Finding spot shape in cdna microarray by using a deformable grid and a Markov segmentation

L'intérêt de l'utilisation des biopuces cdna pour la génétique n'est plus à démontrer [EISE-99]. Cette technologie complexe arrive maintenant à une certaine maturité et son utilisation s'étend notamment dans la modélisation des relations gène expression individu. De ce fait, le défi actuel est l'amélioration de la précision des mesures réalisées de fac¸on à augmenter la qualité des expressions estimées et donc les résultats fonctionnels. En effet, le plus souvent les réponses cherchées jusqu'à présent étaient binaires, alors que maintenant la recherche s'oriente vers des mesures moins tranchées où l'on veut mesurer un quantum d'expression

PRT: Parallel program for a full backtranslation of oligopeptides

DNA hybridization methods have become the most widely used tools in molecular biology to identify organisms and evaluate gene expression levels. PCR (Polymerase Chain Reaction)-based methods, fluorescent in situ hybridization (FISH) and the recent development of DNA microarrays as a high throughput technology need efficient primers or probes design. Evaluation of the metabolic capacities of complex microbial communities found in terrestrial or aquatic environments requires new probe design algorithms that reflect the genetic diversity. As only a small part of the microbial diversity is known, gene sequences deposited in international databases do not reflect the entire diversity. In this context we propose to use oligopeptide sequences for the design of complete set of DNA probes that are able to target the entire genetic diversity of genes encoding enzymes. Due to the degenerated genetic code backtranslation must be managed efficiently. To our knowledge no software has been developed to propose a full backtranslation. This complexity is tractable since we only need to focus on short oligopeptides for DNA probe design. We propose new algorithms that perform a high performance oligopeptide backtranslation into all potential nucleic sequences. We use different efficient techniques such as memory mapping to perform such a computing. We also propose a MPI parallel computing that reduces the whole execution time using data load balancing and network file stream distribution on a cluster architecture

Experimental Evidence of Pitch Control of an All-Terrain AGV during a Ballistic Phase

International audienceIn some conditions, four-wheeled high speed mobile robots designed for open-field applications may take off and land badly. In order to avoid this dead-end situation, it is possible to use the mechanical principle of angular momentum conservation for correcting the pitch angle of the vehicle during the ballistic phases of actual jumps. In this study, the mechanical model of pitch control has been verified in laboratory experiments with a prototype of all-terrain AGV called "RobCat". Two series of trials have been realized on a specific test bench in which RobCat was hanged on a transversal axis passing through its CoM. In each series, RobCat was equipped either with its original hollow rubber tyres or with solid wheels having equivalent inertial parameters. The results of these experiments validated the mechanical model of angular momentum conservation of RobCat during an airborne phase and the feasibility of controlling RobCat's orientation around its pitch axis by accelerating or braking its wheels. The conclusions of this experimental study are highly encouraging for building agile mobile robots able to roll at high velocities on irregular grounds and that will combine the speed of aerial drones with the large autonomy and interaction capacity of terrestrial robots

Modélisation du comportement en roulis d'un véhicule capable d'auto-retournement en phase balistique

Les véhicules terrestres usuels peuvent maintenir une inclinaison adéquate par rappoert à l'horizontale lorsqu'ils sont au sol, mais ne peuvent se réorienter que de manière limitée en phase balistique. Par contre, il est crucial de pouvoir restaurer l'assiette durant les phases balistiques des robots se déplaçant à haute vitesse en terrain accidenté. Nous proposons un modèle analytique et un modèle numérique de véhicule, adaptés à la simulation de différentes techniques d'auto-retournement en roulis, et comparons deux solutions pratiques

Monte Carlo Simulation With The GATE Software Using Grid Computing

DémonstrationInternational audienceMonte Carlo simulations needing many replicates to obtain good statistical results can be easily executed in parallel using the "Multiple Replications In Parallel" approach. However, several precautions have to be taken in the generation of the parallel streams of pseudo-random numbers. In this paper, we present the distribution of Monte Carlo simulations performed with the GATE software using local clusters and grid computing. We obtained very convincing results with this large medical application, thanks to the EGEE Grid (Enabling Grid for E-sciencE), achieving in one week computations that could have taken more than 3 years of processing on a single computer. This work has been achieved thanks to a generic object-oriented toolbox called DistMe which we designed to automate this kind of parallelization for Monte Carlo simulations. This toolbox, written in Java is freely available on SourceForge and helped to ensure a rigorous distribution of pseudo-random number streams. It is based on the use of a documented XML format for random numbers generators statuses

HiSpOD: probe design for functional DNA microarrays.

International audienceMOTIVATION: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. RESULTS: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contaminated environmental sample proved the specificity and the sensitivity of probes designed with the HiSpOD program. AVAILABILITY: http://fc.isima.fr/~g2im/hispod/

SAR Image Fusion in Multi Sensor Context for Small Urban Area Detection

International audienceThe purpose of this work is to provide new fusion methods adapted to multi sensor SAR use for urban area segmentation. We explain first backscattering of radar signal from urban object and characterize variation due to sensors characteristics. Then, we propose two new data fusion methods suitable for radar images. The first one will use similar response to enhance quality of building backscattering and the second one will use two images to calibrate a statistical scheme based on the differences in backscattering from speckled area to urban area. We will show the results of our work applied on tropical areas

Simulation of Microarray images Experiments

International audienceDNA chips allow to simultaneously study the expression of thousands of genes over a wide range of conditions, and are likely to revolutionize our ability to understand how microorganisms act. We propose in this article a simulator of DNA chips. We first introduce the biological fabrication of these chips, then we present the geometrical and physical models involved in the simulator, and we finally shed light on the potential interests of such a simulator w.r.t. microarray image analysis

A Multi-thread GRASPxELS for the Heterogeneous Capacitated Vehicle Routing Problem

International audienceThis chapter focuses on the definition of an efficient parallel metaheuristic which takes advantage of the multi-core design of recent processors. The approach is designed as a Greedy Randomized Adaptive Search Procedure (GRASP) hybridized with a multi-threaded version of an Evolutionary Local Search (ELS) metaheuristic scheme. Our approach is evaluated on an extension of the Vehicle Routing Problem where a heterogeneous fleet of vehicles is available to service a set of customers. The objective consists in designing a set of trips for a limited heterogeneous fleet of vehicles located at a depot node which minimizes the total transportation cost. Each type of vehicles is defined by a capacity and by the number of available vehicles. The efficiency of the parallel approach is evaluated on a new set of real-life instances built out of data from the French districts. A fair comparative study, using a same implementation, is done to evaluate the impact of the number of threads on the convergence rate. Thus, a better trade-off between solution quality and computational time can be reached. The numerical experiments show that the hybrid GRASPxparallel ELS outperforms the classical iterative version and provides numerous new best solutions

Experimental Evaluation of the Pitch Angle Righting Capabilities of a High Speed Terrestrial Vehicle in Ballistic Phase

International audienc