From access and integration to mining of secure genomic data sets across the grid

The UK Department of Trade and Industry (DTI) funded BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services) has developed a Grid infrastructure to support cardiovascular research. This includes the provision of a compute Grid and a data Grid infrastructure with security at its heart. In this paper we focus on the BRIDGES data Grid. A primary aim of the BRIDGES data Grid is to help control the complexity in access to and integration of a myriad of genomic data sets through simple Grid based tools. We outline these tools, how they are delivered to the end user scientists. We also describe how these tools are to be extended in the BBSRC funded Grid Enabled Microarray Expression Profile Search (GEMEPS) to support a richer vocabulary of search capabilities to support mining of microarray data sets. As with BRIDGES, fine grain Grid security underpins GEMEPS

Visually Characterizing Source Code Changes

International audienceRevision Control Systems (e.g., SVN, Git, Mercurial) include automatic and advanced merging algorithms that help developers to merge their modifications with development repositories. While these systems can help to textually detect conflicts, they do not help to identify the semantic consequences of a change. Unfortunately, there is little support to help release masters (integrators) to take decisions about the integration of changes into the system release. Most of the time, the release master needs to read all the modified code, check the diffs to build an idea of a change, and dig for details from related unchanged code to understand the context and potential impact of some changes. As a result, such a task can be overwhelming. In this article we present a visualization tool to support integrators of object-oriented programs in comprehending changes. Our approach named Torch characterizes changes based on structural informa- tion, authors and symbolic information. It mixes text-based diff information with visual representation and metrics characterizing the changes. The current implementation of our approach analyses Smalltalk programs, and thus we de- scribe our experiments applying it to Pharo, a large open-source system. We also report on the evaluations of our approach by release masters and developers of several open-source projects

Tagging Spanish Texts: the Problem of ‘se’

Automatic tagging in Spanish has historically faced many problems because of some specific grammatical constructions. One of these traditional pitfalls is the ‘se’ particle. This particle is a multifunctional and polysemous word used in many different contexts. Many taggers do not distinguish the possible uses of ‘se’ and thus provide poor results at this point. In tune with the philosophy of free software, we have taken a free annotation tool as a basis, we have improved and enhanced its behaviour by adding new rules at different levels and by modifying certain parts in the code to allow for its possible implementation in other EAGLES-compliant tools. In this paper, we present the analysis carried out with different annotators for selecting the tool, the results obtained in all cases as well as the improvements added and the advantages of the modified tagger

Service-oriented architecture for device lifecycle support in industrial automation

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores Especialidade: Robótica e Manufactura IntegradaThis thesis addresses the device lifecycle support thematic in the scope of service oriented industrial automation domain. This domain is known for its plethora of heterogeneous equipment encompassing distinct functions, form factors, network interfaces, or I/O specifications supported by dissimilar software and hardware platforms. There is then an evident and crescent need to take every device into account and improve the agility performance during setup, control, management, monitoring and diagnosis phases. Service-oriented Architecture (SOA) paradigm is currently a widely endorsed approach for both business and enterprise systems integration. SOA concepts and technology are continuously spreading along the layers of the enterprise organization envisioning a unified interoperability solution. SOA promotes discoverability, loose coupling, abstraction, autonomy and composition of services relying on open web standards – features that can provide an important contribution to the industrial automation domain. The present work seized industrial automation device level requirements, constraints and needs to determine how and where can SOA be employed to solve some of the existent difficulties. Supported by these outcomes, a reference architecture shaped by distributed, adaptive and composable modules is proposed. This architecture will assist and ease the role of systems integrators during reengineering-related interventions throughout system lifecycle. In a converging direction, the present work also proposes a serviceoriented device model to support previous architecture vision and goals by including embedded added-value in terms of service-oriented peer-to-peer discovery and identification, configuration, management, as well as agile customization of device resources. In this context, the implementation and validation work proved not simply the feasibility and fitness of the proposed solution to two distinct test-benches but also its relevance to the expanding domain of SOA applications to support device lifecycle in the industrial automation domain

Aide à l'Intégration de Branches Grâce à la Réification des Changements

Developers typically change codebases in parallel from each other, which results in diverging codebases. Such diverging codebases must be integrated when finished. Integrating diverging codebases involves difficult activities. For example, two changes that are correct independently can introduce subtle bugs when integrated together. Integration can be difficult with existing tools, which, instead of dealing with the evolution of the actual program entities being changed, handle code changes as lines of text in files. Tools are important: software development tools have greatly improved from generic text editors to IDEs by providing high-level code manipulation such as automatic refactorings and code completion. This improvement was possible by the reification of program entities. Nevertheless, integration tools did not benefit from a similarreification of change entities to improve productivity in integration.In this work we first conducted a study to learn which integration activities are important and have little tool support. We discovered that one of such activities is the detection of tangled commits (that contain unrelated tasks such as a bug fix and a refactoring). Then we proposed Epicea, a reified change model and associated IDE tools, and EpiceaUntangler, an approach to help developers share untangled commits based on Epicea. The results of our evaluations with real-world studies show the usefulness of our approaches.Les développeurs changent le code source en parallèle les uns des autres, ce qui fait diverger les bases de code. Ces divergences se doivent d'être réintégrées.L'intégration de bases de code divergentes est une activité complexe. Par exemple, réunir deux bases de code indépendamment correctes peut générer des problèmes. L'intégration peut être difficile avec les outils existants, qui, au lieu de gérer l'évolution des entités réelles du programme modifié, gère les changements de code au niveau des lignes de texte dans les fichiers sources.Les outils sont importants: les outils de développement de logiciels se sont grandement améliorés en passant par exemple d'éditeurs de textegénériques à des IDEs qui fournissent de la manipulation de code de haut niveau tels que la refactorisation automatique et la complétion de code. Cette amélioration a été possible grâce à la réification des entités de programme. Néanmoins, les outils d'intégration n'ont pas profité d'une réification similaire des entités de changement pour améliorer l'intégration.Dans cette thèse nous avons d'abord conduit une étude auprès de développeurs pourcomprendre quelles sont les activités menées durant une intégration quisont peu supportées par les outils. L'une d'elle est la détection de commits mêlés (qui contiennent des tâches non liées telles qu'une correction de bug et une refactorisation).Ensuite, nous proposons Epicea, un modèle de changement réifié et des outils d'IDE associés, et EpiceaUntangler, une approche pour aider les développeurs à démêler les commits en se basant sur Epicea.Les résultats de nos évaluations avec des études de cas issues du monde réel montrent l’utilité de nos approches

Adaptive object management for distributed systems

This thesis describes an architecture supporting the management of pluggable software components and evaluates it against the requirement for an enterprise integration platform for the manufacturing and petrochemical industries. In a distributed environment, we need mechanisms to manage objects and their interactions. At the least, we must be able to create objects in different processes on different nodes; we must be able to link them together so that they can pass messages to each other across the network; and we must deliver their messages in a timely and reliable manner. Object based environments which support these services already exist, for example ANSAware(ANSA, 1989), DEC's Objectbroker(ACA,1992), Iona's Orbix(Orbix,1994)Yet such environments provide limited support for composing applications from pluggable components. Pluggability is the ability to install and configure a component into an environment dynamically when the component is used, without specifying static dependencies between components when they are produced. Pluggability is supported to a degree by dynamic binding. Components may be programmed to import references to other components and to explore their interfaces at runtime, without using static type dependencies. Yet thus overloads the component with the responsibility to explore bindings. What is still generally missing is an efficient general-purpose binding model for managing bindings between independently produced components. In addition, existing environments provide no clear strategy for dealing with fine grained objects. The overhead of runtime binding and remote messaging will severely reduce performance where there are a lot of objects with complex patterns of interaction. We need an adaptive approach to managing configurations of pluggable components according to the needs and constraints of the environment. Management is made difficult by embedding bindings in component implementations and by relying on strong typing as the only means of verifying and validating bindings. To solve these problems we have built a set of configuration tools on top of an existing distributed support environment. Specification tools facilitate the construction of independent pluggable components. Visual composition tools facilitate the configuration of components into applications and the verification of composite behaviours. A configuration model is constructed which maintains the environmental state. Adaptive management is made possible by changing the management policy according to this state. Such policy changes affect the location of objects, their bindings, and the choice of messaging system