Orientador: Ney Lemke / Coorientador: Marcio Luis Acencio / Banca: Cesar Martins / Banca: Lucas Bleicher / Resumo: Fatores de transcrição são proteínas que interagem com sequências nucleotídicas específicas situadas nas regiões promotoras de genes e, através dessa interação, regulam a transcrição dos genes. Devido a essa função reguladora, a identificação e a caracterização da rede de interações entre fatores de transcrição e seus genes alvos são importantes por que essa rede representa o arcabouço molecular através do qual os estímulos ambientais são convertidos em expressão diferencial dos genes. Como essa expressão diferencial, por sua vez, determina o comportamento da célula em resposta a um certo estímulo, a rede de interações de regulação transcricional pode, portanto, fornecer uma compreensão sistêmica de como os comportamentos celulares emergem a partir dos estímulos ambientais. A primeira etapa para a construção de uma rede de regulação transcricional consiste na coleta de dados relacionados às interações entre os fatores de transcrição e seus genes alvos. Porém, como esses dados são encontrados de forma dispersa na literatura ou em bancos de dados pagos, essa etapa demanda muito tempo. Com o objetivo de centralizar esses dados de forma a facilitar sua coleta e, consequentemente, a construção da rede de interações de regulação transcricional, desenvolvemos um banco de dados relacional chamado Human Transcriptional Regulation Interaction Database (HTRIdb). Desenvolvido em PostgreSQL e Java, o HTRIdb contém uma coleção de milhares de interações de regulação transcricional experimentalmente verificadas em seres humanos que podem ser acessadas e obtidas gratuitamente por toda a comunidade científica. Além do acesso gratuito e livre permissão para a obtenção dos dados, o HTRIdb oferece... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Transcription factors are proteins that interact with specific nucleotide sequences located in promoter regions of genes and, through this interaction, regulate gene transcription. Due of this regulatory function, the identification and characterization of the network of interactions between transcription factors and their target genes are important since this network represents the molecular framework that explains how environmental stimuli are converted into differential expression of genes. This network provides a systemic understanding of how cellular behaviors emerge from the environmental stimuli. The first step for the transcriptional regulatory network construction is the collection of data about interactions between transcription factors and their target genes. This step is very time-consuming as these data are found dispersed on the literature or in commercial databases. In an effort to provide researchers with a repository of transcriptional regulatory interactions from which such interactions can be directly and easily extracted, we developed a relational database called the Human Interaction Database Transcriptional Regulation (HTRIdb). HTRIdb was implemented using PostgreSQL and Java and contains a collection of thousands of experimentally verified human transcriptional regulation interactions. HTRIdb can be freely accessed by the scientific community and offers a visualization tool for the regulatory network and provides a communication interface between users and developers to enhance... (Complete abstract click electronic access below) / Mestre

[pt] O presente trabalho faz um detalhado estudo visando enriquecer o conhecimento sobre Processo de Desenvolvimento de Software (das questões técnicas às gerenciais). Uma abordagem sistêmica a esses tópicos, buscando um rigoroso e formal tratamento de seus conceitos e definições, é realizada e suas características essenciais sçao levantadas e avaliadas dentro de uma visão de Engenharia e sob a perspectiva de uma Modelagem de Essência. / [en] This work does a detailed study aiming to increase the knowledge about Software Development Process (from technical to management questions). A systemic approach to these topics, seeking a rigorous and formal treatment of their concepts and definitions, is done and their essential and fundamental characteristics are raised and evaluated from a view of engineering and under the perspective of Essential Modeling. A Vocabulary is established aiming to formulate a language (basics of all discussion of this work) with the minimum of ambiguities. A Social-Technical Systems Modeling Structure is presented and an Essential Model to the Software Development Process is proposed. The use of the Modeling Structure in this work is evaluated and it is analyzed under the perspective of the Essential Model proposed. At last, suggestions to further works in research and experimentation are presented.

There has been an increased focus in recent years on the development of re-usable software, in the form of objects and software components. This increase, together with pressures from enterprises conducting transactions on the Web to support all business interactions on all scales, has encouraged research towards the development of easily reconfigurable and highly adaptable Web services. This work investigates the ability of Component-Based Software Development (CBSD) to produce such systems, and proposes a more manageable use of CBSD methodologies. Component-Driven Software Development (CDSD) is introduced to enable better component manageability. Current Web service technologies are also examined to determine their ability to support extensible Web services, and a dynamic Web service architecture is proposed. The work also describes the development of two proof-of-concept systems, DREW Chat and Hamilton Bank. DREW Chat and Hamilton Bank are implementations of Web services that support extension dynamically and at run-time. DREW Chat is implemented on the client side, where the user is given the ability to change the client as required. Hamilton Bank is a server-side implementation, which is run-time customisable by both the user and the party offering the service. In each case, a generic architecture is produced to support dynamic Web services. These architectures are combined to produce CREWS, a Component-driven Runtime Extensible Web Service solution that enables Web services to support the ever changing needs of enterprises. A discussion of similar work is presented, identifying the strengths and weaknesses of our architecture when compared to other solutions.

Técnicas que partem de modelos de alto nível de abstração são requeridas para lidar com a complexidade encontrada nas novas gerações de sistemas embarcados, sendo cruciais para o sucesso do projeto. Uma grande redução do esforço pode ser obtida com o uso de modelos quando código em uma linguagem de programação pode ser gerado automaticamente a partir desses. Porém, ferramentas disponíveis para modelagem e geração de código normalmente são dependentes de domínio e o software embarcado normalmente possui comportamento heterogêneo, requerendo suporte a múltiplos modelos de computação. Nesta tese, estratégias para desenvolvimento de software embarcado baseado em modelos de alto nível usando UML e Simulink são analisadas. A partir desta análise, observaram-se as principais limitações das abordagens para geração de código baseadas em UML e Simulink. Esta tese, então, propõe estratégias para melhorar a automação provida por estas ferramentas, como por exemplo, propondo uma abordagem para geração de código multithread a partir de modelos Simulink. A comparação feita entre UML e Simulink mostra que, embora UML seja a linguagem mais usada no domínio de engenharia de software, UML é baseada em eventos e não é adequada para modelar sistemas dataflow. Por outro lado, Simulink é largamente usado por engenheiros de hardware e de controle, além de suportar dataflow e geração de código. Porém, Simulink provê abstrações de mais baixo nível, quando comparado a UML. Conclui-se que tanto UML como Simulink possuem prós e contras, o que motiva a integração de ambas linguagens em um único fluxo de projeto. Neste contexto, esta tese propõe também uma abordagem integradora para desenvolvimento de software embarcado que inicia com uma especificação de alto nível descrita usando diagramas UML, a partir da qual modelos dataflow e control-flow podem ser gerados. Desta maneira, o modelo UML pode ser usado como front-end para diferentes abordagens de geração de código, incluindo UML e a proposta geração de código multithread a partir de modelos Simulink. / The use of techniques starting from higher abstraction levels is required to cope with the complexity that is found in the new generations of embedded systems, being crucial to the design success. A large reduction of design effort when using models in the development can be achieved when there is a possibility to automatically generate code from them. Using these techniques, the designer specifies the system model using some abstraction and code in a programming language is generated from that. However, available tools for modeling and code generation are domain-specific and embedded software usually shows heterogeneous behavior, which pushes the need for supporting software automation under different models of computation. In this thesis, strategies for embedded software development based on high-level models using UML and Simulink were analyzed. We observed that the embedded software generation approaches based on UML and Simulink have limitations, and hence this thesis proposes strategies to improve the automation provided on those approaches, for example, proposing a Simulink-based multithread code generation. UML is a well used language in the software engineering domain, and we consider that it has several advantages. However, UML is event-based and not suitable to model dataflow systems. On the other side, Simulink is widely used by control and hardware engineers and supports dataflow, and time-continuous models. Moreover, tools are available to generate code from a Simulink model. However, Simulink models represent lower abstraction level compared to UML ones. This comparison shows that UML and Simulink have pros and cons, which motivates the integration of both languages in a single design process. As the main contribution, we propose in this thesis an integrated approach to embedded software design, which starts from a high-level specification using UML diagrams. Both dataflow and control-flow models can be generated from that. In this way, an UML model can be used as front-end for different code generation approaches, including UML-based one and the proposed Simulink-based multithread code generation.

An approach using dot plots as an aid to visualizing smells within Java source files is presented. Dot plots are a visual tool that allows for viewing duplication in a document or text string. Our approach uses a plug-in for the Eclipse Java IDE to convert Java source files into dot plots. The goal here is to find problem areas in the code, known as "Code Smells", that could indicate that the source file needs to be modified or refactored. In the dot plot these problem areas appear as sections that contain interesting dot formations. Color is also used to enhance places of the dot plot that could be important. Duplication is a common problem in source code and also an important Code Smell. We will show that through finding the Duplicate Code smell we will also be able to find other code smells creating a plug-in that a programmer can use during the coding process to help improve code design.

This dissertation discusses risk management in the context of software development. It commences by investigating why so many software development projects fail. It then focuses on approaches to software development that emerged as attempts to improve the success rate. A common shortcoming to these approaches is identified, namely that they only cater for the tasks that need to be done, ignoring possible unexpected problems. After having motivated the need for risk management, the framework for a risk management methodology is discussed, outlining the steps in the risk management process. Decision-making guidelines and best practices follow, as well as a discussion about the way they should be implemented as part of the risk management effort. Guidelines are provided for the implementation of risk management as part of software development. Finally, the risks that may cause the failure of the implementation of risk management are identified and guidelines provided to address them. / Computing / M. Sc. (Information Systems)

Técnicas que partem de modelos de alto nível de abstração são requeridas para lidar com a complexidade encontrada nas novas gerações de sistemas embarcados, sendo cruciais para o sucesso do projeto. Uma grande redução do esforço pode ser obtida com o uso de modelos quando código em uma linguagem de programação pode ser gerado automaticamente a partir desses. Porém, ferramentas disponíveis para modelagem e geração de código normalmente são dependentes de domínio e o software embarcado normalmente possui comportamento heterogêneo, requerendo suporte a múltiplos modelos de computação. Nesta tese, estratégias para desenvolvimento de software embarcado baseado em modelos de alto nível usando UML e Simulink são analisadas. A partir desta análise, observaram-se as principais limitações das abordagens para geração de código baseadas em UML e Simulink. Esta tese, então, propõe estratégias para melhorar a automação provida por estas ferramentas, como por exemplo, propondo uma abordagem para geração de código multithread a partir de modelos Simulink. A comparação feita entre UML e Simulink mostra que, embora UML seja a linguagem mais usada no domínio de engenharia de software, UML é baseada em eventos e não é adequada para modelar sistemas dataflow. Por outro lado, Simulink é largamente usado por engenheiros de hardware e de controle, além de suportar dataflow e geração de código. Porém, Simulink provê abstrações de mais baixo nível, quando comparado a UML. Conclui-se que tanto UML como Simulink possuem prós e contras, o que motiva a integração de ambas linguagens em um único fluxo de projeto. Neste contexto, esta tese propõe também uma abordagem integradora para desenvolvimento de software embarcado que inicia com uma especificação de alto nível descrita usando diagramas UML, a partir da qual modelos dataflow e control-flow podem ser gerados. Desta maneira, o modelo UML pode ser usado como front-end para diferentes abordagens de geração de código, incluindo UML e a proposta geração de código multithread a partir de modelos Simulink. / The use of techniques starting from higher abstraction levels is required to cope with the complexity that is found in the new generations of embedded systems, being crucial to the design success. A large reduction of design effort when using models in the development can be achieved when there is a possibility to automatically generate code from them. Using these techniques, the designer specifies the system model using some abstraction and code in a programming language is generated from that. However, available tools for modeling and code generation are domain-specific and embedded software usually shows heterogeneous behavior, which pushes the need for supporting software automation under different models of computation. In this thesis, strategies for embedded software development based on high-level models using UML and Simulink were analyzed. We observed that the embedded software generation approaches based on UML and Simulink have limitations, and hence this thesis proposes strategies to improve the automation provided on those approaches, for example, proposing a Simulink-based multithread code generation. UML is a well used language in the software engineering domain, and we consider that it has several advantages. However, UML is event-based and not suitable to model dataflow systems. On the other side, Simulink is widely used by control and hardware engineers and supports dataflow, and time-continuous models. Moreover, tools are available to generate code from a Simulink model. However, Simulink models represent lower abstraction level compared to UML ones. This comparison shows that UML and Simulink have pros and cons, which motivates the integration of both languages in a single design process. As the main contribution, we propose in this thesis an integrated approach to embedded software design, which starts from a high-level specification using UML diagrams. Both dataflow and control-flow models can be generated from that. In this way, an UML model can be used as front-end for different code generation approaches, including UML-based one and the proposed Simulink-based multithread code generation.

Made available in DSpace on 2014-06-11T19:23:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-03-01Bitstream added on 2014-06-13T20:49:46Z : No. of bitstreams: 1 bovolenta_la_me_botib.pdf: 1243263 bytes, checksum: ae0c358db6c21782ceadf7284345fd8a (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fatores de transcrição são proteínas que interagem com sequências nucleotídicas específicas situadas nas regiões promotoras de genes e, através dessa interação, regulam a transcrição dos genes. Devido a essa função reguladora, a identificação e a caracterização da rede de interações entre fatores de transcrição e seus genes alvos são importantes por que essa rede representa o arcabouço molecular através do qual os estímulos ambientais são convertidos em expressão diferencial dos genes. Como essa expressão diferencial, por sua vez, determina o comportamento da célula em resposta a um certo estímulo, a rede de interações de regulação transcricional pode, portanto, fornecer uma compreensão sistêmica de como os comportamentos celulares emergem a partir dos estímulos ambientais. A primeira etapa para a construção de uma rede de regulação transcricional consiste na coleta de dados relacionados às interações entre os fatores de transcrição e seus genes alvos. Porém, como esses dados são encontrados de forma dispersa na literatura ou em bancos de dados pagos, essa etapa demanda muito tempo. Com o objetivo de centralizar esses dados de forma a facilitar sua coleta e, consequentemente, a construção da rede de interações de regulação transcricional, desenvolvemos um banco de dados relacional chamado Human Transcriptional Regulation Interaction Database (HTRIdb). Desenvolvido em PostgreSQL e Java, o HTRIdb contém uma coleção de milhares de interações de regulação transcricional experimentalmente verificadas em seres humanos que podem ser acessadas e obtidas gratuitamente por toda a comunidade científica. Além do acesso gratuito e livre permissão para a obtenção dos dados, o HTRIdb oferece... / Transcription factors are proteins that interact with specific nucleotide sequences located in promoter regions of genes and, through this interaction, regulate gene transcription. Due of this regulatory function, the identification and characterization of the network of interactions between transcription factors and their target genes are important since this network represents the molecular framework that explains how environmental stimuli are converted into differential expression of genes. This network provides a systemic understanding of how cellular behaviors emerge from the environmental stimuli. The first step for the transcriptional regulatory network construction is the collection of data about interactions between transcription factors and their target genes. This step is very time-consuming as these data are found dispersed on the literature or in commercial databases. In an effort to provide researchers with a repository of transcriptional regulatory interactions from which such interactions can be directly and easily extracted, we developed a relational database called the Human Interaction Database Transcriptional Regulation (HTRIdb). HTRIdb was implemented using PostgreSQL and Java and contains a collection of thousands of experimentally verified human transcriptional regulation interactions. HTRIdb can be freely accessed by the scientific community and offers a visualization tool for the regulatory network and provides a communication interface between users and developers to enhance... (Complete abstract click electronic access below)

Thesis submitted in fulfilment of the requirements for the degree Master of Technology: Information Technology in the Faculty of Informatics and Design at the Cape Peninsula University of Technology 2013 / The application of software systems in business organizations continue to increase as the Internet technology grows. Business processes that previously required manual interventions are becoming automated using software systems. The use of software systems is fundamental to electronic processing of business transactions. More business organizations, large and small, are utilizing information technology in order to have competitive advantage in the business arena. Software is ubiquitous. Among areas where software plays core roles are e-Banking where software systems are used to process banking transactions, e-Health where software systems are used to facilitate activities in the health sector, e-Commerce where software systems are used to facilitate online business transactions, e-Government where software system are used to facilitate government activities and e-Learning where software systems are used to facilitate the teaching and learning process. Nevertheless, the large number of failing software projects and the increase in software security problems coupled with shortage of skilled software developers are still major obstacles in the software development industry. Among others, the solution can be achieved by improving the competency of software developers so that software systems developed are of good quality, safe, robust, and support business objectives. Software companies and business organizations stand a big chance to increase their return on investment (ROI), if competencies of software developers are improved. A software developer plays critical roles in software development projects. A software developer, however, requires specific skills and knowledge in order to develop software systems that solve problems and deliver solutions. This research is about competencies of software developers. The research focuses on software development activities performed by software companies and business organizations within the Western Cape Province. The unit of analysis is software developers. Data pertaining to tasks performed by software developers, tools used by software developers and skills required were collected, examined and analysed. The objective of the research is to develop a competency framework for software developers. It can be used by institutions and the industry to provide better education. Most importantly, the industry will have access to competent software developers who can perform their job well. As justified in this research, knowledge of a competency framework for software developers is extremely essential.ÿ

Thesis Submitted in fulfilment of the requirements for the degree Master of Technology in Information Technology in the Faculty of Informatics and Design at the Cape Peninsula University of Technonlogy / The use of Information and Communication Technology (ICT) in business has evolved to such an extent that many organizations (if not all) rely on Information Technology (IT) systems to better manage their processes, get competitive advantage, improve performance (efficiency and effectiveness), provide quality services on time and most importantly to keep customers happy. This has changed the way people communicate and conduct businesses, lowering processing cost, time and improving a return on investment. Therefore, high quality software systems are essential. Organizations adopt Agile Scrum methodologies in order to develop applications that help them to obtain a return on investment quickly, to improve customer satisfaction and to maintain competitive advantage. However, the IT industry is yet to develop error-free software that meets the expected quality standards. Therefore, the aim of this study was to explore the extent to which software quality assurance measures can be understood and applied to maximize the quality of software projects developed under Scrum methodology. A qualitative research method informed by an interpretive approach was used to collect and analyse data. Following the purposive sampling technique, five Scrum teams operating in different environments and two academics from one academic institution were interviewed. Structuration Theory (ST) was then used as an analytical framework to analyse data and to improve the understanding of Scrum practices and related quality assurance (QA) processes. Drawing on the major terms of ST, the contextual terrain of the Scrum development process was mapped. It reflected that rules are important aspects of Scrum functions. However, rules are not as strictly applied as in the traditional methodologies. The developer skill, project type and size have a direct influence on the practice/s. In Scrum, rules are flexible in that they can be modified to meet the environment and conditions of the team. Equally significant are resources, most particularly, time and the human resources in the form of developers and Scrum leaders. Otherwise, unit testing, user acceptance testing, close collaboration and code reviews were perceived as the most important practices in Scrum projects. In view of the findings, recommendations can be summed up into 4 main points; (1) that to ensure quality assurance in Scrum, Scrum teams, especially team leaders, should enforce compliance to standards, regardless of time pressures and tight deadlines; (2) It seems that the practice of working with the client to test final products as a quality assurance mechanism is working for all parties. This practice is encouraged and must be maintained; (3) Code reviews must be enforced, and that organisations invest in resources including the constant training of developers; (4) Project product owners, project managers, team leaders and business analysts should regularly meet with the user to verify requirements prior to the implementation phase. Active stakeholder involvement can minimize development costs and time.