Megamodeling Software Platforms: Automated Discovery of Usable Cartography from Available Metadata

International audienceModel-driven reverse engineering focuses on automatically discovering models from different kinds of available information on existing software systems. Although the source code of an application is often used as a basic input, this information may take various forms such as: design "models", bug reports, or any kind of documentation in general. All this metadata may have been either built manually or generated (semi)automatically during the whole software life cycle, from the specification and development phase to the effective running of the system. This paper proposes an automated and extensible MDE approach to build a usable cartography of a given platform from available metadata by combining several MDE techniques. As a running example, the approach has been applied to the TopCased MDE platform for Embedded & Real-Time Systems

Browsing repeats in genomes: Pygram and an application to non-coding region analysis

BACKGROUND: A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires specialized methods, including visualization techniques, to achieve optimum exploratory power. RESULTS: This article presents Pygram, a new visualization application for investigating the organization of repeated sequences in complete genome sequences. The application projects data from a repeat index file on the analysed sequences, and by combining this principle with a query system, is capable of locating repeated sequences with specific properties. In short, Pygram provides an efficient, graphical browser for studying repeats. Implementation of the complete configuration is illustrated in an analysis of CRISPR structures in Archaea genomes and the detection of horizontal transfer between Archaea and Viruses. CONCLUSION: By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes

Model-Driven Interoperability of Dependencies Visualizations

International audienceSoftware tools and corresponding knowledge tend to be collected and packaged into platforms like Eclipse, MathLab or KDE. Their success and usefulness combined with their growing size and complexity rise issues about management of dependencies between their components and between the platform and other applications which rely on its plug-in system and/or provided functionalities. Such problems imply need for dependencies management tools in which visualization is a core feature. As dependencies are also a concern in domains like Object-Oriented Programming or Operating System packaging, we may expect to reuse corresponding works in visualization. But each domain and its related dependencies problem have induced their own hard coded viewing and browsing tools. In this article we present how we have reuse existing visualization tools for our platform cartography together with our own displays using a Model-Driven Interoperability approach to easily realize bindings between visualization tools

Droit, mœurs et politique dans les théories sociales

Alain Mahé, maître de conférencesAvec Bruno Karsenti, maître de conférences à l’Université de Paris-Iet Frédéric Audren, Université de Paris-II Problèmes d’anthropologie juridique Dernier volet du programme « Droit, mœurs et politique dans les théories sociales » inauguré quatre ans auparavant, le séminaire de cette année a eu pour objectif d’illustrer l’ensemble des questions théoriques et méthodologiques débattues les années précédentes à partir d’études de cas empiriques. C’est ainsi que l..

Droit, mœurs et politique dans les théories sociales

Alain Mahé, maître de conférencesAvec Bruno Karsenti, maître de conférences à l’Université de Paris-Iet Frédéric Audren, Université de Paris-II Problèmes d’anthropologie juridique Dernier volet du programme « Droit, mœurs et politique dans les théories sociales » inauguré quatre ans auparavant, le séminaire de cette année a eu pour objectif d’illustrer l’ensemble des questions théoriques et méthodologiques débattues les années précédentes à partir d’études de cas empiriques. C’est ainsi que l..

Interpreting phylogenetic placements for taxonomic assignment of environmental DNA

Taxonomic assignment of operational taxonomic units (OTUs) is an important bioinformatics step in analyzing environmental sequencing data. Pairwise alignment and phylogenetic-placement methods represent two alternative approaches to taxonomic assignments, but their results can differ. Here we used available colpodean ciliate OTUs from forest soils to compare the taxonomic assignments of VSEARCH (which performs pairwise alignments) and EPA-ng (which performs phylogenetic placements). We showed that when there are differences in taxonomic assignments between pairwise alignments and phylogenetic placements at the subtaxon level, there is a low pairwise similarity of the OTUs to the reference database. We then showcase how the output of EPA-ng can be further evaluated using GAPPA to assess the taxonomic assignments when there exist multiple equally likely placements of an OTU, by taking into account the sum over the likelihood weights of the OTU placements within a subtaxon, and the branch distances between equally likely placement locations. We also inferred the evolutionary and ecological characteristics of the colpodean OTUs using their placements within subtaxa. This study demonstrates how to fully analyze the output of EPA-ng, by using GAPPA in conjunction with knowledge of the taxonomic diversity of the clade of interest

Droit, mœurs et politique dans les théories sociales

Alain Mahé, maître de conférences avec Bruno Karsenti, maître de conférences à l’Université de Paris-I et Frédéric Audren, Université de Paris-II La refondation des sciences sociales au XIXe siècle à l’épreuve de la croyance La refondation des sciences sociales, notamment dans le cadre du projet de Durkheim, procède d’une nouvelle réflexion sur les rapports entre droit et religion, dans laquelle l’analyse des diverses modalités de la croyance prend une place essentielle. Le séminaire a procéd..