Versions toolkit for authors, researchers and repository staff

This toolkit is a practical guide to help you when taking decisions about disseminating your research on the web. The toolkit is written in the context of open access (OA) self-archiving of research outputs by authors, alongside traditional publication in refereed journals and other academic publications. The focus is on open access institutional repositories established by universities worldwide. There is also relevance in the context of subject repositories. The full result of the VERSIONS Project survey are available on the project website (see published item link)

Data replication and update propagation in XML P2P data management systems

XML P2P data management systems are P2P systems that use XML as the underlying data format shared between peers in the network. These systems aim to bring the benefits of XML and P2P systems to the distributed data management field. However, P2P systems are known for their lack of central control and high degree of autonomy. Peers may leave the network at any time at will, increasing the risk of data loss. Despite this, most research in XML P2P systems focus on novel and efficient XML indexing and retrieval techniques. Mechanisms for ensuring data availability in XML P2P systems has received comparatively little attention. This project attempts to address this issue. We design an XML P2P data management framework to improve data availability. This framework includes mechanisms for wide-spread data replication, replica location and update propagation. It allows XML documents to be broken down into fragments. By doing so, we aim to reduce the cost of replicating data by distributing smaller XML fragments throughout the network rather than entire documents. To tackle the data replication problem, we propose a suite of selection and placement algorithms that may be interchanged to form a particular replication strategy. To support the placement of replicas anywhere in the network, we use a Fragment Location Catalogue, a global index that maintains the locations of replicas. We also propose a lazy update propagation algorithm to propagate updates to replicas. Experiments show that the data replication algorithms improve data availability in our experimental network environment. We also find that breaking XML documents into smaller pieces and replicating those instead of whole XML documents considerably reduces the replication cost, but at the price of some loss in data availability. For the update propagation tests, we find that the probability that queries return up-to-date results increases, but improvements to the algorithm are necessary to handle environments with high update rates

Improving reproducibility and reuse of modelling results in the life sciences

Research results are complex and include a variety of heterogeneous data. This entails major computational challenges to (i) to manage simulation studies, (ii) to ensure model exchangeability, stability and validity, and (iii) to foster communication between partners. I describe techniques to improve the reproducibility and reuse of modelling results. First, I introduce a method to characterise differences in computational models. Second, I present approaches to obtain shareable and reproducible research results. Altogether, my methods and tools foster exchange and reuse of modelling results.Die verteilte Entwicklung von komplexen Simulationsstudien birgt eine große Zahl an informationstechnischen Herausforderungen: (i) Modelle müssen verwaltet werden; (ii) Reproduzierbarkeit, Stabilität und Gültigkeit von Ergebnissen muss sichergestellt werden; und (iii) die Kommunikation zwischen Partnern muss verbessert werden. Ich stelle Techniken vor, um die Reproduzierbarkeit und Wiederverwendbarkeit von Modellierungsergebnissen zu verbessern. Meine Implementierungen wurden erfolgreich in internationalen Anwendungen integriert und fördern das Teilen von wissenschaftlichen Ergebnissen

Supporting Project Comprehension with Revision Control System Repository Analysis

Context: Project comprehension is an activity relevant to all aspects of software engineering, from requirements specification to maintenance. The historical, transactional data stored in revision control systems can be mined and analysed to produce a great deal of information about a project. Aims: This research aims to explore how the data-mining, analysis and presentation of revision control systems can be used to augment aspects of project comprehension, including change prediction, maintenance, visualization, management, profiling, sampling and assessment. Method: A series of case studies investigate how transactional data can be used to support project comprehension. A thematic analysis of revision logs is used to explore the development process and developer behaviour. A benchmarking study of a history-based model of change prediction is conducted to assess how successfully such a technique can be used to augment syntax-based models. A visualization tool is developed for managers of student projects with the aim of evaluating what visualizations best support their roles. Finally, a quasi-experiment is conducted to determine how well an algorithmic model can automatically select a representative sample of code entities from a project, in comparison with expert strategies. Results: The thematic analysis case study classified maintenance activities in 22 undergraduate projects and four real-world projects. The change prediction study calculated information retrieval metrics for 34 undergraduate projects and three real-world projects, as well as an in-depth exploration of the model's performance and applications in two selected projects. File samples for seven projects were generated by six experts and three heuristic models and compared to assess agreement rates, both within the experts and between the experts and the models. Conclusions: When the results from each study are evaluated together, the evidence strongly shows that the information stored in revision control systems can indeed be used to support a range of project comprehension activities in a manner which complements existing, syntax-based techniques. The case studies also help to develop the empirical foundation of repository analysis in the areas of visualization, maintenance, sampling, profiling and management; the research also shows that students can be viable substitutes for industrial practitioners in certain areas of software engineering research, which weakens one of the primary obstacles to empirical studies in these areas

Annotation-based storage and retrieval of models and simulation descriptions in computational biology

This work aimed at enhancing reuse of computational biology models by identifying and formalizing relevant meta-information. One type of meta-information investigated in this thesis is experiment-related meta-information attached to a model, which is necessary to accurately recreate simulations. The main results are: a detailed concept for model annotation, a proposed format for the encoding of simulation experiment setups, a storage solution for standardized model representations and the development of a retrieval concept.Die vorliegende Arbeit widmete sich der besseren Wiederverwendung biologischer Simulationsmodelle. Ziele waren die Identifikation und Formalisierung relevanter Modell-Meta-Informationen, sowie die Entwicklung geeigneter Modellspeicherungs- und Modellretrieval-Konzepte. Wichtigste Ergebnisse der Arbeit sind ein detailliertes Modellannotationskonzept, ein Formatvorschlag für standardisierte Kodierung von Simulationsexperimenten in XML, eine Speicherlösung für Modellrepräsentationen sowie ein Retrieval-Konzept