Evolutionary changes applied to a framework API may invalidate existing framework-based applications. While manually adapting applications is expensive and error-prone, automatic adaptation demands cumbersome specifications, which the developers are reluctant to write and maintain. Considering structural changes (so-called refactorings) of framework APIs, our adaptation technology supports backward-compatible framework upgrade. The technology is rigorous defining precisely the structure and automatic derivation of compensating adapters. It is also practical compensating for most application-breaking API changes automatically, while requiring neither manual adaptation nor recompilation of existing application code.

A área de sistemas multiagentes é um promissor domínio tecnológico para uso em performances musicais interativas. Em trabalhos recentes, essa tecnologia vem sendo utilizada para resolver problemas musicais de escopo específico e alcance limitado, como a detecção de pulsação, a simulação de instrumentos e o acompanhamento musical automático. Neste trabalho, apresentamos uma taxonomia desses sistemas multiagentes musicais e uma arquitetura e implementação de um arcabouço computacional que generaliza os trabalhos anteriores e aborda problemas usuais como a sincronização em tempo real, a comunicação sonora e a mobilidade espacial dos agentes. Através do arcabouço, um usuário pode desenvolver um sistema multiagente musical focado em suas necessidades musicais, enquanto deixa grande parte dos problemas técnicos a cargo do arcabouço. Para validar o arcabouço, implementamos e discutimos dois estudos de caso que exploram diversos aspectos de um sistema multiagente musical, como a comunicação simbólica, a troca de áudio digital, o uso de trajetórias espaciais, a simulação acústica e conceitos de vida artificial, como códigos genéticos e reprodução, demonstrando a usabilidade do arcabouço em uma grande variedade de aplicações musicais. / Multiagent system technology is a promising new venue for interactive musical performance. In recent works, this technology has been tailored to solve specific, limited scope musical problems, such as pulse detection, instrument simulation or automatic accompaniment. In this work, we pre- sent a taxonomy of such musical multiagent systems, and an implementation of a computational framework that subsumes previous works and addresses general-interest low-level problems such as real-time synchronization, sound communication and spatial agent mobility. By using it, a user may develop a musical multiagent system focusing primarily in his/her musical needs, while leaving most of the technical problems to the framework. To validate this framework, we implemented and discussed two cases studies that explored several aspects of musical multiagent systems, such as symbolic and audio communication, spatial trajectories and acoustical simulation, and artificial life concepts, like genetic codes and reproduction, thus indicating the usefulness of this framework in a variety of musical applications.

The ability of the software engineering community to achieve high levels of reuse from software frameworks has been tempered by the difficulty in understanding how to reuse them properly. When written correctly, a plugin can take advantage of the framework’s code and architecture to provide a rich application with relatively few lines of code. Unfortunately, doing this correctly is difficult because frameworks frequently require plugin developers to be aware of complex protocols between objects, and improper use of these protocols causes exceptions and unexpected behavior at run time. This dissertation introduces collaboration constraints, rules governing how multiple objects may interact in a complex protocol. These constraints are particularly difficult to understand and analyze because they may extend across type boundaries and even programming language boundaries. This thesis improves the state of the art through two mechanisms. First, it provides a deep understanding of these collaboration constraints and the framework designs which create them. Second, it introduces Fusion, an adoptable specification language and static analysis tool, that detects broken collaboration constraints in plugin code and demonstrates how to achieve this goal in a cost-effective manner that is practical for industry use. In this dissertation, I have done an empirical study of framework help forums which showed that collaboration constraints are burdensome for developers, as they take hours or even days to resolve. From this empirical study, I have identified several common properties of collaboration constraints. This motivated a new specification language, called Fusion, that is tailored for specifying collaboration constraints in a practical way. The specification language uses relationships to describe the abstract associations between objects and allows developers to specify collaboration constraints as logical predicates of relationships. Since a relationship is an abstraction above the code, this allows developers to easily specify constraints that cross type and language boundaries. There are three variants of the analysis: a sound variant that has false positives but no false negatives, a complete variant that has false negatives but no false positives, and a pragmatic variant that attempts to balance this tradeoff. In this dissertation, I successfully used Fusion to specify and analyze constraints from examples found in the help forums of the ASP.NET and Spring frameworks. Additionally, I ran Fusion on DaCapo, a 1.5 MLOC DaCapo benchmark for program analysis, to show that Fusion is scalable and provides precise enough results for industry with low specification cost. This dissertation examines many tradeoffs: the tradeoffs of framework designs, the tradeoffs of specification precision, and the tradeoffs of program analysis results are all featured. A central theme of this work is that there is no single right solution to collaboration constraints; there are only solutions that work better for a particular instance of the problem.

A área de sistemas multiagentes é um promissor domínio tecnológico para uso em performances musicais interativas. Em trabalhos recentes, essa tecnologia vem sendo utilizada para resolver problemas musicais de escopo específico e alcance limitado, como a detecção de pulsação, a simulação de instrumentos e o acompanhamento musical automático. Neste trabalho, apresentamos uma taxonomia desses sistemas multiagentes musicais e uma arquitetura e implementação de um arcabouço computacional que generaliza os trabalhos anteriores e aborda problemas usuais como a sincronização em tempo real, a comunicação sonora e a mobilidade espacial dos agentes. Através do arcabouço, um usuário pode desenvolver um sistema multiagente musical focado em suas necessidades musicais, enquanto deixa grande parte dos problemas técnicos a cargo do arcabouço. Para validar o arcabouço, implementamos e discutimos dois estudos de caso que exploram diversos aspectos de um sistema multiagente musical, como a comunicação simbólica, a troca de áudio digital, o uso de trajetórias espaciais, a simulação acústica e conceitos de vida artificial, como códigos genéticos e reprodução, demonstrando a usabilidade do arcabouço em uma grande variedade de aplicações musicais. / Multiagent system technology is a promising new venue for interactive musical performance. In recent works, this technology has been tailored to solve specific, limited scope musical problems, such as pulse detection, instrument simulation or automatic accompaniment. In this work, we pre- sent a taxonomy of such musical multiagent systems, and an implementation of a computational framework that subsumes previous works and addresses general-interest low-level problems such as real-time synchronization, sound communication and spatial agent mobility. By using it, a user may develop a musical multiagent system focusing primarily in his/her musical needs, while leaving most of the technical problems to the framework. To validate this framework, we implemented and discussed two cases studies that explored several aspects of musical multiagent systems, such as symbolic and audio communication, spatial trajectories and acoustical simulation, and artificial life concepts, like genetic codes and reproduction, thus indicating the usefulness of this framework in a variety of musical applications.

This thesis deals with the general problem of robot motion planning and control. It proposes the hypothesis that it should bepossible to create a generic software framework capable of dealing with all robot motion planning and control problems, independent of the robot being used, the task being solved, the workspace obstacles or the algorithms employed. The thesis work then consisted of identifying the requirements and creating a design and implementation of such a framework. This report motivates and documents the entire process. The framework developed was tested on two different robot arms under varying conditions. The testing method and results are also presented.The thesis concludes that the proposed hypothesis is indeed valid.

The objective of this thesis is to address the challenges faced in sustaining efficient, high-performance and scalable Distributed Software Frameworks (DSFs), such as MapReduce, Hadoop, Dryad, and Pregel, for supporting data-intensive scientific and enterprise applications on emerging heterogeneous compute, storage and network infrastructure. Large DSF deployments in the cloud continue to grow both in size and number, given DSFs are cost-effective and easy to deploy. DSFs are becoming heterogeneous with the use of advanced hardware technologies and due to regular upgrades to the system. For instance, low-cost, power-efficient clusters that employ traditional servers along with specialized resources such as FPGAs, GPUs, powerPC, MIPS and ARM based embedded devices, and high-end server-on-chip solutions will drive future DSFs infrastructure. Similarly, high-throughput DSF storage is trending towards hybrid and tiered approaches that use large in-memory buffers, SSDs, etc., in addition to disks. However, the schedulers and resource managers of these DSFs assume the underlying hardware to be similar or homogeneous. Another problem faced in evolving applications is that they are typically complex workflows comprising of different kernels. The kernels can be diverse, e.g., compute-intensive processing followed by data-intensive visualization and each kernel will have a different affinity towards different hardware. Because of the inability of the DSFs to understand heterogeneity of the underlying hardware architecture and applications, existing resource managers cannot ensure appropriate resource-application match for better performance and resource usage. In this dissertation, we design, implement, and evaluate DerbyhatS, an application-characteristics-aware resource manager for DSFs, which predicts the performance of the application under different hardware configurations and dynamically manage compute and storage resources as per the application needs. We adopt a quantitative approach where we first study the detailed behavior of various Hadoop applications running on different hardware configurations and propose application-attuned dynamic system management in order to improve the resource-application match. We re-design the Hadoop Distributed File System (HDFS) into a multi-tiered storage system that seamlessly integrates heterogeneous storage technologies into the HDFS. We also propose data placement and retrieval policies to improve the utilization of the storage devices based on their characteristics such as I/O throughput and capacity. DerbyhatS workflow scheduler is an application-attuned workflow scheduler and is constituted by two components. phi-Sched coupled with epsilon-Sched manages the compute heterogeneity and DUX coupled with AptStore manages the storage substrate to exploit heterogeneity. DerbyhatS will help realize the full potential of the emerging infrastructure for DSFs, e.g., cloud data centers, by offering many advantages over the state of the art by ensuring application-attuned, dynamic heterogeneous resource management. / Ph. D.

In der vorliegenden Arbeit wird die flexible Steuerungsarchitektur Apeca für Systeme der Robotik sowie der robotergestützten Fertigungstechnik vorgestellt. Dafür werden verschiedene Anforderungen identifiziert und innerhalb eines Entwurfs vereint. Ein Hauptaugenmerk des dabei entstandenen Konzeptes ist es, einen vereinfachten Engineeringprozess für den Steuerungsentwurf zu ermöglichen. Dieser Ansatz wird durch die Verwendung von Aktionsprimitiven ermöglicht, die in Form atomarer Systemverhalten in einer speziellen Modulhierarchie eingesetzt werden. Hierzu erfolgt innerhalb der Steuerungsarchitektur eine Trennung zwischen einem funktionsorientierten verhaltensbasierten Modell zur hierarchischen sowie funktionell parallelen Ausführung von Aktionsprimitiven und einem ablauforientierten Modell zur aufgabenabhängigen Aktivierung derselben. Mit Hilfe eines Nutzerkonzepts werden diese Modelle verschiedenen Anwendern zugeordnet. Die objektorientierte Realisierung dieses Entwurfs ermöglicht die Verwendung und Synchronisation von mehreren Teilsystemen innerhalb einer Steuerung. In der Arbeit wird sowohl der entstandene Entwurf diskutiert als auch eine prototypische Implementierung vorgestellt. Abschließend werden die Ergebnisse anhand verschiedener Demonstrationsszenarien präsentiert. / In this present work, the Apeca framework, a flexible control architecture for robotic systems, is introduced. The conceptual design combines different requirements identified in miscellaneous robotic control approaches. The main focus of the resulting concept is on a simplified engineering process for the controller design. This approach is supported by the use of atomic system behaviors, the so called action primitives, in a special module hierarchy. For this purpose a distinction between a functional behavior based system model with hierarchically and also parallelly executed action primitives and a sequential control system model with a task-dependent activation of the primitives is proposed. These models are assigned to different users through a distinct user concept. An object-oriented implementation of the proposed architecture allows the utilization and synchronisation of multiple (sub-)systems within one framework. In this work the proposed framework will be discussed, a prototypical implementation will be presented and results based on different experimental scenarios will be shown.

In der vorliegenden Arbeit wird die flexible Steuerungsarchitektur Apeca für Systeme der Robotik sowie der robotergestützten Fertigungstechnik vorgestellt. Dafür werden verschiedene Anforderungen identifiziert und innerhalb eines Entwurfs vereint. Ein Hauptaugenmerk des dabei entstandenen Konzeptes ist es, einen vereinfachten Engineeringprozess für den Steuerungsentwurf zu ermöglichen. Dieser Ansatz wird durch die Verwendung von Aktionsprimitiven ermöglicht, die in Form atomarer Systemverhalten in einer speziellen Modulhierarchie eingesetzt werden. Hierzu erfolgt innerhalb der Steuerungsarchitektur eine Trennung zwischen einem funktionsorientierten verhaltensbasierten Modell zur hierarchischen sowie funktionell parallelen Ausführung von Aktionsprimitiven und einem ablauforientierten Modell zur aufgabenabhängigen Aktivierung derselben. Mit Hilfe eines Nutzerkonzepts werden diese Modelle verschiedenen Anwendern zugeordnet. Die objektorientierte Realisierung dieses Entwurfs ermöglicht die Verwendung und Synchronisation von mehreren Teilsystemen innerhalb einer Steuerung. In der Arbeit wird sowohl der entstandene Entwurf diskutiert als auch eine prototypische Implementierung vorgestellt. Abschließend werden die Ergebnisse anhand verschiedener Demonstrationsszenarien präsentiert. / In this present work, the Apeca framework, a flexible control architecture for robotic systems, is introduced. The conceptual design combines different requirements identified in miscellaneous robotic control approaches. The main focus of the resulting concept is on a simplified engineering process for the controller design. This approach is supported by the use of atomic system behaviors, the so called action primitives, in a special module hierarchy. For this purpose a distinction between a functional behavior based system model with hierarchically and also parallelly executed action primitives and a sequential control system model with a task-dependent activation of the primitives is proposed. These models are assigned to different users through a distinct user concept. An object-oriented implementation of the proposed architecture allows the utilization and synchronisation of multiple (sub-)systems within one framework. In this work the proposed framework will be discussed, a prototypical implementation will be presented and results based on different experimental scenarios will be shown.

Research in information retrieval deals with the theories and models that constitute the foundations for any kind of service that provides access or pointers to particular elements of a collection of documents in response to a submitted information need. The specific field of information retrieval evaluation is concerned with the critical assessment of the quality of search systems. Empirical evaluation based on the Cranfield paradigm using a specific collection of test queries in combination with relevance assessments in a laboratory environment is the classic approach to compare the impact of retrieval systems and their underlying models on retrieval effectiveness. In the past two decades international campaigns, like the Text Retrieval Conference, have led to huge advances in the design of experimental information retrieval evaluations. But in general the focus of this system-driven paradigm remained on the comparison of system results, i.e. retrieval systems are treated as black boxes. This approach to the evaluation of retrieval system has been criticised for treating systems as black boxes. Recent works on this subject have proposed the study of the system configurations and their individual components. This thesis proposes a generic approach to the evaluation of retrieval systems at the component-level. The focus of the thesis at hand is on the key components that are needed to address typical ad-hoc search tasks, like finding books on a particular topic in a large set of library records. A central approach in this work is the further development of the Xtrieval framework by the integration of widely-used IR toolkits in order to eliminate the limitations of individual tools. Strong empirical results at international campaigns that provided various types of evaluation tasks confirm both the validity of this approach and the flexibility of the Xtrieval framework. Modern information retrieval systems contain various components that are important for solving particular subtasks of the retrieval process. This thesis illustrates the detailed analysis of important system components needed to address ad-hoc retrieval tasks. Here, the design and implementation of the Xtrieval framework offers a variety of approaches for flexible system configurations. Xtrieval has been designed as an open system and allows the integration of further components and tools as well as addressing search tasks other than ad-hoc retrieval. This approach ensures that it is possible to conduct automated component-level evaluation of retrieval approaches. Both the scale and impact of these possibilities for the evaluation of retrieval systems are demonstrated by the design of an empirical experiment that covers more than 13,000 individual system configurations. This experimental set-up is tested on four test collections for ad-hoc search. The results of this experiment are manifold. For instance, particular implementations of ranking models fail systematically on all tested collections. The exploratory analysis of the ranking models empirically confirms the relationships between different implementations of models that share theoretical foundations. The obtained results also suggest that the impact on retrieval effectiveness of most instances of IR system components depends on the test collections that are being used for evaluation. Due to the scale of the designed component-level evaluation experiment, not all possible interactions of the system component under examination could be analysed in this work. For this reason the resulting data set will be made publicly available to the entire research community. / Das Forschungsgebiet Information Retrieval befasst sich mit Theorien und Modellen, die die Grundlage für jegliche Dienste bilden, die als Antwort auf ein formuliertes Informationsbedürfnis den Zugang zu oder einen Verweis auf entsprechende Elemente einer Dokumentsammlung ermöglichen. Die Qualität von Suchalgorithmen wird im Teilgebiet Information Retrieval Evaluation untersucht. Der klassische Ansatz für den empirischen Vergleich von Retrievalsystemen basiert auf dem Cranfield-Paradigma und nutzt einen spezifischen Korpus mit einer Menge von Beispielanfragen mit zugehörigen Relevanzbewertungen. Internationale Evaluationskampagnen, wie die Text Retrieval Conference, haben in den vergangenen zwei Jahrzehnten zu großen Fortschritten in der Methodik der empirischen Bewertung von Suchverfahren geführt. Der generelle Fokus dieses systembasierten Ansatzes liegt jedoch nach wie vor auf dem Vergleich der Gesamtsysteme, dass heißt die Systeme werden als Black Box betrachtet. In jüngster Zeit ist diese Evaluationsmethode vor allem aufgrund des Black-Box-Charakters des Untersuchungsgegenstandes in die Kritik geraten. Aktuelle Arbeiten fordern einen differenzierteren Blick in die einzelnen Systemeigenschaften, bzw. ihrer Komponenten. In der vorliegenden Arbeit wird ein generischer Ansatz zur komponentenbasierten Evaluation von Retrievalsystemen vorgestellt und empirisch untersucht. Der Fokus der vorliegenden Dissertation liegt deshalb auf zentralen Komponenten, die für die Bearbeitung klassischer Ad-Hoc Suchprobleme, wie dem Finden von Büchern zu einem bestimmten Thema in einer Menge von Bibliothekseinträgen, wichtig sind. Ein zentraler Ansatz der Arbeit ist die Weiterentwicklung des Xtrieval Frameworks mittels der Integration weitverbreiteter Retrievalsysteme mit dem Ziel der gegenseitigen Eliminierung systemspezifischer Schwächen. Herausragende Ergebnisse im internationalen Vergleich, für verschiedenste Suchprobleme, verdeutlichen sowohl das Potenzial des Ansatzes als auch die Flexibilität des Xtrieval Frameworks. Moderne Retrievalsysteme beinhalten zahlreiche Komponenten, die für die Lösung spezifischer Teilaufgaben im gesamten Retrievalprozess wichtig sind. Die hier vorgelegte Arbeit ermöglicht die genaue Betrachtung der einzelnen Komponenten des Ad-hoc Retrievals. Hierfür wird mit Xtrieval ein Framework dargestellt, welches ein breites Spektrum an Verfahren flexibel miteinander kombinieren lässt. Das System ist offen konzipiert und ermöglicht die Integration weiterer Verfahren sowie die Bearbeitung weiterer Retrievalaufgaben jenseits des Ad-hoc Retrieval. Damit wird die bislang in der Forschung verschiedentlich geforderte aber bislang nicht erfolgreich umgesetzte komponentenbasierte Evaluation von Retrievalverfahren ermöglicht. Mächtigkeit und Bedeutung dieser Evaluationsmöglichkeiten werden anhand ausgewählter Instanzen der Komponenten in einer empirischen Analyse mit über 13.000 Systemkonfigurationen gezeigt. Die Ergebnisse auf den vier untersuchten Ad-Hoc Testkollektionen sind vielfältig. So wurden beispielsweise systematische Fehler bestimmter Ranking-Modelle identifiziert und die theoretischen Zusammenhänge zwischen spezifischen Klassen dieser Modelle anhand empirischer Ergebnisse nachgewiesen. Der Maßstab des durchgeführten Experiments macht eine Analyse aller möglichen Einflüsse und Zusammenhänge zwischen den untersuchten Komponenten unmöglich. Daher werden die erzeugten empirischen Daten für weitere Studien öffentlich bereitgestellt.

[pt] Os projetos para estudo de genomas partem de uma fase de sequenciamento onde são gerados em laboratório dados brutos, ou seja, sequências de DNA sem significado biológico. As sequências de DNA possuem códigos responsáveis pela produção de proteínas e RNAs, enquanto que as proteínas participam de todos os fenômenos biológicos, como a replicação celular, produção de energia, defesa imunológica, contração muscular, atividade neurológica e reprodução. As sequências de DNA, RNA e proteínas são chamadas nesta tese de biossequências. Porém, o grande desafio destes projetos consiste em analisar essas biossequências, e obter informações biologicamente relevantes. Durante a fase de análise, os pesquisadores usam diversas ferramentas, programas de computador, e um grande volume de informações armazenadas em fontes de dados de Biologia Molecular. O crescente volume e a distribuição das fontes de dados e a implementação de novos processos em Bioinformática facilitaram enormemente a fase de análise, porém criaram uma demanda por ferramentas e sistemas semi-automáticos para lidar com tal volume e complexidade. Neste cenário, esta tese aborda o uso de workflows para compor processos de Bioinformática, facilitando a fase de análise. Inicialmente apresenta uma ontologia modelando processos e dados comumente utilizados em Bioinformática. Esta ontologia foi derivada de um estudo cuidadoso, resumido na tese, das principais tarefas feitas pelos pesquisadores em Bioinformática. Em seguida, a tese propõe um framework para um sistema de gerência de análises em biossequências, composto por dois sub-sistemas. O primeiro é um sistema de gerência de workflows de Bioinformática, que auxilia os pesquisadores na definição, validação, otimização e execução de workflows necessários para se realizar as análises. O segundo é um sistema de gerência de dados em Bioinformática, que trata do armazenamento e da manipulação dos dados envolvidos nestas análises. O framework inclui um gerente de ontologias, armazenando ontologias para Bioinformática, nos moldes da apresentada anteriormente. Por fim, a tese descreve instanciações do framework para três tipos de ambiente de trabalho comumente encontrados e sugestivamente chamados de ambiente pessoal, ambiente de laboratório e ambiente de comunidade. Para cada um destes ambientes, a tese discute em detalhe os aspectos particulares da execução e otimização de workflows. / [en] Genome projects usually start with a sequencing phase, where experimental data, usually DNA sequences, is generated, without any biological interpretation. DNA sequences have codes which are responsible for the production of protein and RNA sequences, while protein sequences participate in all biological phenomena, such as cell replication, energy production, immunological defense, muscular contraction, neurological activity and reproduction. DNA, RNA and protein sequences are called biosequences in this thesis. The fundamental challenge researchers face lies exactly in analyzing these sequences to derive information that is biologically relevant. During the analysis phase, researchers use a variety of analysis programs and access large data sources holding Molecular Biology data. The growing number of Bioinformatics data sources and analysis programs indeed enormously facilitated the analysis phase. However, it creates a demand for systems that facilitate using such computational resources. Given this scenario, this thesis addresses the use of workflows to compose Bioinformatics analysis programs that access data sources, thereby facilitating the analysis phase. An ontology modeling the analysis program and data sources commonly used in Bioinformatics is first described. This ontology is derived from a careful study, also summarized in the thesis, of the computational resources researchers in Bioinformatics presently use. A framework for biosequence analysis management systems is next described. The system is divided into two major components. The first component is a Bioinformatics workflow management system that helps researchers define, validate, optimize and run workflows combining Bioinformatics analysis programs. The second component is a Bioinformatics data management system that helps researchers manage large volumes of Bioinformatics data. The framework includes an ontology manager that stores Bioinformatics ontologies, such as that previously described. Lastly, instantiations for the Bioinformatics workflow management system framework are described. The instantiations cover three types of working environments commonly found and suggestively called personal environment, laboratory environment and community environment. For each of these instantiations, aspects related to workflow optimization and execution are carefully discussed.