The LHCb experiment is dedicated to precision measurements of CP violation and rare decays of B hadrons at the Large Hadron Collider (LHC) at CERN (Geneva). The initial configuration and expected performance of the detector and associated systems, as established by test beam measurements and simulation studies, is described.
Carrier-grade networks of the future are currently being standardized and designed under the umbrella name of Next Generation Network (NGN). The goal of NGN is to provide a more flexible network infrastructure that supports not just data and voice traffic routing, but also higher level services and interfaces for thirdparty enhancements. Within this paper, opportunities to integrate grid and cloud computing
Parallel sequence and structure alignment tools have become ubiquitous and invaluable at all levels in the study of biological systems. We demonstrate the application and utility of this same parallel search paradigm to the process of protein structure determination, benefitting from the large and growing corpus of known structures. Such searches were previously computationally intractable. Through the method of Wide Search Molecular Replacement, developed here, they can be completed in a few hours with the aide of national-scale federated cyberinfrastructure. By dramatically expanding the range of models considered for structure determination, we show that small (less than 12% structural coverage) and low sequence identity (less than 20% identity) template structures can be identified through multidimensional template scoring metrics and used for structure determination. Many new macromolecular complexes can benefit significantly from such a technique due to the lack of known homologous protein folds or sequences. We demonstrate the effectiveness of the method by determining the structure of a full-length p97 homologue from Trichoplusia ni. Example cases with the MHC/T-cell receptor complex and the EmoB protein provide systematic estimates of minimum sequence identity, structure coverage, and structural similarity required for this method to succeed. We describe how this structure-search approach and other novel computationally intensive workflows are made tractable through integration with the US national computational cyberinfrastructure, allowing, for example, rapid processing of the entire Structural Classification of Proteins protein fragment database.p97 ATPase | likelihood functions | scoring methods | grid computing C an access to vast quantities of computational power be leveraged to advance the study of biological systems in previously unexplored ways? Whereas many domains have driven demand for computational power and novel computational techniques in the process of scientific investigation, there remain areas where the opportunities provided by the most advanced computational infrastructures and tools have not been fully explored. The last decade has quietly seen the development of significant national and international federated cyberinfrastructures, established primarily to support the half dozen globally distributed particle physics collaborations. In the same way this community established the World Wide Web as a simple, standards-based system for information sharing, the particle physics community has also facilitated sharing of data and computing through development of what is known as "grid computing." An area within the field of macromolecular structural biology that can leverage grid computing is harnessing the large and growing set of known protein structures to accelerate protein structure determination. The question of how to benefit from known structures was posed even as the earliest protein structures emerged, following observation of the similarity of the hemoglobin subunits to each ...
The GridPP Collaboration is building a UK computing Grid for particle physics, as part of the international effort towards computing for the Large Hadron Collider. The project, funded by the UK Particle Physics and Astronomy Research Council (PPARC), began in September 2001 and completed its first phase 3 years later. GridPP is a collaboration of approximately 100 researchers in 19 UK university particle physics groups, the Council for the Central Laboratory of the Research Councils and CERN, reflecting the strategic importance of the project. In collaboration with other European and US efforts, the first phase of the project demonstrated the feasibility of developing, deploying and operating a Grid-based computing system to meet the UK needs of the Large Hadron Collider experiments. This note describes the work undertaken to achieve this goal. S Supplementary documentation is available from stacks.iop.org/JPhysG/32/N1. References to sections S1, S2.1, etc are to sections within this online supplement.
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