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PIPA: A high-Throughput Pipeline for Protein Function Annotation

PIPA: A High-Throughput Pipeline for Protein Function Annota...

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conference on high performance Computer modernization program

作者： Yu, Chenggang Desai, Valmik Zavaljevski, Nela Reifman, Jaques USA MRMC Biotechnol HPC Software Applicat Inst Telemed & Adv Technol Res Ctr Ft Detrick MD USA

ISBN: (纸本)9780769535159

Traditional experimental methods to determine the functions of proteins encoded in genomic sequences cannot keep pace with the avalanche of sequence data produced by new high-throughput sequencing technologies. This prompted the development of numerous bioinformatics approaches for automated protein function annotation. However, different function classification terminologies are frequently used by these different approaches, precluding the integration of multisource predictions. We developed Pipeline for Protein Annotation (PIPA), a genome-wide protein/function annotation pipeline that runs in a high-performance computing environment. PIPA integrates different tools and employs the Gene Ontology (GO) to provide consistent annotation and resolve prediction conflicts. PIPA has three modules that allow for easy development of specialized databases and integration of various bioinformatics tools. The first module, the pipeline execution module, consists of programs that enable the user access to and control of the pipeline's parallel execution of multiple jobs, each searching a particular database for a chunk of the input data. The execution module wraps the second module, the core pipeline module. The integrated resources, the program for terminology conversion to GO, and the consensus annotation program constitute the main components Of the core module. The third module is the preprocessing module. This last module contains the program for customized generation of protein function databases and the GO-mapping generation program, which creates GO mappings for the terminology conversion program. The current implementation of PIPA annotates protein functions by combining the results of an in-house-developed database for enzyme catalytic function prediction (CatFam) and the results of multiple integrated resources, such as the 11 member databases of InterPro and the Conserved Domains Database, into common GO terms. A Web-page-based graphical user interface is developed b

关键词： Gene Ontology

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Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Effects of Chirality and Diameter on the Pullout Force in a Carbon Nanotube Bundle

Large-Scale Atomic/Molecular Massively Parallel Simulator (L...

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conference on high performance Computer modernization program

作者： Majure, D. L. Haskins, R. W. Lee, N. J. Ebeling, R. M. Maier, R. S. Marsh, C. P. Bednar, A. J. Kirgan, R. A. Welch, C. R. Cornwell, Charles F. USACE Engineer Res & Dev Ctr Vicksburg MS USA High Performance Technol Inc Aberdeen Proving Ground MD USA

ISBN: (纸本)9780769535159

The unique mechanical, electrical, and thermal properties of carbon nanotube (CNT) molecules place them at the forefront of nanotechnology. The mechanical properties of carbon nanotubes such as high tensile strength and modulus provide an effective pathway for better construction materials. Before this potential can be realized, effective techniques of creating load transfer in bulk material must be developed. Carbon nanotubes possess a variety of chiralities and diameters and can cluster into self-organizing, aligned bundles caused by van der Waals (vdW) forces. This paper describes the results of molecular mechanics simulations using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular dynamics code to examine the effect that chirality and diameter have on the pullout force of a single tube from a bundle with hexagonal closest packing (HCP). Pullout force is defined as the force required to extract a tube from a bundle. The different chiralities and diameters create different corrugated surfaces and different areas of contact that influence pullout force. Studying the interaction between CNTs is essential for improving the fundamental understanding of load transfer from CNT to CNT. Additionally, since larger diameter CNTs deform against one another in a bundle, the relationship between diameter and pullout force is quantified in this paper. This research will be used as a basis for studying more advanced load transfer techniques such as twisting, sidewall functionalization, and knotting.

关键词： Carbon nanotubes

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Editor's preface: Proceedings of the 2008 dod hpcmp users group conference

2008 Proceedings of the Department of Defense High Performan...

引用

2008 Proceedings of the Department of Defense high performance computing modernization program: users group conference - Solving the Hard Problems 2008年 xii-xiii页

作者： Post, Douglass E. Scientist, Chief dod, hpcmp

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Ab-Initio Molecular Dynamics Simulations of Molten Ni-Based Superalloys

Ab-Initio Molecular Dynamics Simulations of Molten Ni-Based ...

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conference on high performance Computer modernization program

作者： Woodward, Christopher Asta, Mark Trinkle, Dallas R. Lill, James Angioletti-Uberti, Stefano USAF Res Lab Mat & Mfg Directorate Wright Patterson AFB OH 45433 USA Univ Calif Dept Chem Engn & Mat Davis CA 95616 USA Univ Illinois Dept Mat Sci & Engn Urbana IL 61801 USA High Performance Technol Inc Wright Patterson AFB OH USA Imperial Coll London Dept Mat London England

ISBN: (纸本)9780769535159

Variations in composition and temperature of the liquid-phase molar volume (V(c, T)) play a critical role in driving convective instabilities during the casting of single-crystal turbine blades, These instabilities have long been associated with the formation of large highly mis-oriented grains (i.e., freckle defects) that produce significant degradation in materials properties of these critical aerospace components. Ab initio molecular dynamics (AIMD) simulations have been performed,for elemental, binary and ternary alloys of Ni with Al, W, Re, and Ta, as well as a RENE-N4 multi-component superalloy, to compute equations of state at 1830 and 1750K. Where comparisons with measurements are available, AIMD-calculated volumes agree to within 0.6-1.8% of experiment. Results are compared with recently published parameterizations of V(c,T) developed using binary experimental data from a narrow range of compositions. Also, structural analysis of the AIMD results based on radial distribution functions augmented with common-neighbor analysis and bond angle distributions reveal a strong tendency for icosahedral short range order for Ni-W and Ni-Re alloys. Finally, a new constant pressure methodology was added to the AIMD package that has allowed the efficient simulation of highly complex alloys, such as an eight component model of a RENE-N4 Ni-based superalloy.

关键词： Binary alloys

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Evaluating high performance computing systems at the Naval Research Laboratory

Evaluating high performance computing systems at the Naval R...

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Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Anderson, Wendell Osburn, Jeanie Rosenberg, Robert Lanzagorta, Marco Washington DC United States ITT Corp. Washington DC United States

ISBN: (纸本)0769530885

As a leading edge center within the high performance computing modernization program (hpcmp), the Center for Computational Science (CCS) of the Naval Research Laboratory evaluates new high performance computing (HPC) assets. The center is currently evaluating two systems - an Altix 3700 running the SUSE Linux Enterprise Server (SLES) 10 operating systems and a Cray XD1. With respect to the Altix system, Naval Research Laboratory is looking at applications requiring large memory and testing the new Intel 10.0 compilers. For the XD1, we are examining the applicability of dual core processors and Field programmable Gate Arrays (FPGAs) to HPC applications. © 2007 IEE.

关键词： Research laboratories

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Characterization of high altitude turbulence for air force platforms

Characterization of high altitude turbulence for air force p...

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Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Ruggiero, Frank H. Werne, Joe Mahalov, Alex Nichols, Basil Wroblewski, Donald E. Hanscom AFB MA United States NorthWest Research Associates Colorado Research Associates Division Boulder CO United States Arizona State University Tempe AZ United States Boston University Boston MA United States

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ISBN: (纸本)0769530885

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ezHPC: Adopting a program-wide, user-centered design approach to the ezHPC user interface

ezHPC: Adopting a program-wide, user-centered design approac...

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Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Baca, Julie Monceaux, Wes Rappold, Keith Duett, Patti Buchanan, Kimba Swillie, Scotty Browning, Glen Mississippi State University Mississippi State MS United States Vicksburg MS United States

ISBN: (纸本)0769530885

The Engineer Research and Development Center Major Shared Resource Center (ERDC MSRC) has been tasked by the Department of Defense (dod) high performance computing modernization program (hpcmp) to adopt a program-wide design for the development of the recently introduced ezHPC user interface. The purpose of ezHPC is to provide all hpcmp users intuitive, efficient access to high performance computing (HPC) resources needed in their regular course of work. At the core of user-centered design is an emphasis on fully understanding HPC users and their work environment, enabling support for user needs, not developer concerns, to drive the design process. Fulfilling this goal requires the use of a variety of methods from the field of usability engineering. For ezHPC, methods have included to date (1) inclusion of users as part of the design team, (2) a facilitated focus group session, (3) a usability walkthrough, (4) a usability evaluation, and (5) rapid prototyping. In adherence to user-centered design, a user group (UG) was formed to serve as participants in the design of the ezHPC software. ezHPC UG members participated in a recent workshop for the purpose of assessing and improving the usability of the program-wide version of ezHPC. Results are currently being used to guide the new design of the ezHPC interface using rapid prototyping. Prototypes are under development for regular reviews by the UG, followed by iterative refinement. This direct early involvement of users ensures more responsive, user-centered interfaces. Formal, large-scale usability evaluations are expected in the latter half of the software cycle. © 2007 IEEE.

关键词： User centered design

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Reconfigurable computing for high performance computing computational science

Reconfigurable computing for high performance computing comp...

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Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Song, Jun Park Henz, Brian Shires, Dale High Performance Computing Division Aberdeen Proving Ground MD United States

ISBN: (纸本)0769530885

Parallel computing systems with thousands of processors are now common and more affordable due to the focus on clustered commodity processors. However, both market and physical factors are converging that will limit the performance of these systems in the future. Hardware advances over the past several decades have been empirically observed with remarkable precision to obey Moore's law, predicting an increase in transistor density by about a factor of two every eighteen months. Maintaining these improvements has become problematic as power dissipation and other size-limiting factors become more pronounced at smaller feature size. Reconfigurable computing, or heterogeneous computing, is offering hope to the scientific computing community as a way to provide continued growth in computing capability. This paper discusses some of the hardware and software associated with this new technology. It also provides a discussion on the overall state of the technology for use by computational scientists. This is done by exploring a sample problem related to bit- and integer-based applications. © 2007 IEEE.

关键词： Reconfigurable architectures

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DOVIS: A tool for high-throughput virtual screening

DOVIS: A tool for high-throughput virtual screening

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Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Jiang, Xiaohui Kumar, Kamal Wallqvist, Anders Reifman, Jaques Telemedicine and Advanced Technology Research Center Ft. Detrick MD United States

ISBN: (纸本)0769530885

We developed a DOcking-based VIrtual Screening (DOVIS) pipeline to predict how small molecules may interact with a given protein, so that we can rank a large database of molecules based on their predicted affinities to the protein. We used the program AutoDock as the docking engine and OpenBabel as the molecular data model. We designed and implemented a novel parallelization scheme using a file-based inter-process communication protocol to control parallel jobs. A Web-server/Web-page architecture was developed based on the User Interface Toolkit (UIT) to manage DOVIS jobs on high performance computing (HPC) platforms and provide a Web-page-based graphical user interface (GUI). The DOVIS pipeline is running on JVN at the Army Research Laboratory (ARL) Major Shared Resource Center (MSRC). Scientists at several Department of Defense (dod) labs are currently using the DOVIS pipeline in their research projects. © 2007 IEEE.

关键词： Websites

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Memory leak detection in FORTRAN applications using TAU

Memory leak detection in FORTRAN applications using TAU

引用

Department of Defense - hpcmp users group conference 2007;high performance computing modernization program: A Bridge to Future Defense, dod hpcmp ugc

作者： Shende, Sameer Malony, Allen Moore, Shirley Cronk, David ParaTools Inc. Eugene OR United States Innovative Computing Laboratory University of Tennessee-Knoxville Knoxville TN United States

ISBN: (纸本)0769530885

There is a growing awareness that high-end performance evaluation and tuning requires holistic program analysis. In addition to CPU performance characterization, observation of memory, network, and input/output (I/O) performance can help to identify execution bottlenecks related to these factors. Correctness of memory and communication operations is also an issue and can affect performance indirectly. This paper describes extensions to the TAU performance system to incorporate direct source-level code instrumentation for tracking dynamic memory management in FORTRAN codes that use allocate and de-allocate statements. TAU's lightweight profiling can then generate a detailed report of memory usage including the sizes of memory blocks allocated and de-allocated with precise program attribution: variable name, source line number, and file name. We report on results and experiences in applying TAU to the PTURBO application. © 2007 IEEE.

关键词： FORTRAN (programming language)

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