Rachid Gherbi

University of Paris-Sud | Paris 11 · Département d'Informatique

The talk will highlight the general idea of Virtual and Augmented Reality (V&AR), from design specifications to evaluation methods. After a short introduction into the history of V&AR, we will have a look at various types and concepts of V&AR known today. We then discuss some experimental cases to highlight the need of specification of all V&AR par...

Currently, visualization techniques in the genetic field require a very important modeling phase in terms of resources. 2D based projections of traditional visualization techniques are rarely adapted to manage and process such huge mass of information. To overcome such limitation, we propose to use a new graph modeling technique. This,when used in...

Visualization and manipulation of complex and multivariate data in virtual worlds is important for both holders of these data and for their users. Indeed, Virtual Reality helps to make multidimensional data more intelligible and to bring useful information and knowledge. Offering Virtual Reality to browsers, also known as Web Virtual Reality, moreo...

Cet article vise à établir une méthodologie permettant d'aider à la comparaison de classifications réalisées par différents experts sur un ensemble de termes identiques. Les termes spécifiques ont été extraits de façon automatique à partir d'un corpus spécialisé à l'aide d'un outil d'extraction de terminologie et ont été regroupés en classes, défin...

Biologists are leading current research on genome characterization (sequencing, alignment, transcription), providing a huge quantity of raw data about many genome organisms. Extracting knowledge from this raw data is an important process for biologists, using usually data mining approaches. However, it is difficult to deals with these genomic infor...

Biologists usually work with textual DNA sequences (succession of A, C, G and T). This representation allows biologists to study the syntax and other linguistic properties of DNA sequences. Nevertheless, such a linear coding offers only a local and a one-dimensional vision of the molecule. The 3D structure of DNA is known to be very important in ma...

RESUME Si les séquences génomiques sont d'abord connues sous leur forme linéaire, elles ont aussi une structure tri-dimensionnelle potentiellement utilisable pour l'analyse des génomes. Cette représentation de la structure 3D apporte un point de vue nouveau pour l'analyse des séquences. Les propriétés géométriques de l'ADN sont très peu étudiées, e...

This paper presents a new structural-based approach to explore spatial organization of naked DNA on a whole chromosome sequence and its biological features related to gene regulation. A 3D trajectory representation on full-length yeast chromosomes based on Bolshoy’s conformation model is discussed. These trajectories are predicted by our visualizin...

Most of biologists work on textual DNA sequences that are limited to the linear representation of DNA. In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of naked DNA allows biologists to observe and analyze genomes in an i...

Many databases and software tools are available for biologists in order to have access to genomic information. In a SQL manner, our information system GenoMEDIA addresses the problem of integrating heterogeneous data-bases and software utilities within a generic distributed platform. Lysa increases the GenoMEDIA SQL interface by adding an interacti...

We present Genome3DExploerer, an immersive visual mining tool to explore microarray data with other sources. The paper addresses the problem of exploring huge genome expression data, allowing biologists to group gene expression data in immersive environment. This could be a solution to explore augmented microarray data with other gene information s...

Genomic and post-genomic data processing comprising genome sequencing, annotation and large scale genome technology produce increasing amounts of data which need to be analyzed. Visualization is a powerful analytical technique that uses the ability of the human brain to process complex data. Biological data were already explored by virtual-reality....

Gesture and motion analysis is a highly needed process in the athletics field. This is especially true for sports dealing with acrobatics, because acrobatics mix complex spatial rotations over multiple axes and may be combined with various postures. This paper presents a new vision-based system focused on the analysis of acrobatic gestures of sever...

Many databases and software tools are currently available for accessing genomic data. In general, each tool uses a different type of data in exchange protocols, and usually they offer specific services. The presented system approach, named GenoMEDIA, addresses the problem of integrating these heterogeneous databases and software utilities within a...

Biological databases have become increasingly important distributed resources in this field. These databases contain a mix of data types, including sequence data, structured data such as molecular weights or GC content, and annotations in terms of controlled vocabularies and, increasingly, ontology such as the gene ontology, as well as free text da...

Huge volumes of bioinformatics data are emerging from sequencing efforts, gene expression assays, X-ray crystallography of proteins, and many other activities. High-throughput experimental methods produce masses of data, so that the whole of biology has changed from a data-light science into a data-driven science. Currently there are a lot of datab...

Genomic information shows some characteristics that make them very difficult to interpret and to exploit. Such data constitute an important factual resource (GenBank, SwissProt, GeneOntology, or Decrypthon…), are heterogeneous, huge in quantity, and are geographically distributed. They are also recorded in structured or semi-structured formats with...

In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of DNA allows biologists to observe and analyze genomes in an interactive way at different levels. We developed a powerful software platform that provides a new point of vi...

The aim of this paper is to explore the clustering capabilities of our visual genome explorer software. Genome3DExplorer is a new modeling and software solution to explore textual and factual genomic data. It offers a powerful and user-centered visu- alization of this information within an immersive environment. The visualization is based on a grap...

This work presents the problem of integrating heterogeneous software tools and databases in a generic distributed platform focused on genomic applications. A new system concept, named GenoMEDIA is presented. This platform allows users to access in a uniform and transparent manner these heterogeneous data and tools. The user submits both data and go...

This paper addresses the positioning and identification of markers for 3D tracking within Virtual Reality (VR) applications. Many VR applications need to know the position and the orientation of the body of users in order to make possible intuitive user interactions as stereoscopy calculation, navigation control or gesture dialog. This work is base...

In this paper, we address the potential offered by Virtual Reality and scientific simulation for 3D modeling and immersive visualization of huge genomic sequences. Advanced work on 3D data modeling and structuring is proposed. In Bioinformatics, DNA sequences are often represented within linear format. However, they also have a three-dimensional st...

We present a real-time camera-based system designed for gaze tracking focused on human-computer communication. We aim to equip computer systems with a tool which can provide visual information about the user. This tool must satisfy interaction constraints and be non intrusive. Therefore we use a CCD camera, placed between the keyboard and the scree...

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementa...

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementa...

References

A general approach for the three-dimensional representation and visualization of DNA molecule is proposed. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. This approach makes it possible to have a global point of view of the sequence, in opposition to the textual representation. This b...

This paper deals with knowledge sharing over Internet. After defining the concept, we will discuss work aimed at creating a technical system to implement it and at measuring the quality of results obtained. However, the reader will quickly see that the text is organized to address the theme of this special issue of Scientometrics. Models, methods a...

Multimodal user interfaces under UNIX / X11 rarely do the fusion of monomodal events on a temporal criterion. The main difficulties to achieve this are the representation and the dating of non-standard events (vocal, gesture, touch screen, eye movement,... ) by the X server. To begin with, we study a modality server which extends the control of X e...

We present in this paper a system named PoG. Its role is to recognise and interpret natural pointing gestures in the context of a multimodal interaction. The user’s hand gestures are tracked by a camera located above a building plan. The user points to a room on the plan with his index finger while using speech to ask for some information from the...

We propose a reconstruction technique which consists in defining a parametric surface lying on a closed curve by setting the extremal behavior of the surface along the curve on which it lies. Therefore, we most build a set of curves in space from a stereo reconstruction of matched and closed contours in an image pair. Then, we use photometric infor...

We propose a reconstruction technique which consists in defining a parametric surface lying on a closed curve by setting the extremal behavior of the surface along the curve on which it lies. Therefore, we most build a set of curves in space from a stereo reconstruction of matched and closed contours in an image pair. Then, we use photometric infor...

In this paper we present a vision system with the aim of building a perceptual tool in order to make machines aware of humans allowing natural interaction in human-machine communication. The system must satisfy interaction constraints and be non-intrusive. Such a real-time camera-based system is designed for gaze tracking from an image sequence of...

We present a real-time camera-based system designed for gaze tracking focused on human-computer communication. We aim to equip computer systems with a tool which can provide visual information about the user. This tool must satisfy interaction constraints and not intrusive. Therefore, we use a CCD camera placed between the keyboard and the screen....

Introduction La reconstruction 3D vise `a 'elaborer la maquette virtuelle d'objets r'eels capt'es sous forme d'images. L'un des int'erets de ce type de traitement serait de donner aux outils de CAO une capacit'e de perception du r'eel. De fa¸con g'en'erale, il s'agit de permettre l'automatisation partielle de la saisie de formes issues de l'existan...

From the early steps of sketching to final engineering, a frequent and very important activity in designing objects is to perform graphical and spatial simulations to solve the constraints on the objects which are being designed. But when we analyse work situations involving the use of CAD systems, it is today an acknowledged fact that these tools...

In this paper we address the problem of the choice of visual primitives structure in multi- images analysis systems. We consider that this problem has a great consequences over the robustness of such systems, over their using in different vision tasks and over their computation time. Usually, methods used in image analysis systems (pattern recognit...

We present a new edge-based matching algorithm that can be applied for unstructured stereo images. We first review briefly a major recent development in establishing stereo correspondences and show that a great deal of research in stereo is needed in order to apply stereo techniques to solve more real-world problems. We then discuss why we use edge...

We present a new edge detection algorithm that is specially suited for stereopsis. We first define the quality criteria to be met and the properties required: structural stability, accurate localization, detailed representation, safe extraction, and fast computation. Then we describe the classic methods, explain their defects, and derive our algori...

At present, the biologists in genomic study the genomic sequences in textual form. Unfortunately, this representation does not offer a global vision of these sequences. Our goal was then to develop a tool allowing a representation and a three- dimensional visualization of the sequences. The interaction with the user is appreciably increased by mult...

In the field of computer vision, the motion analysis tech- niques are increasingly robust and beginning to have an impact beyond laboratories. Computers are able nowa- days to perform image processing in real time. Indeed, they could be used to build non-intrusive systems for gesture analysis. In particular, gesture and motion analysis is in strong...

1-Sciences du Langage, Université Paris 8 2-CAMS-LaLIC, université Paris 4 3-IRIT-TCI, université Toulouse 3 4-LIMSI, CNRS, Orsay Introduction En 1999, le Ministère de l'Education Nationale, de la Recherche et de la Technologie lançait une action concertée incitative de recherche en sciences de la cognition, appelée "Cognitique". L'objectif était d...