Data, Software, and Advanced Computational Usage of University of Washington Research Leaders

Scientific research is increasingly data-intensive, relying more and more upon advanced computational resources to be able to answer the questions most pressing to our society at large. This report presents findings from a brief descriptive survey sent to a sample of 342 leading researchers at the University of Washington (UW), Seattle, Washington in 2010 and 2011 as the first stage of the larger National Science Foundation project “Interacting with Cyberinfrastructure in the Face of Changing Science.” This survey assesses these researcher’s use of advanced computational resources, data, and software in their research. We present high-level findings that describe UW researchers’: demographics, interdisciplinarity, research groups, data use, software and computational use—including software development and use, data storage and transfer activities, and collaboration tools, and computing resources. These findings offer insights into the state of computational resources in use during this time period as well as offering a look at the data intensiveness of UW researchers.

Surveying Scientists About Their Software

Software is an important infrastructural component of scientific research practice. The work of research often requires scientists to develop, use, and share software in order to address their research questions. This report presents findings from a survey of researchers at the University of Washington in three broad areas: Oceanography, Biology, and Physics. This survey is part of the National Science Foundation funded study Scientists and their Software: A Sociotechnical Investigation of Scientific Software Development and Sharing (ACI-1302272). We inquired about each respondent’s research area and data use along with their use, development, and sharing of software. Finally, we asked about challenges researchers face with and about concerns regarding software’s effect on study replicability. These findings are part of ongoing efforts to develop deeper characterizations of the role of software in twenty-first century scientific research.

Sviluppo del software di un sistema per l'analisi in tempo reale della combustione di motori endotermici alternativi

Limiti sempre più stringenti sulle emissioni inquinanti ed una maggiore attenzione ai consumi, all'incremento di prestazioni e alla guidabilità, portano allo sviluppo di algoritmi di controllo motore sempre più complicati. Allo stesso tempo, l'unità di propulsione sta diventando un insieme sempre più variegato di sottosistemi che devono lavorare all'unisono. L'ingegnere calibratore si trova di fronte ad una moltitudine di variabili ed algoritmi che devono essere calibrati e testati e necessita di strumenti che lo aiutino ad analizzare il comportamento del motore fornendo risultati sintetici e facilmente accessibili. Nel seguente lavoro è riportato lo sviluppo di un sistema di analisi della combustione: l'obbiettivo è stato quello di sviluppare un software che fornisca le migliori soluzioni per l'analisi di un motore a combustione interna, in termini di accuratezza dei risultati, varietà di calcoli messi a disposizione, facilità di utilizzo ed integrazione con altri sistemi tramite la condivisione dei risultati calcolati in tempo reale.

Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Insulin and leptin relations in obesity: a multimedia approach

Obesity has been recognized as a worldwide public health problem. It significantly increases the chances of developing several diseases, including Type II diabetes. The roles of insulin and leptin in obesity involve reactions that can be better understood when they are presented step by step. The aim of this work was to design software with data from some of the most recent publications on obesity, especially those concerning the roles of insulin and leptin in this metabolic disturbance. The most notable characteristic of this software is the use of animations representing the cellular response together with the presentation of recently discovered mechanisms on the participation of insulin and leptin in processes leading to obesity. The software was field tested in the Biochemistry of Nutrition web-based course. After using the software and discussing its contents in chatrooms, students were asked to answer an evaluation survey about the whole activity and the usefulness of the software within the learning process. The teaching assistants (TA) evaluated the software as a tool to help in the teaching process. The students' and TAs' satisfaction was very evident and encouraged us to move forward with the software development and to improve the use of this kind of educational tool in biochemistry classes.

API documentation with executable examples

The rise of component-based software development has created an urgent need for effective application program interface (API) documentation. Experience has shown that it is hard to create precise and readable documentation. Prose documentation can provide a good overview but lacks precision. Formal methods offer precision but the resulting documentation is expensive to develop. Worse, few developers have the skill or inclination to read formal documentation. We present a pragmatic solution to the problem of API documentation. We augment the prose documentation with executable test cases, including expected outputs, and use the prose plus the test cases as the documentation. With appropriate tool support, the test cases are easy to develop and read. Such test cases constitute a completely formal, albeit partial, specification of input/output behavior. Equally important, consistency between code and documentation is demonstrated by running the test cases. This approach provides an attractive bridge between formal and informal documentation. We also present a tool that supports compact and readable test cases; and generation of test drivers and documentation, and illustrate the approach with detailed case studies. (C) 2002 Elsevier Science Inc. All rights reserved.

A mobile systems interface protocol

Recent progresses in the software development world has assisted a change in hardware from heavy mainframes and desktop machines to unimaginable small devices leading to the prophetic "third computing paradigm", Ubiquitous Computing. Still, this novel unnoticeable devices lack in various capabilities, like computing power, storage capacity and human interface. Connectivity associated to this devices is also considered an handicap which comes generally associated expensive and limited protocols like GSM and UMTS. Considering this scenario as background, this paper presents a minimal communication protocol introducing better interfaces for limited devices. Special attention has been paid to the limitations of connectivity, storage capacity and scalability of the developed software applications. Illustrating this new protocol, a case-study is presented addressing car sensors communicating with a central

Uma Abordagem para a Geração de Casos de Teste Baseada em Modelos

Abstract — The analytical methods based on evaluation models of interactive systems were proposed as an alternative to user testing in the last stages of the software development due to its costs. However, the use of isolated behavioral models of the system limits the results of the analytical methods. An example of these limitations relates to the fact that they are unable to identify implementation issues that will impact on usability. With the introduction of model-based testing we are enable to test if the implemented software meets the specified model. This paper presents an model-based approach for test cases generation from the static analysis of source code.

Architectural prototyping: from CCS to .Net

Over the last decade, software architecture emerged as a critical issue in Software Engineering. This encompassed a shift from traditional programming towards software development based on the deployment and assembly of independent components. The specification of both the overall systems structure and the interaction patterns between their components became a major concern for the working developer. Although a number of formalisms to express behaviour and to supply the indispensable calculational power to reason about designs, are available, the task of deriving architectural designs on top of popular component platforms has remained largely informal. This paper introduces a systematic approach to derive, from CCS behavioural specifications the corresponding architectural skeletons in the Microsoft .Net framework, in the form of executable C and Cω code. The prototyping process is fully supported by a specific tool developed in Haskell

Slicing for architectural analysis

Current software development often relies on non-trivial coordination logic for combining autonomous services, eventually running on different platforms. As a rule, however, such a coordination layer is strongly woven within the application at source code level. Therefore, its precise identification becomes a major methodological (and technical) problem and a challenge to any program understanding or refactoring process. The approach introduced in this paper resorts to slicing techniques to extract coordination data from source code. Such data are captured in a specific dependency graph structure from which a coordination model can be recovered either in the form of an Orc specification or as a collection of code fragments corresponding to the identification of typical coordination patterns in the system. Tool support is also discussed

Type checking cryptography implementations

Cryptographic software development is a challenging eld: high performance must be achieved, while ensuring correctness and com- pliance with low-level security policies. CAO is a domain speci c language designed to assist development of cryptographic software. An important feature of this language is the design of a novel type system introducing native types such as prede ned sized vectors, matrices and bit strings, residue classes modulo an integer, nite elds and nite eld extensions, allowing for extensive static validation of source code. We present the formalisation, validation and implementation of this type system

Extracting and verifying coordination models from source code

Current software development relies increasingly on non-trivial coordination logic for com- bining autonomous services often running on di erent platforms. As a rule, however, in typical non-trivial software systems, such a coordination layer is strongly weaved within the application at source code level. Therefore, its precise identi cation becomes a major methodological (and technical) problem which cannot be overestimated along any program understanding or refactoring process. Open access to source code, as granted in OSS certi cation, provides an opportunity for the devel- opment of methods and technologies to extract, from source code, the relevant coordination information. This paper is a step in this direction, combining a number of program analysis techniques to automatically recover coordination information from legacy code. Such information is then expressed as a model in Orc, a general purpose orchestration language

SHACC: a functional prototyper for a component calculus

Over the last decade component-based software development arose as a promising paradigm to deal with the ever increasing complexity in software design, evolution and reuse. SHACC is a prototyping tool for component-based systems in which components are modelled coinductively as generalized Mealy machines. The prototype is built as a HASKELL library endowed with a graphical user interface developed in Swing

Plataforma de gestão de incidentes

Mestrado em Engenharia Electrotécnica e de Computadores. Área de Especialização de Telecomunicações.

Controlador dedicado de Ecrãs LCD/TFT

Para dar resposta aos grandes avanços tecnológicos e, consequentemente, à postura mais exigente dos clientes, a empresa Francisco Parracho – Electrónica Industrial, Lda., que tem actividade no ramo dos elevadores, decidiu introduzir no mercado um controlador dedicado de ecrãs Liquid Crystal Display / Thin Film Transistor (LCD / TFT). O objectivo é substituir um sistema suportado por um computador, caracterizado pelas suas elevadas dimensões e custos, mas incontornável até à data, nomeadamente para resoluções de ecrã elevadas. E assim nasceu este trabalho. Com uma selecção criteriosa de todos os componentes e, principalmente, sem funcionalidades inúteis, obteve-se um sistema embebido com dimensões e custos bem mais reduzidos face ao seu opositor. O ecrã apontado para este projecto é um Thin Film Transistor – Liquid Crystal Display (TFT-LCD) da Sharp de 10.4” de qualidade industrial, com uma resolução de 800 x 600 píxeis a 18 bits por píxel. Para tal, foi escolhido um micro-controlador da ATMEL, um AVR de 32 bits que, entre outras características, possui um controlador LCD que suporta resoluções até 2048 x 2048 píxeis, de 1 a 24 bits por píxel. Atendendo ao facto deste produto ser inserido na área dos elevadores, as funcionalidades, quer a nível do hardware quer a nível do software, foram projectadas para este âmbito. Contudo, o conceito aqui exposto é adjacente a quaisquer outras áreas onde este produto se possa aplicar, até porque o software está feito para se tornar bem flexível. Com a ajuda de um kit de desenvolvimento, foram validados os drivers dos controladores e periféricos base deste projecto. De seguida, aplicou-se esse software numa placa de circuito impresso, elaborada no âmbito deste trabalho, para que fossem cumpridos todos os requisitos requeridos pela empresa patrocinadora: - Apresentação de imagens no ecrã consoante o piso; - Possibilidade de ter um texto horizontalmente deslizante;Indicação animada do sentido do elevador; - Representação do piso com deslizamento vertical; - Descrição sumária do directório de pisos também com deslizamento vertical; - Relógio digital; - Leitura dos conteúdos pretendidos através de um cartão SD/MMC; - Possibilidade de actualização dos conteúdos via USB flash drive.