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5th International Workshop on science Gateways, IWSG 2013

作者： De La Garza, Luis Krüger, Jens Schärfe, Charlotta Röttig, Marc Aiche, Stephan Reinert, Knut Kohlbacher, Oliver Applied Bioinformatics Group University of Tübingen Germany Department of Mathematics and Computer Science Freie Universität Berlin Berlin Germany International Max Planck Research School Computational Biology and Scientific Computing Berlin Germany Algorithms in Bioinformatics Freie Universität Berlin Berlin Germany

The Konstanz Information Miner is a user-friendly graphical workflow designer with a broad user base in industry and academia. Its broad range of embedded tools and its powerful data mining and visualization tools render it ideal for scientific workflows. It is thus used more and more in a broad range of applications. However, the free version typically runs on a desktop computer, restricting users if they want to tap into computing power. The grid and cloud User Support Environment is a free and open source project created for parallelized and distributed systems, but the creation of workflows with the included components has a steeper learning curve. In this work we suggest an easy to implement solution combining the ease-of-use of the Konstanz Information Miner with the computational power of distributed computing infrastructures. We present a solution permitting the conversion of workflows between the two platforms. This enables a convenient development, debugging, and maintenance of scientific workflows on the desktop. These workflows can then be deployed on a cloud or grid, thus permitting large-scale computation. To achieve our goals, we relied on a Common Tool Description XML file format which describes the execution of arbitrary programs in a structured and easily readable and parseable way. In order to integrate external programs into we employed the Generic KNIME Nodes extension.

关键词： Miners

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Erratum to: Measurement of the inclusive jet cross-section in proton-proton collisions at s = 7 TeV using 4.5 fb −1 of data with the ATLAS detector

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Journal of High Energy Physics 2015年第9期2015卷 1-39页

作者： G. Aad B. Abbott J. Abdallah S. Abdel Khalek O. Abdinov R. Aben B. Abi M. Abolins O. S. AbouZeid H. Abramowicz H. Abreu R. Abreu Y. Abulaiti B. S. Acharya L. Adamczyk D. L. Adams J. Adelman S. Adomeit T. Adye T. Agatonovic-Jovin J. A. Aguilar-Saavedra M. Agustoni S. P. Ahlen F. Ahmadov G. Aielli H. Akerstedt T. P. A. Åkesson G. Akimoto A. V. Akimov G. L. Alberghi J. Albert S. Albrand M. J. Alconada Verzini M. Aleksa I. N. Aleksandrov C. Alexa G. Alexander G. Alexandre T. Alexopoulos M. Alhroob G. Alimonti L. Alio J. Alison B. M. M. Allbrooke L. J. Allison P. P. Allport J. Almond A. Aloisio A. Alonso F. Alonso C. Alpigiani A. Altheimer B. Alvarez Gonzalez M. G. Alviggi K. Amako Y. Amaral Coutinho C. Amelung D. Amidei S. P. Amor Dos Santos A. Amorim S. Amoroso N. Amram G. Amundsen C. Anastopoulos L. S. Ancu N. Andari T. Andeen C. F. Anders G. Anders K. J. Anderson A. Andreazza V. Andrei X. S. Anduaga S. Angelidakis I. Angelozzi P. Anger A. Angerami F. Anghinolfi A. V. Anisenkov N. Anjos A. Annovi A. Antonaki M. Antonelli A. Antonov J. Antos F. Anulli M. Aoki L. Aperio Bella R. Apolle G. Arabidze I. Aracena Y. Arai J. P. Araque A. T. H. Arce J-F. Arguin S. Argyropoulos M. Arik A. J. Armbruster O. Arnaez V. Arnal H. Arnold M. Arratia O. Arslan A. Artamonov G. Artoni S. Asai N. Asbah A. Ashkenazi B. Åsman L. Asquith K. Assamagan R. Astalos M. Atkinson N. B. Atlay B. Auerbach K. Augsten M. Aurousseau G. Avolio G. Azuelos Y. Azuma M. A. Baak A. Baas C. Bacci H. Bachacou K. Bachas M. Backes M. Backhaus J. Backus Mayes E. Badescu P. Bagiacchi P. Bagnaia Y. Bai T. Bain J. T. Baines O. K. Baker P. Balek F. Balli E. Banas Sw. Banerjee A. A. E. Bannoura V. Bansal H. S. Bansil L. Barak S. P. Baranov E. L. Barberio D. Barberis M. Barbero T. Barillari M. Barisonzi T. Barklow N. Barlow B. M. Barnett R. M. Barnett Z. Barnovska A. Baroncelli G. Barone A. J. Barr F. Barreiro J. Barreiro Guimarães da Costa R. Bartoldus A. E. Barton P. Bartos V. Bartsch A. Bassalat A. Basye R. L. Bates J. R. Batley M. Battaglia M. Battistin F. Bauer H CPPM Aix-Marseille Université and CNRS/IN2P3 Marseille France Homer L. Dodge Department of Physics and Astronomy University of Oklahoma Norman United States Institute of Physics Academia Sinica Taipei Taiwan LAL Université Paris-Sud and CNRS/IN2P3 Orsay France Institute of Physics Azerbaijan Academy of Sciences Baku Azerbaijan Nikhef National Institute for Subatomic Physics and University of Amsterdam Amsterdam Netherlands Department of Physics Oklahoma State University Stillwater United States Department of Physics and Astronomy Michigan State University East Lansing United States Department of Physics University of Toronto Toronto Canada Raymond and Beverly Sackler School of Physics and Astronomy Tel Aviv University Tel Aviv Israel Department of Physics Technion: Israel Institute of Technology Haifa Israel CERN Geneva Switzerland Department of Physics Stockholm University Stockholm Sweden The Oskar Klein Centre Stockholm Sweden INFN Gruppo Collegato di Udine Sezione di Trieste Udine Italy ICTP Trieste Italy Department of Physics King’s College London London United Kingdom AGH University of Science and Technology Faculty of Physics and Applied Computer Science Krakow Poland Physics Department Brookhaven National Laboratory Upton United States Department of Physics Yale University New Haven United States Fakultät für Physik Ludwig-Maximilians-Universität München München Germany Particle Physics Department Rutherford Appleton Laboratory Didcot United Kingdom Institute of Physics University of Belgrade Belgrade Serbia Laboratorio de Instrumentacao e Fisica Experimental de Particulas - LIP Lisboa Portugal Departamento de Fisica Teorica y del Cosmos and CAFPE Universidad de Granada Granada Spain Albert Einstein Center for Fundamental Physics and Laboratory for High Energy Physics University of Bern Bern Switzerland Department of Physics Boston University Boston United States Joint Institute for Nuclear Research JINR Dubna Dubna Russia INFN

It was found that the non-perturbative corrections calculated using Pythia with the Perugia 2011 tune did not include the effect of the underlying event. The affected correction factors were recomputed using the Pythia 6.427 generator. These corrections are applied as baseline to the NLO pQCD calculations and thus the central values of the theoretical predictions have changed by a few percent with the new corrections. This has a minor impact on the agreement between the data and the theoretical predictions. Figures 2 and 6 to 13, and all the tables have been updated with the new values. A few sentences in the discussion in sections 5.2 and 9 were altered or removed.

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Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

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Human genomics 2016年第1期10 Suppl 1卷 12页

作者： A. K. Srivastava Y. Wang R. Huang C. Skinner T. Thompson L. Pollard T. Wood F. Luo R. Stevenson R. Polimanti J. Gelernter X. Lin I. Y. Lim Y. Wu A. L. Teh L. Chen I. M. Aris S. E. Soh M. T. Tint J. L. MacIsaac F. Yap K. Kwek S. M. Saw M. S. Kobor M. J. Meaney K. M. Godfrey Y. S. Chong J. D. Holbrook Y. S. Lee P. D. Gluckman N. Karnani A. Kapoor D. Lee A. Chakravarti C. Maercker F. Graf M. Boutros G. Stamoulis F. Santoni P. Makrythanasis A. Letourneau M. Guipponi N. Panousis M. Garieri P. Ribaux E. Falconnet C. Borel S. E. Antonarakis S. Kumar J. Curran J. Blangero S. Chatterjee J. Akiyama D. Auer C. Berrios L. Pennacchio T. R. Donti G. Cappuccio M. Miller P. Atwal A. Kennedy A. Cardon C. Bacino L. Emrick J. Hertecant F. Baumer B. Porter M. Bainbridge P. Bonnen B. Graham R. Sutton Q. Sun S. Elsea Z. Hu P. Wang Y. Zhu J. Zhao M. Xiong David A. Bennett A. Hidalgo-Miranda S. Romero-Cordoba S. Rodriguez-Cuevas R. Rebollar-Vega E. Tagliabue M. Iorio E. D’Ippolito S. Baroni B. Kaczkowski Y. Tanaka H. Kawaji A. Sandelin R. Andersson M. Itoh T. Lassmann Y. Hayashizaki P. Carninci A. R. R. Forrest C. A. Semple E. A. Rosenthal B. Shirts L. Amendola C. Gallego M. Horike-Pyne A. Burt P. Robertson P. Beyers C. Nefcy D. Veenstra F. Hisama R. Bennett M. Dorschner D. Nickerson J. Smith K. Patterson D. Crosslin R. Nassir N. Zubair T. Harrison U. Peters G. Jarvik F. Menghi K. Inaki X. Woo P. Kumar K. Grzeda A. Malhotra H. Kim D. Ucar P. Shreckengast K. Karuturi J. Keck J. Chuang E. T. Liu B. Ji A. Tyler G. Ananda G. Carter H. Nikbakht M. Montagne M. Zeinieh A. Harutyunyan M. Mcconechy N. Jabado P. Lavigne J. Majewski J. B. Goldstein M. Overman G. Varadhachary R. Shroff R. Wolff M. Javle A. Futreal D. Fogelman L. Bravo W. Fajardo H. Gomez C. Castaneda C. Rolfo J. A. Pinto K. C. Akdemir L. Chin S. Patterson C. Statz S. Mockus S. N. Nikolaev X. I. Bonilla L. Parmentier B. King F. Bezrukov G. Kaya V. Zoete V. Seplyarskiy H. Sharpe T. McKee K. Popadin N. Basset-Seguin R. Ben Chaabene M. Andrianova C. Verdan K. Grosdemange O. Sumara M. E JCSRI Greenwood Genetic Center Greenwood USA School of Computing Clemson University Clemson USA Biochemical Genetics Laboratory Greenwood Genetic Center Greenwood USA Department Psychiatry Yale Sch Med and VA CT Healthcare Center West Haven USA Department Genetics Yale Sch Med and VA CT Healthcare Center West Haven USA Department Neurobiology Yale Sch Med and VA CT Healthcare Center West Haven USA Singapore Institute for Clinical Sciences Singapore Singapore National University of Singapore Singapore Singapore University of British Columbia Vancouver Canada KK Women’s and Children’s Hospital Singapore Singapore University of Southampton and University Hospital Southampton NHS Foundation Trust Southampton UK University of Auckland Auckland New Zealand McKusick-Nathans Institute of Genetic Medicine Johns Hopkins University School of Medicine Baltimore USA Esslingen University of Applied Sciences Esslingen Germany German Cancer Research Center Heidelberg Germany Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Geneva University Hospitals-HUG Service of Genetic Medicine Geneva Switzerland GE3 Institute of Genetics and Genomics of Geneva University of Geneva Medical School Geneva Switzerland South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Edinburg USA South Texas Diabetes and Obesity Institute School of Medicine University of Texas Rio-Grande Valley Brownsville USA Institute of Genetic Medicine Johns Hopkins University Baltimore USA Genomics Division Lawrence Berkeley National Laboratory Berkeley USA Molecular and Human Genetics Baylor College of Medicine Houston USA Department of Translational Medical Sciences Federico II University Naples Italy Metabolon Inc Durham USA Section of Pediatric Neurology and Neuroscience Baylor College of Medicine Houston USA Tawam Hospital Abu Dhabi United Arab Emirates Stanford Medical School Stanford USA Sch

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s

关键词： Pulmonary Arterial Hypertension Oral Squamous Cell Carcinoma Deep Neural Network Autosomal Recessive Polycystic Kidney Disease Whole Genome Bisulfite Sequencing

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Using a low-cost open source hardware development platform in teaching young students programming skills 13

Using a low-cost open source hardware development platform i...

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2013 13th ACM SIGITE Annual Conference on Information Technology Education, SIGITE 2013

作者： Hill, Lawrence Ciccarelli, Steven Information Sciences and Technologies Department Golisano College of Computing and Information Sciences Rochester Institute of Technology 102 Lomb Memorial Drive Rochester NY 14623-5603 United States Electrical Computer and Telecommunications Technology Department College of Applied Science and Technology Rochester Institute of Technology 78 Lomb Memorial Drive Rochester NY 14623-5604 United States

ISBN: (纸本)9781450322393

The teaching of programming skills to young students is often described by those educators involved as problematic at best. Student issues like mathematical maturity, readiness for complex thought, basic problem solving skills, short attention span especially related to the boredom of traditional programming teaching methodologies, and the lack of exciting problems and their solutions with respect to programming assignments contribute to the angst of many a programming instructor. A small fraction of students who "were just made for programming" always seem to succeed at whatever programming problem is given to them. However, a majority of students, especially precollege and college freshmen tend to have difficulty in overcoming these issues. It is with that observation that something new, in terms of programming pedagogy, needed to be investigated by this paper's authors. An ideal opportunity requiring successful programming instruction for 7-12 graders in the local metropolitan area presented itself in the winter of 2012. The students were involved in a statewide competition where groups of students self-selected into project options offered by various sponsoring institutions. Under the "Technology" choice heading of the state program, the student team and the instructor agreed to program a microprocessor to send messages in International Morse Code. The object of the exercise was to learn basic programming skills and to apply them to solving a problem. The hook was to do something brand new the students had never engaged in, keeping their attention on the end goal, and to see the immediate real-time results of some programming effort along the development cycle as the completed final program took form. The effort was a resounding success;the students learned in a few Saturday morning sessions more about programming than the authors have experienced over weeks of effort in traditional programming classes at the college freshman level. © 2013 ACM.

关键词： Students

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Bonding and Structure of Ceramic-Ceramic Interfaces

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Physical Review Letters 2013年第6期111卷 066103-066103页

作者： Kohei Shimamura Fuyuki Shimojo Rajiv K. Kalia Aiichiro Nakano Priya Vashishta Collaboratory for Advanced Computing and Simulations Department of Physics and Astronomy Department of Computer Science Department of Chemical Engineering and Materials Science University of Southern California Los Angeles California 90089-0242 USA Department of Physics Kumamoto University Kumamoto 860-8555 Japan Department of Applied Quantum Physics and Nuclear Engineering Kyushu University Fukuoka 819-0395 Japan

Quantum molecular dynamics simulations of α−Al2O3(0001)/3C−SiC(111) interfaces reveal profound effects of thermal annealing for producing strong interfaces consisting solely of cation-anion bonds and their consequence on interfacial structures. A Si-terminated SiC surface and Al2O3 form a stronger interface (Si-interface) with a Si-O bond density of 12.2 nm−2, whereas the C interface has an Al-C bond density of 9.46 nm−2. The interfacial bond strengthening is accompanied by the formation of an Al2O3 interphase with a thickness of 2–8 Å. Such atomistic understanding may help rational interfacial design of high-temperature ceramic composites for broad applications such as power generation systems.

关键词： MOLECULAR dynamics ANNEALING of metals INTERFACIAL bonding CERAMIC materials TRANSMISSION electron microscopes SILICON carbide

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Corrigendum to “A novel approach to collaborative testing in a crowdsourcing environment” in the Journal of Systems and Software 86 (2013) 2143–2153

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Journal of Systems and Software 2014年 87卷 137-137页

作者： Yuan-Hsin Tung Shian-Shyong Tseng Wei-Tek Tsai Department of Computer Science and Information Engineering National Chiao Tung University Taiwan ROC Telecommunication Laboratory Chunghwa Telecom Co. Ltd. Taiwan ROC Department of Applied Informatics and Multimedia Asia University Taiwan ROC School of Computing Informatics and Decision Systems Engineering Arizona State University Tempe AZ USA

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Systematic Reduction of Data Movement in Algebraic Multigrid Solvers

Systematic Reduction of Data Movement in Algebraic Multigrid...

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IEEE International Symposium on Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Hormozd Gahvari William Gropp Kirk E. Jordan Martin Schulz Ulrike Meier Yang Department of Computer Science University of Illinois at Urbana-Champaign Urbana IL Computational Science Center IBM TJ Watson Research Center Cambridge MA Center for Applied Scientific Computing Lawrence Livermore National Laboratory Livermore CA

ISBN: (纸本)9781479913725

Algebraic Multigrid (AMG) solvers find wide use in scientific simulation codes. Their ideal computational complexity makes them especially attractive for solving large problems on parallel machines. However, they also involve a substantial amount of data movement, posing challenges to performance and scalability. In this paper, we present an algorithm that provides a systematic means of reducing data movement in AMG. The algorithm operates by gathering and redistributing the problem data to reduce the need to move it on the communication-intensive coarse grid portion of AMG. The data is gathered in a way that ensures data locality by keeping data movement confined to specific regions of the machine. Any decision to gather data is made systematically through the means of a performance model. This approach results in substantial speedups on a multicore cluster when using AMG to solve a variety of test problems.

关键词： Switches Interpolation Computational modeling Data models Bandwidth Multicore processing Heuristic algorithms

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An analysis of replication and retrieval of medical image data using a database management system and a distributed file system

An analysis of replication and retrieval of medical image da...

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IEEE Symposium on computers and Communications (ISCC)

作者： Elias Amaral Santos Eros Comunello Douglas D.J. de Macedo Miriam A.M. Capretz Thiago Coelho Prado M.A.R. Dantas Master of Science in Applied Computing University of Itajai Valley (UNIVALI) Itajaí SC Brazil Informatics and Statistic Department Federal University of Santa Catarina (UFSC) Florianopolis SC Brazil Department of Electrical and Computer Engineering Western University London ON Canada

This paper presents a research study consisting of a comparison analysis of replication and retrieval of medical image data which use the Digital Imaging and Communications in Medicine (DICOM) standard. These data are stored in a relational database management system (RDBMS) and in the Hierarchical Data Format (HDF) using a distributed file system as a data backend. The importance of this work was measured by verification of elapsed-time reduction for medical image data replication and retrieval in a real telemedicine environment.

关键词： Arrays Angiography DICOM Indexes US department of Defense

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Performance Analysis of the Lattice Boltzmann Model Beyond Navier-Stokes

Performance Analysis of the Lattice Boltzmann Model Beyond N...

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International Symposium on Parallel and Distributed Processing (IPDPS)

作者： Amanda Peters Randles Vivek Kale Jeff Hammond William Gropp Efthimios Kaxiras School of Engineering and Applied Sciences Harvard University Cambridge MA USA Department of Computer Science University of Illinois Urbana-Champaign Urbana IL USA Leadership Computing Facility Argonne National Laboratory Argonne IL USA

ISBN: (纸本)9781467360661

The lattice Boltzmann method is increasingly important in facilitating large-scale fluid dynamics simulations. To date, these simulations have been built on discretized velocity models of up to 27 neighbors. Recent work has shown that higher order approximations of the continuum Boltzmann equation enable not only recovery of the Navier-Stokes hydrodynamics, but also simulations for a wider range of Knudsen numbers, which is especially important in micro- and nanoscale flows. These higher-order models have significant impact on both the communication and computational complexity of the application. We present a performance study of the higher-order models as compared to the traditional ones, on both the IBM Blue Gene/P and Blue Gene/Q architectures. We study the tradeoffs of many optimizations methods such as the use of deep halo level ghost cells that, alongside hybrid programming models, reduce the impact of extended models and enable efficient modeling of extreme regimes of computational fluid dynamics.

关键词： Computational modeling Lattices Mathematical model Bandwidth computer architecture Optimization Load modeling

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Training sessions in a Master degree “Informatics as a Second Competence”

Training sessions in a Master degree “Informatics as a Seco...

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IEEE Education Engineering (EDUCON)

作者： Agathe Merceron Jean-Michel Adam Daniel Bardou Jerome David Sergio Lujan-Mora Marek Milosz Media Informatics department Beuth University of Applied Sciences Berlin Germany Department of Software and Computing Systems University of Alicante Alicante Spain Laboratory of Informatics of Grenoble Pierre Mendes France University Grenoble France Institute of Computer Science Lublin University of Technology Lublin Poland

The ERAMIS acronym stands for European-Russian-Central Asian Network of Master's degrees “Informatics as a Second Competence”. The aim of this project is to create a Master degree “computer science as a Second Competence” in 9 beneficiary universities located in Kazakhstan, Kirghizstan and Russia. One crucial aspect of the project is training. In this contribution we describe how training sessions have been organized, the pedagogical issues that are involved and ways to address them.

关键词： Educational institutions Training Data models Data mining Databases computer science

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