CyberLiveApp: a secure sharing and migration approach for live virtual desktop applications in a cloud environment

In recent years we have witnessed the rapid advent of cloud computing, in which the remote software is delivered as a service and accessed by users using a thin client over the Internet. In particular, the traditional desktop application can execute in the remote virtual machines without re-architecture providing a personal desktop experience to users through remote display technologies. However, existing cloud desktop applications mainly achieve isolation environments using virtual machines (VMs), which cannot adequately support application-oriented collaborations between multiple users and VMs. In this paper, we propose a flexible collaboration approach, named CyberLiveApp, to enable live virtual desktop applications sharing based on a cloud and virtualization infrastructure. The CyberLiveApp supports secure application sharing and on-demand migration among multiple users or equipment. To support VM desktop sharing among multiple users, a secure access mechanism is developed to distinguish view privileges allowing window operation events to be tracked to compute hidden window areas in real time. A proxy-based window filtering mechanism is also proposed to deliver desktops to different users. To support application sharing and migration between VMs, we use the presentation streaming redirection mechanism and VM cloning service. These approaches have been preliminary evaluated on an extended MetaVNC. Results of evaluations have verified that these approaches are effective and useful

A query processing system for very large spatial databases using a new map algebra

Dans cette thèse nous introduisons une approche de traitement de requêtes pour des bases de donnée spatiales. Nous expliquons aussi les concepts principaux que nous avons défini et développé: une algèbre spatiale et une approche à base de graphe utilisée dans l'optimisateur. L'algèbre spatiale est défini pour exprimer les requêtes et les règles de transformation pendant les différentes étapes de l'optimisation de requêtes. Nous avons essayé de définir l'algèbre la plus complète que possible pour couvrir une grande variété d'application. L'opérateur algébrique reçoit et produit seulement des carte. Les fonctions reçoivent des cartes et produisent des scalaires ou des objets. L'optimisateur reçoit la requête en expression algébrique et produit un QEP (Query Evaluation Plan) efficace dans deux étapes: génération de QEG (Query Evaluation Graph) et génération de QEP. Dans première étape un graphe (QEG) équivalent de l'expression algébrique est produit. Les règles de transformation sont utilisées pour transformer le graphe a un équivalent plus efficace. Dans deuxième étape un QEP est produit de QEG passé de l'étape précédente. Le QEP est un ensemble des opérations primitives consécutives qui produit les résultats finals (la réponse finale de la requête soumise au base de donnée). Nous avons implémenté l'optimisateur, un générateur de requête spatiale aléatoire, et une base de donnée simulée. La base de donnée spatiale simulée est un ensemble de fonctions pour simuler des opérations spatiales primitives. Les requêtes aléatoires sont soumis à l'optimisateur. Les QEPs générées sont soumis au simulateur de base de données spatiale. Les résultats expérimentaux sont utilisés pour discuter les performances et les caractéristiques de l'optimisateur.Abstract: In this thesis we introduce a query processing approach for spatial databases and explain the main concepts we defined and developed: a spatial algebra and a graph based approach used in the optimizer. The spatial algebra was defined to express queries and transformation rules during different steps of the query optimization. To cover a vast variety of potential applications, we tried to define the algebra as complete as possible. The algebra looks at the spatial data as maps of spatial objects. The algebraic operators act on the maps and result in new maps. Aggregate functions can act on maps and objects and produce objects or basic values (characters, numbers, etc.). The optimizer receives the query in algebraic expression and produces one efficient QEP (Query Evaluation Plan) through two main consecutive blocks: QEG (Query Evaluation Graph) generation and QEP generation. In QEG generation we construct a graph equivalent of the algebraic expression and then apply graph transformation rules to produce one efficient QEG. In QEP generation we receive the efficient QEG and do predicate ordering and approximation and then generate the efficient QEP. The QEP is a set of consecutive phases that must be executed in the specified order. Each phase consist of one or more primitive operations. All primitive operations that are in the same phase can be executed in parallel. We implemented the optimizer, a randomly spatial query generator and a simulated spatial database. The query generator produces random queries for the purpose of testing the optimizer. The simulated spatial database is a set of functions to simulate primitive spatial operations. They return the cost of the corresponding primitive operation according to input parameters. We put randomly generated queries to the optimizer, got the generated QEPs and put them to the spatial database simulator. We used the experimental results to discuss on the optimizer characteristics and performance. The optimizer was designed for databases with a very large number of spatial objects nevertheless most of the concepts we used can be applied to all spatial information systems."--Résumé abrégé par UMI

PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results

BACKGROUND: BLAST searches are widely used for sequence alignment. The search results are commonly adopted for various functional and comparative genomics tasks such as annotating unknown sequences, investigating gene models and comparing two sequence sets. Advances in sequencing technologies pose challenges for high-throughput analysis of large-scale sequence data. A number of programs and hardware solutions exist for efficient BLAST searching, but there is a lack of generic software solutions for mining and personalized management of the results. Systematically reviewing the results and identifying information of interest remains tedious and time-consuming. RESULTS: Personal BLAST Navigator (PLAN) is a versatile web platform that helps users to carry out various personalized pre- and post-BLAST tasks, including: (1) query and target sequence database management, (2) automated high-throughput BLAST searching, (3) indexing and searching of results, (4) filtering results online, (5) managing results of personal interest in favorite categories, (6) automated sequence annotation (such as NCBI NR and ontology-based annotation). PLAN integrates, by default, the Decypher hardware-based BLAST solution provided by Active Motif Inc. with a greatly improved efficiency over conventional BLAST software. BLAST results are visualized by spreadsheets and graphs and are full-text searchable. BLAST results and sequence annotations can be exported, in part or in full, in various formats including Microsoft Excel and FASTA. Sequences and BLAST results are organized in projects, the data publication levels of which are controlled by the registered project owners. In addition, all analytical functions are provided to public users without registration. CONCLUSION: PLAN has proved a valuable addition to the community for automated high-throughput BLAST searches, and, more importantly, for knowledge discovery, management and sharing based on sequence alignment results. The PLAN web interface is platform-independent, easily configurable and capable of comprehensive expansion, and user-intuitive. PLAN is freely available to academic users at . The source code for local deployment is provided under free license. Full support on system utilization, installation, configuration and customization are provided to academic users

Visualization and analysis of software clones

Code clones are identical or similar fragments of code in a software system. Simple copy-paste programming practices of developers, reusing existing code fragments instead of implementing from the scratch, limitations of both programming languages and developers are the primary reasons behind code cloning. Despite the maintenance implications of clones, it is not possible to conclude that cloning is harmful because there are also benefits in using them (e.g. faster and independent development). As a result, researchers at least agree that clones need to be analyzed before aggressively refactoring them. Although a large number of state-of-the-art clone detectors are available today, handling raw clone data is challenging due to the textual nature and large volume. To address this issue, we propose a framework for large-scale clone analysis and develop a maintenance support environment based on the framework called VisCad. To manage the large volume of clone data, VisCad employs the Visual Information Seeking Mantra: overview first, zoom and filter, then provide details-on-demand. With VisCad users can analyze and identify distinctive code clones through a set of visualization techniques, metrics covering different clone relations and data filtering operations. The loosely coupled architecture of VisCad allows users to work with any clone detection tool that reports source-coordinates of the found clones. This yields the opportunity to work with the clone detectors of choice, which is important because each clone detector has its own strengths and weaknesses. In addition, we extend the support for clone evolution analysis, which is important to understand the cause and effect of changes at the clone level during the evolution of a software system. Such information can be used to make software maintenance decisions like when to refactor clones. We propose and implement a set of visualizations that can allow users to analyze the evolution of clones from a coarse grain to a fine grain level. Finally, we use VisCad to extract both spatial and temporal clone data to predict changes to clones in a future release/revision of the software, which can be used to rank clone classes as another means of handling a large volume of clone data. We believe that VisCad makes clone comprehension easier and it can be used as a test-bed to further explore code cloning, necessary in building a successful clone management system

Animating the evolution of software

The use and development of open source software has increased significantly in the last decade. The high frequency of changes and releases across a distributed environment requires good project management tools in order to control the process adequately. However, even with these tools in place, the nature of the development and the fact that developers will often work on many other projects simultaneously, means that the developers are unlikely to have a clear picture of the current state of the project at any time. Furthermore, the poor documentation associated with many projects has a detrimental effect when encouraging new developers to contribute to the software. A typical version control repository contains a mine of information that is not always obvious and not easy to comprehend in its raw form. However, presenting this historical data in a suitable format by using software visualisation techniques allows the evolution of the software over a number of releases to be shown. This allows the changes that have been made to the software to be identified clearly, thus ensuring that the effect of those changes will also be emphasised. This then enables both managers and developers to gain a more detailed view of the current state of the project. The visualisation of evolving software introduces a number of new issues. This thesis investigates some of these issues in detail, and recommends a number of solutions in order to alleviate the problems that may otherwise arise. The solutions are then demonstrated in the definition of two new visualisations. These use historical data contained within version control repositories to show the evolution of the software at a number of levels of granularity. Additionally, animation is used as an integral part of both visualisations - not only to show the evolution by representing the progression of time, but also to highlight the changes that have occurred. Previously, the use of animation within software visualisation has been primarily restricted to small-scale, hand generated visualisations. However, this thesis shows the viability of using animation within software visualisation with automated visualisations on a large scale. In addition, evaluation of the visualisations has shown that they are suitable for showing the changes that have occurred in the software over a period of time, and subsequently how the software has evolved. These visualisations are therefore suitable for use by developers and managers involved with open source software. In addition, they also provide a basis for future research in evolutionary visualisations, software evolution and open source development

BamView: visualizing and interpretation of next-generation sequencing read alignments.

So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user

ICD Management (ICDM) tool for embedded systems on aircrafts

International audienceIn the scope of on-board systems development and integration for aircrafts, ICDs (Interface Control Document/Description) are fundamental sources of information at same level that the functional requirements. ICD description must include feasible (bus capacity not exceeded, processing load under specific limits) and accurate (data precision, data retransmission rate, data consistency) inter-connectivity mechanisms, to support the application requirements needs, as well as the information must be easy to update and to maintain.On the other hand, DOORS (IBM) is a tool specialized on requirements management. It faces with aspects as traceability, version control, security (access control), changes control, data persistency and accessibility. DOORS is widely used and it is recognized as a reference tool in the scope of aeronautic developments.Nevertheless, ICD information usually is not managed with DOORS. The reason can be found in the specificities of the nature of ICD information, which suggests other approaches more suitable than DOORS.The alternative approaches are very diverse but most of them focus on handling information typified according to specific meta-models for ICD: databases, customized spreadsheets, and tabular descriptions. But whatever is the solution, it must address also, by its own means, the features of ICD derived of its “requirement nature”.This paper presents a solution based on the integration of DOORS with a user front-end developed with Model Driven Architecture (MDA) and Open Source technologies. It is intended to provide means to manage ICD data in a robust way (guaranteeing the correctness -syntactic, completeness, non ambiguity- of data, changes, versions, dependencies, ...) and additionally, to provide mechanisms to focus the effort on the data transformation rather than on the manual elaboration of derived artefacts