Recongurable computing technology has progressed to a stage where it is now possible to achieve orders of magnitude performance and power eciency gains over conventional computer architectures for a subset of high performance computing applications. In this thesis, we investigate the potential of recongurable computers to accelerate genomic sequence alignment specically for genome sequencing applications. We present a highly optimized implementation of a parallel sequence alignment algorithm for the Berkeley Emulation Engine (BEE2) recongurable computer, allowing a single BEE2 to align simultaneously hundreds of sequences. For each recongurable processor (FPGA), we demonstrate a 61X speedup versus a state-of-the-art implementation on a modern conventional CPU core, and a 56X improvement in performance-per-Watt. We also show that our implementation is highly scalable and we provide performance results from a cluster implementation using 32 FPGAs. We conclude that reconfigurable computers provide an excellent platform on which to run sequence alignment, and that clusters of recongurable computers will be able to cope far more easily with the vast quantities of data produced by new ultra-high-throughput sequencers.

There exist several challenges in supporting mobile applications. For example, creating a separate target application for each device type, leaving developers with a huge maintenance chore. Most desktop applications run on largely homogenous hardware so instead of writing the same code over and over again, developers only need to write modules to implement a particular need. This is because even though there are differences in PC hardware configurations, the same desktop application will work fine on any hardware as the operating system provides an abstract layer. This is the way mobile applications are expected to work. However, this has been divided into dozens of ill-assorted versions. Java mobile applications developers spend more time rewriting code to run on different versions of mobile devices more than they do actually creating application in the first place. This is an intolerable burden for small mobile developers, and it stifles mobile software innovation overall. Mobile devices differ in a variety of attributes, such as screen size, colour depth and the optional hardware devices they support such as cameras, GPS etc. The differences often require special code or project settings for successful deployment for each device a developer is targeting but this creates a huge logistical overhead. One potential solution that is shipped with NetBeans IDE is to add a new configuration for each device, modify the project properties, add some pre-processing code, then build and deploy the application. In most cases, one configuration for each distribution of the Java Archive (JAR) one plans to build for the project is created. For example, if a developer is planning to support three different screen sizes using two sets of vendor specific APIs, one needs to create six configurations. This reduces the performance of the application drastically and increases the size at the same time. This is not acceptable for mobile devices where memory size and processor performance are limited. The goal of this research work is to support mobile application development through a Java IDE (the NetBeans IDE in this case). Therefore, our approach will be to modify the NetBeans IDE to better address the difficulty that was mentioned above – namely targeting applications for different platforms. Our solution is to integrate another type of a preprocessor into the NetBeans IDE that will help alleviate the problems of the existing tool. Our approach is to directly implement this inside the NetBeans IDE to further support mobile application development with the NetBeans IDE.

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Programming by demonstration is an end-user programming technique that allows people to create programs by showing the computer examples of what they want to do. Users do not need specialised programming skills. Instead, they instruct the computer by demonstrating examples, much as they might show another person how to do the task. Programming by demonstration empowers users to create programs that perform tedious and time-consuming computer chores. However, it is not in widespread use, and is instead confined to research applications that end users never see. This makes it difficult to evaluate programming by demonstration tools and techniques. This thesis claims that domain-independent programming by demonstration can be made available in existing applications and used to automate iterative tasks by end users. It is supported by Familiar, a domain-independent, AppleScript-based programming-by-demonstration tool embodying standard machine learning algorithms. Familiar is designed for end users, so works in the existing applications that they regularly use. The assertion that programming by demonstration can be made available in existing applications is validated by identifying the relevant platform requirements and a range of platforms that meet them. A detailed scrutiny of AppleScript highlights problems with the architecture and with many implementations, and yields a set of guidelines for designing applications that support programming-by-demonstration. An evaluation shows that end users are capable of using programming by demonstration to automate iterative tasks. However, the subjects tended to prefer other tools, choosing Familiar only when the alternatives were unsuitable or unavailable. Familiar's inferencing is evaluated on an extensive set of examples, highlighting the tasks it can perform and the functionality it requires.

Extensible programming languages allow users to create fundamentally new syntax and translate this syntax into language primitives. The concept of compile-time meta-programming has been around for decades, but systems that provide such abilities generally disallow the creation of new syntactic forms, or have heavy restrictions on how, or where, this may be done. Genesis is an extension to Java that supports compile-time meta-programming by allowing users to create their own arbitrary syntax. This is achieved through macros that operate on a mix of both concrete and abstract syntax, and produce abstract syntax. Genesis attempts to provide a minimal design whilst maintaining, and extending, the expressive power of other similar macro systems. The core Genesis language definition lacks many of the desirable features found in other systems, such as quasi-quote, hygiene, and static expression-type dispatch, but is expressive enough to define these as syntax extensions. User-defined macros produce only well-formed syntactic structures via the use of a predefined set of classes that define a Java abstract syntax. At the heart of Genesis is a flexible parser that is capable of parsing any context-free grammars - even ambiguous ones. The parser is capable of arbitrary speculation and will consider all possible parses. The parser constructs a graph of possible paths, and is capable of dynamically pruning this graph, or combining nodes, based on precedence or associativity rules. This general parser allows macro programmers to forget about parsing, and concentrate on defining new syntax. One key goal of this system was to address the programmer's learning curve by providing as simple a system as possible. This was achieved by the use of the flexible parser, the introduction of only one new construct to standard Java, and extensions to make programming macros more user friendly. The expressiveness of Genesis is wide ranging; it is capable of providing small scale limited use macros, large scale semantic modifications, through to complete language replacements. To demonstrate this expressiveness, we implement many of the simple test cases found in other systems, such as a type-safe printf, assertions, and iteration statements. These test cases require an ability to perform static type-checking and to manipulate compile-time values and abstract syntax trees. As additional examples of Genesis' expressive power we also provide implementations of embedded subsets of SQL and Haskell. As a final proof of power, the Haskell subset can operate as a stand-alone extension independent of any recognisable Java code.

As technology becomes ever more pervasive, the challenges of home automation are increasingly apparent. Seamless home control, home monitoring and home programming by the end user have yet to enter the mainstream. This could be attributed to the challenge of developing a fully autonomous and extensible home system that can support devices and technologies of differing protocols and functionalities. In order to offer programming facilities to the user, the underlying rule system must be fully independent, allowing support for current and future devices. Additional challenges arise from the need to detect and handle conflicts that may arise among user rules and yield undesirable results. Non-technical individuals typically struggle when faced with a programming task. It is therefore vital to encourage and ease the process of programming the home. This thesis presents Homer, a home system that has been developed to support three key features of a home system: control, monitoring and programming. Homer supports any third-party hardware or software service that can expose its functionality through Java and conform to the Homer interface. Stand-alone end user interfaces can be written by developers to offer any of Homer's functionality. Where policies (i.e. rules) for the home are concerned, Homer offers a fully independent policy system. The thesis presents a custom policy language, Homeric, that has been designed specifically for writing home rules. The Homer policy system detects overlaps and conflicts among rules using constraint satisfaction and the effect on environment variables. The thesis also introduces the notion of perspectives to ease user interactivity. These have been integrated into Homer to accommodate the range of ways in which a user may think about different aspects and features of their home. These perspectives include location, device type, time and people-oriented points of view. Design guidelines are also discussed to aid end user programming of the home. The work presented in this thesis demonstrates a system that supports control, monitoring and programming of the home. Developers can quickly and easily add functionality to the home through components. Conflicts can be detected amongst rules within the home. Finally, design guidelines and a prototype interface have been developed to allow both technically minded and non-technical people to program their home.

En esta tesis presentamos un nuevo enfoque para concebir, diseñar y desarrollar aplicaciones web accesibles usando conceptos de la Orientación a Aspectos. Con el fin de alcanzar nuestro objetivo, proveemos algunas técnicas de modelado que desarrollamos explícitamente para manejar las características no-funcionales, genéricas y transversales de la accesibilidad. Concretamente, enriquecimos la técnica UID con puntos de integración para registrar los intereses de accesibilidad que serán considerados en el diseño de la interfaz de usuario. Luego, instanciando la plantilla SIG con tablas de asociación, trabajamos en el modelo de interfaz abstracta con softgoals de accesibilidad para obtener un modelo de interfaz concreta y accesible de la aplicación web en desarrollo. Para ilustrar nuestras ideas y señalar las ventajas de una clara separación de intereses durante el ciclo de vida de desarrollo, utilizamos un ejemplo de aplicación real. De esta manera, nuestra propuesta se fundamenta en técnicas de diseño reconocidas, las cuales hemos embebido en una herramienta de software, con el propósito de facilitar la transferencia del enfoque a la industria. <i>(del texto de la contratapa)</i> / Tesis doctoral de la Facultad de Informática (UNLP). Grado alcanzado: Doctor en Ciencias Informáticas. Director de tesis: Alejandra Cechich; co-director de tesis: Gustavo Rossi. La tesis, presentada en el año 2012, obtuvo el Premio "Dr. Raúl Gallard" en el 2013.

This paper reviews numerous theoretical results on control structures and demonstrates their practical examples. This study deals with the design of run-time support routines by using top-down structured programming technique. A number of examples are given as illustration of this method. In conclusion, structured programming has proved to be an important methodology for systematic program design and development.

In the computer science community, there is considerable debate about the appropriate sequence for introducing object-oriented concepts to novice programmers. Research into novice programming has struggled to identify the critical aspects that would provide a consistently successful approach to teaching introductory object-oriented programming. Starting from the premise that the conceptions of a task determine the type of output from the task, assisting novice programmers to become aware of what the required output should be, may lay a foundation for improving learning. This study adopted a phenomenographic approach. Thirty one practitioners were interviewed about the ways in which they experience object-oriented programming and categories of description and critical aspects were identified. These critical aspects were then used to examine the spaces of learning provided in twenty introductory textbooks. The study uncovered critical aspects that related to the way that practitioners expressed their understanding of an object-oriented program and the influences on their approach to designing programs. The study of the textbooks revealed a large variability in the cover of these critical aspects.

The Weighted Histogram Analysis Method (WHAM) is a technique used to calculate free energy from molecular simulation data. WHAM recombines biased distributions of samples from multiple Umbrella Sampling simulations to yield an estimate of the global unbiased distribution. The WHAM algorithm iterates two coupled, non-linear, equations, until convergence at an acceptable level of accuracy. The equations have quadratic time complexity for a single reaction coordinate. However, this increases exponentially with the number of reaction coordinates under investigation, which makes multidimensional WHAM a computationally expensive procedure. There is potential to use general purpose graphics processing units (GPGPU) to accelerate the execution of the algorithm. Here we develop and evaluate a multidimensional GPGPU WHAM implementation to investigate the potential speed-up attained over its CPU counterpart. In addition, to avoid the cost of multiple Molecular Dynamics simulations and for validation of the implementations we develop a test system to generate samples analogous to Umbrella Sampling simulations. We observe a maximum problem size dependent speed-up of approximately 19 for the GPGPU optimized WHAM implementation over our single threaded CPU optimized version. We find that the WHAM algorithm is amenable to GPU acceleration, which provides the means to study ever more complex molecular systems in reduced time periods.