Multiple hierarchies : new aspects of an old solution

In this paper, we present the Multiple Annotation approach, which solves two problems: the problem of annotating overlapping structures, and the problem that occurs when documents should be annotated according to different, possibly heterogeneous tag sets. This approach has many advantages: it is based on XML, the modeling of alternative annotations is possible, each level can be viewed separately, and new levels can be added at any time. The files can be regarded as an interrelated unit, with the text serving as the implicit link. Two representations of the information contained in the multiple files (one in Prolog and one in XML) are described. These representations serve as a base for several applications

Transparent interface composition in web applications

In this paper we present an approach for oblivious composition of Web user interfaces, particularly for volatile functionality. Our approach, which is inspired on well-known techniques for advanced separation of concerns such as aspect-oriented software design, allows to clearly separate the design of the core's interface from the one corresponding to more volatile services, i.e. those that are offered for short periods of time. Both interfaces are oblivious from each other and can be seamlessly composed using a transformation language. We show that in this way we simplify the application's evolution by preventing intrusive edition of the interface code. Using some illustrative examples we focus both on design and implementation issues, presenting an extension of the OOHDM design model which supports modular design of volatile functionality.Publicado en Lecture Notes in Computer Science book series (LNCS, vol. 4607).Laboratorio de Investigación y Formación en Informática Avanzad

Concern-sensitive navigation: Improving navigation in web software through separation of concerns

Traditionally, the use of good techniques to improve software modularity, such as advanced separation of concerns, has no impact in the user experience, for example while navigating Web software. While the intent of these techniques is to simplify evolution and maintenance, navigation design quality is often seen as an unrelated concern. In this paper we present a novel approach for improving navigation in Web applications by using some of the core application's concerns (called navigational concerns) to derive their navigational structure. Using some realistic examples we show that, by carefully using these concerns, we can improve the user experience. Some implementation issues are discussed and a thorough comparison with related ideas in the Web Engineering field is presented.Publicado en Lecture Notes in Computer Science book series (LNCS, vol. 5074).Facultad de Informátic

Error propagation metrics from XMI

This work describes the production of an application Error Propagation Metrics from XMI which can extract process and display software design metrics from XMI files. The tool archives these design metrics in a standard XML format defined by a metric document type definition.;XMI is a flavour of XML allowing the description of UML models. As such, the XMI representation of a software design will include information from which a variety of software design metrics can be extracted. These metrics are potentially useful in improving the software design process, either throughout the early stages of design if a suitable XMI-enabled modelling tool is deployed, or to enable the comparison of completed software projects, by extracting design metrics from UML models reverse engineered from the implemented source code.;The tool is able to derive the error propagation of metrics from test XMI files created from UML sequence and state diagrams and from reverse engineered Java source code. However, variation was observed between the XMI representations generated by different software design tools, limiting the ability of the tool to process XMI from all sources. Furthermore, it was noted that subtle differences between UML design representations might have a marked effect on the quality of metrics derived.;In conclusion in order to validate the usefulness of these metrics that can be extracted from XMI files it would be useful to follow well-documented design projects throughout the total design and implementation process. Alternatively, the tool might be used to compare metrics from well-matched design implementations. In either case design metrics will only be of true value to software engineers if they can be associated empirically with a validated measure of system quality

Concern-sensitive navigation: Improving navigation in web software through separation of concerns

Traditionally, the use of good techniques to improve software modularity, such as advanced separation of concerns, has no impact in the user experience, for example while navigating Web software. While the intent of these techniques is to simplify evolution and maintenance, navigation design quality is often seen as an unrelated concern. In this paper we present a novel approach for improving navigation in Web applications by using some of the core application's concerns (called navigational concerns) to derive their navigational structure. Using some realistic examples we show that, by carefully using these concerns, we can improve the user experience. Some implementation issues are discussed and a thorough comparison with related ideas in the Web Engineering field is presented.Publicado en Lecture Notes in Computer Science book series (LNCS, vol. 5074).Facultad de Informátic

A Model Driven Approach to Model Transformations

The OMG's Model Driven Architecture (MDA) initiative has been the focus of much attention in both academia and industry, due to its promise of more rapid and consistent software development through the increased use of models. In order for MDA to reach its full potential, the ability to manipulate and transform models { most obviously from the Platform Independent Model (PIM) to the Platform Specific Models (PSM) { is vital. Recognizing this need, the OMG issued a Request For Proposals (RFP) largely concerned with finding a suitable mechanism for trans- forming models. This paper outlines the relevant background material, summarizes the approach taken by the QVT-Partners (to whom the authors belong), presents a non-trivial example using the QVT-Partners approach, and finally sketches out what the future holds for model transformations

Processing Structured Hypermedia : A Matter of Style

With the introduction of the World Wide Web in the early nineties, hypermedia has become the uniform interface to the wide variety of information sources available over the Internet. The full potential of the Web, however, can only be realized by building on the strengths of its underlying research fields. This book describes the areas of hypertext, multimedia, electronic publishing and the World Wide Web and points out fundamental similarities and differences in approaches towards the processing of information. It gives an overview of the dominant models and tools developed in these fields and describes the key interrelationships and mutual incompatibilities. In addition to a formal specification of a selection of these models, the book discusses the impact of the models described on the software architectures that have been developed for processing hypermedia documents. Two example hypermedia architectures are described in more detail: the DejaVu object-oriented hypermedia framework, developed at the VU, and CWI's Berlage environment for time-based hypermedia document transformations

Improving task modelling to support the co-evolution of information systems and business processes

In business environments, information systems are required to change in response to changes in business processes. We refer to this process as co-evolution: the process of reciprocal change in a software system and the activities and goals of the system's users. This research focuses on improving task modelling techniques to support the co-evolution of information systems and business processes.We propose the Interaction Template approach to improve task modelling to support co-evolution. Interaction Templates make the task modelling process less tedious in both the design phase and the evolution phase of a system's lifecycle. Our approach adds data schemas and presentation components to task models, allowing us to build task models that adapt to data elements and parameters. Binding presentation components to task models allows us to generate user interface prototypes from task models. The generated user interface prototypes improve task model simulation and help make the effects of changes to business processes more clear. This thesis describes a study of the seven year evolution of a real world information system. Through this study, we gain a better understanding of how information systems evolve in response to the evolution of an organization's business processes. This thesis presents the Interaction Template approach, as well as a notation for specifying Interaction Templates. A prototype system supporting the Interaction Template approach is provided, along with examples demonstrating the approach

Encoding, Storing and Searching of Analytical Properties and Assigned Metabolite Structures

Informationen über Metabolite und andere kleine organische Moleküle sind von entscheidender Bedeutung in vielen verschiedenen Bereichen der Naturwissenschaften. Sie spielen z.B. eine entscheidende Rolle in metabolischen Netzwerken und das Wissen über ihre Eigenschaften, hilft komplexe biologische Prozesse und komplette biologische Systeme zu verstehen. Da in biologischen und chemischen Laboren täglich Daten anfallen, welche diese Moleküle beschreiben, existiert eine umfassende Datengrundlage, die sich kontinuierlich erweitert. Um Wissenschaftlern die Verarbeitung, den Austausch, die Archivierung und die Suche innerhalb dieser Informationen unter Erhaltung der semantischen Zusammenhänge zu ermöglichen, sind komplexe Softwaresysteme und Datenformate nötig. Das Ziel dieses Projektes bestand darin, Anwendungen und Algorithmen zu entwickeln, welche für die effiziente Kodierung, Sammlung, Normalisierung und Analyse molekularer Daten genutzt werden können. Diese sollen Wissenschaftler bei der Strukturaufklärung, der Dereplikation, der Analyse von molekularen Wechselwirkungen und bei der Veröffentlichung des so gewonnenen Wissens unterstützen. Da die direkte Beschreibung der Struktur und der Funktionsweise einer unbekannten Verbindung sehr schwierig und aufwändig ist, wird dies hauptsächlich indirekt, mit Hilfe beschreibender Eigenschaften erreicht. Diese werden dann zur Vorhersage struktureller und funktioneller Charakteristika genutzt. In diesem Zusammenhang wurden Programmmodule entwickelt, welche sowohl die Visualisierung von Struktur- und Spektroskopiedaten, die gegliederte Darstellung und Veränderung von Metadaten und Eigenschaften, als auch den Import und Export von verschiedenen Datenformaten erlauben. Diese wurden durch Methoden erweitert, welche es ermöglichen, die gewonnenen Informationen weitergehend zu analysieren und Struktur- und Spektroskopiedaten einander zuzuweisen. Außerdem wurde ein System zur strukturierten Archivierung und Verwaltung großer Mengen molekularer Daten und spektroskopischer Informationen, unter Beibehaltung der semantischen Zusammenhänge, sowohl im Dateisystem, als auch in Datenbanken, entwickelt. Um die verlustfreie Speicherung zu gewährleisten, wurde ein offenes und standardisiertes Datenformat definiert (CMLSpect). Dieses erweitert das existierende CML (Chemical Markup Language) Vokabular und erlaubt damit die einfache Handhabung von verknüpften Struktur- und Spektroskopiedaten. Die entwickelten Anwendungen wurden in das Bioclipse System für Bio- und Chemoinformatik eingebunden und bieten dem Nutzer damit eine hochqualitative Benutzeroberfläche und dem Entwickler eine leicht zu erweiternde modulare Programmarchitektur