Stuart Pook

Mapping the whole human genome by fingerprinting yeast artificial chromosomes.

Physical mapping of the human genome has until now been envisioned through single chromosome strategies. We demonstrate that by using large insert yeast artificial chromosomes (YACs) a whole genome approach becomes feasible. YACs (22,000) of 810 kb mean size (5 genome equivalents) have been fingerprinted to obtain individual patterns of restriction fragments detected by a LINE-1 (L1) probe. More than 1000 contigs were assembled. Ten randomly chosen contigs were validated by metaphase chromosome fluorescence in situ hybridization, as well as by analyzing the inter-Alu PCR patterns of their constituent YACs. We estimate that 15% to 20% of the human genome, mainly the L1-rich regions, is already covered with contigs larger than 3 Mb.

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

BackgroundMolecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them.ResultsNaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system.ConclusionsNaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Zomit: biological data visualization and browsing.

MOTIVATION The problems caused by the difficulty in visualizing and browsing biological databases have become crucial. Scientists can no longer interact directly with the huge amount of available data. However, future breakthroughs in biology depend on this interaction. We propose a new metaphor for biological data visualization and browsing that allows navigation in very large databases in an intuitive way. The concepts underlying our approach are based on navigation and visualization with zooming, semantic zooming and portals; and on data transformation via magic lenses. We think that these new visualization and navigation techniques should be applied globally to a federation of biological databases. RESULTS We have implemented a generic tool, called Zomit, that provides an application programming interface for developing servers for such navigation and visualization, and a generic architecture-independent client (Javatrade mark applet) that queries such servers. As an illustration of the capabilities of our approach, we have developed ZoomMap, a prototype browser for the HuGeMap human genome map database. AVAILABILITY Zomit and ZoomMap are available at the URL http://www.infobiogen.fr/services/zomit.

The HuGeMap Database: interconnection and visualization of human genome maps

The HuGeMap database stores the major genetic and physical maps of the human genome. HuGeMap is accessible on the Web at http://www. infobiogen.fr/services/Hugemap and through a CORBA server. A standard genome map data format for the interconnection of genome map databases was defined in collaboration with the EBI. The HuGeMap CORBA server provides this interconnection using the interface definition language IDL. Two graphical user interfaces were developed for the visualization of the HuGeMap data: ZoomMap (http://www.infobiogen.fr/services/zomit/Zoom Map.html) for navigation by zooming and data transformation via magic lenses, and MappetShow (http://www.infobiogen.fr/services/Mappet) for visualizing and comparing maps.

Augmentation de cours et de réunions dans un campus

This paper presents two prototypes for augmenting lectures and small group meetings that have been developped in the context of a digital campus. The various aspects that have been developped (augmented whiteboard interaction, annotation management, multimedia, wireless communication strategies, single display groupware, user centred conception...) are described and analyzed relatively to the considered scenarios. Some preliminary observations are presented and compared to other studies.