RT models dedicated to this modeling language. To this end we use a formal internal representation of UML-RT models that preserves the important features of these models, such as hierarchical structures of components, asynchronous communication and action code. This provides us with formalized models using straightforward transformation. In addition, this approach enables the use of MDD-specific abstractions aiming to reduce the size of the state space necessary. To this end we introduce several MDD-specific types of abstractions for: data (using symbolic execution), structure and behavior. The work also includes model checking algorithms, which use the modular nature of UML-RT models. The proposed approach is implemented in a toolset that enables analysis directly of UML-RT models. We show the results of experiments with UML-RT models developed in-house and obtained from our industrial partner. / Thesis (Ph.D, Computing) -- Queen's University, 2014-06-24 17:58:05.973

There are many companies operating in the current electricity market and new companies are still forming. This gives every consumer an option to choose a company selling electricity. Electricity dealers can even buy or sell electricity from abroad. Although this situation seems to be natural, it's very complicated to achieve. It's necessary to follow a lot of rules and business processes to be able to establish a functional liberalized market. Because of the amount of business processes it's obvious that liberalized market depends first of all on information systems. However, to develop an information system is usually big investment and it is necessary to find some way to cut the information systems prices. This thesis introduces an effective way of system development for the electricity market domain. This method is introduced as Model Driven Development (MDD) methodology. The idea promoted by MDD is to use models to describe programs and automation code generators to transform models into source code. Model creation is obviously much faster than writing source code, which makes software development more effective. In the category of supporting MDD tools, Damas Energy platform is introduced. The main goal of this thesis is to analyze the usability of Damas Energy with MDD and to show which method to choose when developing information systems for the electricity market domain.

To be able to create quality software system, one need to analyse it well, design, program and test it. The whole process is called software life-cycle and is studied by software engineering. Today, there are many tools making this process easier. For analysing and designing software UML language became favourite. It enables programmers to describe different aspects of software by graphical diagrams and enables them to comprehend them better. Some of them can be translated into source code in chosen programming language. Problem is maintaining those diagrams during later phases when source code was already generated and is used exclusively. This problem is trying to be solved by Model-Driven Development, where programmer is working with well-defined models that can be automatically transformed into the source code that don't have to be edited by hand. Unfortunately this approach is not universal. This work tries to design and create tool that can work with use case diagrams, class diagrams and object-oriented Petri nets. This tool should allow designing those diagrams and be able to synchronise information between them to make the software design easier.

A indústria de desenvolvimento de software está em constante evolução e em busca de novos desafios, como por exemplo: novas tecnologias, linguagens de programação e estratégias para aumentar a produtividade no desenvolvimento. Com o passar do tempo, essa evolução desejada tem se concretizado, em especial com o surgimento de conceitos como Service Oriented Architecture (SOA) e Model-Driven Development (MDD). Nesse contexto, ganha importância a reutilização de software, por exemplo por meio do uso de serviços que facilitam a interoperabilidade entre diferentes sistemas. Ambientes de desenvolvimento de software, em especial ambientes de reúso de software, poderiam se adequar à arquitetura SOA para facilitar a disponibilização de serviços a outros ambientes, promovendo sua integração e aumentando a possibilidade de reúso. Após um levantamento bibliográfico sobre ambientes integrados de reúso que utilizassem serviços para permitir o compartilhamento de recursos, percebeu-se que os trabalhos nessa direção são poucos. Ao mesmo tempo, observou-se que para integração de sistemas por meio de serviços é necessário criar camadas de acesso às entidades dos sistemas que compartilharão informações. A implementação desses serviços de forma manual é repetitiva e sujeita a erros, principalmente por programadores que não estão familiarizados com SOA. Por outro lado, diagramas de classes em UML (Unified Modeling Language) são de amplo conhecimento por parte de desenvolvedores e estão em um nível de abstração que é suficientemente detalhado para permitir a derivação de serviços de acesso às suas classes. Desta forma, para atender uma demanda crescente de sistemas que precisam oferecer serviços para possibilitar sua integração com outros sistemas, este mestrado tem por objetivo promover a geração automatizada de código de serviços por meio de transformações de modelo para texto, em que o modelo de entrada é um diagrama de classes derivado da UML e os serviços gerados cobrem operações básicas do tipo CRUD. O gerador resultante foi validado por meio de duas provas de conceito e mostrou-se adequado para cumprir os objetivos estabelecidos, visto que o desenvolvedor trabalha com um modelo em alto nível de abstração, não precisando conhecer os detalhes inerentes à implementação dos serviços. / The software development industry is constantly evolving and looking for challenges, such as: new technologies, programming languages and strategies to increase developers productivity. During the course of time, this required evolution has been concretized, especially with the emergency of concepts such as Service Oriented Architecture (SOA) and Model-Driven Development (MDD). In this context, software reuse gains importance, for example through the use of services that ease the interoperability of different systems. Software development environments, in special reuse environments, could be adapted to the SOA architecture to ease the availability of services to other environments, thus promoting its integration and possibility of reuse. After a literature review about integrated reuse environments that use services to allow resources sharing, it has been observed that there are only a few works in this direction. At the same time, it was observed that for system integration through services it is required to create an access layer for the system entities that share information. The manual implementation of these services is repetitive and error prone, especially for programmers who are not familiar with SOA. On the other hand, UML (Unified Modeling Language) class diagrams are widely known by developers and are at a level of abstraction that is sufficiently detailed to allow the derivation of access services to their classes. Thus, to meet a growing demand for systems that need to provide services to enable its integration with other systems, this masters dissertation aims to promote the automated generation of service code through transformations from model to text, where the input model is a class diagram derived from UML, and the generated services cover the basic CRUD operations. The resulting generator has been validated through two proofs of concepts and was adequate to meet the stated objectives, as the developer works with a model in a high abstraction level, and does not need to know the details related with the service implementation.

Este trabalho tem por objetivo propor a utilização de soluções pré-definidas e comprovadas na abordagem MDA, auxiliando o desenvolvedor na resolução de problemas recorrentes ao desenvolvimento de software. A utilização destas soluções pré-definidas leva a um aumento de produtividade no contexto MDA e na geração de software baseado em boas práticas. Para que este objetivo seja cumprido, é empreendida uma análise sobre o MDA e sobre como operacionalizar as transformações entre modelos. Também é empreendida uma análise sobre o suporte fornecido pela UML e sobre reutilização em desenvolvimento orientado a modelos. Por fim este trabalho apresenta partes de uma aplicação protótipo, construída para ser uma prova de conceito de código gerado através da combinação de UML e soluções pré-definidas. / The goal of this work is to propose the use of pre-defined solutions on MDA approach, supporting the developer in solving recurrent problems of software development. The use of these pre-defined solutions leads to an increase of productivity in MDA context, and in the generation of software based on best practices. To reach this goal, an analysis of MDA is undertaken, as well as an analysis of how to enable the transformations between models. It is also undertaken an analysis about the use of UML and the reuse in model driven development. Finally this work presents portions of a prototype application, constructed to be a proof-of-concept of generated code, combining UML and the pre-defined solutions.