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High performance computing workflow for protein functional annotation 13

High performance computing workflow for protein functional a...

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conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013

作者： Stanberry, Larissa Rekepalli, Bhanu Giblock, Paul Liu, Yuan Higdon, Roger Broomall, William DELSA Global 1900 9th Ave C9S-9 Seattle WA 98101 United States Oak Ridge National Laboratory Joint Institute for Computational Sciences University of Tennessee ǍŞ United States High-Throughput Analysis Core SCRI DELSA Global United States

ISBN: (纸本)9781450321709

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the PSU (Protein Sequence Universe) expands exponentially. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. the rate of data generation has far surpassed that of protein annotation. the volume of protein data makes manual curation infeasible whereas a high compute cost limits the utility of existing automated approaches. In this study, we built an automated workflow to enable large-scale protein annotation into existing orthologous groups using HPC (High Performance computing) architectures. We developed a low complexity classification algorithm to assign proteins into bacterial COGs (Clusters of Orthologous Groups of proteins). Based on the PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool), the algorithm was validated on simulated and archaeal data to ensure at least 80% specificity and sensitivity. the workflow with highly scalable parallel applications for classification and sequence alignment was developed on XSEDE (Extreme Science and Engineering Discovery Environment) supercomputers. Using the workflow, we have classified one million newly sequenced bacterial proteins. With the rapid expansion of the PSU, the proposed workflow will enable scientists to annotate big genome data. © 2013 by the Association for computing Machinery, Inc.

关键词： Proteins

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Medical software - Issues and best practices

Medical software - Issues and best practices

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9th international conference on distributed computing and Internet Technology, ICDCIT 2013

作者： Jetley, Raoul Sudarsan, Sithu Sampath, R. Ramaswamy, Srini Industrial Software Systems ABB Corporate Research Bangalore India Device Security Assurance Center India Development Center ABB Corporate Research Bangalore India CEO BeWo Technologies Chennai India

ISBN: (纸本)9783642360701

Introduction: the design and functional complexity of medical software has increased during the past 50 years, evolving from the use of a metronome circuit for the initial cardiac pacemaker to functions that include electrocardiogram (EKG) analysis, laser surgery, and networked systems for monitoring patients across various healthcare environments. Software has become ubiquitous in healthcare applications, as is evident from its prevalent use for controlling medical devices, maintaining electronic patient health data, and enabling healthcare information technology (HIT) systems. As the software functionality becomes more intricate, concerns arise regarding efficacy, safety and reliability. It thus becomes imperative to adopt an approach or methodology based on best engineering practices to ensure that the possibility of any defect or malfunction in these devices is minimized. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Application programs

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Graphical Programming and Program Correctness Proof

Graphical Programming and Program Correctness Proof

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9th international conference on Computer Science and Information technologies (CSIT)

作者： Velbitskiy, Igor V. Glushkovs Fund UA-01001 Kiev Ukraine

ISBN: (纸本)9781479924608

the next generation visual programming technology (VTR), which uses so-called R-charts (ISO/IEC 8631) is defined here. R-charts - are being the oriented graphs loaded through the arcs. the main difference of VTR is its simplicity and single graphic form of the program writing during its entire life cycle, which ensures new principles of design, debugging, visual and compact (by more than one order) writing compared to writing in existing programming languages (PL). Due to its simplicity, it is acceptable to broad circle of the specialists, but not only to the programmers. Graphic paradigm of VTR is set, which is based on a single graphical shell for all existing PLs without goto, if, for, while, break, labels, brackets: begin-end, {-} etc. Evidentiary, linguistic, parallel, three-and multidimensional programming is introduced for controlling and computing systems. Colour is used extensively for writing of graphic programs. It is integrated well with available programming systems. At present, graphic programming VTR is realized in the environment Qt Creator C++ (***). this allowed carrying out justified analysis of VTR advantages in comparison with traditional technologies that use modern PLs, UML, and OOP.

关键词： use only of graphs during the entire program life cycle programming without goto, if, for, while, labels, brackets begin-end, {-} etc. use of colour programming of special processors - linguistic, control, parallel, three-dimensional, multi-dimensional etc. program correctness proof

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Topic 6: Grid, Cluster and Cloud computing (Introduction)

Topic 6: Grid, Cluster and Cloud Computing (Introduction)

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19th international conference on Euro-Par

作者： Laure, Erwin Kao, Odej Badia, Rosa M. Lefevre, Laurent Di Martino, Beniamino Prodan, Radu Turilli, Matteo Warneke, Daniel KTH Royal Institute of Technology Sweden Technische Universität Berlin Germany Barcelona Supercomputing Center CSIC Spain INRIA University of Lyon France Seconda Universitá di Napoli Italy University of Innsbruck Austria University of Oxford United Kingdom International Computer Science Institute Berkeley United States

ISBN: (纸本)9783642400476

Grid and cloud computing have changed the IT landscape in the way we access and manage IT infrastructures. the use of computing resources has become essential for many applications in various areas. Both technologies provide easyto- use and on-demand access to large-scale infrastructures. the high number of submissions to “Topic 6: Grid, Cluster and Cloud computing-reflected the importance of the research area. the papers addressed key challenges regarding design, deployment, operation and use of Grid and cloud infrastructures. Moreover, several innovative algorithms and methods for fundamental capabilities and services that are required in a heterogeneous environment, such as adaptability, scalability, reliability and security, and to support applications as diverse as ubiquitous local services, enterprise-scale virtual organizations, and internet-scale distributed supercomputing were proposed. Finally, many experimental evaluations and use-cases delivered an insight into the deployment in real-world scenarios and showed interesting future application domains. Each submission was reviewed by at least four reviewers and, finally, we were able to select nine high-quality papers. the papers were grouped in four sessions that are briefly summarized in following.

关键词： Cluster computing

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A parallel 2-approximation NC-algorithm for range assignment problem in packet radio networks

A parallel 2-approximation NC-algorithm for range assignment...

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9th international conference on distributed computing and Internet Technology, ICDCIT 2013

作者： Bhatta, Bijaya Kishor Shetty, D. Pushparaj School of Math.-Stat-Computer Science Utkal University Bhubaneswar 751004 India Computer Science and Application Group Department of Mathematics Indian Institute of Technology Delhi Hauz Khas New Delhi 110016 India

ISBN: (纸本)9783642360701

Given a set of sensors in a plane or in higher dimension, the strong minimum energy topology problem is to assign transmission range to each of the sensor nodes, so as to minimize the total power consumption. Here the constraint is that the network must be strongly connected. this problem is known to be NP-hard. As this problem has lot of practical application, several approximation algorithms and heuristics has been proposed. there exist a MST based 2-approximation algorithm for this problem having running time complexity of O(n 2 logn). In this paper we propose a simple parallel version of the 2-approximation algorithm. We prove that this parallel algorithm is a NC-algorithm and is also cost optimal for a dense graph. We prove that the algorithm has a time complexity O(logn) and work complexity O(n 2) when the number of processor used is O(n 2). © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Approximation algorithms

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MPI parallel implementation of 3D object categorization using spin-images

MPI parallel implementation of 3D object categorization usin...

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作者： Eleliemy, A. Hegazy, D. Elkilani, Wail S. Computers Systems Department Ain Shams University Egypt

ISBN: (纸本)9781479933709

Object recognition and categorization are two important key features of computer vision. Accuracy aspects represent research challenge fo r both object recognition and categorization techniques. High performance computing (HPC) technologies usually manage the increasing time and complexity of computations. In this paper, a new approach that use 3D spin-images for 3D object categorization is introduced. the main contribution of our approach i s that it employs the MPI techniques in a unique way to extract spin-images. the technique proposed utilizes the independence between spin-images generated at each point. Time estimation of our technique ha ve shown dramatic decrease of the categorization time proportional to number of workers used. © 2013 IEEE.

关键词： Object recognition

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the use of distributed version control systems in advanced programming courses 9

The use of distributed version control systems in advanced p...

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9th international conference on Information and Communication technologies in Education, Research and Industrial applications: Integration, Harmonization and Knowledge Transfer, ICTERI 2013

作者： Cochez, Michael Isomöttönen, Ville Tirronen, Ville Itkonen, Jonne Jyväskylä40014 Finland

Version Control Systems are essential tools in software development. Educational institutions offering education to future computer scientists should embed the use of such systems in their curricula in order to prepare the student for real life situations. the use of a version control system also has several potential benefits for the teacher. the teacher might, for instance, use the tool to monitor students' progress and to give feedback efficiently. this study analyzes how students used the distributed version control system Git in advanced programming related *** also have data from a second year course, which enables us to compare between introductory level and master's level *** found out that students do not use the system in an optimal way;they do not commit changes often enough and regard the version control system as file storage. they also often write commitmessages which are meaningless. Further, it seems that in group work settings there is usually one dominant user of the system.

关键词： Students

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Impact of mediating technologies on talk and emotion: Questioning “commonsense”

Impact of mediating technologies on talk and emotion: Questi...

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international conference on Collaborative computing: Networking, applications and Worksharing (CollaborateCom)

作者： Joon-Suk Lee Deborah Tatar Dept. of Computer Science Virginia State University Petersburg VA USA Dept. of Computer Science Virginia Tech Blacksburg VA USA

Much CSCW research predominantly focuses on investigating how distributed, mediated interactions are different from collocated interactions, but rarely looks at how the use of technologies affect collocated people. We argue that the needs for studying the impact of mediating technologies among collocated people are current and large. A situation of seeing the other but not being able to see what captures his/her attention is endemic. In this paper, we investigate collocated triads as they play a collaborative, problem-solving game on laptops, on tablets or on a shared paper. People's positive emotion rose more when they talked about the complex relationships of the puzzle specifics and added new perspectives to other people's contributions during the game. People in computer conditions talked less about the specifics on the game board than people in the paper condition, but only people in the laptop condition experienced a significant decrease in positive emotion.

关键词： Games Portable computers Atmospheric measurements Particle measurements Collaboration Problem-solving

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Seeds for a heterogeneous interconnect

Seeds for a heterogeneous interconnect

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2013 IEEE 37th Annual Computer Software and applications conference, COMPSAC 2013

作者： Hackett, Adam Ajwani, Deepak Ali, Shoukat Kirkland, Steve Morrison, John P. Hamilton Institute National University of Ireland Maynooth Ireland Exascale Systems Group IBM Research Ireland Centre for Unified Computing University College Cork Ireland Industrial Mathematics and Operations Research Group Emerging Computing Technologies Bell Laboratories Ireland

ISBN: (纸本)9780769549798

Traditionally, a parallel application is partitioned, mapped and then routed on a network of compute nodes where the topology of the interconnection network is known beforehand and is homogeneous. However, such homogeneity in interconnects is rarely required or needed for several important classes of applications. Nevertheless such interconnects are designed this way, i.e., with redundant links, to accommodate the communication patterns of a wide range of applications. However, with recent advances in technology for optical circuit switches, it is now possible to construct network with much fewer links, and to make the link endpoints configurable to suit the communication pattern of a given application. While this is economical (saving both links and the power to run them), it raises the difficult problem of how to configure the network and how to reconfigure it quickly when the application's communication pattern changes. Since the space of all configurable topologies is large and determining the quality of a topology is a time-consuming process, it is not feasible to explore the entire space. One way of dealing with this limitation is to start the search from a "good" initial topology and then conduct a restricted search around it. the success of such a strategy crucially depends on the choice of the initial or seed topology. In the past, such an initial topology was computed by mimicking the communication requirements of the application. In this paper, we propose a different approach by showing that interconnect topologies such as chordal rings(circulant graphs) chosen based on metrics such as bisection width and average shortest path length can provide a better starting point. the topology obtained by searching around such an initial topology provides almost as good a performance as an application-specific initial topology, and the search time is significantly reduced. © 2013 IEEE.

关键词： Interconnection networks (circuit switching)

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Efficient position sharing for location privacy using binary space partitioning 9th

Efficient position sharing for location privacy using binary...

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9th international conference on Mobile and Ubiquitous Systems: computing, Networking and Services, MobiQuitous 2012

作者： Wernke, Marius Dürr, Frank Rothermel, Kurt Institute of Parallel and Distributed Systems Universitätsstraße 38 Stuttgart70569 Germany

ISBN: (纸本)9783642402371

Millions of users use location-based applications (LBAs) to share their positions with friends, request information from points of interest finders, or get notifications from event finders, etc. Such LBAs are typically based on location servers (LSs) managing mobile object positions in a scalable fashion. However, storing precise user positions on LSs raises privacy concerns, in particular, if LS providers are non-trusted. To solve this problem, we present PShare-BSP, a novel approach for the secure management of private user positions on non-trusted LSs. PShare-BSP splits up precise user positions into position shares and distributes them to different LSs of different providers. thus, a compromised provider only reveals user positions with degraded precision. Nevertheless, LBAs can combine several shares from different LSs to increase their precision. PShare-BSP improves on our previous position sharing approaches [4,15,17]: It uses a deterministic share generation approach based on binary space partitioning to avoid probabilistic attacks based, for instance, on Monte Carlo simulations. Moreover, it significantly decreases the computational complexity and increases the efficiency by reducing the update costs for succeeding position updates. © Institute for Computer Sciences, Social Informatics and Telecommunications Engineering 2013.

关键词： Location

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