Fusion of 3D B-Spline Surface Patches Reconstructed from Image Sequences

International audienceThis paper considers the problem of merging a set of distinct three dimensional B-spline surface patches, which are reconstructed from observations of the motion of occluding contours in image sequences. We propose an original method of fusing these partially overlapping patches in order to obtain a whole surface. This approach is based on a triangular mesh and surface interpolation through regularized uniform bicubic B-spline surface patches. Experimental results are presented for both synthetic and real data

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community

Analysis of variation at transcription factor binding sites in Drosophila and humans

Background: Advances in sequencing technology have boosted population genomics and made it possible to map the positions of transcription factor binding sites (TFBSs) with high precision. Here we investigate TFBS variability by combining transcription factor binding maps generated by ENCODE, modENCODE, our previously published data and other sources with genomic variation data for human individuals and Drosophila isogenic lines. Results: We introduce a metric of TFBS variability that takes into account changes in motif match associated with mutation and makes it possible to investigate TFBS functional constraints instance-by-instance as well as in sets that share common biological properties. We also take advantage of the emerging per-individual transcription factor binding data to show evidence that TFBS mutations, particularly at evolutionarily conserved sites, can be efficiently buffered to ensure coherent levels of transcription factor binding. Conclusions: Our analyses provide insights into the relationship between individual and interspecies variation and show evidence for the functional buffering of TFBS mutations in both humans and flies. In a broad perspective, these results demonstrate the potential of combining functional genomics and population genetics approaches for understanding gene regulation.European Molecular Biology Laboratory (interdisciplinary fellowship (EIPOD))Deutsche Forschungsgemeinschaft (DFG FU 750/1-1

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes

Ensembl’s 10th year

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure

Modèle groupe réflexif pour la construction d'applications réparties

L'objet de cette thèse concerne l'étude et la réalisation d'un modèle de composition simplifiant la construction d'applications ouvertes. Nous proposons dans un premier temps d'étendre la relation classique de compatibilité de types avec une relation de compatibilité coercitive afin de lier dynamiquement des composants dont les types sont a priori incompatibles. La +-glua entre les composants est fournie par un connecteur appelé groupe qui adapte le type et le comportement d'un ou plusieurs composants fournis au type et au comportement attendu par d'autres composants. La problématique abordée dans un second temps se concentre sur la reconfiguration des composants de granularité variable à l'exécution. Nous proposons un modèle où les groupes servent à définir des composants de granularité variable. L'originalité de notre approche provient de l'introduction de mécanismes réflexifs tant structurels que comportementaux. Un groupe représente un composant reconfigurable à l'exécution.RENNES1-BU Sciences Philo (352382102) / SudocSudocFranceF