The RAST Server: Rapid Annotations using Subsystems Technology

<p>Abstract</p> <p>Background</p> <p>The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.</p> <p>Description</p> <p>We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment.</p> <p>The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service.</p> <p>Conclusion</p> <p>By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.</p

A SOFTWARE PARADIGM FOR THE DEVELOPMENT OF PORTABLE MULTIPROCESS-ORIENTED COMPUTER GRAPHICS ALGORITHMS (PARALLEL PROCESSING).

A SOFTWARE PARADIGM FOR THE DEVELOPMENT OF PORTABLE MULTIPROCESS-ORIENTED COMPUTER GRAPHICS ALGORITHMS (PARALLEL PROCESSING)

Performance Model of the Argonne Voyager Multimedia Server

The Argonne Voyager Multimedia Server is being developed in the Futures Lab of the Mathematics and Computer Science Division at Argonne National Laboratory. As a network-based service for recording and playing multimedia streams, it is important that the Voyager system be capable of sustaining certain minimal levels of performance in order for it to be a viable system. In this article, we examine the performance characteristics of the server. As we examine the architecture of the system, we try to determine where bottlenecks lie, show actual vs potential performance, and recommend areas for improvement through custom architectures and system tuning. 1 Introduction The Argonne Computing and Communications Infrastructure Futures Laboratory (Futures Lab) [1] was created to explore, develop, and prototype nextgeneration computing and communications infrastructure systems. An important goal of the Futures Lab project is to understand how to incorporate advanced display and media server sy..

UbiWorld: An EnvironmentIntegrating Virtual Reality, Supercomputing, and Design

UbiWorld is a concept being developedbytheFutures Laboratory group at Argonne National Laboratory that ties together the notion of ubiquitous computing (Ubicomp) with that of using virtual reality for rapid prototyping. The goal is to develop an environment where one can exploreUbicomp-typeconcepts without having to build real Ubicomp hardware. The basic notion is to extend object models in a virtual world by using distributed wide area heterogeneous computing technology to provide complex networking and processing capabilities to virtual reality objects

The Argonne Voyager multimedia server

With the growing presence of multimedia-enabled systems, we will see an integration of collaborative computing concepts into future scientific and technical workplaces. Desktop teleconferencing is common today,while more complex teleconferencing technology that relies on the availability of multipoint-enabled tools is starting to become available on PCs. A critical problem when using these collaborative tools is archiving multistream, multipoint meetings and making the content available to others. Ideally, one would like the ability to capture, record, play back, index, annotate, and distribute multimedia stream data as easily as we currently handle text or still-image data. The Argonne Voyager project is exploring and developing media server technology needed to provide such a flexible, virtual multipoint recording/playback capability. In this article we describe the motivating requirements, architecture, implementation, operation, performance, and related work.

Sharing Visualization Experiences among Remote Virtual Environments

Virtual reality has become an increasingly familiar part of the science of visualization and communication of information. This, combined with the increase in connectivity of remote sites via high-speed networks, allows for the development of a collaborative distributed virtual environment. Such an environment enables the development of supercomputer simulations with virtual reality visualizations that can be displayed at multiple sites, with each site interacting, viewing, and communicating about the results being discovered. The early results of an experimental collaborative virtual reality environment are discussed in this paper. The issues that need to be addressed in the implementation, as well as preliminary results are covered. Also provided are a discussion of plans and a generalized application programmers interface for CAVE to CAVE will be provided. 1 Introduction Sharing a visualization experience among remote virtual environments is a new area of research within the field ..

Virtual Reality Visualization of Parallel Molecular Dynamics Simulation

: When performing communications mapping experiments for massively parallel processors, it is important to be able to visualize the mappings and resulting communications. In a molecular dynamics model, visualization of the atom to atom interaction and the processor mappings provides insight into the effectiveness of the communications algorithms. The basic quantities available for visualization in a model of this type are the number of molecules per unit volume, the mass, and velocity of each molecule. The computational information available for visualization is the atom to atom interaction within each time step, the atom to processor mapping, and the energy rescaling events. We use the CAVE (CAVE Automatic Virtual Environment) to provide interactive, immersive visualization experiences. 1 Introduction Molecular dynamic simulations are increasingly being used to perform simulations of materials and in the modeling of drug compounds. The validation of these simulations is done by comp..