Simulation of a viscous fluid spreading by a bidimensional shallow water model

In this paper we propose a numerical method to solve the Cauchy problem based on the viscous shallow water equations in an horizontally moving domain. More precisely, we are interested in a flooding and drying model, used to modelize the overflow of a river or the intrusion of a tsunami on ground. We use a non conservative form of the two-dimensional shallow water equations, in eight velocity formulation and we build a numerical approximation, based on the Arbitrary Lagrangian Eulerian formulation, in order to compute the solution in the moving domain

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future

On the two-dimensional compressible isentropic Navier–Stokes equations

We analyze the compressible isentropic Navier–Stokes equations (Lions, 1998) in the two-dimensional case with $\gamma= \displaystyle{{c_{p}}/{c_{v}}}=2$. These equations also modelize the shallow water problem in height-flow rate formulation used to solve the flow in lakes and perfectly well-mixed sea. We establish a convergence result for the time-discretized problem when the momentum equation and the continuity equation are solved with the Galerkin method, without adding a penalization term in the continuity equation as it is made in Lions (1998). The second part is devoted to the numerical analysis and mainly deals with problems of geophysical fluids. We compare the simulations obtained with this compressible isentropic Navier–Stokes model and those obtained with a shallow water model (Di Martino et al., 1999). At first, the computations are executed on a simplified domain in order to validate the method by comparison with existing numerical results and then on a real domain: the dam of Calacuccia (France). At last, we numerically implement an analytical example presented by Weigant (1995) which shows that even if the data are rather smooth, we cannot have bounds on ρ in Lp for p large if $\gamma<2$ when N=2

Sequence analyses of Megabase-sized contigs of the wheat genome

International audienceWith 17 Gb and an hexaploid composition, molecular characterization of the bread wheat (Triticum aestivum L.) genome is a challenge and its genome structure and composition remain largely unknown. Our current knowledge is limited to the analysis of individual BAC sequences and of random BAC end and plasmid sequences. To improve our knowledge on the structure and evolution of the wheat genome, we have sequenced a dozen of Mb-sized contigs (up to 3.2 Mb; 8-12x coverage) originating from different regions of chromosome 3B for which a physical map has been recently established in our laboratory. Altogether, these data account for 16.5 Mb of sequences and represent the first set of large contiguous wheat genome sequences to be analyzed. Automatic annotation has been performed using the web-based TriAnnot pipeline (http://urgi.versailles.inra.fr/projects/TriAnnot/; EU-Auvergne Lifegrid project) that is under final stage of development. TriAnnot allows direct submission of BAC sequences and uses Triticeae specific libraries, algorithms and combiners to provide gene models. Similarity-based identification of the transposable elements is also computed and a more sophisticated approach for characterization of nested elements is under development. TriAnnot benefits from a user friendly interface and from a modular grid-based architecture. The gene density over the 16.5 Mb is 1 gene per 139 kb. Locally, important variations of the gene content is detected, from 0 to 10 genes per BAC, revealing a non-random distribution of the genes along the chromosome. Intergenic region as small as 500 bps were observed while a region of 620 kb without genes has also been found. Curation of the TE annotation has been performed over the larger contig (3.2 Mb). With 60 different TE families detected in the region, it revealed that the wheat genome is characterized by an important diversity of TEs. However, a few number of elements are over-represented suggesting that wheat genome expansion has occurred by a massive amplification of a small number of specific TEs. Finally comparative analyses has been performed with other available cereal genomes. First comparisons reveal that, for some regions, wheat may have undergone many DNA rearrangements that led to numerous micro-synteny breaks when compared to the other cereal genomes that exhibit a more ancestral genome structure. The latest results on gene and TE annotation, on the architecture of the annotation pipeline and on comparative analyses will be presented. This project is supported by the Agence Nationale de la Recherche (ANR-Genoplante-SMART)

Vers une annotation RMN 1D et 2D ciblée à partir de matrices de référence

National audienc