WorldWideScience

Sample records for genome atlas program

  1. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  2. ATLAS forward physics program

    CERN Document Server

    HELLER, M; The ATLAS collaboration

    2010-01-01

    The variety of forward detectors installed in the vicinity of the ATLAS experiment allows to look over a wide range of forward physics topics. They ensure a good information about rapidity gaps, and the installation of very forward detectors (ALFA and AFP) will allow to tag the leading proton(s) remaining from the different processes studied. Most of the studies have to be done at low luminosity to avoid pile-up, but the AFP project offers a really exiting future for the ATLAS forward physics program. We also present how these forward detectors can be used to measure the relative and absolute luminosity.

  3. The ATLAS Forward Physics Program

    CERN Document Server

    Pinfold, J L

    2009-01-01

    The ATLAS forward physics program is discussed in the light of the future detector upgrades under study. These developments will enhance the overall physics potential of the experiment. The physics topics presented include: luminosity determination using the LUCID and ALFA detectors; diffractive measurements that should be possible with early data; and, the AFP project which plans to deploy proton taggers at 220 and 420 m from the ATLAS IP. The AFP program includes such physics topics as hard diffraction; diffractive Higgs production,two photon physics; and, new physics in the forward region.

  4. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  5. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  6. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  7. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  8. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  9. Programs | Office of Cancer Genomics

    Science.gov (United States)

    OCG facilitates cancer genomics research through a series of highly-focused programs. These programs generate and disseminate genomic data for use by the cancer research community. OCG programs also promote advances in technology-based infrastructure and create valuable experimental reagents and tools. OCG programs encourage collaboration by interconnecting with other genomics and cancer projects in order to accelerate translation of findings into the clinic. Below are OCG’s current, completed, and initiated programs:

  10. The Education and Outreach Program of ATLAS

    CERN Multimedia

    Barnett, M.

    2006-01-01

    The ATLAS Education and Outreach (E&O) program began in 1997, but the advent of LHC has placed a new urgency in our efforts. Even a year away, we can feel the approaching impact of starting an experiment that could make revolutionary discoveries. The public and teachers are beginning to turn their attention our way, and the newsmedia are showing growing interest in ATLAS. When datataking begins, the interest will peak, and the demands on us are likely to be substantial. The collaboration is responding to this challenge in a number of ways. ATLAS management has begun consultation with experts. The official budget for the E&O group has been growing as have the contributions of many ATLAS institutions. The number of collaboration members joining these efforts has grown, and their time and effort is increasing. We are in ongoing consultation with the CERN Public Affairs Office, as well as the other LHC experiments and the European Particle Physics Outreach Group. The E&O group has expanded the scope...

  11. Methods for visual mining of genomic and proteomic data atlases.

    Science.gov (United States)

    Boyle, John; Kreisberg, Richard; Bressler, Ryan; Killcoyne, Sarah

    2012-04-23

    As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations

  12. Methods for visual mining of genomic and proteomic data atlases

    Directory of Open Access Journals (Sweden)

    Boyle John

    2012-04-01

    Full Text Available Abstract Background As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing. Results This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas and the genomic characterization of cancer (The Cancer Genome Atlas. Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types. Conclusions The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make

  13. Human genome. 1993 Program report

    Energy Technology Data Exchange (ETDEWEB)

    1994-03-01

    The purpose of this report is to update the Human Genome 1991-92 Program Report and provide new information on the DOE genome program to researchers, program managers, other government agencies, and the interested public. This FY 1993 supplement includes abstracts of 60 new or renewed projects and listings of 112 continuing and 28 completed projects. These two reports, taken together, present the most complete published view of the DOE Human Genome Program through FY 1993. Research is progressing rapidly toward 15-year goals of mapping and sequencing the DNA of each of the 24 different human chromosomes.

  14. Follicular cell thyroid neoplasia: insights from genomics and The Cancer Genome Atlas research network.

    Science.gov (United States)

    Giordano, Thomas J

    2016-01-01

    The present review is focused on the recently published study on the genomics of papillary thyroid carcinoma performed by The Cancer Genome Atlas Research Network and its implications for the follicular variant of papillary carcinoma. The Cancer Genome Atlas study of papillary thyroid carcinoma comprehensively examined the cancer genome of nearly 500 primary tumors. Using a highly integrated bioinformatic analysis, papillary carcinoma was shown at the genomic level to consist of two highly distinct classes that reflected both tumor histology and underlying genotype. Tumors with true papillary architecture were dominated by BRAF(V600E) mutations and RET kinase fusions and were designated as BRAF(V600E)-like. Tumors with follicular architecture were conversely dominated by RAS mutations and were designated as RAS-like. Given the strong genotype:phenotype correlation known to be present in thyroid cancer, the separation of BRAF(V600E)-like and RAS-like tumors has profound implications for its classification, especially the follicular variant of papillary carcinoma. The recent genomic characterization of papillary thyroid carcinoma is challenging the established pathological classification of thyroid cancer with significance for the care of patients.

  15. Insights into the Genetic Basis of the Renal Cell Carcinomas from The Cancer Genome Atlas.

    Science.gov (United States)

    Haake, Scott M; Weyandt, Jamie D; Rathmell, W Kimryn

    2016-07-01

    The renal cell carcinomas (RCC), clear cell, papillary, and chromophobe, have recently undergone an unmatched genomic characterization by The Cancer Genome Atlas. This analysis has revealed new insights into each of these malignancies and underscores the unique biology of clear cell, papillary, and chromophobe RCC. Themes that have emerged include distinct mechanisms of metabolic dysregulation and common mutations in chromatin modifier genes. Importantly, the papillary RCC classification encompasses a heterogeneous group of diseases, each with highly distinct genetic and molecular features. In conclusion, this review summarizes RCCs that represent a diverse set of malignancies, each with novel biologic programs that define new paradigms for cancer biology. Mol Cancer Res; 14(7); 589-98. ©2016 AACR. ©2016 American Association for Cancer Research.

  16. Future of the ATLAS heavy ion program

    CERN Document Server

    ATLAS-Collaboration, The; The ATLAS collaboration

    2012-01-01

    The primary goal of the heavy ion program at the LHC is to study the properties of deconfined strongly interacting matter, often referred to as ``quark-gluon plasma'' (QGP), created in ultra-relativistic nuclear collisions. That matter is found to be strongly coupled with a viscosity to entropy ratio near a conjectured quantum lower bound. ATLAS foresees a rich program of studies using jets, Upsilons, measurements of global event properties and measurements in proton-nucleus collisions that will measure fundamental transport properties of the QGP, probe the nature of the interactions between constituents of the QGP, elucidate the origin of the strong coupling, and provide insight on the initial state of nuclear collisions. The heavy ion program through the third long shutdown should provide one inverse nb of 5.5~TeV Pb+Pb data. That data will provide more than an order of magnitude increase in statistics over currently available data for high-pT observables such as gamma-jet and Z-jet pairs. However, potentia...

  17. A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

    Energy Technology Data Exchange (ETDEWEB)

    Mockler, Todd [Oregon State Univ., Corvallis, OR (United States)

    2017-04-17

    Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes of plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.

  18. Complete mitochondrial genome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae) and the phylogenetic relationship of Saturniidae species.

    Science.gov (United States)

    Chen, Miao-Miao; Li, Yan; Chen, Mo; Wang, Huan; Li, Qun; Xia, Run-Xi; Zeng, Cai-Yun; Li, Yu-Ping; Liu, Yan-Qun; Qin, Li

    2014-07-15

    Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect with the largest wing surface area of all moths. The mitogenome of A. atlas is a circular molecule of 15,282 bp long, and its nucleotide composition shows heavily biased towards As and Ts, accounting for 79.30%. This genome comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A+T-rich region. It is of note that this genome exhibits a slightly positive AT skew, which is different from the other known Saturniidae species. All PCGs are initiated by ATN codons, except for COI with CGA instead. Only six PCGs use a common stop codon of TAA or TAG, whereas the remaining seven use an incomplete termination codon T or TA. All tRNAs have the typical clover-leaf structure, with an exception for tRNA(Ser)(AGN). The A. atlas A+T-rich region contains non-repetitive sequences, but harbors several features common to the Bombycoidea insects. The phylogenetic relationships based on Maximum Likelihood method provide a well-supported outline of Saturniidae, which is in accordance with the traditional morphological classification and recent molecular works.

  19. Feature selection and survival modeling in The Cancer Genome Atlas

    Directory of Open Access Journals (Sweden)

    Kim H

    2013-09-01

    Full Text Available Hyunsoo Kim,1 Markus Bredel2 1Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, USA; 2Department of Radiation Oncology, and Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL, USA Purpose: Personalized medicine is predicated on the concept of identifying subgroups of a common disease for better treatment. Identifying biomarkers that predict disease subtypes has been a major focus of biomedical science. In the era of genome-wide profiling, there is controversy as to the optimal number of genes as an input of a feature selection algorithm for survival modeling. Patients and methods: The expression profiles and outcomes of 544 patients were retrieved from The Cancer Genome Atlas. We compared four different survival prediction methods: (1 1-nearest neighbor (1-NN survival prediction method; (2 random patient selection method and a Cox-based regression method with nested cross-validation; (3 least absolute shrinkage and selection operator (LASSO optimization using whole-genome gene expression profiles; or (4 gene expression profiles of cancer pathway genes. Results: The 1-NN method performed better than the random patient selection method in terms of survival predictions, although it does not include a feature selection step. The Cox-based regression method with LASSO optimization using whole-genome gene expression data demonstrated higher survival prediction power than the 1-NN method, but was outperformed by the same method when using gene expression profiles of cancer pathway genes alone. Conclusion: The 1-NN survival prediction method may require more patients for better performance, even when omitting censored data. Using preexisting biological knowledge for survival prediction is reasonable as a means to understand the biological system of a cancer, unless the analysis goal is to identify completely unknown genes relevant to cancer biology. Keywords: brain, feature selection

  20. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation

    Science.gov (United States)

    Background A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juvenile and fetal cattle tissues and three cattle cell lines. Results The Bovine Gene...

  1. The Implementation of Full ATLAS Detector Simulation Program

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The ATLAS detector is one of the most sophisticated and huge detectors ever designed up to now.A detailed,flexible and complete simulation program is needed in order to study the characteristics and possible problems of such a challenging apparatus and to answer to all raising questions in terms of physics,design optimization,etc.To cope with these needs we are implementing an application based on the simulation framework FADS/Goofy(Framework for ATLAS Detector Simulation /Geant4-based Object-Oriented Folly)in the Geant4 environment.The user's specific code implementation is presented in detalils for the different applications implemented until now,from the various components of the ATLAS spectrometer top some particular testbeam facilities,particular emphasis is put in describing the simulation of the Muon Spectrometer and its subsystems as a test case for the implementation of the whole detector simulation program:the intrinsic complexity in the geometry description of the Muon System is one of the more demanding problems that are faced.The magnetic field handling,the physics impact in the event processing in presence of backgrounds from different sources and the implementation of different possible generators(including Pythia) are also discussed.

  2. Genomic Signal Search by Dynamic Programming

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wei-Mou

    2003-01-01

    A general and flexible multi-motif model is proposed based on dynamic programming. By extending theGibbs sampler to the dynamic programming and introducing temperature, an efficient algorithm is developed. Branchpoint signalsequences and translation initiation sequences extracted from the rice genome are then examined.

  3. Recent results from the ATLAS heavy ion program

    CERN Document Server

    Slovak, Radim; The ATLAS collaboration

    2017-01-01

    The heavy ion program in the ATLAS experiment at the Large Hadron Collider aims to probe and characterize the hot, dense matter created in relativistic lead-lead collisions, in the context of smaller collision systems involving nuclei and hadrons. This talk presents recent results based on LHC Run 1 and Run 2 data, including measurements of bulk collectivity, electroweak bosons, jet modifications, and quarkonium suppression. Results will also be presented on electromagnetic processes in ultra-peripheral collisions, including forward dilepton production and light-by-light scattering.

  4. Large-scale profiling of microRNAs for The Cancer Genome Atlas.

    Science.gov (United States)

    Chu, Andy; Robertson, Gordon; Brooks, Denise; Mungall, Andrew J; Birol, Inanc; Coope, Robin; Ma, Yussanne; Jones, Steven; Marra, Marco A

    2016-01-01

    The comprehensive multiplatform genomics data generated by The Cancer Genome Atlas (TCGA) Research Network is an enabling resource for cancer research. It includes an unprecedented amount of microRNA sequence data: ~11 000 libraries across 33 cancer types. Combined with initiatives like the National Cancer Institute Genomics Cloud Pilots, such data resources will make intensive analysis of large-scale cancer genomics data widely accessible. To support such initiatives, and to enable comparison of TCGA microRNA data to data from other projects, we describe the process that we developed and used to generate the microRNA sequence data, from library construction through to submission of data to repositories. In the context of this process, we describe the computational pipeline that we used to characterize microRNA expression across large patient cohorts.

  5. Review of the ATLAS B0 model coil test program

    CERN Document Server

    Dolgetta, N; Acerbi, E; Berriaud, C; Boxman, H; Broggi, F; Cataneo, F; Daël, A; Delruelle, N; Dudarev, A; Foussat, A; Haug, F; ten Kate, H H J; Mayri, C; Paccalini, A; Pengo, R; Rivoltella, G; Sbrissa, E

    2004-01-01

    The ATLAS B0 model coil has been extensively tested, reproducing the operational conditions of the final ATLAS Barrel Toroid coils. Two test campaigns have taken place on B0, at the CERN facility where the individual BT coils are about to be tested. The first campaign aimed to test the cool-down, warm-up phases and to commission the coil up to its nominal current of 20.5 kA, reproducing Lorentz forces similar to the ones on the BT coil. The second campaign aimed to evaluate the margins above the nominal conditions. The B0 was tested up to 24 kA and specific tests were performed to assess: the coil temperature margin with respect to the design value, the performance of the double pancake internal joints, static and dynamic heat loads, behavior of the coil under quench conditions. The paper reviews the overall test program with emphasis on second campaign results not covered before. 10 Refs.

  6. [Mapping and human genome sequence program].

    Science.gov (United States)

    Weissenbach, J

    1997-03-01

    Until recently, human genome programs focused primarily on establishing maps that would provide signposts to researchers seeking to identify genes responsible for inherited diseases, as well as a basis for genome sequencing studies. Preestablished gene mapping goals have been reached. The over 7,000 microsatellite markers identified to date provide a map of sufficient density to allow localization of the gene of a monogenic disease with a precision of 1 to 2 million base pairs. The physical map, based on systematically arranged overlapping sets of artificial yeast chromosomes (YACs), has also made considerable headway during the last few years. The most recently published map covers more than 90% of the genome. However, currently available physical maps cannot be used for sequencing studies because multiple rearrangements occur in YACs. The recently developed sets of radioinduced hybrids are extremely useful for incorporating genes into existing maps. A network of American and European laboratories has successfully used these radioinduced hybrids to map 15,000 gene tags from large-scale cDNA library sequencing programs. There are increasingly pressing reasons for initiating large scale human genome sequencing studies.

  7. ATLAS

    Data.gov (United States)

    Federal Laboratory Consortium — ATLAS is a particle physics experiment at the Large Hadron Collider at CERN, the European Organization for Nuclear Research. Scientists from Brookhaven have played...

  8. ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard A.; Brown, Joseph M.; Colby, Sean M.; Overall, Christopher C.; Lee, Joon-Yong; Zucker, Jeremy D.; Glaesemann, Kurt R.; Jansson, Georg C.; Jansson, Janet K.

    2017-03-02

    ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.

  9. Endometrial and acute myeloid leukemia cancer genomes characterized

    Science.gov (United States)

    Two studies from The Cancer Genome Atlas (TCGA) program reveal details about the genomic landscapes of acute myeloid leukemia (AML) and endometrial cancer. Both provide new insights into the molecular underpinnings of these cancers.

  10. Virtual Visit to the ATLAS Control Room by QuarkNet program in Portland

    CERN Multimedia

    2013-01-01

    The LHC fellows of the U.S. QuarkNet program will hold a workshop "Real LHC Data for the Classroom" for teachers using elements of the ATLAS masterclass on July 13, 2013. The workshop is part of the Summer 2013 Meeting of the American Association of Physics Teachers. In the workshop, teachers are introduced to particle physics, the ATLAS experiment, and ways to use actual data from the Large Hadron Collider at CERN to help their students understand fundamental physics. One of the highlights of this one-day workshop is an ATLAS Virtual Visit, in which the teachers connect by videoconference with the ATLAS control room. In the videoconferecne, the participants will be able to to ask questions of and have discussions with an ATLAS physicist.

  11. ATLAS

    CERN Multimedia

    2002-01-01

    Barrel and END-CAP Toroids In order to produce a powerful magnetic field to bend the paths of the muons, the ATLAS detector uses an exceptionally large system of air-core toroids arranged outside the calorimeter volumes. The large volume magnetic field has a wide angular coverage and strengths of up to 4.7tesla. The toroids system contains over 100km of superconducting wire and has a design current of 20 500 amperes. (ATLAS brochure: The Technical Challenges)

  12. Wind Atlas Analysis and Application Program: WAsP 11 Help Facility

    DEFF Research Database (Denmark)

    2014-01-01

    The Wind Atlas Analysis and Application Program (WAsP) is a PC-program for horizontal and vertical extrapolation of wind climates. The program contains a complete set of models to calculate the effects on the wind of sheltering obstacles, surface roughness changes and terrain height variations....... The analysis part consists of a transformation of an observed wind climate (wind speed and direction distributions) to a generalised wind climate (wind atlas data set). The generalised wind climate can subsequently be applied for estimation of the wind climate and wind power potential, as well as for siting...

  13. The Cancer Genome Atlas expression profiles of low-grade gliomas.

    Science.gov (United States)

    Gonda, David D; Cheung, Vincent J; Muller, Karra A; Goyal, Amit; Carter, Bob S; Chen, Clark C

    2014-04-01

    Differentiating between low-grade gliomas (LGGs) of astrocytic and oligodendroglial origin remains a major challenge in neurooncology. Here the authors analyzed The Cancer Genome Atlas (TCGA) profiles of LGGs with the goal of identifying distinct molecular characteristics that would afford accurate and reliable discrimination of astrocytic and oligodendroglial tumors. They found that 1) oligodendrogliomas are more likely to exhibit the glioma-CpG island methylator phenotype (G-CIMP), relative to low-grade astrocytomas; 2) relative to oligodendrogliomas, low-grade astrocytomas exhibit a higher expression of genes related to mitosis, replication, and inflammation; and 3) low-grade astrocytic tumors harbor microRNA profiles similar to those previously described for glioblastoma tumors. Orthogonal intersection of these molecular characteristics with existing molecular markers, such as IDH1 mutation, TP53 mutation, and 1p19q status, should facilitate accurate and reliable pathological diagnosis of LGGs.

  14. ATLAS

    CERN Multimedia

    Akhnazarov, V; Canepa, A; Bremer, J; Burckhart, H; Cattai, A; Voss, R; Hervas, L; Kaplon, J; Nessi, M; Werner, P; Ten kate, H; Tyrvainen, H; Vandelli, W; Krasznahorkay, A; Gray, H; Alvarez gonzalez, B; Eifert, T F; Rolando, G; Oide, H; Barak, L; Glatzer, J; Backhaus, M; Schaefer, D M; Maciejewski, J P; Milic, A; Jin, S; Von torne, E; Limbach, C; Medinnis, M J; Gregor, I; Levonian, S; Schmitt, S; Waananen, A; Monnier, E; Muanza, S G; Pralavorio, P; Talby, M; Tiouchichine, E; Tocut, V M; Rybkin, G; Wang, S; Lacour, D; Laforge, B; Ocariz, J H; Bertoli, W; Malaescu, B; Sbarra, C; Yamamoto, A; Sasaki, O; Koriki, T; Hara, K; Da silva gomes, A; Carvalho maneira, J; Marcalo da palma, A; Chekulaev, S; Tikhomirov, V; Snesarev, A; Buzykaev, A; Maslennikov, A; Peleganchuk, S; Sukharev, A; Kaplan, B E; Swiatlowski, M J; Nef, P D; Schnoor, U; Oakham, G F; Ueno, R; Orr, R S; Abouzeid, O; Haug, S; Peng, H; Kus, V; Vitek, M; Temming, K K; Dang, N P; Meier, K; Schultz-coulon, H; Geisler, M P; Sander, H; Schaefer, U; Ellinghaus, F; Rieke, S; Nussbaumer, A; Liu, Y; Richter, R; Kortner, S; Fernandez-bosman, M; Ullan comes, M; Espinal curull, J; Chiriotti alvarez, S; Caubet serrabou, M; Valladolid gallego, E; Kaci, M; Carrasco vela, N; Lancon, E C; Besson, N E; Gautard, V; Bracinik, J; Bartsch, V C; Potter, C J; Lester, C G; Moeller, V A; Rosten, J; Crooks, D; Mathieson, K; Houston, S C; Wright, M; Jones, T W; Harris, O B; Byatt, T J; Dobson, E; Hodgson, P; Hodgkinson, M C; Dris, M; Karakostas, K; Ntekas, K; Oren, D; Duchovni, E; Etzion, E; Oren, Y; Ferrer, L M; Testa, M; Doria, A; Merola, L; Sekhniaidze, G; Giordano, R; Ricciardi, S; Milazzo, A; Falciano, S; De pedis, D; Dionisi, C; Veneziano, S; Cardarelli, R; Verzegnassi, C; Soualah, R; Ochi, A; Ohshima, T; Kishiki, S; Linde, F L; Vreeswijk, M; Werneke, P; Muijs, A; Vankov, P H; Jansweijer, P P M; Dale, O; Lund, E; Bruckman de renstrom, P; Dabrowski, W; Adamek, J D; Wolters, H; Micu, L; Pantea, D; Tudorache, V; Mjoernmark, J; Klimek, P J; Ferrari, A; Abdinov, O; Akhoundov, A; Hashimov, R; Shelkov, G; Khubua, J; Ladygin, E; Lazarev, A; Glagolev, V; Dedovich, D; Lykasov, G; Zhemchugov, A; Zolnikov, Y; Ryabenko, M; Sivoklokov, S; Vasilyev, I; Shalimov, A; Lobanov, M; Paramoshkina, E; Mosidze, M; Bingul, A; Nodulman, L J; Guarino, V J; Yoshida, R; Drake, G R; Calafiura, P; Haber, C; Quarrie, D R; Alonso, J R; Anderson, C; Evans, H; Lammers, S W; Baubock, M; Anderson, K; Petti, R; Suhr, C A; Linnemann, J T; Richards, R A; Tollefson, K A; Holzbauer, J L; Stoker, D P; Pier, S; Nelson, A J; Isakov, V; Martin, A J; Adelman, J A; Paganini, M; Gutierrez, P; Snow, J M; Pearson, B L; Cleland, W E; Savinov, V; Wong, W; Goodson, J J; Li, H; Lacey, R A; Gordeev, A; Gordon, H; Lanni, F; Nevski, P; Rescia, S; Kierstead, J A; Liu, Z; Yu, W W H; Bensinger, J; Hashemi, K S; Bogavac, D; Cindro, V; Hoeferkamp, M R; Coelli, S; Iodice, M; Piegaia, R N; Alonso, F; Wahlberg, H P; Barberio, E L; Limosani, A; Rodd, N L; Jennens, D T; Hill, E C; Pospisil, S; Smolek, K; Schaile, D A; Rauscher, F G; Adomeit, S; Mattig, P M; Wahlen, H; Volkmer, F; Calvente lopez, S; Sanchis peris, E J; Pallin, D; Podlyski, F; Says, L; Boumediene, D E; Scott, W; Phillips, P W; Greenall, A; Turner, P; Gwilliam, C B; Kluge, T; Wrona, B; Sellers, G J; Millward, G; Adragna, P; Hartin, A; Alpigiani, C; Piccaro, E; Bret cano, M; Hughes jones, R E; Mercer, D; Oh, A; Chavda, V S; Carminati, L; Cavasinni, V; Fedin, O; Patrichev, S; Ryabov, Y; Nesterov, S; Grebenyuk, O; Sasso, J; Mahmood, H; Polsdofer, E; Dai, T; Ferretti, C; Liu, H; Hegazy, K H; Benjamin, D P; Zobernig, G; Ban, J; Brooijmans, G H; Keener, P; Williams, H H; Le geyt, B C; Hines, E J; Fadeyev, V; Schumm, B A; Law, A T; Kuhl, A D; Neubauer, M S; Shang, R; Gagliardi, G; Calabro, D; Conta, C; Zinna, M; Jones, G; Li, J; Stradling, A R; Hadavand, H K; Mcguigan, P; Chiu, P; Baldelomar, E; Stroynowski, R A; Kehoe, R L; De groot, N; Timmermans, C; Lach-heb, F; Addy, T N; Nakano, I; Moreno lopez, D; Grosse-knetter, J; Tyson, B; Rude, G D; Tafirout, R; Benoit, P; Danielsson, H O; Elsing, M; Fassnacht, P; Froidevaux, D; Ganis, G; Gorini, B; Lasseur, C; Lehmann miotto, G; Kollar, D; Aleksa, M; Sfyrla, A; Duehrssen-debling, K; Fressard-batraneanu, S; Van der ster, D C; Bortolin, C; Schumacher, J; Mentink, M; Geich-gimbel, C; Yau wong, K H; Lafaye, R; Crepe-renaudin, S; Albrand, S; Hoffmann, D; Pangaud, P; Meessen, C; Hrivnac, J; Vernay, E; Perus, A; Henrot versille, S L; Le dortz, O; Derue, F; Piccinini, M; Polini, A; Terada, S; Arai, Y; Ikeno, M; Fujii, H; Nagano, K; Ukegawa, F; Aguilar saavedra, J A; Conde muino, P; Castro, N F; Eremin, V; Kopytine, M; Sulin, V; Tsukerman, I; Korol, A; Nemethy, P; Bartoldus, R; Glatte, A; Chelsky, S; Van nieuwkoop, J; Bellerive, A; Sinervo, J K; Battaglia, A; Barbier, G J; Pohl, M; Rosselet, L

    2002-01-01

    % ATLAS \\\\ \\\\ ATLAS is a general-purpose experiment for recording proton-proton collisions at LHC. The ATLAS collaboration consists of 144 participating institutions (June 1998) with more than 1750~physicists and engineers (700 from non-Member States). The detector design has been optimized to cover the largest possible range of LHC physics: searches for Higgs bosons and alternative schemes for the spontaneous symmetry-breaking mechanism; searches for supersymmetric particles, new gauge bosons, leptoquarks, and quark and lepton compositeness indicating extensions to the Standard Model and new physics beyond it; studies of the origin of CP violation via high-precision measurements of CP-violating B-decays; high-precision measurements of the third quark family such as the top-quark mass and decay properties, rare decays of B-hadrons, spectroscopy of rare B-hadrons, and $ B ^0 _{s} $-mixing. \\\\ \\\\The ATLAS dectector, shown in the Figure includes an inner tracking detector inside a 2~T~solenoid providing an axial...

  15. A genomic atlas of human adrenal and gonad development [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Ignacio del Valle

    2017-04-01

    Full Text Available Background: In humans, the adrenal glands and gonads undergo distinct biological events between 6-10 weeks post conception (wpc, such as testis determination, the onset of steroidogenesis and primordial germ cell development. However, relatively little is currently known about the genetic mechanisms underlying these processes. We therefore aimed to generate a detailed genomic atlas of adrenal and gonad development across these critical stages of human embryonic and fetal development. Methods: RNA was extracted from 53 tissue samples between 6-10 wpc (adrenal, testis, ovary and control. Affymetrix array analysis was performed and differential gene expression was analysed using Bioconductor. A mathematical model was constructed to investigate time-series changes across the dataset. Pathway analysis was performed using ClueGo and cellular localisation of novel factors confirmed using immunohistochemistry. Results: Using this approach, we have identified novel components of adrenal development (e.g. ASB4, NPR3 and confirmed the role of SRY as the main human testis-determining gene. By mathematical modelling time-series data we have found new genes up-regulated with SOX9 in the testis (e.g. CITED1, which may represent components of the testis development pathway. We have shown that testicular steroidogenesis has a distinct onset at around 8 wpc and identified potential novel components in adrenal and testicular steroidogenesis (e.g. MGARP, FOXO4, MAP3K15, GRAMD1B, RMND2, as well as testis biomarkers (e.g. SCUBE1. We have also shown that the developing human ovary expresses distinct subsets of genes (e.g. OR10G9, OR4D5, but enrichment for established biological pathways is limited. Conclusion: This genomic atlas is revealing important novel aspects of human development and new candidate genes for adrenal and reproductive disorders.

  16. TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

    Science.gov (United States)

    Cumbo, Fabio; Fiscon, Giulia; Ceri, Stefano; Masseroli, Marco; Weitschek, Emanuel

    2017-01-03

    Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration. Additionally, it supports the conversion in CSV, GTF, JSON, and XML standard formats. Furthermore, TCGA2BED extends TCGA data with information extracted from other genomic databases (i.e., NCBI Entrez Gene, HGNC, UCSC, and miRBase). We also provide and maintain an automatically updated data repository with publicly available Copy Number Variation, DNA-methylation, DNA-seq, miRNA-seq, and RNA-seq (V1,V2) experimental data of TCGA converted into the BED format, and their associated clinical and biospecimen meta data in attribute-value text format. The availability of the valuable TCGA data in BED format reduces the time spent in taking advantage of them: it is possible to efficiently and effectively deal with huge amounts of cancer genomic data integratively, and to search, retrieve and extend them with additional information. The BED format facilitates the investigators allowing several knowledge discovery analyses on all tumor types in TCGA with the final aim of understanding pathological mechanisms and aiding cancer treatments.

  17. VIGOR, an annotation program for small viral genomes

    Directory of Open Access Journals (Sweden)

    Wang Shiliang

    2010-09-01

    Full Text Available Abstract Background The decrease in cost for sequencing and improvement in technologies has made it easier and more common for the re-sequencing of large genomes as well as parallel sequencing of small genomes. It is possible to completely sequence a small genome within days and this increases the number of publicly available genomes. Among the types of genomes being rapidly sequenced are those of microbial and viral genomes responsible for infectious diseases. However, accurate gene prediction is a challenge that persists for decoding a newly sequenced genome. Therefore, accurate and efficient gene prediction programs are highly desired for rapid and cost effective surveillance of RNA viruses through full genome sequencing. Results We have developed VIGOR (Viral Genome ORF Reader, a web application tool for gene prediction in influenza virus, rotavirus, rhinovirus and coronavirus subtypes. VIGOR detects protein coding regions based on sequence similarity searches and can accurately detect genome specific features such as frame shifts, overlapping genes, embedded genes, and can predict mature peptides within the context of a single polypeptide open reading frame. Genotyping capability for influenza and rotavirus is built into the program. We compared VIGOR to previously described gene prediction programs, ZCURVE_V, GeneMarkS and FLAN. The specificity and sensitivity of VIGOR are greater than 99% for the RNA viral genomes tested. Conclusions VIGOR is a user friendly web-based genome annotation program for five different viral agents, influenza, rotavirus, rhinovirus, coronavirus and SARS coronavirus. This is the first gene prediction program for rotavirus and rhinovirus for public access. VIGOR is able to accurately predict protein coding genes for the above five viral types and has the capability to assign function to the predicted open reading frames and genotype influenza virus. The prediction software was designed for performing high

  18. Genomic prediction in a breeding program of perennial ryegrass

    DEFF Research Database (Denmark)

    Fé, Dario; Ashraf, Bilal; Greve-Pedersen, Morten;

    2015-01-01

    We present a genomic selection study performed on 1918 rye grass families (Lolium perenne L.), which were derived from a commercial breeding program at DLF-Trifolium, Denmark. Phenotypes were recorded on standard plots, across 13 years and in 6 different countries. Variants were identified...... in utilizing genomic selection in rye grass....

  19. EnviroAtlas - Ecosystem Services Market-Based Programs Web Service, U.S., 2016, Forest Trends' Ecosystem Marketplace

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service contains layers depicting market-based programs and projects addressing ecosystem services protection in the United States. Layers...

  20. Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.

    Science.gov (United States)

    Nulton, Tara J; Olex, Amy L; Dozmorov, Mikhail; Morgan, Iain M; Windle, Brad

    2017-03-14

    Human papillomavirus (HPV) DNA is detected in up to 80% of oropharyngeal carcinomas (OPC) and this HPV positive disease has reached epidemic proportions. To increase our understanding of the disease, we investigated the status of the HPV16 genome in HPV-positive head and neck cancers (HNC). Raw RNA-Seq and Whole Genome Sequence data from The Cancer Genome Atlas HNC samples were analyzed to gain a full understanding of the HPV genome status for these tumors. Several remarkable and novel observations were made following this analysis. Firstly, there are three main HPV genome states in these tumors that are split relatively evenly: An episomal only state, an integrated state, and a state in which the viral genome exists as a hybrid episome with human DNA. Secondly, none of the tumors expressed high levels of E6; E6*I is the dominant variant expressed in all tumors. The most striking conclusion from this study is that around three quarters of HPV16 positive HNC contain episomal versions of the viral genome that are likely replicating in an E1-E2 dependent manner. The clinical and therapeutic implications of these observations are discussed.

  1. GenomePixelizer--a visualization program for comparative genomics within and between species.

    Science.gov (United States)

    Kozik, A; Kochetkova, E; Michelmore, R

    2002-02-01

    GenomePixelizer is a visualization tool that generates custom images of the physical or genetic positions of specified sets of genes in whole genomes or parts of genomes. Multiple sets of genes can be shown simultaneously with user-defined characteristics displayed. It allows the analysis of duplication events within and between species based on sequence similarities. The program is written in Tcl/Tk and works on any platform that supports the Tcl/Tk toolkit. GenomePixelizer generates HTML ImageMap tags for each gene in the image allowing links to databases. Images can be saved and presented on web pages.

  2. Genomic connectivity networks based on the BrainSpan atlas of the developing human brain

    Science.gov (United States)

    Mahfouz, Ahmed; Ziats, Mark N.; Rennert, Owen M.; Lelieveldt, Boudewijn P. F.; Reinders, Marcel J. T.

    2014-03-01

    The human brain comprises systems of networks that span the molecular, cellular, anatomic and functional levels. Molecular studies of the developing brain have focused on elucidating networks among gene products that may drive cellular brain development by functioning together in biological pathways. On the other hand, studies of the brain connectome attempt to determine how anatomically distinct brain regions are connected to each other, either anatomically (diffusion tensor imaging) or functionally (functional MRI and EEG), and how they change over development. A global examination of the relationship between gene expression and connectivity in the developing human brain is necessary to understand how the genetic signature of different brain regions instructs connections to other regions. Furthermore, analyzing the development of connectivity networks based on the spatio-temporal dynamics of gene expression provides a new insight into the effect of neurodevelopmental disease genes on brain networks. In this work, we construct connectivity networks between brain regions based on the similarity of their gene expression signature, termed "Genomic Connectivity Networks" (GCNs). Genomic connectivity networks were constructed using data from the BrainSpan Transcriptional Atlas of the Developing Human Brain. Our goal was to understand how the genetic signatures of anatomically distinct brain regions relate to each other across development. We assessed the neurodevelopmental changes in connectivity patterns of brain regions when networks were constructed with genes implicated in the neurodevelopmental disorder autism (autism spectrum disorder; ASD). Using graph theory metrics to characterize the GCNs, we show that ASD-GCNs are relatively less connected later in development with the cerebellum showing a very distinct expression of ASD-associated genes compared to other brain regions.

  3. BSMAP: whole genome bisulfite sequence MAPping program

    Directory of Open Access Journals (Sweden)

    Li Wei

    2009-07-01

    Full Text Available Abstract Background Bisulfite sequencing is a powerful technique to study DNA cytosine methylation. Bisulfite treatment followed by PCR amplification specifically converts unmethylated cytosines to thymine. Coupled with next generation sequencing technology, it is able to detect the methylation status of every cytosine in the genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge due to the increased searching space, reduced complexity of bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation. Results We developed an efficient bisulfite reads mapping algorithm BSMAP to address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping. Compared with existing bisulfite mapping approaches, BSMAP is faster, more sensitive and more flexible. Conclusion BSMAP is the first general-purpose bisulfite mapping software. It is able to map high-throughput bisulfite reads at whole genome level with feasible memory and CPU usage. It is freely available under GPL v3 license at http://code.google.com/p/bsmap/.

  4. DOE Human Genome Program contractor-grantee workshop

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-01-01

    This volume contains the proceedings for the DOE Human Genome Program`s Contractor-Grantee Workshop V held in Sante Fe, New Mexico January 28, February 1, 1996. Presentations were divided into sessions entitled Sequencing; Mapping; Informatics; Ethical, Legal, and Social Issues; and Infrastructure. Reports of individual projects described herein are separately indexed and abstracted for the database.

  5. Human Genome Program Report. Part 1, Overview and Progress

    Science.gov (United States)

    1997-11-01

    This report contains Part 1 of a two-part report to reflect research and progress in the U.S. Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 1 consists of the program overview and report on progress.

  6. Human genome program report. Part 1, overview and progress

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    This report contains Part 1 of a two-part report to reflect research and progress in the U.S. Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 1 consists of the program overview and report on progress.

  7. The National Toxicology Program Web-based nonneoplastic lesion atlas: a global toxicology and pathology resource.

    Science.gov (United States)

    Cesta, Mark F; Malarkey, David E; Herbert, Ronald A; Brix, Amy; Hamlin, Melvin H; Singletary, Emily; Sills, Robert C; Bucher, John R; Birnbaum, Linda S

    2014-01-01

    Toxicologists and pathologists worldwide will benefit from a new, website-based, and completely searchable Nonneoplastic Lesion Atlas just released by the U.S. National Toxicology Program (NTP). The atlas is a much-needed resource with thousands of high-quality, zoomable images and diagnostic guidelines for each rodent lesion. Liver, gallbladder, nervous system, bone marrow, lower urinary tract and skin lesion images, and diagnostic strategies are available now. More organ and biological systems will be added with a total of 22 chapters planned for the completed project. The atlas will be used by the NTP and its many pathology partners to standardize lesion diagnosis, terminology, and the way lesions are recorded. The goal is to improve our understanding of nonneoplastic lesions and the consistency and accuracy of their diagnosis between pathologists and laboratories. The atlas is also a useful training tool for pathology residents and can be used to bolster any organization's own lesion databases. Researchers have free access to this online resource at www.ntp.niehs.nih.gov/nonneoplastic.

  8. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

    Directory of Open Access Journals (Sweden)

    King Nichole L

    2009-02-01

    Full Text Available Abstract Background Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments. Results In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s in which it was observed. Conclusion PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1 reduction of the complexity inherently associated with performing targeted proteomic studies, (2 designing and accelerating shotgun proteomics experiments, (3 confirming or questioning gene models, and (4 adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.

  9. Report to users of ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Ahmad, I.; Glagola, B. [eds.

    1995-05-01

    This report contains discussing in the following areas: Status of the Atlas accelerator; highlights of recent research at Atlas; concept for an advanced exotic beam facility based on Atlas; program advisory committee; Atlas executive committee; and Atlas and ANL physics division on the world wide web.

  10. Wind Atlas Analysis and Application Program: WAsP 11 Help Facility

    DEFF Research Database (Denmark)

    2014-01-01

    The Wind Atlas Analysis and Application Program (WAsP) is a PC-program for horizontal and vertical extrapolation of wind climates. The program contains a complete set of models to calculate the effects on the wind of sheltering obstacles, surface roughness changes and terrain height variations...... of specific wind turbines and wind farms. The WAsP Help Facility includes a Quick Start Tutorial, a User's Guide and a Technical Reference. It further includes descriptions of the Observed Wind Climate Wizard, the WAsP Climate Analyst, the WAsP Map Editor tool, the WAsP Turbine Editor tool, the Air Density...

  11. Primer on Molecular Genetics; DOE Human Genome Program

    Science.gov (United States)

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  12. Primer on molecular genetics. DOE Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  13. Clarifying the biological significance of the CHK2 K373E somatic mutation discovered in The Cancer Genome Atlas database.

    Science.gov (United States)

    Higashiguchi, Masayoshi; Nagatomo, Izumi; Kijima, Takashi; Morimura, Osamu; Miyake, Kotaro; Minami, Toshiyuki; Koyama, Shohei; Hirata, Haruhiko; Iwahori, Kota; Takimoto, Takayuki; Takeda, Yoshito; Kida, Hiroshi; Kumanogoh, Atsushi

    2016-12-01

    We identified CHK2 K373E as a recurrent mutation in The Cancer Genome Atlas (TCGA) database. In this study, we demonstrate that the K373E mutation disrupts CHK2 autophosphorylation as well as kinase activity, thus leading to impairment of CHK2 functions in suppressing cell proliferation and promoting cell survival after ionizing radiation. We propose that K373E impairs p53-independent induction of p21(WAF)(1/)(CIP)(1) by CHK2. Our data implicate the K373E mutation of CHK2 in tumorigenesis. © 2016 Federation of European Biochemical Societies.

  14. Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues.

    Science.gov (United States)

    Chisanga, David; Keerthikumar, Shivakumar; Pathan, Mohashin; Ariyaratne, Dinuka; Kalra, Hina; Boukouris, Stephanie; Mathew, Nidhi Abraham; Al Saffar, Haidar; Gangoda, Lahiru; Ang, Ching-Seng; Sieber, Oliver M; Mariadason, John M; Dasgupta, Ramanuj; Chilamkurti, Naveen; Mathivanan, Suresh

    2016-01-04

    In order to advance our understanding of colorectal cancer (CRC) development and progression, biomedical researchers have generated large amounts of OMICS data from CRC patient samples and representative cell lines. However, these data are deposited in various repositories or in supplementary tables. A database which integrates data from heterogeneous resources and enables analysis of the multidimensional data sets, specifically pertaining to CRC is currently lacking. Here, we have developed Colorectal Cancer Atlas (http://www.colonatlas.org), an integrated web-based resource that catalogues the genomic and proteomic annotations identified in CRC tissues and cell lines. The data catalogued to-date include sequence variations as well as quantitative and non-quantitative protein expression data. The database enables the analysis of these data in the context of signaling pathways, protein-protein interactions, Gene Ontology terms, protein domains and post-translational modifications. Currently, Colorectal Cancer Atlas contains data for >13 711 CRC tissues, >165 CRC cell lines, 62 251 protein identifications, >8.3 million MS/MS spectra, >18 410 genes with sequence variations (404 278 entries) and 351 pathways with sequence variants. Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Recent highlights from the ATLAS heavy-ion program

    Science.gov (United States)

    Angerami, Aaron

    2016-12-01

    These proceedings report on recent measurements performed with the ATLAS Detector at the LHC presented at the Quark Matter 2015 Conference. These include measurements of two-particle correlations in pp collisions at √{ s} = 2.76 and 13 TeV. These results are the first to show a second harmonic modulation in the azimuthal dependence of the particle yields in pp collisions, a signature closely associated with collective flow in ion-ion collisions. Measurements of p+Pb collisions at √{sNN} = 5.02 TeV are presented including charged particle multiplicities, Bose-Einstein correlations and yields of jets and electroweak bosons that provide insight into the initial stages of these collisions including the nuclear geometry. Finally, measurements of dijet asymmetry and jet structure in Pb+Pb and pp collisions at √{sNN} = 2.76 TeV are presented that further illuminate the phenomenon of partonic energy loss.

  16. Human genome program report. Part 2, 1996 research abstracts

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  17. Human Genome Program Report. Part 2, 1996 Research Abstracts

    Science.gov (United States)

    1997-11-01

    This report contains Part 2 of a two-part report to reflect research and progress in the US Department of Energy Human Genome Program from 1994 through 1996, with specified updates made just before publication. Part 2 consists of 1996 research abstracts. Attention is focused on the following: sequencing; mapping; informatics; ethical, legal, and social issues; infrastructure; and small business innovation research.

  18. Recent highlights from the ATLAS heavy-ion program

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00210782; The ATLAS collaboration

    2016-01-01

    These proceedings report on recent measurements performed by with ATLAS Detector at the LHC presented at the Quark Matter 2015 Conference. These include measurements of two-particle correlations in $pp$ collisions at $\\sqrt{s}=2.76$ and 13 TeV. These results are the first to show a second harmonic modulation in the azimuthal dependence of the particle yields in $pp$ collisions, a signature closely associated with collective flow in ion-ion collisions. Measurements of $p$+Pb collisions at $\\sqrt{s_{\\mathrm{NN}}}=5.02$ TeV are presented including charged particle multiplicities, Bose-Einstein correlations and yields of jets and electroweak bosons that provide insight into the initial stages of these collisions including the nuclear geometry. Finally, measurements of dijet asymmetry and jet structure in Pb+Pb and $pp$ collisions at $\\sqrt{s_{\\mathrm{NN}}}=2.76$ TeV are presented that further illuminate the phenomenon of partonic energy loss.

  19. WAsP prediction errors due to site orography[Wind Atlas Analysis and Application Program

    Energy Technology Data Exchange (ETDEWEB)

    Bowen, A.J.; Mortensen, N.G.

    2004-12-01

    The influence of rugged terrain on the prediction accuracy of the Wind Atlas Analysis and Application Program (WAsP) is investigated using a case study of field measurements taken in rugged terrain. The parameters that could cause substantial errors in a prediction are identified and discussed. In particular, the effects from extreme orography are investigated. A suitable performance indicator is developed which predicts the sign and approximate magnitude of such errors due to orography. This procedure allows the user to assess the consequences of using WAsP outside its operating envelope and could provide a means of correction for rugged terrain effects. (au)

  20. Assembling networks of microbial genomes using linear programming

    Directory of Open Access Journals (Sweden)

    Holloway Catherine

    2010-11-01

    Full Text Available Abstract Background Microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. Assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem. Results We have developed a new approach that uses linear programming to find between-genome relationships, by treating tables of genetic affinities (here, represented by transformed BLAST e-values as an optimization problem. Validation trials on simulated data demonstrate the effectiveness of the approach in recovering and representing vertical and lateral relationships among genomes. Application of the technique to a set comprising Aquifex aeolicus and 75 other thermophiles showed an important role for large genomes as 'hubs' in the gene sharing network, and suggested that genes are preferentially shared between organisms with similar optimal growth temperatures. We were also able to discover distinct and common genetic contributors to each sequenced representative of genus Pseudomonas. Conclusions The linear programming approach we have developed can serve as an effective inference tool in its own right, and can be an efficient first step in a more-intensive phylogenomic analysis.

  1. Genomic resources in mungbean for future breeding programs

    Directory of Open Access Journals (Sweden)

    Sue K Kim

    2015-08-01

    Full Text Available Among the legume family, mungbean (Vigna radiata has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.

  2. FoldAtlas: a repository for genome-wide RNA structure probing data

    Science.gov (United States)

    Norris, Matthew; Kwok, Chun Kit; Cheema, Jitender; Hartley, Matthew; Morris, Richard J.; Aviran, Sharon; Ding, Yiliang

    2017-01-01

    Summary: Most RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work. Availability and Implementation: The FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985. Contact: yiliang.ding@jic.ac.uk or matthew.norris@jic.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27663500

  3. [Strategies of the study on herb genome program].

    Science.gov (United States)

    Chen, Shi-lin; Sun, Yong-zhen; Xu, Jiang; Luo, Hong-mei; Sun, Chao; He, Liu; Cheng, Xiang-lin; Zhang, Bo-li; Xiao, Pei-gen

    2010-07-01

    Herb Genome Program (HerbGP) includes a series of projects on whole genome sequencing (WGS) and post-genomics research of medicinal plants with unique secondary metabolism pathways or/and those of great medical and pharmaceutical importance. In this paper, we systematically discussed the strategy of HerbGP, from species selection, whole-genome sequencing, assembly and bioinformatics analysis, to postgenomics research. HerbGP will push study on Chinese traditional medicines into the front field of life science, by selecting a series of plants with unique secondary metabolism pathways as models and introducing "omics" methods into the research of these medicinal plants. HerbGP will provide great opportunities for China to be the leader in the basic research field of traditional Chinese medicine. HerbGP shall also have significant impacts on the R&D of natural medicines and the development of medicinal farming by analysis of secondary metabolic pathways and selection of cultivars with good agricultural traits.

  4. EnviroAtlas - Acres of USDA Farm Service Agency Conservation Reserve Program land by 12-Digit HUC for the Conterminous United States.

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the acres of land enrolled in the US Department of Agriculture (USDA)'s Conservation Reserve Program (CRP). The CRP is administered by...

  5. 78 FR 18680 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Science.gov (United States)

    2013-03-27

    ... Medicine Program Advisory Committee will meet on April 11, 2013, in Suite 1000 at the United States Access... AFFAIRS Genomic Medicine Program Advisory Committee, Notice of Meeting The Department of Veterans Affairs... Million Veteran Program, as well as the clinical Genomic Medicine Service. The emerging implications...

  6. ATLAS Forward Detectors and Physics

    CERN Document Server

    Soni, N

    2010-01-01

    In this communication I describe the ATLAS forward physics program and the detectors, LUCID, ZDC and ALFA that have been designed to meet this experimental challenge. In addition to their primary role in the determination of ATLAS luminosity these detectors - in conjunction with the main ATLAS detector - will be used to study soft QCD and diffractive physics in the initial low luminosity phase of ATLAS running. Finally, I will briefly describe the ATLAS Forward Proton (AFP) project that currently represents the future of the ATLAS forward physics program.

  7. Molecular characteristics of non-small cell lung cancer with reduced CHFR expression in The Cancer Genome Atlas (TCGA) project.

    Science.gov (United States)

    Brodie, Seth A; Li, Ge; Brandes, Johann C

    2015-01-01

    CHFR expression has previously been established as a powerful predictor for response to taxane based first-line chemotherapy in non-small cell lung cancer. It is currently unknown however, if reduced CHFR expression correlates with certain molecular subtypes of lung cancer. In order to determine which patients may benefit from CHFR biomarker testing we conducted the present study to characterize clinical and molecular characteristics of patients with reduced vs. high CHFR expression. We utilized the extensive molecular and clinical data of the most recent adeno- and squamous cell carcinoma datasets from The Cancer Genome Atlas (TCGA) project. CHFR expression, analyzed by RNA-seq, was classified as high vs. low based on the median CHFR expression level and correlated with the presence or absence of lung cancer specific mutations (EGFR, KRAS, ALK, MET, ERBB2, TP53, STK11, ROS1, RET, NF1, Pik3CA for adenocarcinomas and FGFR1, FGFR2, FGFR3, TP53, STK11, EGFR for squamous cell carcinomas). Reduced CHFR expression was associated with EGFR exon19/21 mutations in adenocarcinoma OR 0.23 (95%CI: 0.06-0.88) and male gender in squamous cell carcinoma (OR 0.46 (95%CI 0.23-0.92), p = 0.02). Published by Elsevier Ltd.

  8. Bioinformatics analyses of the differences between lung adenocarcinoma and squamous cell carcinoma using The Cancer Genome Atlas expression data.

    Science.gov (United States)

    Sun, Fenghao; Yang, Xiaodong; Jin, Yulin; Chen, Li; Wang, Lin; Shi, Mengkun; Zhan, Cheng; Shi, Yu; Wang, Qun

    2017-07-01

    The present study aimed to explore gene and microRNA (miRNA) expression differences between lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) were identified by analyzing mRNA and miRNA expression data in normal and cancerous lung tissues that were obtained from The Cancer Genome Atlas database. A total of 778 DEGs and 7 DEMs were identified. Altered gene functions and signaling pathways were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, which revealed that DEGs were significantly enriched in extracellular matrix organization, cell differentiation, negative regulation of toll signaling pathway, and several other terms and pathways. Transcription factor (TF)‑miRNA‑gene networks in LUAD and LUSC were predicted using the TargetScan, Miranda, and TRANSFAC databases, which revealed the regulatory links among the TFs, DEMs, and DEGs. The central TFs, i.e., the TFs in the middle of the TF‑miRNA‑gene network, of LUAD and LUSC were similar. Although LUAD and LUSC shared similar miRNAs in the predicted networks, miR‑29b‑3p was demonstrated to be upregulated only in LUAD, whereas miR‑1, miR‑105‑5p, and miR‑193b‑5p were altered in LUSC. These findings may improve our understanding of the different molecular mechanisms in non‑small cell lung cancers and may promote new and accurate strategies for prevention, diagnosis, and treatment.

  9. Expression profile analysis of head and neck squamous cell carcinomas using data from The Cancer Genome Atlas.

    Science.gov (United States)

    Yan, Li; Zhan, Cheng; Wu, Jihong; Wang, Shengzi

    2016-05-01

    Head and neck squamous cell carcinoma (HNSCC) is the major histological type of head and neck cancer and no curative treatments are currently available. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) has produced large‑scale sequencing data, which provide unprecedented opportunities to reveal molecular mechanisms of cancer. The present study analyzed the mRNA and micro (mi)RNA expression data of HNSCC and normal control tissues released by the TCGA database using a bioinformatics approach to explore underlying molecular mechanisms. The mRNA and miRNA expression data were downloaded from the TCGA database and differentially expressed genes (DEGs) and miRNAs (DEMs) between HNSCC and normal head and neck tissues were identified using TwoClassDif. Subsequently, the gene functions and pathways which are significantly altered in HNSCC were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Regulatory networks among DEGs and DEMs were then constructed, and transcription factors (TFs) potentially regulating the DEGs and DEMs were determined and a TF ‑ miRNA ‑ gene network was established. A total of 2,594 significant DEGs (1,087 upregulated and 1,507 downregulated), and 25 DEMs (8 upregulated and 17 downregulated) were identified in HNSCC compared with normal control samples. These DEGs were significantly enriched in GOs and KEGG pathways such as mitosis, cell cycle, Wnt, JAK/STAT and TLR signaling pathway. CPBP, NF‑AT1 and miR‑1 were situated in the central hub of the TF ‑ miRNA ‑ gene network, underlining their central roles in regulatory processes specific for HNSCC. The present study enhanced the current understanding of the molecular mechanisms underlying HNSCC and may offer novel strategies for its prevention, diagnosis and treatment.

  10. Genomic prediction in a breeding program of perennial ryegrass

    DEFF Research Database (Denmark)

    Fé, Dario; Ashraf, Bilal; Greve-Pedersen, Morten

    2015-01-01

    We present a genomic selection study performed on 1918 rye grass families (Lolium perenne L.), which were derived from a commercial breeding program at DLF-Trifolium, Denmark. Phenotypes were recorded on standard plots, across 13 years and in 6 different countries. Variants were identified...... this set. Estimated Breeding Value and prediction accuracies were calculated trough two different cross-validation schemes: (i) k-fold (k=10); (ii) leaving out one parent combination at the time, in order to test for accuracy of predicting new families. Accuracies ranged between 0.56 and 0.97 for scheme (i....... A larger set of 1791 F2s were used as training set to predict EBVs of 127 synthetic families (originated from poly-crosses between 5-11 single plants) for heading date and crown rust resistance. Prediction accuracies were 0.93 and 0.57 respectively. Results clearly demonstrate considerable potential...

  11. Genomic tools in cowpea breeding programs: status and perspectives

    Directory of Open Access Journals (Sweden)

    Ousmane eBoukar

    2016-06-01

    Full Text Available Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA. It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS, promises an increase in the number of

  12. Genomic Tools in Cowpea Breeding Programs: Status and Perspectives.

    Science.gov (United States)

    Boukar, Ousmane; Fatokun, Christian A; Huynh, Bao-Lam; Roberts, Philip A; Close, Timothy J

    2016-01-01

    Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

  13. DO CANCER CLINICAL TRIAL POPULATIONS TRULY REPRESENT CANCER PATIENTS? A COMPARISON OF OPEN CLINICAL TRIALS TO THE CANCER GENOME ATLAS.

    Science.gov (United States)

    Geifman, Nophar; Butte, Atul J

    2016-01-01

    Open clinical trial data offer many opportunities for the scientific community to independently verify published results, evaluate new hypotheses and conduct meta-analyses. These data provide a springboard for scientific advances in precision medicine but the question arises as to how representative clinical trials data are of cancer patients overall. Here we present the integrative analysis of data from several cancer clinical trials and compare these to patient-level data from The Cancer Genome Atlas (TCGA). Comparison of cancer type-specific survival rates reveals that these are overall lower in trial subjects. This effect, at least to some extent, can be explained by the more advanced stages of cancer of trial subjects. This analysis also reveals that for stage IV cancer, colorectal cancer patients have a better chance of survival than breast cancer patients. On the other hand, for all other stages, breast cancer patients have better survival than colorectal cancer patients. Comparison of survival in different stages of disease between the two datasets reveals that subjects with stage IV cancer from the trials dataset have a lower chance of survival than matching stage IV subjects from TCGA. One likely explanation for this observation is that stage IV trial subjects have lower survival rates since their cancer is less likely to respond to treatment. To conclude, we present here a newly available clinical trials dataset which allowed for the integration of patient-level data from many cancer clinical trials. Our comprehensive analysis reveals that cancer-related clinical trials are not representative of general cancer patient populations, mostly due to their focus on the more advanced stages of the disease. These and other limitations of clinical trials data should, perhaps, be taken into consideration in medical research and in the field of precision medicine.

  14. Prognostic microRNA signatures derived from The Cancer Genome Atlas for head and neck squamous cell carcinomas.

    Science.gov (United States)

    Wong, Nathan; Khwaja, Shariq S; Baker, Callie M; Gay, Hiram A; Thorstad, Wade L; Daly, Mackenzie D; Lewis, James S; Wang, Xiaowei

    2016-07-01

    Identification of novel prognostic biomarkers typically requires a large dataset which provides sufficient statistical power for discovery research. To this end, we took advantage of the high-throughput data from The Cancer Genome Atlas (TCGA) to identify a set of prognostic biomarkers in head and neck squamous cell carcinomas (HNSCC) including oropharyngeal squamous cell carcinoma (OPSCC) and other subtypes. In this study, we analyzed miRNA-seq data obtained from TCGA patients to identify prognostic biomarkers for OPSCC. The identified miRNAs were further tested with an independent cohort. miRNA-seq data from TCGA was also analyzed to identify prognostic miRNAs in oral cavity squamous cell carcinoma (OSCC) and laryngeal squamous cell carcinoma (LSCC). Our study identified that miR-193b-3p and miR-455-5p were positively associated with survival, and miR-92a-3p and miR-497-5p were negatively associated with survival in OPSCC. A combined expression signature of these four miRNAs was prognostic of overall survival in OPSCC, and more importantly, this signature was validated in an independent OPSCC cohort. Furthermore, we identified four miRNAs each in OSCC and LSCC that were prognostic of survival, and combined signatures were specific for subtypes of HNSCC. A robust 4-miRNA prognostic signature in OPSCC, as well as prognostic signatures in other subtypes of HNSCC, was developed using sequencing data from TCGA as the primary source. This demonstrates the power of using TCGA as a potential resource to develop prognostic tools for improving individualized patient care. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  15. GIANT API: an application programming interface for functional genomics

    Science.gov (United States)

    Roberts, Andrew M.; Wong, Aaron K.; Fisk, Ian; Troyanskaya, Olga G.

    2016-01-01

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

  16. GIANT API: an application programming interface for functional genomics.

    Science.gov (United States)

    Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

    2016-07-08

    GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu.

  17. Programming biological operating systems: genome design, assembly and activation.

    Science.gov (United States)

    Gibson, Daniel G

    2014-05-01

    The DNA technologies developed over the past 20 years for reading and writing the genetic code converged when the first synthetic cell was created 4 years ago. An outcome of this work has been an extraordinary set of tools for synthesizing, assembling, engineering and transplanting whole bacterial genomes. Technical progress, options and applications for bacterial genome design, assembly and activation are discussed.

  18. 76 FR 65563 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Science.gov (United States)

    2011-10-21

    ... (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic Medicine... incorporate genomic information into its health care program while applying appropriate ethical oversight and... the public. The purpose of the Committee is to provide advice and make recommendations to the...

  19. Genomic selection needs to be carefully assessed to meet specific requirements in livestock breeding programs

    Directory of Open Access Journals (Sweden)

    Elisabeth eJonas

    2015-02-01

    Full Text Available Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies. It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating genomic selection into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken and fish. It outlines tasks to help understanding possible consequences when applying genomic information in

  20. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Ussery, David

    2004-01-01

    , these results counts to more than 220 pieces of information. The backbone of this solution consists of a program package written in Perl, which enables administrators to synchronize and update the database content. The MySQL database has been connected to the CBS web-server via PHP4, to present a dynamic web...... content for users outside the center. This solution is tightly fitted to existing server infrastructure and the solutions proposed here can perhaps serve as a template for other research groups to solve database issues....

  1. ATLAS Virtual Visits

    CERN Document Server

    Goldfarb, Steven; The ATLAS collaboration

    2015-01-01

    ATLAS Virtual Visits is a project initiated in 2011 for the Education & Outreach program of the ATLAS Experiment at CERN. Its goal is to promote public appreciation of the LHC physics program and particle physics, in general, through direct dialogue between ATLAS physicists and remote audiences. A Virtual Visit is an IP-based videoconference, coupled with a public webcast and video recording, between ATLAS physicists and remote locations around the world, that typically include high school or university classrooms, Masterclasses, science fairs, or other special events, usually hosted by collaboration members. Over the past two years, more than 10,000 people, from all of the world’s continents, have actively participated in ATLAS Virtual Visits, with many more enjoying the experience from the publicly available webcasts and recordings. We present an overview of our experience and discuss potential development for the future.

  2. SIS: a program to generate draft genome sequence scaffolds for prokaryotes

    Directory of Open Access Journals (Sweden)

    Dias Zanoni

    2012-05-01

    Full Text Available Abstract Background Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of sis, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that sis has overall better performance. Conclusions sis is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of sis in our tests adds evidence that large

  3. Genomic tools in pea breeding programs: status and perspectives

    Directory of Open Access Journals (Sweden)

    Nadim eTAYEH

    2015-11-01

    Full Text Available Pea (Pisum sativum L. is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25 percent protein, complex starch and fibre constituents and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tonnes produced in 2013. Pea breeding has achieved great success since the time of Mendel’s experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress towards deciphering the pea genome.

  4. Expression profiles of pivotal microRNAs and targets in thyroid papillary carcinoma: an analysis of The Cancer Genome Atlas

    Directory of Open Access Journals (Sweden)

    Cong D

    2015-08-01

    Full Text Available Dan Cong,1 Mengzi He,2 Silin Chen,2 Xiaoli Liu,1 Xiaodong Liu,2 Hui Sun11Jilin Provincial Key Laboratory of Surgical Translational Medicine, Department of Thyroid and Parathyroid Surgery, People’s Republic of China–Japan Union Hospital, 2Key Laboratory of Radiobiology (Ministry of Health, School of Public Health, Jilin University, Changchun, Jilin, People’s Republic of ChinaAbstract: In the present study, we analyzed microRNA (miRNA and gene expression profiles using 499 papillary thyroid carcinoma (PTC samples and 58 normal thyroid tissues obtained from The Cancer Genome Atlas database. A pivotal regulatory network of 18 miRNA and 16 targets was identified. Upregulated miRNAs (miR-222, miR-221, miR-146b, miR-181a/b/d, miR-34a, and miR-424 and downregulated miRNAs (miR-9-1, miR-138, miR-363, miR-20b, miR-195, and miR-152 were identified. Among them, the upregulation of miR-424 and downregulation of miR-363, miR-195, and miR-152 were not previously identified. The genes CCNE2 (also known as cyclin E2, E2F1, RARA, CCND1 (cyclin D1, RUNX1, ITGA2, MET, CDKN1A (p21, and COL4A1 were overexpressed, and AXIN2, TRAF6, BCL2, RARB, HSP90B1, FGF7, and PDGFRA were downregulated. Among them, CCNE2, COL4A1, TRAF6, and HSP90B1 were newly identified. Based on receiver operating characteristic curves, several miRNAs (miR-222, miR-221, and miR-34a and genes (CCND1 and MET were ideal diagnostic indicators, with sensitivities and specificities greater than 90%. The combination of inversely expressed miRNAs and targets improved diagnostic accuracy. In a clinical feature analysis, several miRNAs (miR-34a, miR-424, miR-20b, and miR-152 and genes (CCNE2, COL4A1, TRAF6, and HSP90B1 were associated with aggressive clinical features, which have not previously been reported. Our study not only identified a pivotal miRNA regulatory network associated with PTC but also provided evidence that miRNAs and target genes can be used as biomarkers in PTC diagnosis and clinical

  5. Flexible approaches for teaching computational genomics in a health information management program.

    Science.gov (United States)

    Zhou, Leming; Watzlaf, Valerie; Abdelhak, Mervat

    2013-01-01

    The astonishing improvement of high-throughput biotechnologies in recent years makes it possible to access a huge amount of genomic data. The association between genomic data and genetic disease has already been and will continue to be applied to personalized healthcare. Health information management (HIM) professionals are the ones who will handle personal genetic information and provide solid evidence to support physicians' diagnoses and personalized treatment strategies, and therefore they will need to have the knowledge and skills to process genomic data. In this paper, we describe flexible approaches for teaching a computational genomics course in the HIM program at the University of Pittsburgh. HIM programs at other universities may choose an appropriate approach to fit into their own curriculum.

  6. Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae

    OpenAIRE

    2006-01-01

    In viruses, programmed −1 ribosomal frameshifting (−1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify −1 PRF signals in genomic databases, (ii) apply the protocol to the yeast genome and (iii) test selected candidates at the bench. Computational analyses revealed the presence of 10 340 consensus −1 PRF signals in the yeast genome. Of...

  7. Genome-wide alterations of the DNA replication program during tumor progression

    Science.gov (United States)

    Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

    2016-08-01

    Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

  8. A Genome Sequencing Program for Novel Undiagnosed Diseases

    Science.gov (United States)

    Bloss, Cinnamon S.; Scott-Van Zeeland, Ashley A.; Topol, Sarah E.; Darst, Burcu F.; Boeldt, Debra L.; Erikson, Galina A.; Bethel, Kelly J.; Bjork, Robert L.; Friedman, Jennifer R.; Hwynn, Nelson; Patay, Bradley A.; Pockros, Paul J.; Scott, Erick R.; Simon, Ronald A.; Williams, Gary W.; Schork, Nicholas J.; Topol, Eric J.; Torkamani, Ali

    2015-01-01

    Purpose The Scripps Idiopathic Diseases of huMan (IDIOM) study aims to discover novel gene-disease relationships and provide molecular genetic diagnosis and treatment guidance for individuals with novel diseases using genome sequencing integrated with clinical assessment and multidisciplinary case review. Methods Here we describe the IDIOM study operational protocol and initial results. Results 121 cases underwent first tier review by the principal investigators to determine if the primary inclusion criteria were satisfied, 59 (48.8%) underwent second tier review by our clinician-scientist review panel, and 17 (14.0%) patients and their family members were enrolled. 60% of cases resulted in a plausible molecular diagnosis. 18% of cases resulted in a confirmed molecular diagnosis. 2 of 3 confirmed cases led to the identification of novel gene-disease relationships. In the third confirmed case, a previously described but unrecognized disease was revealed. In all three confirmed cases, a new clinical management strategy was initiated based on the genetic findings. Conclusions Genome sequencing provides tangible clinical benefit for individuals with idiopathic genetic disease, not only in the context of molecular genetic diagnosis of known rare conditions, but also in cases where prior clinical information regarding a new genetic disorder is lacking. PMID:25790160

  9. Protein - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available eins Research Program (TPRP). Data file File name: at_atlas_protein.zip File URL:... ftp://ftp.biosciencedbc.jp/archive/at_atlas/LATEST/at_atlas_protein.zip File size: 1.13 KB Simple search UR...L http://togodb.biosciencedbc.jp/togodb/view/at_atlas_protein#en Data acquisition method - Data analysis met

  10. 77 FR 16898 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Science.gov (United States)

    2012-03-22

    ... (VA) gives notice under Public Law 92-463 (Federal Advisory Committee Act) that the Genomic Medicine... health care program while applying appropriate ethical oversight and protecting the privacy of Veterans... Highway, Arlington, Virginia, from 9 a.m. to 5 p.m. The meeting is open to the public. The purpose of the...

  11. Potential benefits of genomic selection on genetic gain of small ruminant breeding programs.

    Science.gov (United States)

    Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Elsen, J M

    2013-08-01

    In conventional small ruminant breeding programs, only pedigree and phenotype records are used to make selection decisions but prospects of including genomic information are now under consideration. The objective of this study was to assess the potential benefits of genomic selection on the genetic gain in French sheep and goat breeding designs of today. Traditional and genomic scenarios were modeled with deterministic methods for 3 breeding programs. The models included decisional variables related to male selection candidates, progeny testing capacity, and economic weights that were optimized to maximize annual genetic gain (AGG) of i) a meat sheep breeding program that improved a meat trait of heritability (h(2)) = 0.30 and a maternal trait of h(2) = 0.09 and ii) dairy sheep and goat breeding programs that improved a milk trait of h(2) = 0.30. Values of ±0.20 of genetic correlation between meat and maternal traits were considered to study their effects on AGG. The Bulmer effect was accounted for and the results presented here are the averages of AGG after 10 generations of selection. Results showed that current traditional breeding programs provide an AGG of 0.095 genetic standard deviation (σa) for meat and 0.061 σa for maternal trait in meat breed and 0.147 σa and 0.120 σa in sheep and goat dairy breeds, respectively. By optimizing decisional variables, the AGG with traditional selection methods increased to 0.139 σa for meat and 0.096 σa for maternal traits in meat breeding programs and to 0.174 σa and 0.183 σa in dairy sheep and goat breeding programs, respectively. With a medium-sized reference population (nref) of 2,000 individuals, the best genomic scenarios gave an AGG that was 17.9% greater than with traditional selection methods with optimized values of decisional variables for combined meat and maternal traits in meat sheep, 51.7% in dairy sheep, and 26.2% in dairy goats. The superiority of genomic schemes increased with the size of the

  12. The Ethical, Legal, and Social Implications Program of the National Human Genome Research Institute: reflections on an ongoing experiment.

    Science.gov (United States)

    McEwen, Jean E; Boyer, Joy T; Sun, Kathie Y; Rothenberg, Karen H; Lockhart, Nicole C; Guyer, Mark S

    2014-01-01

    For more than 20 years, the Ethical, Legal, and Social Implications (ELSI) Program of the National Human Genome Research Institute has supported empirical and conceptual research to anticipate and address the ethical, legal, and social implications of genomics. As a component of the agency that funds much of the underlying science, the program has always been an experiment. The ever-expanding number of issues the program addresses and the relatively low level of commitment on the part of other funding agencies to support such research make setting priorities especially challenging. Program-supported studies have had a significant impact on the conduct of genomics research, the implementation of genomic medicine, and broader public policies. The program's influence is likely to grow as ELSI research, genomics research, and policy development activities become increasingly integrated. Achieving the benefits of increased integration while preserving the autonomy, objectivity, and intellectual independence of ELSI investigators presents ongoing challenges and new opportunities.

  13. Renal cell tumors with clear cell histology and intact VHL and chromosome 3p: a histological review of tumors from the Cancer Genome Atlas database.

    Science.gov (United States)

    Favazza, Laura; Chitale, Dhananjay A; Barod, Ravi; Rogers, Craig G; Kalyana-Sundaram, Shanker; Palanisamy, Nallasivam; Gupta, Nilesh S; Williamson, Sean R

    2017-07-21

    Clear cell renal cell carcinoma is by far the most common form of kidney cancer; however, a number of histologically similar tumors are now recognized and considered distinct entities. The Cancer Genome Atlas published data set was queried (http://cbioportal.org) for clear cell renal cell carcinoma tumors lacking VHL gene mutation and chromosome 3p loss, for which whole-slide images were reviewed. Of the 418 tumors in the published Cancer Genome Atlas clear cell renal cell carcinoma database, 387 had VHL mutation, copy number loss for chromosome 3p, or both (93%). Of the remaining, 27/31 had whole-slide images for review. One had 3p loss based on karyotype but not sequencing, and three demonstrated VHL promoter hypermethylation. Nine could be reclassified as distinct or emerging entities: translocation renal cell carcinoma (n=3), TCEB1 mutant renal cell carcinoma (n=3), papillary renal cell carcinoma (n=2), and clear cell papillary renal cell carcinoma (n=1). Of the remaining, 6 had other clear cell renal cell carcinoma-associated gene alterations (PBRM1, SMARCA4, BAP1, SETD2), leaving 11 specimens, including 2 high-grade or sarcomatoid renal cell carcinomas and 2 with prominent fibromuscular stroma (not TCEB1 mutant). One of the remaining tumors exhibited gain of chromosome 7 but lacked histological features of papillary renal cell carcinoma. Two tumors previously reported to harbor TFE3 gene fusions also exhibited VHL mutation, chromosome 3p loss, and morphology indistinguishable from clear cell renal cell carcinoma, the significance of which is uncertain. In summary, almost all clear cell renal cell carcinomas harbor VHL mutation, 3p copy number loss, or both. Of tumors with clear cell histology that lack these alterations, a subset can now be reclassified as other entities. Further study will determine whether additional entities exist, based on distinct genetic pathways that may have implications for treatment.Modern Pathology advance online publication, 21

  14. Atlas – a data warehouse for integrative bioinformatics

    Directory of Open Access Journals (Sweden)

    Yuen Macaire MS

    2005-02-01

    Full Text Available Abstract Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL calls that are implemented in a set of Application Programming Interfaces (APIs. The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD, Biomolecular Interaction Network Database (BIND, Database of Interacting Proteins (DIP, Molecular Interactions Database (MINT, IntAct, NCBI Taxonomy, Gene Ontology (GO, Online Mendelian Inheritance in Man (OMIM, LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First

  15. Data Standards for the Genomes to Life Program

    Energy Technology Data Exchange (ETDEWEB)

    Arkin, Adam; Ambrosiano, John; Babnigg, Gyorgy; Frank, Ed; Geist,Al; Giometti, Carol; Jacobsen, Janet; Samatova, Nagiza; Slater, Nancy; Taylor, Ron

    2004-01-31

    Existing GTL Projects already have produced volumes of dataand, over the course of the next five years, will produce an estimatedhundreds, or possibly thousands, of terabytes of data from hundreds ofexperiments conducted at dozens of laboratories in National Labs anduniversities across the nation. These data will be the basis forpublications by individual researchers, research groups, andmulti-institutional collaborations, and the basis for future DOEdecisions on funding further research in bioremediation. The short-termand long-term value of the data to project participants, to the DOE, andto the nation depends, however, on being able to access the data and onhow, or whether, the data are archived. The ability to access data is thestarting point for data analysis and interpretation, data integration,data mining, and development of data-driven models. Limited orinefficient data access means that less data are analyzed in acost-effective and timely manner. Data production in the GTL Program willlikely outstrip, or may have already outstripped, the ability to analyzethe data. Being able to access data depends on two key factors: datastandards and implementation of the data standards. For the purpose ofthis proposal, a data standard is defined as a standard, documented wayin which data and information about the data are describe. The attributesof the experiment in which the data were collected need to be known andthe measurements corresponding to the data collected need to bedescribed. In general terms, a data standard could be a form (electronicor paper) that is completed by a researcher or a document that prescribeshow a protocol or experiment should be described in writing.Datastandards are critical to data access because they provide a frameworkfor organizing and managing data. Researchers spend significant amountsof time managing data and information about experiments using labnotebooks, computer files, Excel spreadsheets, etc. In addition, dataoutput format

  16. Smoking correlates with increased cytoskeletal protein-related coding region mutations in the lung and head and neck datasets of the cancer genome atlas.

    Science.gov (United States)

    Yavorski, John M; Blanck, George

    2016-12-01

    Cancer from smoking tobacco is considered dependent on mutagens, but significant molecular aspects of smoking-specific, cancer development remain unknown. We defined sets of coding regions for oncoproteins, tumor suppressor proteins, and cytoskeletal-related proteins that were compared between nonsmokers and smokers, for mutation occurrences, in the lung adenocarcinoma (LUAD), head and neck squamous carcinoma (HNSC), bladder carcinoma (BLCA), and pancreatic adenocarcinoma ( PAAD) datasets from the cancer genome atlas (TCGA). We uncovered significant differences in overall mutation rates, and in mutation rates in cytoskeletal protein-related coding regions (CPCRs, including extracellular matrix protein coding regions), between nonsmokers and smokers in LUAD and HNSC (P < 0.001), raising the question of whether the CPCR mutation differences lead to different clinical courses for nonsmoker and smoker cancers. Another important question inspired by these results is, whether high smoker cancer mutation rates would facilitate genotoxicity or neoantigen-based therapies. No significant, mutation-based differences were found in the BLCA or PAAD datasets, between nonsmokers and smokers. However, a significant difference was uncovered for the average number of overall cancer mutations, in LUAD, for persons who stopped smoking more than 15 years ago, compared with more recent smokers (P < 0.032).

  17. Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the Cancer Genome Atlas.

    Science.gov (United States)

    Miller, Daniel L; Davis, J Wade; Taylor, Kristen H; Johnson, Jeff; Shi, Zonggao; Williams, Russell; Atasoy, Ulus; Lewis, James S; Stack, M Sharon

    2015-03-01

    High-risk human papillomavirus (HPV) is a causative agent for an increasing subset of oropharyngeal squamous cell carcinomas (OPSCCs), and current evidence supports these tumors as having identifiable risk factors and improved response to therapy. However, the biochemical and molecular alterations underlying the pathobiology of HPV-associated OPSCC (designated HPV(+) OPSCC) remain unclear. Herein, we profile miRNA expression patterns in HPV(+) OPSCC to provide a more detailed understanding of pathologic molecular events and to identify biomarkers that may have applicability for early diagnosis, improved staging, and prognostic stratification. Differentially expressed miRNAs were identified in RNA isolated from an initial clinical cohort of HPV(+/-) OPSCC tumors by quantitative PCR-based miRNA profiling. This oncogenic miRNA panel was validated using miRNA sequencing and clinical data from The Cancer Genome Atlas and miRNA in situ hybridization. The HPV-associated oncogenic miRNA panel has potential utility in diagnosis and disease stratification and in mechanistic elucidation of molecular factors that contribute to OPSCC development, progression, and differential response to therapy. Copyright © 2015 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  18. Efficient and exact maximum likelihood quantisation of genomic features using dynamic programming.

    Science.gov (United States)

    Song, Mingzhou; Haralick, Robert M; Boissinot, Stéphane

    2010-01-01

    An efficient and exact dynamic programming algorithm is introduced to quantise a continuous random variable into a discrete random variable that maximises the likelihood of the quantised probability distribution for the original continuous random variable. Quantisation is often useful before statistical analysis and modelling of large discrete network models from observations of multiple continuous random variables. The quantisation algorithm is applied to genomic features including the recombination rate distribution across the chromosomes and the non-coding transposable element LINE-1 in the human genome. The association pattern is studied between the recombination rate, obtained by quantisation at genomic locations around LINE-1 elements, and the length groups of LINE-1 elements, also obtained by quantisation on LINE-1 length. The exact and density-preserving quantisation approach provides an alternative superior to the inexact and distance-based univariate iterative k-means clustering algorithm for discretisation.

  19. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database

    Science.gov (United States)

    Tian, Feng; Zhao, Jinlong; Kang, Zhenxing

    2017-01-01

    Background Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. Methods We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. Results Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. Conclusions The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.

  20. Weighted gene co-expression network analysis in identification of metastasis-related genes of lung squamous cell carcinoma based on the Cancer Genome Atlas database.

    Science.gov (United States)

    Tian, Feng; Zhao, Jinlong; Fan, Xinlei; Kang, Zhenxing

    2017-01-01

    Lung squamous cell carcinoma (lung SCC) is a common type of malignancy. Its pathogenesis mechanism of tumor development is unclear. The aim of this study was to identify key genes for diagnosis biomarkers in lung SCC metastasis. We searched and downloaded mRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database to identify differences in mRNA expression of primary tumor tissues from lung SCC with and without metastasis. Gene co-expression network analysis, protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and quantitative real-time polymerase chain reactions (qRT-PCR) were used to explore the biological functions of the identified dysregulated genes. Four hundred and eighty-two differentially expressed genes (DEGs) were identified between lung SCC with and without metastasis. Nineteen modules were identified in lung SCC through weighted gene co-expression network analysis (WGCNA). Twenty-three DEGs and 26 DEGs were significantly enriched in the respective pink and black module. KEGG pathway analysis displayed that 26 DEGs in the black module were significantly enriched in bile secretion pathway. Forty-nine DEGs in the two gene co-expression module were used to construct PPI network. CFTR in the black module was the hub protein, had the connectivity with 182 genes. The results of qRT-PCR displayed that FIGF, SFTPD, DYNLRB2 were significantly down-regulated in the tumor samples of lung SCC with metastasis and CFTR, SCGB3A2, SSTR1, SCTR, ROPN1L had the down-regulation tendency in lung SCC with metastasis compared to lung SCC without metastasis. The dysregulated genes including CFTR, SCTR and FIGF might be involved in the pathology of lung SCC metastasis and could be used as potential diagnosis biomarkers or therapeutic targets for lung SCC.

  1. Anatomy atlases.

    Science.gov (United States)

    Rosse, C

    1999-01-01

    Anatomy atlases are unlike other knowledge sources in the health sciences in that they communicate knowledge through annotated images without the support of narrative text. An analysis of the knowledge component represented by images and the history of anatomy atlases suggest some distinctions that should be made between atlas and textbook illustrations. Textbook and atlas should synergistically promote the generation of a mental model of anatomy. The objective of such a model is to support anatomical reasoning and thereby replace memorization of anatomical facts. Criteria are suggested for selecting anatomy texts and atlases that complement one another, and the advantages and disadvantages of hard copy and computer-based anatomy atlases are considered.

  2. TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.

    Science.gov (United States)

    Iwayanagi, Takao; Miyamoto, Sei; Konno, Takeshi; Mizutani, Hisashi; Hirai, Tomohiro; Shigemoto, Yasumasa; Gojobori, Takashi; Sugawara, Hideaki

    2012-09-01

    The Targeted Proteins Research Program (TPRP) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan is the phase II of structural biology project (2007-2011) following the Protein 3000 Project (2002-2006) in Japan. While the phase I Protein 3000 Project put partial emphasis on the construction and maintenance of pipelines for structural analyses, the TPRP is dedicated to revealing the structures and functions of the targeted proteins that have great importance in both basic research and industrial applications. To pursue this objective, 35 Targeted Proteins (TP) Projects selected in the three areas of fundamental biology, medicine and pharmacology, and food and environment are tightly collaborated with 10 Advanced Technology (AT) Projects in the four fields of protein production, structural analyses, chemical library and screening, and information platform. Here, the outlines and achievements of the 35 TP Projects are summarized in the system named TP Atlas. Progress in the diversified areas is described in the modules of Graphical Summary, General Summary, Tabular Summary, and Structure Gallery of the TP Atlas in the standard and unified format. Advances in TP Projects owing to novel technologies stemmed from AT Projects and collaborative research among TP Projects are illustrated as a hallmark of the Program. The TP Atlas can be accessed at http://net.genes.nig.ac.jp/tpatlas/index_e.html .

  3. A genome resource to address mechanisms of developmental programming: determination of the fetal sheep heart transcriptome.

    Science.gov (United States)

    Cox, Laura A; Glenn, Jeremy P; Spradling, Kimberly D; Nijland, Mark J; Garcia, Roy; Nathanielsz, Peter W; Ford, Stephen P

    2012-06-15

    The pregnant sheep has provided seminal insights into reproduction related to animal and human development (ovarian function, fertility, implantation, fetal growth, parturition and lactation). Fetal sheep physiology has been extensively studied since 1950, contributing significantly to the basis for our understanding of many aspects of fetal development and behaviour that remain in use in clinical practice today. Understanding mechanisms requires the combination of systems approaches uniquely available in fetal sheep with the power of genomic studies. Absence of the full range of sheep genomic resources has limited the full realization of the power of this model, impeding progress in emerging areas of pregnancy biology such as developmental programming. We have examined the expressed fetal sheep heart transcriptome using high-throughput sequencing technologies. In so doing we identified 36,737 novel transcripts and describe genes, gene variants and pathways relevant to fundamental developmental mechanisms. Genes with the highest expression levels and with novel exons in the fetal heart transcriptome are known to play central roles in muscle development. We show that high-throughput sequencing methods can generate extensive transcriptome information in the absence of an assembled and annotated genome for that species. The gene sequence data obtained provide a unique genomic resource for sheep specific genetic technology development and, combined with the polymorphism data, augment annotation and assembly of the sheep genome. In addition, identification and pathway analysis of novel fetal sheep heart transcriptome splice variants is a first step towards revealing mechanisms of genetic variation and gene environment interactions during fetal heart development.

  4. Strategies for use of reproductive technologies in genomic dairy cattle breeding programs

    DEFF Research Database (Denmark)

    Thomasen, Jørn Rind; Sørensen, Anders Christian

    A simulation study was performed for testing the effect of using reproductive technologies in a genomic dairy cattle young bull breeding scheme. The breeding scheme parameters: 1) number of donors, 2) number of progeny per donor, 3) age of the donor, 4) number of sires, and 5) reliability...... of genomic breeding values. The breeding schemes were evaluated according to genetic gain and rate of inbreeding. The relative gain by use of reproductive technologies is 11 to 84 percent points depending on the choice of other breeding scheme parameters. A large donor program with high selection intensity...... of sires provides the highest genetic gain. A relatively higher genetic gain is obtained for higher reliability of GEBV. Extending the donor program and number of selected bulls has a major effect of reducing the rate of inbreeding without compromising genetic gain....

  5. Economic evaluation of genomic selection in small ruminants: a sheep meat breeding program.

    Science.gov (United States)

    Shumbusho, F; Raoul, J; Astruc, J M; Palhiere, I; Lemarié, S; Fugeray-Scarbel, A; Elsen, J M

    2016-06-01

    Recent genomic evaluation studies using real data and predicting genetic gain by modeling breeding programs have reported moderate expected benefits from the replacement of classic selection schemes by genomic selection (GS) in small ruminants. The objectives of this study were to compare the cost, monetary genetic gain and economic efficiency of classic selection and GS schemes in the meat sheep industry. Deterministic methods were used to model selection based on multi-trait indices from a sheep meat breeding program. Decisional variables related to male selection candidates and progeny testing were optimized to maximize the annual monetary genetic gain (AMGG), that is, a weighted sum of meat and maternal traits annual genetic gains. For GS, a reference population of 2000 individuals was assumed and genomic information was available for evaluation of male candidates only. In the classic selection scheme, males breeding values were estimated from own and offspring phenotypes. In GS, different scenarios were considered, differing by the information used to select males (genomic only, genomic+own performance, genomic+offspring phenotypes). The results showed that all GS scenarios were associated with higher total variable costs than classic selection (if the cost of genotyping was 123 euros/animal). In terms of AMGG and economic returns, GS scenarios were found to be superior to classic selection only if genomic information was combined with their own meat phenotypes (GS-Pheno) or with their progeny test information. The predicted economic efficiency, defined as returns (proportional to number of expressions of AMGG in the nucleus and commercial flocks) minus total variable costs, showed that the best GS scenario (GS-Pheno) was up to 15% more efficient than classic selection. For all selection scenarios, optimization increased the overall AMGG, returns and economic efficiency. As a conclusion, our study shows that some forms of GS strategies are more advantageous

  6. A survey of application: genomics and genetic programming, a new frontier.

    Science.gov (United States)

    Khan, Mohammad Wahab; Alam, Mansaf

    2012-08-01

    The aim of this paper is to provide an introduction to the rapidly developing field of genetic programming (GP). Particular emphasis is placed on the application of GP to genomics. First, the basic methodology of GP is introduced. This is followed by a review of applications in the areas of gene network inference, gene expression data analysis, SNP analysis, epistasis analysis and gene annotation. Finally this paper concluded by suggesting potential avenues of possible future research on genetic programming, opportunities to extend the technique, and areas for possible practical applications.

  7. Design and implementation of a genomics field trip program aimed at secondary school students.

    Directory of Open Access Journals (Sweden)

    Jennifer McQueen

    Full Text Available With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics tools and concepts to secondary school students. Our approach has been to offer a full-day field trip in our research facility where secondary school students carry out experiments at the laboratory bench and on a laptop computer. This experience offers benefits for students, teachers, and field trip instructors. In delivering a wide variety of science outreach and education programs, we have learned that a number of factors contribute to designing a successful experience for secondary school students. First, it is important to engage students with authentic and fun activities that are linked to real-world applications and/or research questions. Second, connecting with a local high school teacher to pilot programs and linking to curricula taught in secondary schools will enrich the field trip experience. Whether or not programs are linked directly to local teachers, it is important to be flexible and build in mechanisms for collecting feedback in field trip programs. Finally, graduate students can be very powerful mentors for students and should be encouraged to share their enthusiasm for science and to talk about career paths. Our experiences suggest a real need for effective science outreach programs at the secondary school level and that genomics and bioinformatics are ideal areas to explore.

  8. Design and implementation of a genomics field trip program aimed at secondary school students.

    Science.gov (United States)

    McQueen, Jennifer; Wright, Jody J; Fox, Joanne A

    2012-01-01

    With the rapid pace of advancements in biological research brought about by the application of computer science and information technology, we believe the time is right for introducing genomics and bioinformatics tools and concepts to secondary school students. Our approach has been to offer a full-day field trip in our research facility where secondary school students carry out experiments at the laboratory bench and on a laptop computer. This experience offers benefits for students, teachers, and field trip instructors. In delivering a wide variety of science outreach and education programs, we have learned that a number of factors contribute to designing a successful experience for secondary school students. First, it is important to engage students with authentic and fun activities that are linked to real-world applications and/or research questions. Second, connecting with a local high school teacher to pilot programs and linking to curricula taught in secondary schools will enrich the field trip experience. Whether or not programs are linked directly to local teachers, it is important to be flexible and build in mechanisms for collecting feedback in field trip programs. Finally, graduate students can be very powerful mentors for students and should be encouraged to share their enthusiasm for science and to talk about career paths. Our experiences suggest a real need for effective science outreach programs at the secondary school level and that genomics and bioinformatics are ideal areas to explore.

  9. Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, Matthew; Gillette, Michael; Carr, Steven A.; Paulovich, Amanda G.; Smith, Richard D.; Rodland, Karin D.; Townsend, Reid; Kinsinger, Christopher; Mesri, Mehdi; Rodriguez, Henry; Liebler, Daniel

    2013-10-03

    The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium is applying the latest generation of proteomic technologies to genomically annotated tumors from The Cancer Genome Atlas (TCGA) program, a joint initiative of the NCI and the National Human Genome Research Institute. By providing a fully integrated accounting of DNA, RNA, and protein abnormalities in individual tumors, these datasets will illuminate the complex relationship between genomic abnormalities and cancer phenotypes, thus producing biologic insights as well as a wave of novel candidate biomarkers and therapeutic targets amenable to verifi cation using targeted mass spectrometry methods.

  10. Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs.

    Science.gov (United States)

    Gonen, Serap; Jenko, Janez; Gorjanc, Gregor; Mileham, Alan J; Whitelaw, C Bruce A; Hickey, John M

    2017-01-04

    This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome. We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance [Formula: see text], rate of change in inbreeding ([Formula: see text]), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles. Gene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain. Genome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency

  11. Genomics technologies to study structural variations in the grapevine genome

    Directory of Open Access Journals (Sweden)

    Cardone Maria Francesca

    2016-01-01

    Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

  12. Integration of the Atlas of Natural Hazards and the Ecological Territorial Order Program for Puerto Vallarta using GIS.

    Science.gov (United States)

    Trejo-Gómez, E.; Nuñez-Cornu, F.; Suarez-Plascencia, C.; Chavez-Dagostino, R.

    2006-12-01

    The Atlas of Natural Hazards in Puerto Vallarta (ARN) and the Ecological Territorial Order Program (POET), are documents needed to carry out recommendations to the municipal adminitrations for tasks such as the preservation and recoverment of important zones conserning the natural environment in Puerto Vallarta. These tasks can improve the quality level of life and offer security to the financial investors of this tourist destiny. Both documents are generated with the support of HABITAT Program by the Secretary's of Social Development (SEDESOL) and City Council of Puerto Vallarta. The purpose of this work is to recommend the implementation of a Geographical Information System with the ARN and POET, that responds to the necessities of the municipal goverment in areas like State and Municipal Civil Defense, Urban Planning, Tourism and Ecology. The study has a surface of 340.75 square kilometers and the initial information corresponds to a restitution of year 2000; on graphic scale 1:20,000. At the moment, we have alredy included the descriptions of geology, morphology, seismology, hydrology, type of vegetation, flora and fauna with protected and endemic species. By means of field work, we have related 266 sites with geophysical and hydrometereological hazards. The practices performed by the population in these sites increase their own risk. We have also delimited hazard zones by rock fall, flows and floods along the routes. The valuation is obtained like Affectation-Surface including consolidated houses of different surplus values. In the future, it will be necessary to keep updated the ARN and quantify the information of risks caussed by natural hazards in Puerto Vallarta.

  13. Atlas C++ Coding Standard Specification

    CERN Document Server

    Albrand, S; Barberis, D; Bosman, M; Jones, B; Stavrianakou, M; Arnault, C; Candlin, D; Candlin, R; Franck, E; Hansl-Kozanecka, Traudl; Malon, D; Qian, S; Quarrie, D; Schaffer, R D

    2001-01-01

    This document defines the ATLAS C++ coding standard, that should be adhered to when writing C++ code. It has been adapted from the original "PST Coding Standard" document (http://pst.cern.ch/HandBookWorkBook/Handbook/Programming/programming.html) CERN-UCO/1999/207. The "ATLAS standard" comprises modifications, further justification and examples for some of the rules in the original PST document. All changes were discussed in the ATLAS Offline Software Quality Control Group and feedback from the collaboration was taken into account in the "current" version.

  14. 22 March 2012 - Canada Foundation for Innovation Senior Programs Officer H.-C. Bandulet with spouse in the ATLAS visitor centre guided by Former Spokesperson P. Jenni.

    CERN Multimedia

    Maximilien Brice

    2012-01-01

    CERN-HI-1203073 16: Senior Canadian Scientist, ATLAS Collaboration, University of Toronto/IPP R. Teuscher; L. Andrzejewski(Spouse); H.-C. Bandulet; R.Voss (behind);ATLAS Collaboration, University of Toronto N.Ilic; ;ATLAS Collaboration, University of Toronto, R. Rezvani; ATLAS Collaboration Former Spokesperson P. Jenni.

  15. A time for atlases and atlases for time

    Directory of Open Access Journals (Sweden)

    Yoav Livneh

    2010-02-01

    Full Text Available Advances in neuroanatomy and computational power are leading to the construction of new digital brain atlases. Atlases are rising as indispensable tools for comparing anatomical data as well as being stimulators of new hypotheses and experimental designs. Brain atlases describe nervous systems which are inherently plastic and variable. Thus, the levels of brain plasticity and stereotypy would be important to evaluate as limiting factors in the context of static brain atlases. In this review, we discuss the extent of structural changes which neurons undergo over time, and how these changes would impact the static nature of atlases. We describe the anatomical stereotypy between neurons of the same type, highlighting the differences between invertebrates and vertebrates. We review some recent experimental advances in our understanding of anatomical dynamics in adult neural circuits, and how these are modulated by the organism’s experience. In this respect, we discuss some analogies between brain atlases and the sequenced genome and the emerging epigenome. We argue that variability and plasticity of neurons are substantially high, and should thus be considered as integral features of high-resolution digital brain atlases.

  16. Significance of the BRAF mRNA Expression Level in Papillary Thyroid Carcinoma: An Analysis of The Cancer Genome Atlas Data.

    Directory of Open Access Journals (Sweden)

    Young Jun Chai

    Full Text Available BRAFV600E is the most common mutation in papillary thyroid carcinoma (PTC, and it is associated with high-risk prognostic factors. However, the significance of the BRAF mRNA level in PTC remains unknown. We evaluated the significance of BRAF mRNA expression level by analyzing PTC data from The Cancer Genome Atlas (TCGA database.Data from 499 patients were downloaded from the TCGA database. After excluding other PTC variants, we selected 353 cases of classic PTC, including 193 cases with BRAFV600E and 160 cases with the wild-type BRAF. mRNA abundances were measured using RNA-Seq with the Expectation Maximization algorithm.The mean BRAF mRNA level was significantly higher in BRAFV600E patients than in patients with wild-type BRAF (197.6 vs. 179.3, p = 0.031. In wild-type BRAF patients, the mean BRAF mRNA level was higher in cases with a tumor > 2 cm than those with a tumor ≤ 2.0 cm (189.4 vs. 163.8, p = 0.046, and was also higher in cases with lymph node metastasis than in those without lymph node metastasis (188.5 vs. 157.9, p = 0.040. Within BRAFV600E patients, higher BRAF mRNA expression was associated with extrathyroidal extension (186.4 vs. 216.4, p = 0.001 and higher T stage (188.1 vs. 210.2, p = 0.016.A higher BRAF mRNA expression level was associated with tumor aggressiveness in classic PTC regardless of BRAF mutational status. Evaluation of BRAF mRNA level may be helpful in prognostic risk stratification of PTC.

  17. Report on the Imaging Workshop for the Genomes to Life Program, April 16-18, 2002

    Energy Technology Data Exchange (ETDEWEB)

    Colson, STEVEN

    2003-08-04

    This report is a result of the Imaging Workshop for the Genomes to Life (GTL) program held April 16-19, 2002, in Charlotte, North Carolina. The meeting was sponsored by the Office of Biological and Environmental Research and the Office of Advanced Scientific Computing Research of the U.S. Department of Energy's (DOE) Office of Science. The purpose of the workshop was to project a broad vision for future needs and determine the value of imaging to GTL program research. The workshop included four technical sessions with plenary lectures on biology and technology perspectives and technical presentations on needs and approaches as they related to the following areas of the GTL program: (1) Molecular machines (protein complexes); (2) Intracellular and cellular structure, function, and processes; (3) Multicellular: Monoclonal and heterogeneous multicellular systems, cell-cell signaling, and model systems; and (4) Cells in situ and in vivo: Bacteria in the natural environment, microenvironment, and in vivo systems.

  18. Large scale digital atlases in neuroscience

    Science.gov (United States)

    Hawrylycz, M.; Feng, D.; Lau, C.; Kuan, C.; Miller, J.; Dang, C.; Ng, L.

    2014-03-01

    Imaging in neuroscience has revolutionized our current understanding of brain structure, architecture and increasingly its function. Many characteristics of morphology, cell type, and neuronal circuitry have been elucidated through methods of neuroimaging. Combining this data in a meaningful, standardized, and accessible manner is the scope and goal of the digital brain atlas. Digital brain atlases are used today in neuroscience to characterize the spatial organization of neuronal structures, for planning and guidance during neurosurgery, and as a reference for interpreting other data modalities such as gene expression and connectivity data. The field of digital atlases is extensive and in addition to atlases of the human includes high quality brain atlases of the mouse, rat, rhesus macaque, and other model organisms. Using techniques based on histology, structural and functional magnetic resonance imaging as well as gene expression data, modern digital atlases use probabilistic and multimodal techniques, as well as sophisticated visualization software to form an integrated product. Toward this goal, brain atlases form a common coordinate framework for summarizing, accessing, and organizing this knowledge and will undoubtedly remain a key technology in neuroscience in the future. Since the development of its flagship project of a genome wide image-based atlas of the mouse brain, the Allen Institute for Brain Science has used imaging as a primary data modality for many of its large scale atlas projects. We present an overview of Allen Institute digital atlases in neuroscience, with a focus on the challenges and opportunities for image processing and computation.

  19. BAP1 is overexpressed in black compared with white patients with Mx-M1 clear cell renal cell carcinoma: A report from the cancer genome atlas.

    Science.gov (United States)

    Paulucci, David J; Sfakianos, John P; Yadav, Shalini Singh; Badani, Ketan K

    2016-06-01

    Incidence of renal cell carcinoma (RCC) is higher in Black patients with disease-specific and overall survival being lower compared with White patients even though renal tumors among Black patients are more likely to be localized. These disparities have been attributed to higher rates of obesity and hypertension, lower rates of nephrectomy, and a lack of access to quality health care. With scant genomic evidence to account for these disparities, the present study sought to compare BAP1 expression between Black and White patients with clear cell RCC (ccRCC); a gene that inhibits tumor progression when overexpressed and results in poor clinical outcomes when silenced. The cancer genome atlas dataset was used to identify 58 (9.9%) Black and 529 (90.9%) White patients with ccRCC with an initial pathologic diagnosis from 1998 to 2013. BAP1 expression was compared using a Mann-Whitney U test. The association between BAP1 expression and pathologic stage, American Joint Committee on Cancer (AJCC) stage, and Fuhrman grade was assessed for the overall cohort and stratified by race. The association between BAP1 expression and overall survival was assessed using Cox proportion hazards models adjusting for Fuhrman grade, pathologic stage, and the presence of pathologic metastases for the overall cohort and stratified by race. The level of BAP1 expression was significantly higher in Black vs. White patients with ccRCC (10.5 vs. 10.3; P<.001). For the overall cohort, increasing BAP1 expression was associated with decreasing pathologic stage (β =-0.25, P = .004) and decreasing AJCC stage (β =-0.029, P = .006). For Black patients, increasing BAP1 expression was associated with decreasing AJCC stage (β =-0.79, P = .016), decreasing Fuhrman grade (β =-0.55, P = .011), and a decreased risk of pathologic metastases (odds ratio [OR] = 0.83, P = .038). For White patients, increasing BAP1 expression was associated with decreasing pathologic stage (β =-0.20, P = .026). BAP1 is

  20. Data and analysis of the cancer genome atlas%癌症基因组图谱计划数据及分析

    Institute of Scientific and Technical Information of China (English)

    邓祯祥(综述); 李金明(审校)

    2014-01-01

    Multiple chromosomal aberrations, nucleotide substitutions, and epigenetic modifications may occur in human cancer cells, which drive malignant transformation. The Cancer Genome Atlas (TCGA) project aims to promote large-scale multi-dimensional analysis of these molecular characteristics in human cancer and rapidly provide data to researchers. In this study, we introduce four flow paths of the production of TCGA data, the collections of various cancer types, the data category and level, and the standardized pipeline of data analysis, as well as several existing data analytical tools. We used ovarian cancer as an example to introduce the application of the TCGA data in the analyses of mutation, copy number, analysis, and expression. We summarized the important findings of glioblasto-ma by TCGA teams.%人类癌症细胞中通常藏匿着多种引起恶性病变的染色体变异,核酸替换和表观遗传修饰。癌症基因组图谱(the can-cer genome atlas,TCGA)计划的目标是获取、刻画并分析人类癌症中大规模、多种变异的分子特征,并且为癌症研究者迅速地提供数据。本文对TCGA数据的四个产生流程以及包含的癌症种类、数据类型、数据水平、分析流程和常用的几种分析工具等进行阐述,同时以卵巢癌(ovarian cancer)为例详细介绍了TCGA数据在突变分析、拷贝数分析、表达分析和通路分析等方面的应用,并对TCGA研究团队近几年有关胶质母细胞瘤(glioblastoma,GBM)的研究方法和结果以及已经完成分析的癌症类型进行综述。

  1. The Human Genome Project and Mental Retardation: An Educational Program. Final Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Sharon

    1999-05-03

    The Arc, a national organization on mental retardation, conducted an educational program for members, many of whom have a family member with a genetic condition causing mental retardation. The project informed members about the Human Genome scientific efforts, conducted training regarding ethical, legal and social implications and involved members in issue discussions. Short reports and fact sheets on genetic and ELSI topics were disseminated to 2,200 of the Arc's leaders across the country and to other interested individuals. Materials produced by the project can e found on the Arc's web site, TheArc.org.

  2. READSCAN: A fast and scalable pathogen discovery program with accurate genome relative abundance estimation

    KAUST Repository

    Naeem, Raeece

    2012-11-28

    Summary: READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes (Supplementary Material). Availability: http://cbrc.kaust.edu.sa/readscan Contact: or raeece.naeem@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. 2012 The Author(s).

  3. The Herschel ATLAS

    Science.gov (United States)

    Eales, S.; Dunne, L.; Clements, D.; Cooray, A.; De Zotti, G.; Dye, S.; Ivison, R.; Jarvis, M.; Lagache, G.; Maddox, S.; Negrello, M.; Serjeant, S.; Thompson, M. A.; Van Kampen, E.; Amblard, A.; Andreani, P.; Baes, M.; Beelen, A.; Bendo, G. J.; Bertoldi, F.; Benford, D.; Bock, J.

    2010-01-01

    The Herschel ATLAS is the largest open-time key project that will be carried out on the Herschel Space Observatory. It will survey 570 sq deg of the extragalactic sky, 4 times larger than all the other Herschel extragalactic surveys combined, in five far-infrared and submillimeter bands. We describe the survey, the complementary multiwavelength data sets that will be combined with the Herschel data, and the six major science programs we are undertaking. Using new models based on a previous submillimeter survey of galaxies, we present predictions of the properties of the ATLAS sources in other wave bands.

  4. Test Data Sets and Evaluation of Gene Prediction Programs on the Rice Genome

    Institute of Scientific and Technical Information of China (English)

    Heng Li; Tao Liu; Hai-Hong Li; Yan Li; Li-Jun Fang; Hui-Min Xie; Wei-Mou Zheng; Bai-Lin Hao; Jin-Song Liu; Zhao Xu; Jiao Jin; Lin Fang; Lei Gao; Yu-Dong Li; Zi-Xing Xing; Shao-Gen Gao

    2005-01-01

    With several rice genome projects approaching completion gene prediction/finding by computer algorithms has become an urgent task. Two test sets were constructed by mapping the newly published 28,469 full-length KOME rice cDNA to the RGP BAC clone sequences of Oryza sativa ssp. japonica: a single-gene set of 550 sequences and a multi-gene set of 62 sequences with 271 genes. These data sets were used to evaluate five ab initio gene prediction programs: RiceHMM,GlimmerR, GeneMark, FGENSH and BGF. The predictions were compared on nucleotide, exon and whole gene structure levels using commonly accepted measures and several new measures. The test results show a progress in performance in chronological order. At the same time complementarity of the programs hints on the possibility of further improvement and on the feasibility of reaching better performance by combining several gene-finders.

  5. Calorimetry triggering in ATLAS

    CERN Document Server

    Igonkina, O; Adragna, P; Aharrouche, M; Alexandre, G; Andrei, V; Anduaga, X; Aracena, I; Backlund, S; Baines, J; Barnett, B M; Bauss, B; Bee, C; Behera, P; Bell, P; Bendel, M; Benslama, K; Berry, T; Bogaerts, A; Bohm, C; Bold, T; Booth, J R A; Bosman, M; Boyd, J; Bracinik, J; Brawn, I, P; Brelier, B; Brooks, W; Brunet, S; Bucci, F; Casadei, D; Casado, P; Cerri, A; Charlton, D G; Childers, J T; Collins, N J; Conde Muino, P; Coura Torres, R; Cranmer, K; Curtis, C J; Czyczula, Z; Dam, M; Damazio, D; Davis, A O; De Santo, A; Degenhardt, J; Delsart, P A; Demers, S; Demirkoz, B; Di Mattia, A; Diaz, M; Djilkibaev, R; Dobson, E; Dova, M, T; Dufour, M A; Eckweiler, S; Ehrenfeld, W; Eifert, T; Eisenhandler, E; Ellis, N; Emeliyanov, D; Enoque Ferreira de Lima, D; Faulkner, P J W; Ferland, J; Flacher, H; Fleckner, J E; Flowerdew, M; Fonseca-Martin, T; Fratina, S; Fhlisch, F; Gadomski, S; Gallacher, M P; Garitaonandia Elejabarrieta, H; Gee, C N P; George, S; Gillman, A R; Goncalo, R; Grabowska-Bold, I; Groll, M; Gringer, C; Hadley, D R; Haller, J; Hamilton, A; Hanke, P; Hauser, R; Hellman, S; Hidvgi, A; Hillier, S J; Hryn'ova, T; Idarraga, J; Johansen, M; Johns, K; Kalinowski, A; Khoriauli, G; Kirk, J; Klous, S; Kluge, E-E; Koeneke, K; Konoplich, R; Konstantinidis, N; Kwee, R; Landon, M; LeCompte, T; Ledroit, F; Lei, X; Lendermann, V; Lilley, J N; Losada, M; Maettig, S; Mahboubi, K; Mahout, G; Maltrana, D; Marino, C; Masik, J; Meier, K; Middleton, R P; Mincer, A; Moa, T; Monticelli, F; Moreno, D; Morris, J D; Mller, F; Navarro, G A; Negri, A; Nemethy, P; Neusiedl, A; Oltmann, B; Olvito, D; Osuna, C; Padilla, C; Panes, B; Parodi, F; Perera, V J O; Perez, E; Perez Reale, V; Petersen, B; Pinzon, G; Potter, C; Prieur, D P F; Prokishin, F; Qian, W; Quinonez, F; Rajagopalan, S; Reinsch, A; Rieke, S; Riu, I; Robertson, S; Rodriguez, D; Rogriquez, Y; Rhr, F; Saavedra, A; Sankey, D P C; Santamarina, C; Santamarina Rios, C; Scannicchio, D; Schiavi, C; Schmitt, K; Schultz-Coulon, H C; Schfer, U; Segura, E; Silverstein, D; Silverstein, S; Sivoklokov, S; Sjlin, J; Staley, R J; Stamen, R; Stelzer, J; Stockton, M C; Straessner, A; Strom, D; Sushkov, S; Sutton, M; Tamsett, M; Tan, C L A; Tapprogge, S; Thomas, J P; Thompson, P D; Torrence, E; Tripiana, M; Urquijo, P; Urrejola, P; Vachon, B; Vercesi, V; Vorwerk, V; Wang, M; Watkins, P M; Watson, A; Weber, P; Weidberg, T; Werner, P; Wessels, M; Wheeler-Ellis, S; Whiteson, D; Wiedenmann, W; Wielers, M; Wildt, M; Winklmeier, F; Wu, X; Xella, S; Zhao, L; Zobernig, H; de Seixas, J M; dos Anjos, A; Asman, B; Özcan, E

    2009-01-01

    The ATLAS experiment is preparing for data taking at 14 TeV collision energy. A rich discovery physics program is being prepared in addition to the detailed study of Standard Model processes which will be produced in abundance. The ATLAS multi-level trigger system is designed to accept one event in 2 105 to enable the selection of rare and unusual physics events. The ATLAS calorimeter system is a precise instrument, which includes liquid Argon electro-magnetic and hadronic components as well as a scintillator-tile hadronic calorimeter. All these components are used in the various levels of the trigger system. A wide physics coverage is ensured by inclusively selecting events with candidate electrons, photons, taus, jets or those with large missing transverse energy. The commissioning of the trigger system is being performed with cosmic ray events and by replaying simulated Monte Carlo events through the trigger and data acquisition system.

  6. ATLAS Overview Week 2009 Barcelona

    CERN Multimedia

    Claudia Marcelloni

    2009-01-01

    From October 5th to October 9th about 400 physicists from the ATLAS Collaboration met in Barcelona (Catalonia) to discuss the status of the experiment. The event was organized by the Institut de Física d'Altes Energies (IFAE), a member of the ATLAS Collaboration. Besides the Scientific program, few social events were organized, such as Reception at the Palau de Pedralbes, a visit to the Fundacio Joan Miro and a social dinner at Maremagnunm hall.

  7. The forward Detectors of the ATLAS experiment

    CERN Document Server

    Vittori, Camilla; The ATLAS collaboration

    2017-01-01

    In this poster, a review of the ATLAS forward detectors operating in the 2015-2016 data taking is given. This includes a description of LUCID, the preferred ATLAS luminosity provider; of the ALFA detector, aimed to measure elastically scattered protons at small angle for the total proton-proton cross section measurement; of the ATLAS Forward Proton project AFP, which was partially installed and took the first data in 2015, and of the Zero Degree Calorimeter ZDC built for the ATLAS Heavy Ions physics program. The near future plans for these detectors will also be addressed.

  8. Highly precise and developmentally programmed genome assembly in Paramecium requires ligase IV-dependent end joining.

    Directory of Open Access Journals (Sweden)

    Aurélie Kapusta

    2011-04-01

    Full Text Available During the sexual cycle of the ciliate Paramecium, assembly of the somatic genome includes the precise excision of tens of thousands of short, non-coding germline sequences (Internal Eliminated Sequences or IESs, each one flanked by two TA dinucleotides. It has been reported previously that these genome rearrangements are initiated by the introduction of developmentally programmed DNA double-strand breaks (DSBs, which depend on the domesticated transposase PiggyMac. These DSBs all exhibit a characteristic geometry, with 4-base 5' overhangs centered on the conserved TA, and may readily align and undergo ligation with minimal processing. However, the molecular steps and actors involved in the final and precise assembly of somatic genes have remained unknown. We demonstrate here that Ligase IV and Xrcc4p, core components of the non-homologous end-joining pathway (NHEJ, are required both for the repair of IES excision sites and for the circularization of excised IESs. The transcription of LIG4 and XRCC4 is induced early during the sexual cycle and a Lig4p-GFP fusion protein accumulates in the developing somatic nucleus by the time IES excision takes place. RNAi-mediated silencing of either gene results in the persistence of free broken DNA ends, apparently protected against extensive resection. At the nucleotide level, controlled removal of the 5'-terminal nucleotide occurs normally in LIG4-silenced cells, while nucleotide addition to the 3' ends of the breaks is blocked, together with the final joining step, indicative of a coupling between NHEJ polymerase and ligase activities. Taken together, our data indicate that IES excision is a "cut-and-close" mechanism, which involves the introduction of initiating double-strand cleavages at both ends of each IES, followed by DSB repair via highly precise end joining. This work broadens our current view on how the cellular NHEJ pathway has cooperated with domesticated transposases for the emergence of new

  9. The mitochondrial genome of the hexactinellid sponge Aphrocallistes vastus: Evidence for programmed translational frameshifting

    Directory of Open Access Journals (Sweden)

    Leys Sally P

    2008-01-01

    Full Text Available Abstract Background Mitochondrial genomes (mtDNA of numerous sponges have been sequenced as part of an ongoing effort to resolve the class-level phylogeny of the Porifera, as well as to place the various lower metazoan groups on the animal-kingdom tree. Most recently, the partial mtDNA of two glass sponges, class Hexactinellida, were reported. While previous phylogenetic estimations based on these data remain uncertain due to insufficient taxon sampling and accelerated rates of evolution, the mtDNA molecules themselves reveal interesting traits that may be unique to hexactinellids. Here we determined the first complete mitochondrial genome of a hexactinellid sponge, Aphrocallistes vastus, and compared it to published poriferan mtDNAs to further describe characteristics specific to hexactinellid and other sponge mitochondrial genomes. Results The A. vastus mtDNA consisted of a 17,427 base pair circular molecule containing thirteen protein-coding genes, divergent large and small subunit ribosomal RNAs, and a reduced set of 18 tRNAs. The A. vastus mtDNA showed a typical hexactinellid nucleotide composition and shared a large synteny with the other sequenced glass sponge mtDNAs. It also contained an unidentified open reading frame and large intergenic space region. Two frameshifts, in the cox3 and nad6 genes, were not corrected by RNA editing, but rather possessed identical shift sites marked by the extremely rare tryptophan codon (UGG followed by the common glycine codon (GGA in the +1 frame. Conclusion Hexactinellid mtDNAs have shown similar trends in gene content, nucleotide composition, and codon usage, and have retained a large gene syntenty. Analysis of the mtDNA of A. vastus has provided evidence diagnostic for +1 programmed translational frameshifting, a phenomenon disparately reported throughout the animal kingdom, but present in the hexactinellid mtDNAs that have been sequenced to date.

  10. Supporting ATLAS

    CERN Multimedia

    maximilien brice

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator.

  11. A mixed-integer linear programming approach to the reduction of genome-scale metabolic networks.

    Science.gov (United States)

    Röhl, Annika; Bockmayr, Alexander

    2017-01-03

    Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models. In 2015, Erdrich et al. introduced a method called NetworkReducer, which reduces large metabolic networks to smaller subnetworks, while preserving a set of biological requirements that can be specified by the user. Already in 2001, Burgard et al. developed a mixed-integer linear programming (MILP) approach for computing minimal reaction sets under a given growth requirement. Here we present an MILP approach for computing minimum subnetworks with the given properties. The minimality (with respect to the number of active reactions) is not guaranteed by NetworkReducer, while the method by Burgard et al. does not allow specifying the different biological requirements. Our procedure is about 5-10 times faster than NetworkReducer and can enumerate all minimum subnetworks in case there exist several ones. This allows identifying common reactions that are present in all subnetworks, and reactions appearing in alternative pathways. Applying complex analysis methods to genome-scale metabolic networks is often not possible in practice. Thus it may become necessary to reduce the size of the network while keeping important functionalities. We propose a MILP solution to this problem. Compared to previous work, our approach is more efficient and allows computing not only one, but even all minimum subnetworks satisfying the required properties.

  12. Supporting ATLAS

    CERN Multimedia

    2003-01-01

    Eighteen feet made of stainless steel will support the barrel ATLAS detector in the cavern at Point 1. In total, the ATLAS feet system will carry approximately 6000 tons, and will give the same inclination to the detector as the LHC accelerator. The installation of the feet is scheduled to finish during January 2004 with an installation precision at the 1 mm level despite their height of 5.3 metres. The manufacture was carried out in Russia (Company Izhorskiye Zavody in St. Petersburg), as part of a Russian and JINR Dubna in-kind contribution to ATLAS. Involved in the installation is a team from IHEP-Protvino (Russia), the ATLAS technical co-ordination team at CERN, and the CERN survey team. In all, about 15 people are involved. After the feet are in place, the barrel toroid magnet and the barrel calorimeters will be installed. This will keep the ATLAS team busy for the entire year 2004.

  13. Forward Detectors and Physics at ATLAS

    CERN Document Server

    Soni, N; The ATLAS collaboration

    2010-01-01

    This talk will cover the current Atlas forward detectors LUCID, ZDC, ALFA and the upgrade project AFP. The current forward detectors are dedicated for the luminosity measurements and the forward physics measurements at first low luminosity LHC phase. The AFP project will significantly extend the ATLAS physics program at high luminosities by tagging the very forward tagging protons.

  14. Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes.

    Science.gov (United States)

    Reumerman, Richard A; Tucker, Nicholas P; Herron, Paul R; Hoskisson, Paul A; Sangal, Vartul

    2013-09-01

    Next generation sequencing (NGS) has been widely used to study genomic variation in a variety of prokaryotes. Single nucleotide polymorphisms (SNPs) resulting from genomic comparisons need to be annotated for their functional impact on the coding sequences. We have developed a program, TRAMS, for functional annotation of genomic SNPs which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. TRAMS needs a tab delimited text file containing SNP locations, reference nucleotide and SNPs in variant strains along with a reference genome sequence in GenBank or EMBL format. SNPs are annotated as synonymous, nonsynonymous or nonsense. Nonsynonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in multiple overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms within a codon are combined before annotation. We have also developed a workflow for Galaxy, a highly used tool for analysing NGS data, to map short reads to a reference genome and extract and annotate the SNPs. TRAMS is a simple program for rapid and accurate annotation of SNPs that will be very useful for microbiologists in analysing genomic diversity in microbial populations.

  15. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    . RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide...... a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains...

  16. 77 FR 58913 - Genomic Medicine Program Advisory Committee, Notice of Meeting

    Science.gov (United States)

    2012-09-24

    ... applying appropriate ethical oversight and protecting the privacy of Veterans. The meeting focus will be on... challenges, and a continued discussion of the incorporation of genomic data, particularly whole genome...

  17. An Icelandic wind atlas

    Science.gov (United States)

    Nawri, Nikolai; Nína Petersen, Gudrun; Bjornsson, Halldór; Arason, Þórður; Jónasson, Kristján

    2013-04-01

    While Iceland has ample wind, its use for energy production has been limited. Electricity in Iceland is generated from renewable hydro- and geothermal source and adding wind energy has not be considered practical or even necessary. However, adding wind into the energy mix is becoming a more viable options as opportunities for new hydro or geothermal power installation become limited. In order to obtain an estimate of the wind energy potential of Iceland a wind atlas has been developed as a part of the Nordic project "Improved Forecast of Wind, Waves and Icing" (IceWind). The atlas is based on mesoscale model runs produced with the Weather Research and Forecasting (WRF) Model and high-resolution regional analyses obtained through the Wind Atlas Analysis and Application Program (WAsP). The wind atlas shows that the wind energy potential is considerable. The regions with the strongest average wind are nevertheless impractical for wind farms, due to distance from road infrastructure and power grid as well as harsh winter climate. However, even in easily accessible regions wind energy potential in Iceland, as measured by annual average power density, is among the highest in Western Europe. There is a strong seasonal cycle, with wintertime power densities throughout the island being at least a factor of two higher than during summer. Calculations show that a modest wind farm of ten medium size turbines would produce more energy throughout the year than a small hydro power plants making wind energy a viable additional option.

  18. Overview of ATLAS results

    CERN Document Server

    Grabowska-Bold, Iwona; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the Large Hadron Collider has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This talk presents recent results based on Run 2 data on production of jet, electroweak bosons and quarkonium, electromagnetic processes in ultra-peripheral collisions, and bulk particle collectivity from PbPb, pPb and pp collisions.

  19. Mongolian Atlas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Climatic atlas dated 1985, in Mongolian, with introductory material also in Russian and English. One hundred eight pages in single page PDFs.

  20. NCHHSTP Atlas

    Science.gov (United States)

    ... Sets County-level data on poverty, income, education, housing and other social factors tied to health. Buttons ... HIV STD TB DASH Youth Online Citing AtlasPlus Materials We are pleased to make these materials available, ...

  1. Conference Report: The First ATLAS.ti User Conference

    OpenAIRE

    Evers, Jeanine C.; Silver, Christina

    2014-01-01

    This report on the First ATLAS.ti User Conference shares our impressions and experiences as longstanding ATLAS.ti users and trainers about the First ATLAS.ti User Conference in Berlin 2013. The origins, conceptual principles and development of the program are outlined, the conference themes discussed and experiences shared. Finally, the future of the program is discussed.URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs1401197

  2. ATLAS @ LHC: status and recent results

    CERN Document Server

    McPherson, Robert; The ATLAS collaboration

    2017-01-01

    The status and data taking summary of the ATLAS experiment at the CERN Large Hadron Collider is reviewed. Recent physics analysis results are presented, and the detector upgrade program is briefly summarized.

  3. Genetic testing and Alzheimer disease: recommendations of the Stanford Program in Genomics, Ethics, and Society.

    Science.gov (United States)

    McConnell, L M; Koenig, B A; Greely, H T; Raffin, T A

    1999-01-01

    Several genes associated with Alzheimer disease (AD) have been localized and cloned; two genetic tests are already commercially available, and new tests are being developed. Genetic testing for AD--either for disease prediction or for diagnosis--raises critical ethical concerns. The multidisciplinary Alzheimer Disease Working Group of the Stanford Program in Genomics, Ethics, and Society (PGES) presents comprehensive recommendations on genetic testing for AD. The Group concludes that under current conditions, genetic testing for AD prediction or diagnosis is only rarely appropriate. Criteria for judging the readiness of a test for introduction into routine clinical practice typically rely heavily on evaluation of technical efficacy. PGES recommends a broader and more comprehensive approach, considering: 1) the unique social and historical meanings of AD; 2) the availability of procedures to promote good surrogate decision making for incompetent patients and to safeguard confidentiality; 3) access to sophisticated genetic counselors able to communicate complex risk information and effectively convey the social costs and psychological burdens of testing, such as unintentional disclosure of predictive genetic information to family members; 4) protection from inappropriate advertising and marketing of genetic tests; and 5) recognition of the need for public education about the meaning and usefulness of predictive and diagnostic tests for AD. In this special issue of Genetic Testing, the PGES recommendations are published along with comprehensive background papers authored by Working Group members.

  4. MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.

    Science.gov (United States)

    Turki, Turki; Roshan, Usman

    2014-11-15

    Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes. We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the highest scoring fragment for exact alignment. We evaluate MaxSSmap's accuracy and runtime when mapping simulated Illumina E.coli and human chromosome one reads of different lengths and 10% to 30% mismatches with gaps to the E.coli genome and human chromosome one. We also demonstrate applications on real data by mapping ancient horse DNA reads to modern genomes and unmapped paired reads from NA12878 in 1000 genomes. We show that MaxSSmap attains comparable high accuracy and low error to fast Smith-Waterman programs yet has much lower runtimes. We show that MaxSSmap can map reads rejected by BWA and NextGenMap with high accuracy and low error much faster than if Smith-Waterman were used. On short read lengths of 36 and 51 both MaxSSmap and Smith-Waterman have lower accuracy compared to at higher lengths. On real data MaxSSmap produces many alignments with high score and mapping quality that are not given by NextGenMap and BWA. The MaxSSmap source code in CUDA and OpenCL is freely available from http://www.cs.njit.edu/usman/MaxSSmap.

  5. 75 FR 61861 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Science.gov (United States)

    2010-10-06

    ... ethical oversight and protecting the privacy of Veterans; and receive updates on genomics initiatives within Patient Care Services; efforts to increase genetics education among VA Nursing Staff; and...

  6. Networks in ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; The ATLAS collaboration

    2017-01-01

    Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks....

  7. Networks in ATLAS

    CERN Document Server

    Mc Kee, Shawn Patrick; The ATLAS collaboration

    2016-01-01

    Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks....

  8. An Innovative Plant Genomics and Gene Annotation Program for High School, Community College, and University Faculty

    Science.gov (United States)

    Hacisalihoglu, Gokhan; Hilgert, Uwe; Nash, E. Bruce; Micklos, David A.

    2008-01-01

    Today's biology educators face the challenge of training their students in modern molecular biology techniques including genomics and bioinformatics. The Dolan DNA Learning Center (DNALC) of Cold Spring Harbor Laboratory has developed and disseminated a bench- and computer-based plant genomics curriculum for biology faculty. In 2007, a five-day…

  9. Assessment of the scientific-technological production in molecular biology in Brazil (1996-2007): the contribution of genomics programs.

    Science.gov (United States)

    Meneghini, Rogério; Gamba, Estêvão C

    2011-06-01

    Several genome sequencing programs were launched in Brazil by the end of the nineties and the early 2000s.The most important initiatives were supported by the ONSA program (http://watson.fapesp.br/onsa/Genoma3.htm) and aimed at gaining domain in genomic technology and bringing molecular biology to the state of art. Two main sets of data were collected in the 1996-2007 period to evaluate the results of these genome programs: the scientific production (Scopus and Web of Science databases) and the register of patents (US Patent and Trademark Office), both related to the progress of molecular biology along this period. In regard to the former, Brazil took a great leap in comparison to 17 other developed and developing countries, being only surpassed by China. As to the register of patents in the area of molecular biology, Brazil's performance lags far behind most of the countries focused in the present study, confirming the Brazilian long-standing tendency of poor achievements in technological innovations when compared with scientific production. Possible solutions to surpass this inequality are discussed.

  10. Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

    Science.gov (United States)

    Moore, Allan F; Jablonski, Kathleen A; McAteer, Jarred B; Saxena, Richa; Pollin, Toni I; Franks, Paul W; Hanson, Robert L; Shuldiner, Alan R; Knowler, William C; Altshuler, David; Florez, Jose C

    2008-09-01

    Genome-wide association scans (GWASs) have identified novel diabetes-associated genes. We evaluated how these variants impact diabetes incidence, quantitative glycemic traits, and response to preventive interventions in 3,548 subjects at high risk of type 2 diabetes enrolled in the Diabetes Prevention Program (DPP), which examined the effects of lifestyle intervention, metformin, and troglitazone versus placebo. We genotyped selected single nucleotide polymorphisms (SNPs) in or near diabetes-associated loci, including EXT2, CDKAL1, CDKN2A/B, IGF2BP2, HHEX, LOC387761, and SLC30A8 in DPP participants and performed Cox regression analyses using genotype, intervention, and their interactions as predictors of diabetes incidence. We evaluated their effect on insulin resistance and secretion at 1 year. None of the selected SNPs were associated with increased diabetes incidence in this population. After adjustments for ethnicity, baseline insulin secretion was lower in subjects with the risk genotype at HHEX rs1111875 (P = 0.01); there were no significant differences in baseline insulin sensitivity. Both at baseline and at 1 year, subjects with the risk genotype at LOC387761 had paradoxically increased insulin secretion; adjustment for self-reported ethnicity abolished these differences. In ethnicity-adjusted analyses, we noted a nominal differential improvement in beta-cell function for carriers of the protective genotype at CDKN2A/B after 1 year of troglitazone treatment (P = 0.01) and possibly lifestyle modification (P = 0.05). We were unable to replicate the GWAS findings regarding diabetes risk in the DPP. We did observe genotype associations with differences in baseline insulin secretion at the HHEX locus and a possible pharmacogenetic interaction at CDKNA2/B.

  11. The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology.

    Science.gov (United States)

    Hallin, Peter F; Binnewies, Tim T; Ussery, David W

    2008-05-01

    The development of fast and inexpensive methods for sequencing bacterial genomes has led to a wealth of data, often with many genomes being sequenced of the same species or closely related organisms. Thus, there is a need for visualization methods that will allow easy comparison of many sequenced genomes to a defined reference strain. The BLASTatlas is one such tool that is useful for mapping and visualizing whole genome homology of genes and proteins within a reference strain compared to other strains or species of one or more prokaryotic organisms. We provide examples of BLASTatlases, including the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context of regions. Additional information can be added to these plots, and as an example we have added circles showing the probability of the DNA helix opening up under superhelical tension. The tool is SOAP compliant and WSDL (web services description language) files are located on our website: (http://www.cbs.dtu.dk/ws/BLASTatlas), where programming examples are available in Perl. By providing an interoperable method to carry out whole genome visualization of homology, this service offers bioinformaticians as well as biologists an easy-to-adopt workflow that can be directly called from the programming language of the user, hence enabling automation of repeated tasks. This tool can be relevant in many pangenomic as well as in metagenomic studies, by giving a quick overview of clusters of insertion sites, genomic islands and overall homology between a reference sequence and a data set.

  12. Clinical value of miR-452-5p expression in lung adenocarcinoma: A retrospective quantitative real-time polymerase chain reaction study and verification based on The Cancer Genome Atlas and Gene Expression Omnibus databases.

    Science.gov (United States)

    Gan, Xiao-Ning; Luo, Jie; Tang, Rui-Xue; Wang, Han-Lin; Zhou, Hong; Qin, Hui; Gan, Ting-Qing; Chen, Gang

    2017-05-01

    The role and mechanism of miR-452-5p in lung adenocarcinoma remain unclear. In this study, we performed a systematic study to investigate the clinical value of miR-452-5p expression in lung adenocarcinoma. The expression of miR-452-5p in 101 lung adenocarcinoma patients was detected by quantitative real-time polymerase chain reaction. The Cancer Genome Atlas and Gene Expression Omnibus databases were joined to verify the expression level of miR-452-5p in lung adenocarcinoma. Via several online prediction databases and bioinformatics software, pathway and network analyses of miR-452-5p target genes were performed to explore its prospective molecular mechanism. The expression of miR-452-5p in lung adenocarcinoma in house was significantly lower than that in adjacent tissues (p < 0.001). Additionally, the expression level of miR-452-5p was negatively correlated with several clinicopathological parameters including the tumor size (p = 0.014), lymph node metastasis (p = 0.032), and tumor-node-metastasis stage (p = 0.036). Data from The Cancer Genome Atlas also confirmed the low expression of miR-452 in lung adenocarcinoma (p < 0.001). Furthermore, reduced expression of miR-452-5p in lung adenocarcinoma (standard mean deviations = -0.393, 95% confidence interval: -0.774 to -0.011, p = 0.044) was validated by a meta-analysis. Five hub genes targeted by miR-452-5p, including SMAD family member 4, SMAD family member 2, cyclin-dependent kinase inhibitor 1B, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta, were significantly enriched in the cell-cycle pathway. In conclusion, low expression of miR-452-5p tends to play an essential role in lung adenocarcinoma. Bioinformatics analysis might be beneficial to reveal the potential mechanism of miR-452-5p in lung adenocarcinoma.

  13. DOE Human Genome Program: Contractor-Grantee Workshop IV, November 13--17, 1994, Santa Fe, New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    1994-10-01

    This volume contains the proceedings of the fourth Contractor-Grantee Workshop for the Department of Energy (DOE) Human Genome Program. Of the 204 abstracts in this book, some 200 describe the genome research of DOE-funded grantees and contractors located at the multidisciplinary centers at Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory; other DOE-supported laboratories; and more than 54 universities, research organizations, and companies in the United States and abroad. Included are 16 abstracts from ongoing projects in the Ethical, Legal, and Social Issues (ELSI) component, an area that continues to attract considerable attention from a wide variety of interested parties. Three abstracts summarize work in the new Microbial Genome Initiative launched this year by the Office of Health and Environmental Research (OHER) to provide genome sequence and mapping data on industrially important microorganisms and those that live under extreme conditions. Many of the projects will be discussed at plenary sessions held throughout the workshop, and all are represented in the poster sessions.

  14. 75 FR 26846 - Genomic Medicine Program Advisory Committee; Notice of Meeting

    Science.gov (United States)

    2010-05-12

    ... electronic health record; an overview of an upcoming large scale study on the genetics of functional disability of mental illness; and a roll-out of the national genomics initiative, the Million Veteran...

  15. Virtual Visit to the ATLAS Control Room by the University of Genova

    CERN Multimedia

    ATLAS Experiment

    2012-01-01

    The ATLAS Virtual Visit is included in the program of the Course in Particle and Nuclear Experimental Physics at the Physics Department of the Genova University. Students are introduced to experimental techniques and instrumentation and run few experiences in the laboratory. Besides that, they visit the Department groups that are involved both in Nuclear or High Energy Particle physics experiments. In this context, the ATLAS team will open them the doors to laboratory where ~1/3 of the Pixel detector has been built and where we are currently assembling and qualifying part of the electrical services and modules for the Insertable B layer (IBL) that will be installed in 2014 in ATLAS. Students will be introduced to LHC, ATLAS and the physics program before having the possibility to meet ATLAS physicists in ATLAS control room. http://atlas-live-virtual-visit.web.cern.ch/atlas-live-virtual-visit/2012/Genova-2012.html

  16. Virtual Visit to the ATLAS Control Room by the Genova University

    CERN Multimedia

    2013-01-01

    The ATLAS Virtual Visit is included in the program of the Course in Particle and Nuclear Experimental Physics at the Physics Department of the Genova University. Students are introduced to experimental techniques and instrumentation and run few experiences in the laboratory. Besides that, they visit the Department groups that are involved both in Nuclear or High Energy Particle physics experiments. In this context, the ATLAS team will open them the doors to laboratory where ~1/3 of the Pixel detector has been built and where we are currently assembling and qualifying part of the electrical services and modules for the Insertable B layer (IBL) that will be installed in 2014 in ATLAS. Students will be introduced to LHC, ATLAS and the physics program before having the possibility to meet ATLAS physicists in ATLAS control room. http://atlas-live-virtual-visit.web.cern.ch/atlas-live-virtual-visit/2013/Genova-2013_2.html

  17. Virtual Visit to the ATLAS Control Room by the Genova University

    CERN Multimedia

    2013-01-01

    The ATLAS Virtual Visit is included in the program of the Course in Particle and Nuclear Experimental Physics at the Physics Department of the Genova University. Students are introduced to experimental techniques and instrumentation and run few experiences in the laboratory. Besides that, they visit the Department groups that are involved both in Nuclear or High Energy Particle physics experiments. In this context, the ATLAS team will open them the doors to laboratory where ~1/3 of the Pixel detector has been built and where we are currently assembling and qualifying part of the electrical services and modules for the Insertable B layer (IBL) that will be installed in 2014 in ATLAS. Students will be introduced to LHC, ATLAS and the physics program before having the possibility to meet ATLAS physicists in ATLAS control room. http://atlas-live-virtual-visit.web.cern.ch/atlas-live-virtual-visit/2013/Genova-2013_1.html

  18. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-03-27

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Results: Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs.

  19. ATLAS Nightly Build System Upgrade

    CERN Document Server

    Dimitrov, G; The ATLAS collaboration; Simmons, B; Undrus, A

    2014-01-01

    The ATLAS Nightly Build System is a facility for automatic production of software releases. Being the major component of ATLAS software infrastructure, it supports more than 50 multi-platform branches of nightly releases and provides ample opportunities for testing new packages, for verifying patches to existing software, and for migrating to new platforms and compilers. The Nightly System testing framework runs several hundred integration tests of different granularity and purpose. The nightly releases are distributed and validated, and some are transformed into stable releases used for data processing worldwide. The first LHC long shutdown (2013-2015) activities will elicit increased load on the Nightly System as additional releases and builds are needed to exploit new programming techniques, languages, and profiling tools. This paper describes the plan of the ATLAS Nightly Build System Long Shutdown upgrade. It brings modern database and web technologies into the Nightly System, improves monitoring of nigh...

  20. ATLAS Nightly Build System Upgrade

    CERN Document Server

    Dimitrov, G; The ATLAS collaboration; Simmons, B; Undrus, A

    2013-01-01

    The ATLAS Nightly Build System is a facility for automatic production of software releases. Being the major component of ATLAS software infrastructure, it supports more than 50 multi-platform branches of nightly releases and provides ample opportunities for testing new packages, for verifying patches to existing software, and for migrating to new platforms and compilers. The Nightly System testing framework runs several hundred integration tests of different granularity and purpose. The nightly releases are distributed and validated, and some are transformed into stable releases used for data processing worldwide. The first LHC long shutdown (2013-2015) activities will elicit increased load on the Nightly System as additional releases and builds are needed to exploit new programming techniques, languages, and profiling tools. This paper describes the plan of the ATLAS Nightly Build System Long Shutdown upgrade. It brings modern database and web technologies into the Nightly System, improves monitoring of nigh...

  1. Cassini Tour Atlas Automated Generation

    Science.gov (United States)

    Grazier, Kevin R.; Roumeliotis, Chris; Lange, Robert D.

    2011-01-01

    During the Cassini spacecraft s cruise phase and nominal mission, the Cassini Science Planning Team developed and maintained an online database of geometric and timing information called the Cassini Tour Atlas. The Tour Atlas consisted of several hundreds of megabytes of EVENTS mission planning software outputs, tables, plots, and images used by mission scientists for observation planning. Each time the nominal mission trajectory was altered or tweaked, a new Tour Atlas had to be regenerated manually. In the early phases of Cassini s Equinox Mission planning, an a priori estimate suggested that mission tour designers would develop approximately 30 candidate tours within a short period of time. So that Cassini scientists could properly analyze the science opportunities in each candidate tour quickly and thoroughly so that the optimal series of orbits for science return could be selected, a separate Tour Atlas was required for each trajectory. The task of manually generating the number of trajectory analyses in the allotted time would have been impossible, so the entire task was automated using code written in five different programming languages. This software automates the generation of the Cassini Tour Atlas database. It performs with one UNIX command what previously took a day or two of human labor.

  2. SUSY (ATLAS)

    CERN Document Server

    Sopczak, Andre; The ATLAS collaboration

    2017-01-01

    During the data-taking period at LHC (Run-II), several searches for supersymmetric particles were performed. The results from searches by the ATLAS collaborations are concisely reviewed. Model-independent and model-dependent limits on new particle production are set, and interpretations in supersymmetric models are given.

  3. ATLAS Story

    CERN Multimedia

    AUTHOR|(CDS)2108663

    2012-01-01

    This film produced in July 2012 explains how fundamental research connects to Society and what benefits collaborative way of working can and may generate in the future, using ATLAS Collaboration as a case study. The film is intellectually inspired by the book "Collisions and Collaboration" (OUP) by Max Boisot (ed.), see: collisionsandcollaboration.com. The film is directed by Andrew Millington (OMNI Communications)

  4. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.

    Directory of Open Access Journals (Sweden)

    Zoe A Dyson

    2017-01-01

    Full Text Available Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly.

  5. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program

    Science.gov (United States)

    Thanh, Duy Pham; Bodhidatta, Ladaporn; Mason, Carl Jeffries; Srijan, Apichai; Rabaa, Maia A.; Vinh, Phat Voong; Thanh, Tuyen Ha; Thwaites, Guy E.; Baker, Stephen; Holt, Kathryn E.

    2017-01-01

    Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly. PMID:28060810

  6. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program.

    Science.gov (United States)

    Dyson, Zoe A; Thanh, Duy Pham; Bodhidatta, Ladaporn; Mason, Carl Jeffries; Srijan, Apichai; Rabaa, Maia A; Vinh, Phat Voong; Thanh, Tuyen Ha; Thwaites, Guy E; Baker, Stephen; Holt, Kathryn E

    2017-01-01

    Vaccines against Salmonella Typhi, the causative agent of typhoid fever, are commonly used by travellers, however, there are few examples of national immunization programs in endemic areas. There is therefore a paucity of data on the impact of typhoid immunization programs on localised populations of S. Typhi. Here we have used whole genome sequencing (WGS) to characterise 44 historical bacterial isolates collected before and after a national typhoid immunization program that was implemented in Thailand in 1977 in response to a large outbreak; the program was highly effective in reducing typhoid case numbers. Thai isolates were highly diverse, including 10 distinct phylogenetic lineages or genotypes. Novel prophage and plasmids were also detected, including examples that were previously only reported in Shigella sonnei and Escherichia coli. The majority of S. Typhi genotypes observed prior to the immunization program were not observed following it. Post-vaccine era isolates were more closely related to S. Typhi isolated from neighbouring countries than to earlier Thai isolates, providing no evidence for the local persistence of endemic S. Typhi following the national immunization program. Rather, later cases of typhoid appeared to be caused by the occasional importation of common genotypes from neighbouring Vietnam, Laos, and Cambodia. These data show the value of WGS in understanding the impacts of vaccination on pathogen populations and provide support for the proposal that large-scale typhoid immunization programs in endemic areas could result in lasting local disease elimination, although larger prospective studies are needed to test this directly.

  7. ATLAS Outreach Highlights

    CERN Document Server

    Cheatham, Susan; The ATLAS collaboration

    2016-01-01

    The ATLAS outreach team is very active, promoting particle physics to a broad range of audiences including physicists, general public, policy makers, students and teachers, and media. A selection of current outreach activities and new projects will be presented. Recent highlights include the new ATLAS public website and ATLAS Open Data, the very recent public release of 1 fb-1 of ATLAS data.

  8. The genome BLASTatlas - a GeneWiz extension for visualization of whole-genome homology

    DEFF Research Database (Denmark)

    Hallin, Peter Fischer; Binnewies, Tim Terence; Ussery, David

    2008-01-01

    the Clostridium tetani plasmid p88, where homologues for toxin genes can be easily visualized in other sequenced Clostridium genomes, and for a Clostridium botulinum genome, compared to 14 other Clostridium genomes. DNA structural information is also included in the atlas to visualize the DNA chromosomal context...

  9. Probabilistic liver atlas construction

    OpenAIRE

    Dura, Esther; Domingo, Juan; Ayala, Guillermo; Marti-Bonmati, Luis; Goceri, E.

    2017-01-01

    Background Anatomical atlases are 3D volumes or shapes representing an organ or structure of the human body. They contain either the prototypical shape of the object of interest together with other shapes representing its statistical variations (statistical atlas) or a probability map of belonging to the object (probabilistic atlas). Probabilistic atlases are mostly built with simple estimations only involving the data at each spatial location. Results A new method for probabilistic atlas con...

  10. Controlling inbreeding and maximizing genetic gain using semi-definite programming with pedigree-based and genomic relationships.

    Science.gov (United States)

    Schierenbeck, S; Pimentel, E C G; Tietze, M; Körte, J; Reents, R; Reinhardt, F; Simianer, H; König, S

    2011-12-01

    Because of the relatively high levels of genetic relationships among potential bull sires and bull dams, innovative selection tools should consider both genetic gain and genetic relationships in a long-term perspective. Optimum genetic contribution theory using official estimated breeding values for a moderately heritable trait (production index, Index-PROD), and a lowly heritable functional trait (index for somatic cell score, Index-SCS) was applied to find optimal allocations of bull dams and bull sires. In contrast to previous practical applications using optimizations based on Lagrange multipliers, we focused on semi-definite programming (SDP). The SDP methodology was combined with either pedigree (a(ij)) or genomic relationships (f(ij)) among selection candidates. Selection candidates were 484 genotyped bulls, and 499 preselected genotyped bull dams completing a central test on station. In different scenarios separately for PROD and SCS, constraints on the average pedigree relationships among future progeny were varied from a(ij)=0.08 to a(ij)=0.20 in increments of 0.01. Corresponding constraints for single nucleotide polymorphism-based kinship coefficients were derived from regression analysis. Applying the coefficient of 0.52 with an intercept of 0.14 estimated for the regression pedigree relationship on genomic relationship, the corresponding range to alter genomic relationships varied from f(ij) = 0.18 to f(ij) = 0.24. Despite differences for some bulls in genomic and pedigree relationships, the same trends were observed for constraints on pedigree and corresponding genomic relationships regarding results in genetic gain and achieved coefficients of relationships. Generally, allowing higher values for relationships resulted in an increase of genetic gain for Index-PROD and Index-SCS and in a reduction in the number of selected sires. Interestingly, more sires were selected for all scenarios when restricting genomic relationships compared with restricting

  11. Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery

    DEFF Research Database (Denmark)

    Hickey, John M.; Chiurugwi, Tinashe; Mackay, Ian

    2017-01-01

    The rate of annual yield increases for major staple crops must more than double relative to current levels in order to feed a predicted global population of 9 billion by 2050. Controlled hybridization and selective breeding have been used for centuries to adapt plant and animal species for human...... that unifies breeding approaches, biological discovery, and tools and methods. Here we compare and contrast some animal and plant breeding approaches to make a case for bringing the two together through the application of genomic selection. We propose a strategy for the use of genomic selection as a unifying...... use. However, achieving higher, sustainable rates of improvement in yields in various species will require renewed genetic interventions and dramatic improvement of agricultural practices. Genomic prediction of breeding values has the potential to improve selection, reduce costs and provide a platform...

  12. Allele frequency changes due to hitch-hiking in genomic selection programs

    DEFF Research Database (Denmark)

    Liu, Huiming; Sørensen, Anders Christian; Meuwissen, Theo H E

    2014-01-01

    Background Genomic selection makes it possible to reduce pedigree-based inbreeding over best linear unbiased prediction (BLUP) by increasing emphasis on own rather than family information. However, pedigree inbreeding might not accurately reflect the loss of genetic variation and the true level...... of inbreeding due to changes in allele frequencies and hitch-hiking. This study aimed at understanding the impact of using long-term genomic selection on changes in allele frequencies, genetic variation and the level of inbreeding. Methods Selection was performed in simulated scenarios with a population of 400......-BLUP, Genomic BLUP and Bayesian Lasso. Changes in allele frequencies at QTL, markers and linked neutral loci were investigated for the different selection criteria and different scenarios, along with the loss of favourable alleles and the rate of inbreeding measured by pedigree and runs of homozygosity. Results...

  13. Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery.

    Science.gov (United States)

    Hickey, John M; Chiurugwi, Tinashe; Mackay, Ian; Powell, Wayne

    2017-08-30

    The rate of annual yield increases for major staple crops must more than double relative to current levels in order to feed a predicted global population of 9 billion by 2050. Controlled hybridization and selective breeding have been used for centuries to adapt plant and animal species for human use. However, achieving higher, sustainable rates of improvement in yields in various species will require renewed genetic interventions and dramatic improvement of agricultural practices. Genomic prediction of breeding values has the potential to improve selection, reduce costs and provide a platform that unifies breeding approaches, biological discovery, and tools and methods. Here we compare and contrast some animal and plant breeding approaches to make a case for bringing the two together through the application of genomic selection. We propose a strategy for the use of genomic selection as a unifying approach to deliver innovative 'step changes' in the rate of genetic gain at scale.

  14. An anatomically comprehensive atlas of the adult human brain transcriptome

    NARCIS (Netherlands)

    Hawrylycz, M.J.; Beckmann, Christian

    2012-01-01

    Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising

  15. Democratizing Human Genome Project Information: A Model Program for Education, Information and Debate in Public Libraries.

    Science.gov (United States)

    Pollack, Miriam

    The "Mapping the Human Genome" project demonstrated that librarians can help whomever they serve in accessing information resources in the areas of biological and health information, whether it is the scientists who are developing the information or a member of the public who is using the information. Public libraries can guide library…

  16. Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia

    Science.gov (United States)

    Spanier, Katina I.; Jansen, Mieke; Decaestecker, Ellen; Hulselmans, Gert; Becker, Dörthe; Colbourne, John K.; Orsini, Luisa

    2017-01-01

    Abstract Ecological genomics aims to understand the functional association between environmental gradients and the genes underlying adaptive traits. Many genes that are identified by genome-wide screening in ecologically relevant species lack functional annotations. Although gene functions can be inferred from sequence homology, such approaches have limited power. Here, we introduce ecological regulatory genomics by presenting an ontology-free gene prioritization method. Specifically, our method combines transcriptome profiling with high-throughput cis-regulatory sequence analysis in the water fleas Daphnia pulex and Daphnia magna. It screens coexpressed genes for overrepresented DNA motifs that serve as transcription factor binding sites, thereby providing insight into conserved transcription factors and gene regulatory networks shaping the expression profile. We first validated our method, called Daphnia-cisTarget, on a D. pulex heat shock data set, which revealed a network driven by the heat shock factor. Next, we performed RNA-Seq in D. magna exposed to the cyanobacterium Microcystis aeruginosa. Daphnia-cisTarget identified coregulated gene networks that associate with the moulting cycle and potentially regulate life history changes in growth rate and age at maturity. These networks are predicted to be regulated by evolutionary conserved transcription factors such as the homologues of Drosophila Shavenbaby and Grainyhead, nuclear receptors, and a GATA family member. In conclusion, our approach allows prioritising candidate genes in Daphnia without bias towards prior knowledge about functional gene annotation and represents an important step towards exploring the molecular mechanisms of ecological responses in organisms with poorly annotated genomes. PMID:28854641

  17. ATLAS Recordings

    CERN Multimedia

    Steven Goldfarb; Mitch McLachlan; Homer A. Neal

    Web Archives of ATLAS Plenary Sessions, Workshops, Meetings, and Tutorials from 2005 until this past month are available via the University of Michigan portal here. Most recent additions include the Trigger-Aware Analysis Tutorial by Monika Wielers on March 23 and the ROOT Workshop held at CERN on March 26-27.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal.Feedback WelcomeOur group is making arrangements now to record plenary sessions, tutorials, and other important ATLAS events for 2007. Your suggestions for potential recording, as well as your feedback on existing archives is always welcome. Please contact us at wlap@umich.edu. Thank you.Enjoy the Lectures!

  18. Replication of the Wellcome Trust genome-wide association study of essential hypertension: the Family Blood Pressure Program.

    Science.gov (United States)

    Ehret, Georg B; Morrison, Alanna C; O'Connor, Ashley A; Grove, Megan L; Baird, Lisa; Schwander, Karen; Weder, Alan; Cooper, Richard S; Rao, D C; Hunt, Steven C; Boerwinkle, Eric; Chakravarti, Aravinda

    2008-12-01

    Essential hypertension is a principal cardiovascular risk factor whose origin remains unknown. Classical genetic studies have shown that blood pressure is at least partially heritable, opening a window to understanding the pathophysiology of essential hypertension in the human using modern genetic tools. The Wellcome Trust Case Control Consortium has recently published the results of screening the genomes of 2000 essential hypertension cases and 3000 controls using 500 000 genome-wide single nucleotide polymorphisms (SNPs). None of the variants proved to be genome-wide significant after correction for multiple tests but the most significantly associated SNPs (PFamily Blood Pressure Program comprising 11 433 individuals recruited by hypertensive families. The results suggest that only one of the six SNPs might be associated with essential hypertension in Americans of European origin. This SNP shows a significant but opposite effect in Americans of Hispanic origin and no association in African Americans. The significance of the opposing effect estimates is unclear. No replication could be shown for hypertension status, but there are differences in study design. This attempted replication highlights that essential hypertension studies will require more comprehensive and larger genetic screens.

  19. An Introduction to China Rice Functional Genomics Program%中国水稻功能基因组学研究计划介绍

    Institute of Scientific and Technical Information of China (English)

    Yongbiao XUE; Zhihong XU; Jingliu ZHANG; Da LUO; Jiayang LI; Yaoguang LIU; Hongwei XUE; Kang CHONG; Hai HUANG; Guohua LIANG

    2002-01-01

    @@ To discover genes essential for agronomic performances of crops we initiated a program on rice functional genomics of important agronomic traits in rice in 1999. The program was funded by the Ministry of Science and Technology of China through the National Basic Research Initiative and is expected to last for five years.

  20. Ku-mediated coupling of DNA cleavage and repair during programmed genome rearrangements in the ciliate Paramecium tetraurelia.

    Directory of Open Access Journals (Sweden)

    Antoine Marmignon

    2014-08-01

    Full Text Available During somatic differentiation, physiological DNA double-strand breaks (DSB can drive programmed genome rearrangements (PGR, during which DSB repair pathways are mobilized to safeguard genome integrity. Because of their unique nuclear dimorphism, ciliates are powerful unicellular eukaryotic models to study the mechanisms involved in PGR. At each sexual cycle, the germline nucleus is transmitted to the progeny, but the somatic nucleus, essential for gene expression, is destroyed and a new somatic nucleus differentiates from a copy of the germline nucleus. In Paramecium tetraurelia, the development of the somatic nucleus involves massive PGR, including the precise elimination of at least 45,000 germline sequences (Internal Eliminated Sequences, IES. IES excision proceeds through a cut-and-close mechanism: a domesticated transposase, PiggyMac, is essential for DNA cleavage, and DSB repair at excision sites involves the Ligase IV, a specific component of the non-homologous end-joining (NHEJ pathway. At the genome-wide level, a huge number of programmed DSBs must be repaired during this process to allow the assembly of functional somatic chromosomes. To understand how DNA cleavage and DSB repair are coordinated during PGR, we have focused on Ku, the earliest actor of NHEJ-mediated repair. Two Ku70 and three Ku80 paralogs are encoded in the genome of P. tetraurelia: Ku70a and Ku80c are produced during sexual processes and localize specifically in the developing new somatic nucleus. Using RNA interference, we show that the development-specific Ku70/Ku80c heterodimer is essential for the recovery of a functional somatic nucleus. Strikingly, at the molecular level, PiggyMac-dependent DNA cleavage is abolished at IES boundaries in cells depleted for Ku80c, resulting in IES retention in the somatic genome. PiggyMac and Ku70a/Ku80c co-purify as a complex when overproduced in a heterologous system. We conclude that Ku has been integrated in the Paramecium

  1. Ku-mediated coupling of DNA cleavage and repair during programmed genome rearrangements in the ciliate Paramecium tetraurelia.

    Science.gov (United States)

    Marmignon, Antoine; Bischerour, Julien; Silve, Aude; Fojcik, Clémentine; Dubois, Emeline; Arnaiz, Olivier; Kapusta, Aurélie; Malinsky, Sophie; Bétermier, Mireille

    2014-08-01

    During somatic differentiation, physiological DNA double-strand breaks (DSB) can drive programmed genome rearrangements (PGR), during which DSB repair pathways are mobilized to safeguard genome integrity. Because of their unique nuclear dimorphism, ciliates are powerful unicellular eukaryotic models to study the mechanisms involved in PGR. At each sexual cycle, the germline nucleus is transmitted to the progeny, but the somatic nucleus, essential for gene expression, is destroyed and a new somatic nucleus differentiates from a copy of the germline nucleus. In Paramecium tetraurelia, the development of the somatic nucleus involves massive PGR, including the precise elimination of at least 45,000 germline sequences (Internal Eliminated Sequences, IES). IES excision proceeds through a cut-and-close mechanism: a domesticated transposase, PiggyMac, is essential for DNA cleavage, and DSB repair at excision sites involves the Ligase IV, a specific component of the non-homologous end-joining (NHEJ) pathway. At the genome-wide level, a huge number of programmed DSBs must be repaired during this process to allow the assembly of functional somatic chromosomes. To understand how DNA cleavage and DSB repair are coordinated during PGR, we have focused on Ku, the earliest actor of NHEJ-mediated repair. Two Ku70 and three Ku80 paralogs are encoded in the genome of P. tetraurelia: Ku70a and Ku80c are produced during sexual processes and localize specifically in the developing new somatic nucleus. Using RNA interference, we show that the development-specific Ku70/Ku80c heterodimer is essential for the recovery of a functional somatic nucleus. Strikingly, at the molecular level, PiggyMac-dependent DNA cleavage is abolished at IES boundaries in cells depleted for Ku80c, resulting in IES retention in the somatic genome. PiggyMac and Ku70a/Ku80c co-purify as a complex when overproduced in a heterologous system. We conclude that Ku has been integrated in the Paramecium DNA cleavage

  2. ATLAS UPGRADES

    CERN Document Server

    Lacasta, C; The ATLAS collaboration

    2014-01-01

    After the successful LHC operation at the center-of-mass energies of 7 and 8 TeV in 2010 - 2012, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity leveling. The final goal is to extend the dataset from about few hundred fb−1 expected for LHC running to 3000 fb−1 by around 2035 for ATLAS and CMS. In parallel the experiments need to be keep lockstep with the accelerator to accommodate running beyond the nominal luminosity this decade. Current planning in ATLAS envisions significant upgrades to the detector during the consolidation of the LHC to reach full LHC energy and further upgrades. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for ...

  3. Sequential computation of elementary modes and minimal cut sets in genome-scale metabolic networks using alternate integer linear programming.

    Science.gov (United States)

    Song, Hyun-Seob; Goldberg, Noam; Mahajan, Ashutosh; Ramkrishna, Doraiswami

    2017-08-01

    Elementary (flux) modes (EMs) have served as a valuable tool for investigating structural and functional properties of metabolic networks. Identification of the full set of EMs in genome-scale networks remains challenging due to combinatorial explosion of EMs in complex networks. It is often, however, that only a small subset of relevant EMs needs to be known, for which optimization-based sequential computation is a useful alternative. Most of the currently available methods along this line are based on the iterative use of mixed integer linear programming (MILP), the effectiveness of which significantly deteriorates as the number of iterations builds up. To alleviate the computational burden associated with the MILP implementation, we here present a novel optimization algorithm termed alternate integer linear programming (AILP). Our algorithm was designed to iteratively solve a pair of integer programming (IP) and linear programming (LP) to compute EMs in a sequential manner. In each step, the IP identifies a minimal subset of reactions, the deletion of which disables all previously identified EMs. Thus, a subsequent LP solution subject to this reaction deletion constraint becomes a distinct EM. In cases where no feasible LP solution is available, IP-derived reaction deletion sets represent minimal cut sets (MCSs). Despite the additional computation of MCSs, AILP achieved significant time reduction in computing EMs by orders of magnitude. The proposed AILP algorithm not only offers a computational advantage in the EM analysis of genome-scale networks, but also improves the understanding of the linkage between EMs and MCSs. The software is implemented in Matlab, and is provided as supplementary information . hyunseob.song@pnnl.gov. Supplementary data are available at Bioinformatics online.

  4. Proceedings of the relevance of mass spectrometry to DNA sequence determination: Research needs for the Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    Edmonds, C.G.; Smith, R.D. (Pacific Northwest Lab., Richland, WA (USA)); Smith, L.M. (Wisconsin Univ., Madison, WI (USA))

    1990-11-01

    A workshop was sponsored for the US Department of Energy (DOE), Office of Health and Environmental Research by Pacific Northwest Laboratory, April 4--5, 1990, in Seattle, Washington, to examine the potential role of mass spectrometry in the joint DOE/National Institutes of Health (NIH) Human Genome Program. The workshop was occasioned by recent developments in mass spectrometry that are providing new levels for selectivity, sensitivity, and, in particular, new methods of ionization appropriate for large biopolymers such as DNA. During discussions, three general mass spectrometric approaches to the determination of DNA sequence were considered: (1) the mass spectrometric detection of isotopic labels from DNA sequencing mixtures separated using gel electrophoresis, (2) the direct mass spectrometric analysis from direct ionization of unfractionated sequencing mixtures where the measured mass of the constituents functions to identify and order the base sequence (replacing separation by gel electrophoresis), and (3) an approach in which a single highly charged molecular ion of a large DNA segment produced is rapidly sequenced in an ion cyclotron resonance ion trap. The consensus of the workshop was that, on the basis of the new developments, mass spectrometry has the potential to provide the substantial increases in sequencing speed required for the Human Genome Program. 66 refs., 3 tabs.

  5. Proceedings of the relevance of mass spectrometry to DNA sequence determination: Research needs for the Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    Edmonds, C.G.; Smith, R.D. (Pacific Northwest Lab., Richland, WA (USA)); Smith, L.M. (Wisconsin Univ., Madison, WI (USA))

    1990-11-01

    A workshop was sponsored for the US Department of Energy (DOE), Office of Health and Environmental Research by Pacific Northwest Laboratory, April 4--5, 1990, in Seattle, Washington, to examine the potential role of mass spectrometry in the joint DOE/National Institutes of Health (NIH) Human Genome Program. The workshop was occasioned by recent developments in mass spectrometry that are providing new levels for selectivity, sensitivity, and, in particular, new methods of ionization appropriate for large biopolymers such as DNA. During discussions, three general mass spectrometric approaches to the determination of DNA sequence were considered: (1) the mass spectrometric detection of isotopic labels from DNA sequencing mixtures separated using gel electrophoresis, (2) the direct mass spectrometric analysis from direct ionization of unfractionated sequencing mixtures where the measured mass of the constituents functions to identify and order the base sequence (replacing separation by gel electrophoresis), and (3) an approach in which a single highly charged molecular ion of a large DNA segment produced is rapidly sequenced in an ion cyclotron resonance ion trap. The consensus of the workshop was that, on the basis of the new developments, mass spectrometry has the potential to provide the substantial increases in sequencing speed required for the Human Genome Program. 66 refs., 3 tabs.

  6. Educational Gaps in Molecular Diagnostics, Genomics, and Personalized Medicine in Dermatopathology Training: A Survey of US Dermatopathology Fellowship Program Directors.

    Science.gov (United States)

    Torre, Kristin; Russomanno, Kristen; Ferringer, Tammie; Elston, Dirk; Murphy, Michael J

    2017-05-02

    Molecular technologies offer clinicians the tools to provide high-quality, cost-effective patient care. We evaluated education focused on molecular diagnostics, genomics, and personalized medicine in dermatopathology fellowship. A 20-question online survey was emailed to all (n = 53) Accreditation Council for Graduate Medical Education (ACGME)-accredited dermatopathology training programs in the United States. Thirty-one of 53 program directors responded (response rate = 58%). Molecular training is undertaken in 74% of responding dermatopathology fellowships, with levels of instruction varying among dermatology-based and pathology-based programs. Education differed for dermatology- and pathology-trained fellows in approximately one-fifth (19%) of programs. Almost half (48%) of responding program directors believe that fellows are not currently receiving adequate molecular education although the majority (97%) expect to incorporate additional instruction in the next 2-5 years. Factors influencing the incorporation of relevant education include perceived clinical utility and Accreditation Council for Graduate Medical Education/residency review committee (RRC) requirements. Potential benefits of molecular education include increased medical knowledge, improved patient care, and promotion of effective communication with other healthcare professionals. More than two-thirds (68%) of responding program directors believe that instruction in molecular technologies should be required in dermatopathology fellowship training. Although all responding dermatopathology fellowship program directors agreed that molecular education is important, only a little over half of survey participants believe that their fellows receive adequate instruction. This represents an important educational gap. Discussion among those who oversee fellow education is necessary to best integrate and evaluate teaching of molecular dermatopathology.

  7. Validation and calibration of next-generation sequencing to identify Epstein-Barr virus-positive gastric cancer in The Cancer Genome Atlas.

    Science.gov (United States)

    Camargo, M Constanza; Bowlby, Reanne; Chu, Andy; Pedamallu, Chandra Sekhar; Thorsson, Vesteinn; Elmore, Sandra; Mungall, Andrew J; Bass, Adam J; Gulley, Margaret L; Rabkin, Charles S

    2016-04-01

    The Epstein-Barr virus (EBV)-positive subtype of gastric adenocarcinoma is conventionally identified by in situ hybridization (ISH) for viral nucleic acids, but next-generation sequencing represents a potential alternative. We therefore determined normalized EBV read counts by whole-genome, whole-exome, mRNA and miRNA sequencing for 295 fresh-frozen gastric tumor samples. Formalin-fixed, paraffin-embedded tissue sections were retrieved for ISH confirmation of 13 high-EBV and 11 low-EBV cases. In pairwise comparisons, individual samples were either concordantly high or concordantly low by all genomic methods for which data were available. Empiric cutoffs of sequencing counts identified 26 (9 %) tumors as EBV positive. EBV positivity or negativity by molecular testing was confirmed by EBER-ISH in all but one tumor evaluated by both approaches (kappa = 0.91). EBV-positive gastric tumors can be accurately identified by quantifying viral sequences in genomic data. Simultaneous analyses of human and viral DNA, mRNA and miRNA could streamline tumor profiling for clinical care and research.

  8. Genomic Selection for Processing and End-Use Quality Traits in the CIMMYT Spring Bread Wheat Breeding Program

    Directory of Open Access Journals (Sweden)

    Sarah D. Battenfield

    2016-07-01

    Full Text Available Wheat ( L. cultivars must possess suitable end-use quality for release and consumer acceptability. However, breeding for quality traits is often considered a secondary target relative to yield largely because of amount of seed needed and expense. Without testing and selection, many undesirable materials are advanced, expending additional resources. Here, we develop and validate whole-genome prediction models for end-use quality phenotypes in the CIMMYT bread wheat breeding program. Model accuracy was tested using forward prediction on breeding lines ( = 5520 tested in unbalanced yield trials from 2009 to 2015 at Ciudad Obregon, Sonora, Mexico. Quality parameters included test weight, 1000-kernel weight, hardness, grain and flour protein, flour yield, sodium dodecyl sulfate sedimentation, Mixograph and Alveograph performance, and loaf volume. In general, prediction accuracy substantially increased over time as more data was available to train the model. Reflecting practical implementation of genomic selection (GS in the breeding program, forward prediction accuracies ( for quality parameters were assessed in 2015 and ranged from 0.32 (grain hardness to 0.62 (mixing time. Increased selection intensity was possible with GS since more entries can be genotyped than phenotyped and expected genetic gain was 1.4 to 2.7 times higher across all traits than phenotypic selection. Given the limitations in measuring many lines for quality, we conclude that GS is a powerful tool to facilitate early generation selection for end-use quality in wheat, leaving larger populations for selection on yield during advanced testing and leading to better gain for both quality and yield in bread wheat breeding programs.

  9. Expression of lactate/H⁺ symporters MCT1 and MCT4 and their chaperone CD147 predicts tumor progression in clear cell renal cell carcinoma: immunohistochemical and The Cancer Genome Atlas data analyses.

    Science.gov (United States)

    Kim, Younghye; Choi, Jung-Woo; Lee, Ju-Han; Kim, Young-Sik

    2015-01-01

    Clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau protein, leading to the accumulation of hypoxia-inducible factor-α (HIF-α). HIF-1α induces aerobic glycolysis, the Warburg effect, whereas HIF-2α functions as an oncoprotein. Lactate transport through monocarboxylate transporters (MCTs) and the chaperone CD147 is essential for high glycolytic cancer cell survival. To elucidate the clinical significance of MCT1, MCT4, and CD147 expression, we investigated their expressions by immunohistochemistry in ccRCC specimens and validated the results by an open-access The Cancer Genome Atlas data analysis. Overexpression of MCT1, MCT4, and CD147 was observed in 49.4% (89/180), 39.4% (71/180), and 79.4% (143/180) of ccRCC patients, respectively. High MCT1 expression was associated with older age (P = .017), larger tumor size (P = .015), and advanced TNM stage (P = .012). However, MCT4 overexpression was not related to any variables. CD147 overexpression correlated with high grade (P = .005), tumor necrosis (P = .016), and larger tumor size (P = .038). In univariate analysis, high expression of MCT1 (P CD147 (P = .02) was linked to short progression-free survival. In multivariate analysis, high MCT1 expression was associated with worse progression-free survival (P = .001). In conclusion, high expression of MCT1 and CD147 is associated with poor prognostic factors. Overexpression of MCT1, MCT4, and CD147 predicts tumor progression. Reversing the Warburg effect by targeting the lactate transporters may be a useful strategy to prevent ccRCC progression.

  10. [Atlas fractures].

    Science.gov (United States)

    Schären, S; Jeanneret, B

    1999-05-01

    Fractures of the atlas account for 1-2% of all vertebral fractures. We divide atlas fractures into 5 groups: isolated fractures of the anterior arch of the atlas, isolated fractures of the posterior arch, combined fractures of the anterior and posterior arch (so-called Jefferson fractures), isolated fractures of the lateral mass and fractures of the transverse process. Isolated fractures of the anterior or posterior arch are benign and are treated conservatively with a soft collar until the neck pain has disappeared. Jefferson fractures are divided into stable and unstable fracture depending on the integrity of the transverse ligament. Stable Jefferson fractures are treated conservatively with good outcome while unstable Jefferson fractures are probably best treated operatively with a posterior atlanto-axial or occipito-axial stabilization and fusion. The authors preferred treatment modality is the immediate open reduction of the dislocated lateral masses combined with a stabilization in the reduced position using a transarticular screw fixation C1/C2 according to Magerl. This has the advantage of saving the atlanto-occipital joints and offering an immediate stability which makes immobilization in an halo or Minerva cast superfluous. In late instabilities C1/2 with incongruency of the lateral masses occurring after primary conservative treatment, an occipito-cervical fusion is indicated. Isolated fractures of the lateral masses are very rare and may, if the lateral mass is totally destroyed, be a reason for an occipito-cervical fusion. Fractures of the transverse processes may be the cause for a thrombosis of the vertebral artery. No treatment is necessary for the fracture itself.

  11. EnviroAtlas

    Data.gov (United States)

    City and County of Durham, North Carolina — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://www.epa.gov/enviroatlas). The layers in this web...

  12. ATLAS experimentet

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    Filmen innehåller mycket information om fysik och varför LHC behövs tilsammans med stora detektorer och specielt om behovet av ATLAS Experimentet. Mycket bra film för att förklara det okända- som man undersöker i CERN för att ge svar på frågor som människor har försökt förklara under flere tusen år.

  13. Genome-Wide Linkage Analysis for Loci Affecting Pulse Pressure: The Family Blood Pressure Program

    National Research Council Canada - National Science Library

    Bielinski, Suzette J; Lynch, Amy I; Miller, Michael B; Weder, Alan; Cooper, Richard; Oberman, Albert; Chen, Yii-Der Ida; Turner, Stephen T; Fornage, Myriam; Province, Michael; Arnett, Donna K

    2005-01-01

    ... in sequential oligogenic linkage analysis routines. The analysis sample included 10 798 participants in 3320 families who were recruited as part of the Family Blood Pressure Program and were phenotyped with an oscillometric blood pressure measurement...

  14. Deep sequencing revealed genome-wide single-nucleotide polymorphism and plasmid content of Erwinia amylovora strains isolated in Middle Atlas, Morocco.

    Science.gov (United States)

    Hannou, Najat; Mondy, Samuel; Planamente, Sara; Moumni, Mohieddine; Llop, Pablo; López, María; Manceau, Charles; Barny, Marie-Anne; Faure, Denis

    2013-10-01

    Erwinia amylovora causes economic losses that affect pear and apple production in Morocco. Here, we report comparative genomics of four Moroccan E. amylovora strains with the European strain CFBP1430 and North-American strain ATCC49946. Analysis of single nucleotide polymorphisms (SNPs) revealed genetic homogeneity of Moroccan's strains and their proximity to the European strain CFBP1430. Moreover, the collected sequences allowed the assembly of a 65 kpb plasmid, which is highly similar to the plasmid pEI70 harbored by several European E. amylovora isolates. This plasmid was found in 33% of the 40 E. amylovora strains collected from several host plants in 2009 and 2010 in Morocco.

  15. Atlases: Complex models of geospace

    Directory of Open Access Journals (Sweden)

    Ikonović Vesna

    2005-01-01

    Full Text Available Atlas is modeled contexture contents of treated thematic of space on optimal map union. Atlases are higher form of cartography. Atlases content composition of maps which are different by projection, scale, format methods, contents, usage and so. Atlases can be classified by multi criteria. Modern classification of atlases by technology of making would be on: 1. classical or traditional (printed on paper and 2. electronic (made on electronic media - computer or computer station. Electronic atlases divided in three large groups: view-only electronic atlases, 2. interactive electronic atlases and 3. analytical electronic atlases.

  16. Multimedia Presentations on the Human Genome: Implementation and Assessment of a Teaching Program for the Introduction to Genome Science Using a Poster and Animations

    Science.gov (United States)

    Kano, Kei; Yahata, Saiko; Muroi, Kaori; Kawakami, Masahiro; Tomoda, Mari; Miyaki, Koichi; Nakayama, Takeo; Kosugi, Shinji; Kato, Kazuto

    2008-01-01

    Genome science, including topics such as gene recombination, cloning, genetic tests, and gene therapy, is now an established part of our daily lives; thus we need to learn genome science to better equip ourselves for the present day. Learning from topics directly related to the human has been suggested to be more effective than learning from…

  17. Developing the eHistology Atlas.

    Science.gov (United States)

    Richardson, Lorna; Graham, Liz; Moss, Julie; Burton, Nick; Roochun, Yogmatee; Armit, Chris; Baldock, Richard A

    2015-01-01

    The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook 'The Atlas of Mouse Development' by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php. © The Author(s) 2015. Published by Oxford University Press.

  18. Berliner Philarmoniker ATLAS visit

    CERN Multimedia

    ATLAS Collaboration

    2017-01-01

    The Berliner Philarmoniker in on tour through Europe. They stopped on June 27th in Geneva, for a concert at the Victoria Hall. An ATLAS visit was organised the morning after, lead by the ATLAS spokesperson Karl Jakobs (welcome and overview talk) and two ATLAS guides (AVC visit and 3D movie).

  19. ATLAS Data Access Policy

    CERN Document Server

    The ATLAS collaboration

    2015-01-01

    ATLAS has fully supported the principle of open access in its publication policy. This document outlines the policy of ATLAS as regards open access to data at different levels as described in the DPHEP model. The main objective is to make the data available in a usable way to people external to the ATLAS collaboration.

  20. Interactive Atlas of Histology

    Science.gov (United States)

    Goubran, Emile Z.; Vinjamury, Sivarama P.

    2007-01-01

    Purpose: An interactive atlas of histology was developed for online use by chiropractic students to enable them to practice and self-assess their ability to identify various histological structures. This article discusses the steps in the development, implementation, and usefulness of an interactive atlas of histology for students who take histology examinations. Methods: The atlas was developed by digitizing images imported through a video-microscope using actual microscope slides. Leica EWS 2100 and PowerPoint software were used to construct the atlas. The usefulness of the atlas was assessed through a comparison of histology exam scores between four classes before and four classes after the use of the atlas. Analysis of admissions data, including overall grade point average (GPA), science and nonscience GPA, and a number of course units, was done initially to avoid any identifiable differences in the academic competency between the two being compared. A survey of the students was also done to assess atlas usefulness and students' satisfaction with the atlas. Results: Analysis of histology exam scores showed that the average scores in the lab exam were significantly higher for the classes that used the atlas. Survey results showed a high level of student satisfaction with the atlas. Conclusion: The development and use of an online interactive atlas of histology for chiropractic students helped to improve lab exams scores. In addition, students were satisfied with the features and usefulness of this atlas. PMID:18483638

  1. Digital atlas of fetal brain MRI

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, Teresa; Weinberger, E. [Department of Radiology, Seattle Children' s Hospital, Seattle, WA (United States); Matesan, Manuela [University of Washington, Department of Radiology, Seattle, WA (United States); Bulas, Dorothy I. [Division of Diagnostic Imaging and Radiology, Children' s National Medical Center, Washington, DC (United States)

    2010-02-15

    Fetal MRI can be performed in the second and third trimesters. During this time, the fetal brain undergoes profound structural changes. Interpretation of appropriate development might require comparison with normal age-based models. Consultation of a hard-copy atlas is limited by the inability to compare multiple ages simultaneously. To provide images of normal fetal brains from weeks 18 through 37 in a digital format that can be reviewed interactively. This will facilitate recognition of abnormal brain development. T2-W images for the atlas were obtained from fetal MR studies of normal brains scanned for other indications from 2005 to 2007. Images were oriented in standard axial, coronal and sagittal projections, with laterality established by situs. Gestational age was determined by last menstrual period, earliest US measurements and sonogram performed on the same day as the MR. The software program used for viewing the atlas, written in C, permits linked scrolling and resizing the images. Simultaneous comparison of varying gestational ages is permissible. Fetal brain images across gestational ages 18 to 37 weeks are provided as an interactive digital atlas and are available for free download. Improved interpretation of fetal brain abnormalities can be facilitated by the use of digital atlas cataloging of the normal changes throughout fetal development. Here we provide a description of the atlas and a discussion of normal fetal brain development. (orig.)

  2. Recent ATLAS Articles on WLAP

    CERN Multimedia

    J. Herr

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Physics Workshop 6-11 June 2005 June 2005 ATLAS Week Plenary Session Click here to browse WLAP for all ATLAS lectures.

  3. Learning regulatory programs by threshold SVD regression.

    Science.gov (United States)

    Ma, Xin; Xiao, Luo; Wong, Wing Hung

    2014-11-04

    We formulate a statistical model for the regulation of global gene expression by multiple regulatory programs and propose a thresholding singular value decomposition (T-SVD) regression method for learning such a model from data. Extensive simulations demonstrate that this method offers improved computational speed and higher sensitivity and specificity over competing approaches. The method is used to analyze microRNA (miRNA) and long noncoding RNA (lncRNA) data from The Cancer Genome Atlas (TCGA) consortium. The analysis yields previously unidentified insights into the combinatorial regulation of gene expression by noncoding RNAs, as well as findings that are supported by evidence from the literature.

  4. Integrating Public Health and Deliberative Public Bioethics: Lessons from the Human Genome Project Ethical, Legal, and Social Implications Program.

    Science.gov (United States)

    Meagher, Karen M; Lee, Lisa M

    2016-01-01

    Public health policy works best when grounded in firm public health standards of evidence and widely shared social values. In this article, we argue for incorporating a specific method of ethical deliberation--deliberative public bioethics--into public health. We describe how deliberative public bioethics is a method of engagement that can be helpful in public health. Although medical, research, and public health ethics can be considered some of what bioethics addresses, deliberative public bioethics offers both a how and where. Using the Human Genome Project Ethical, Legal, and Social Implications program as an example of effective incorporation of deliberative processes to integrate ethics into public health policy, we examine how deliberative public bioethics can integrate both public health and bioethics perspectives into three areas of public health practice: research, education, and health policy. We then offer recommendations for future collaborations that integrate deliberative methods into public health policy and practice.

  5. ATLAS Recordings

    CERN Multimedia

    Jeremy Herr; Homer A. Neal; Mitch McLachlan

    The University of Michigan Web Archives for the 2006 ATLAS Week Plenary Sessions, as well as the first of 2007, are now online. In addition, there are a wide variety of Software and Physics Tutorial sessions, recorded over the past couple years, to chose from. All ATLAS-specific archives are accessible here.Viewing requires a standard web browser with RealPlayer plug-in (included in most browsers automatically) and works on any major platform. Lectures can be viewed directly over the web or downloaded locally.In addition, you will find access to a variety of general tutorials and events via the portal. Shaping Collaboration 2006The Michigan group is happy to announce a complete set of recordings from the Shaping Collaboration conference held last December at the CICG in Geneva.The event hosted a mix of Collaborative Tool experts and LHC Users, and featured presentations by the CERN Deputy Director General, Prof. Jos Engelen, the President of Internet2, and chief developers from VRVS/EVO, WLAP, and other tools...

  6. EnviroAtlas - Rare Ecosystems in the Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset identifies rare ecosystems using base landcover data from the USGS GAP Analysis Program (Version 2, 2011) combined with landscape ecology...

  7. PREIMS - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available AT Atlas PREIMS Data detail Data name PREIMS Description of data contents It is a table of protocols that were developed in the Techn...ology Development projects of the Targeted Proteins Research Program (TPRP). Data f

  8. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular

  9. Comprehensive genomic characterization defines human glioblastoma genes and core pathways

    NARCIS (Netherlands)

    Chin, L.; Meyerson, M.; Aldape, K.; Bigner, D.; Mikkelsen, T.; VandenBerg, S.; Kahn, A.; Penny, R.; Gerhard, D. S.; Getz, G.; Brennan, C.; Taylor, B. S.; Winckler, W.; Park, P.; Ladanyi, M.; Hoadley, K. A.; Verhaak, R. G. W.; Hayes, D. N.; Spellman, Paul T.; Absher, D.; Weir, B. A.; Ding, L.; Wheeler, D.; Lawrence, M. S.; Cibulskis, K.; Mardis, E.; Zhang, Jinghui; Wilson, R. K.; Donehower, L.; Wheeler, D. A.; Purdom, E.; Wallis, J.; Laird, P. W.; Herman, J. G.; Schuebel, K. E.; Weisenberger, D. J.; Baylin, S. B.; Schultz, N.; Yao, Jun; Wiedemeyer, R.; Weinstein, J.; Sander, C.; Gibbs, R. A.; Gray, J.; Kucherlapati, R.; Lander, E. S.; Myers, R. M.; Perou, C. M.; McLendon, Roger; Friedman, Allan; Van Meir, Erwin G; Brat, Daniel J; Mastrogianakis, Gena Marie; Olson, Jeffrey J; Lehman, Norman; Yung, W. K. Alfred; Bogler, Oliver; Berger, Mitchel; Prados, Michael; Muzny, Donna; Morgan, Margaret; Scherer, Steve; Sabo, Aniko; Nazareth, Lynn; Lewis, Lora; Hall, Otis; Zhu, Yiming; Ren, Yanru; Alvi, Omar; Yao, Jiqiang; Hawes, Alicia; Jhangiani, Shalini; Fowler, Gerald; San Lucas, Anthony; Kovar, Christie; Cree, Andrew; Dinh, Huyen; Santibanez, Jireh; Joshi, Vandita; Gonzalez-Garay, Manuel L.; Miller, Christopher A.; Milosavljevic, Aleksandar; Sougnez, Carrie; Fennell, Tim; Mahan, Scott; Wilkinson, Jane; Ziaugra, Liuda; Onofrio, Robert; Bloom, Toby; Nicol, Rob; Ardlie, Kristin; Baldwin, Jennifer; Gabriel, Stacey; Fulton, Robert S.; McLellan, Michael D.; Larson, David E.; Shi, Xiaoqi; Abbott, Rachel; Fulton, Lucinda; Chen, Ken; Koboldt, Daniel C.; Wendl, Michael C.; Meyer, Rick; Tang, Yuzhu; Lin, Ling; Osborne, John R.; Dunford-Shore, Brian H.; Miner, Tracie L.; Delehaunty, Kim; Markovic, Chris; Swift, Gary; Courtney, William; Pohl, Craig; Abbott, Scott; Hawkins, Amy; Leong, Shin; Haipek, Carrie; Schmidt, Heather; Wiechert, Maddy; Vickery, Tammi; Scott, Sacha; Dooling, David J.; Chinwalla, Asif; Weinstock, George M.; O'Kelly, Michael; Robinson, Jim; Alexe, Gabriele; Beroukhim, Rameen; Carter, Scott; Chiang, Derek; Gould, Josh; Gupta, Supriya; Korn, Josh; Mermel, Craig; Mesirov, Jill; Monti, Stefano; Nguyen, Huy; Parkin, Melissa; Reich, Michael; Stransky, Nicolas; Garraway, Levi; Golub, Todd; Protopopov, Alexei; Perna, Ilana; Aronson, Sandy; Sathiamoorthy, Narayan; Ren, Georgia; Kim, Hyunsoo; Kong, Sek Won; Xiao, Yonghong; Kohane, Isaac S.; Seidman, Jon; Cope, Leslie; Pan, Fei; Van Den Berg, David; Van Neste, Leander; Yi, Joo Mi; Li, Jun Z.; Southwick, Audrey; Brady, Shannon; Aggarwal, Amita; Chung, Tisha; Sherlock, Gavin; Brooks, James D.; Jakkula, Lakshmi R.; Lapuk, Anna V.; Marr, Henry; Dorton, Shannon; Choi, Yoon Gi; Han, Ju; Ray, Amrita; Wang, Victoria; Durinck, Steffen; Robinson, Mark; Wang, Nicholas J.; Vranizan, Karen; Peng, Vivian; Van Name, Eric; Fontenay, Gerald V.; Ngai, John; Conboy, John G.; Parvin, Bahram; Feiler, Heidi S.; Speed, Terence P.; Socci, Nicholas D.; Olshen, Adam; Lash, Alex; Reva, Boris; Antipin, Yevgeniy; Stukalov, Alexey; Gross, Benjamin; Cerami, Ethan; Wang, Wei Qing; Qin, Li-Xuan; Seshan, Venkatraman E.; Villafania, Liliana; Cavatore, Magali; Borsu, Laetitia; Viale, Agnes; Gerald, William; Topal, Michael D.; Qi, Yuan; Balu, Sai; Shi, Yan; Wu, George; Bittner, Michael; Shelton, Troy; Lenkiewicz, Elizabeth; Morris, Scott; Beasley, Debbie; Sanders, Sheri; Sfeir, Robert; Chen, Jessica; Nassau, David; Feng, Larry; Hickey, Erin; Schaefer, Carl; Madhavan, Subha; Buetow, Ken; Barker, Anna; Vockley, Joseph; Compton, Carolyn; Vaught, Jim; Fielding, Peter; Collins, Francis; Good, Peter; Guyer, Mark; Ozenberger, Brad; Peterson, Jane; Thomson, Elizabeth

    2008-01-01

    Human cancer cells typically harbour multiple chromosomal aberrations, nucleotide substitutions and epigenetic modifications that drive malignant transformation. The Cancer Genome Atlas ( TCGA) pilot project aims to assess the value of large- scale multi- dimensional analysis of these molecular char

  10. ATLAS DBM Module Qualification

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gorisek, Andrej [J. Stefan Inst., Ljubljana (Slovenia); Zavrtanik, Marko [J. Stefan Inst., Ljubljana (Slovenia); Sokhranyi, Grygorii [J. Stefan Inst., Ljubljana (Slovenia); McGoldrick, Garrin [Univ. of Toronto, ON (Canada); Cerv, Matevz [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2014-06-18

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of Jozef Stefan Institute, CERN, and University of Toronto who have committed to participate in beam tests to be carried out during the 2014 Fermilab Test Beam Facility program. Chemical Vapour Deposition (CVD) diamond has a number of properties that make it attractive for high energy physics detector applications. Its large band-gap (5.5 eV) and large displacement energy (42 eV/atom) make it a material that is inherently radiation tolerant with very low leakage currents and high thermal conductivity. CVD diamond is being investigated by the RD42 Collaboration for use very close to LHC interaction regions, where the most extreme radiation conditions are found. This document builds on that work and proposes a highly spatially segmented diamond-based luminosity monitor to complement the time-segmented ATLAS Beam Conditions Monitor (BCM) so that, when Minimum Bias Trigger Scintillators (MTBS) and LUCID (LUminosity measurement using a Cherenkov Integrating Detector) have difficulty functioning, the ATLAS luminosity measurement is not compromised.

  11. ATLAS DBM Module Qualification

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States); Gorisek, Andrej [J. Stefan Inst., Ljubljana (Slovenia); Zavrtanik, Marko [J. Stefan Inst., Ljubljana (Slovenia); Sokhranyi, Grygorii [J. Stefan Inst., Ljubljana (Slovenia); McGoldrick, Garrin [Univ. of Toronto, ON (Canada); Cerv, Matevz [European Organization for Nuclear Research (CERN), Geneva (Switzerland)

    2014-06-18

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of Jozef Stefan Institute, CERN, and University of Toronto who have committed to participate in beam tests to be carried out during the 2014 Fermilab Test Beam Facility program. Chemical Vapour Deposition (CVD) diamond has a number of properties that make it attractive for high energy physics detector applications. Its large band-gap (5.5 eV) and large displacement energy (42 eV/atom) make it a material that is inherently radiation tolerant with very low leakage currents and high thermal conductivity. CVD diamond is being investigated by the RD42 Collaboration for use very close to LHC interaction regions, where the most extreme radiation conditions are found. This document builds on that work and proposes a highly spatially segmented diamond based luminosity monitor to complement the time segmented ATLAS Beam Conditions Monitor (BCM) so that when Minimum Bias Trigger Scintillators (MTBS) and LUCID (LUminosity measurement using a Cherenkov Integrating Detector) have difficulty functioning the ATLAS luminosity measurement is not compromised.

  12. EnviroAtlas - Green Bay, WI - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Green Bay, WI Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  13. EnviroAtlas - Portland, ME - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Portland, ME Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  14. EnviroAtlas - Portland, OR - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Portland, OR Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  15. EnviroAtlas - Phoenix, AZ - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Phoenix, AZ Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  16. EnviroAtlas - Paterson, NJ - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Paterson, NJ Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas Area....

  17. EnviroAtlas - Austin, TX - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Austin, TX Atlas Area. It represents the outside edge of all the block groups included in the EnviroAtlas...

  18. A Self-Study Tutorial using the Allen Brain Explorer and Brain Atlas to Teach Concepts of Mammalian Neuroanatomy and Brain Function.

    Science.gov (United States)

    Jenks, Bruce G

    2009-01-01

    The Allen Brain Atlas is a repository of neuroanatomical data concerning the mouse brain. The core of the database is a Nissl-stained reference atlas of the brain accompanied by in situ hybridization data for essentially the entire mouse genome. This database is freely available at the Allen Institute for Brain Science website, as is an innovative tool to explore the database, the Brain Explorer. This tool is downloaded and installed on your own computer. I have developed a self-study tutorial, "Explorations with the Allen Brain Explorer", which uses the Brain Explorer and the Brain Atlas to teach fundamentals of mammalian neuroanatomy and brain function. In this tutorial background information and step-by-step exercises on the use of the Brain Explorer are given using PowerPoint as a platform. To do the tutorial both the PowerPoint and the Brain Explorer are opened on the computer and the students switch from one program to the other as they go, in a step-wise fashion, through the various exercises. There are two main groups of exercises, titled "The Basics" and "Explorations", with both groups accessed from a PowerPoint "Start Menu" by clicking on dynamic links to the appropriate exercises. Most exercises have a number of dynamic links to PowerPoint slides where background information for the exercises is given or the neuroanatomical data collected from the Brain Atlas is discussed.

  19. ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing

    Directory of Open Access Journals (Sweden)

    Kamatani Naoyuki

    2009-10-01

    Full Text Available Abstract Background Since more than a million single-nucleotide polymorphisms (SNPs are analyzed in any given genome-wide association study (GWAS, performing multiple comparisons can be problematic. To cope with multiple-comparison problems in GWAS, haplotype-based algorithms were developed to correct for multiple comparisons at multiple SNP loci in linkage disequilibrium. A permutation test can also control problems inherent in multiple testing; however, both the calculation of exact probability and the execution of permutation tests are time-consuming. Faster methods for calculating exact probabilities and executing permutation tests are required. Methods We developed a set of computer programs for the parallel computation of accurate P-values in haplotype-based GWAS. Our program, ParaHaplo, is intended for workstation clusters using the Intel Message Passing Interface (MPI. We compared the performance of our algorithm to that of the regular permutation test on JPT and CHB of HapMap. Results ParaHaplo can detect smaller differences between 2 populations than SNP-based GWAS. We also found that parallel-computing techniques made ParaHaplo 100-fold faster than a non-parallel version of the program. Conclusion ParaHaplo is a useful tool in conducting haplotype-based GWAS. Since the data sizes of such projects continue to increase, the use of fast computations with parallel computing--such as that used in ParaHaplo--will become increasingly important. The executable binaries and program sources of ParaHaplo are available at the following address: http://sourceforge.jp/projects/parallelgwas/?_sl=1

  20. ParaHaplo: A program package for haplotype-based whole-genome association study using parallel computing.

    Science.gov (United States)

    Misawa, Kazuharu; Kamatani, Naoyuki

    2009-10-21

    Since more than a million single-nucleotide polymorphisms (SNPs) are analyzed in any given genome-wide association study (GWAS), performing multiple comparisons can be problematic. To cope with multiple-comparison problems in GWAS, haplotype-based algorithms were developed to correct for multiple comparisons at multiple SNP loci in linkage disequilibrium. A permutation test can also control problems inherent in multiple testing; however, both the calculation of exact probability and the execution of permutation tests are time-consuming. Faster methods for calculating exact probabilities and executing permutation tests are required. We developed a set of computer programs for the parallel computation of accurate P-values in haplotype-based GWAS. Our program, ParaHaplo, is intended for workstation clusters using the Intel Message Passing Interface (MPI). We compared the performance of our algorithm to that of the regular permutation test on JPT and CHB of HapMap. ParaHaplo can detect smaller differences between 2 populations than SNP-based GWAS. We also found that parallel-computing techniques made ParaHaplo 100-fold faster than a non-parallel version of the program. ParaHaplo is a useful tool in conducting haplotype-based GWAS. Since the data sizes of such projects continue to increase, the use of fast computations with parallel computing--such as that used in ParaHaplo--will become increasingly important. The executable binaries and program sources of ParaHaplo are available at the following address: http://sourceforge.jp/projects/parallelgwas/?_sl=1.

  1. ATLAS note ATL-COM-PHYS-2009.

    Energy Technology Data Exchange (ETDEWEB)

    Chekanov, S.; Boomsma, J.; High Energy Physics

    2009-12-22

    The program InvMass has been developed to perform a general model-independent search for new particles using the ATLAS detector at the Large Hadron Collider (LHC), a proton-proton collider at CERN. The search is performed by examining statistically significant variations from the Standard Model predictions in exclusive event classes classified according to the number of identified objects. The program, called InvMass, finds all relevant particle groups identified with the ATLAS detector and analyzes their production rates, invariant masses and the total transverse momenta. The generic code of InvMass can easily be adapted for any particle types identified with the ATLAS detector. Several benchmark tests are presented.

  2. Multilanguage Package of slow control programs for the ATLAS Hadronic End-Cap Calorimeter Test Beam Experiment

    CERN Document Server

    Sytnik, V V

    1999-01-01

    In this article the package of slow control applications for the Liquid Argon (LAr) Hadronic End-Cap Calorimeter (HEC) test beam set-up is described. As compared to previous release, new applications have been included to fit needs of the experiment. New approaches were used to boost software reliability and to improve timing characteristics. In order to implement different part of the software the relevant programming languages were chosen: - software dealing with apparatus was implemented in Labview; - asynchronous slow control TCP server was implemented in C++; - Web monitoring of slow control system parameters was implemented in Java. The platform of slow control software is Microsoft Windows. The Java applet based monitoring of combined slow control data may also run on any platform using Netscape or Microsoft Internet Explorer.

  3. ATLAS Distributed Computing Automation

    CERN Document Server

    Schovancova, J; The ATLAS collaboration; Borrego, C; Campana, S; Di Girolamo, A; Elmsheuser, J; Hejbal, J; Kouba, T; Legger, F; Magradze, E; Medrano Llamas, R; Negri, G; Rinaldi, L; Sciacca, G; Serfon, C; Van Der Ster, D C

    2012-01-01

    The ATLAS Experiment benefits from computing resources distributed worldwide at more than 100 WLCG sites. The ATLAS Grid sites provide over 100k CPU job slots, over 100 PB of storage space on disk or tape. Monitoring of status of such a complex infrastructure is essential. The ATLAS Grid infrastructure is monitored 24/7 by two teams of shifters distributed world-wide, by the ATLAS Distributed Computing experts, and by site administrators. In this paper we summarize automation efforts performed within the ATLAS Distributed Computing team in order to reduce manpower costs and improve the reliability of the system. Different aspects of the automation process are described: from the ATLAS Grid site topology provided by the ATLAS Grid Information System, via automatic site testing by the HammerCloud, to automatic exclusion from production or analysis activities.

  4. Cultural differences define diagnosis and genomic medicine practice: implications for undiagnosed diseases program in China.

    Science.gov (United States)

    Duan, Xiaohong; Markello, Thomas; Adams, David; Toro, Camilo; Tifft, Cynthia; Gahl, William A; Boerkoel, Cornelius F

    2013-09-01

    Despite the current acceleration and increasing leadership of Chinese genetics research, genetics and its clinical application have largely been imported to China from the Occident. Neither genetics nor the scientific reductionism underpinning its clinical application is integral to the traditional Chinese worldview. Given that disease concepts and their incumbent diagnoses are historically derived and culturally meaningful, we hypothesize that the cultural expectations of genetic diagnoses and medical genetics practice differ between the Occident and China. Specifically, we suggest that an undiagnosed diseases program in China will differ from the recently established Undiagnosed Diseases Program at the United States National Institutes of Health; a culturally sensitive concept will integrate traditional Chinese understanding of disease with the scientific reductionism of Occidental medicine.

  5. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Science.gov (United States)

    Chang, Yi-Feng; Chang, Chuan-Hsiung

    2011-01-01

    CAGO (Comparative Analysis of Genome Organization) is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG) format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  6. CAGO: a software tool for dynamic visual comparison and correlation measurement of genome organization.

    Directory of Open Access Journals (Sweden)

    Yi-Feng Chang

    Full Text Available CAGO (Comparative Analysis of Genome Organization is developed to address two critical shortcomings of conventional genome atlas plotters: lack of dynamic exploratory functions and absence of signal analysis for genomic properties. With dynamic exploratory functions, users can directly manipulate chromosome tracks of a genome atlas and intuitively identify distinct genomic signals by visual comparison. Signal analysis of genomic properties can further detect inconspicuous patterns from noisy genomic properties and calculate correlations between genomic properties across various genomes. To implement dynamic exploratory functions, CAGO presents each genome atlas in Scalable Vector Graphics (SVG format and allows users to interact with it using a SVG viewer through JavaScript. Signal analysis functions are implemented using R statistical software and a discrete wavelet transformation package waveslim. CAGO is not only a plotter for generating complex genome atlases, but also a platform for exploring genome atlases with dynamic exploratory functions for visual comparison and with signal analysis for comparing genomic properties across multiple organisms. The web-based application of CAGO, its source code, user guides, video demos, and live examples are publicly available and can be accessed at http://cbs.ym.edu.tw/cago.

  7. Constraining Dark Matter with ATLAS

    CERN Document Server

    Czodrowski, Patrick; The ATLAS collaboration

    2017-01-01

    The presence of a non-baryonic dark matter component in the Universe is inferred from the observation of its gravitational interaction. If dark matter interacts weakly with the Standard Model it would be produced at the LHC, escaping the detector and leaving a large missing transverse momentum as their signature. The ATLAS detector has developed a broad and systematic search program for dark matter production in LHC collisions. The results of these searches on the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  8. Consumer Energy Atlas

    Energy Technology Data Exchange (ETDEWEB)

    1980-06-01

    This first edition of the Atlas provides, in reference form, a central source of information to consumers on key contacts concerned with energy in the US. Energy consumers need information appropriate to local climates and characteristics - best provided by state and local governments. The Department of Energy recognizes the authority of state and local governments to manage energy programs on their own. Therefore, emphasis has been given to government organizations on both the national and state level that influence, formulate, or administer policies affecting energy production, distribution, and use, or that provide information of interest to consumers and non-specialists. In addition, hundreds of non-government energy-related membership organizations, industry trade associations, and energy publications are included.

  9. Identification of histological correlates of overall survival in lower grade gliomas using a bag-of-words paradigm: A preliminary analysis based on hematoxylin & eosin stained slides from the lower grade glioma cohort of the cancer genome Atlas

    Directory of Open Access Journals (Sweden)

    Reid Trenton Powell

    2017-01-01

    Full Text Available Background: Glioma, the most common primary brain neoplasm, describes a heterogeneous tumor of multiple histologic subtypes and cellular origins. At clinical presentation, gliomas are graded according to the World Health Organization guidelines (WHO, which reflect the malignant characteristics of the tumor based on histopathological and molecular features. Lower grade diffuse gliomas (LGGs (WHO Grade II–III have fewer malignant characteristics than high-grade gliomas (WHO Grade IV, and a better clinical prognosis, however, accurate discrimination of overall survival (OS remains a challenge. In this study, we aimed to identify tissue-derived image features using a machine learning approach to predict OS in a mixed histology and grade cohort of lower grade glioma patients. To achieve this aim, we used H and E stained slides from the public LGG cohort of The Cancer Genome Atlas (TCGA to create a machine learned dictionary of “image-derived visual words” associated with OS. We then evaluated the combined efficacy of using these visual words in predicting short versus long OS by training a generalized machine learning model. Finally, we mapped these predictive visual words back to molecular signaling cascades to infer potential drivers of the machine learned survival-associated phenotypes. Methods: We analyzed digitized histological sections downloaded from the LGG cohort of TCGA using a bag-of-words approach. This method identified a diverse set of histological patterns that were further correlated with OS, histology, and molecular signaling activity using Cox regression, analysis of variance, and Spearman correlation, respectively. A support vector machine (SVM model was constructed to discriminate patients into short and long OS groups dichotomized at 24-month. Results: This method identified disease-relevant phenotypes associated with OS, some of which are correlated with disease-associated molecular pathways. From these image

  10. Radiogenomics of clear cell renal cell carcinoma: preliminary findings of The Cancer Genome Atlas-Renal Cell Carcinoma (TCGA-RCC) Imaging Research Group.

    Science.gov (United States)

    Shinagare, Atul B; Vikram, Raghu; Jaffe, Carl; Akin, Oguz; Kirby, Justin; Huang, Erich; Freymann, John; Sainani, Nisha I; Sadow, Cheryl A; Bathala, Tharakeswara K; Rubin, Daniel L; Oto, Aytekin; Heller, Matthew T; Surabhi, Venkateswar R; Katabathina, Venkat; Silverman, Stuart G

    2015-08-01

    To investigate associations between imaging features and mutational status of clear cell renal cell carcinoma (ccRCC). This multi-institutional, multi-reader study included 103 patients (77 men; median age 59 years, range 34-79) with ccRCC examined with CT in 81 patients, MRI in 19, and both CT and MRI in three; images were downloaded from The Cancer Imaging Archive, an NCI-funded project for genome-mapping and analyses. Imaging features [size (mm), margin (well-defined or ill-defined), composition (solid or cystic), necrosis (for solid tumors: 0%, 1%-33%, 34%-66% or >66%), growth pattern (endophytic, <50% exophytic, or ≥50% exophytic), and calcification (present, absent, or indeterminate)] were reviewed independently by three readers blinded to mutational data. The association of imaging features with mutational status (VHL, BAP1, PBRM1, SETD2, KDM5C, and MUC4) was assessed. Median tumor size was 49 mm (range 14-162 mm), 73 (71%) tumors had well-defined margins, 98 (95%) tumors were solid, 95 (92%) showed presence of necrosis, 46 (45%) had ≥50% exophytic component, and 18 (19.8%) had calcification. VHL (n = 52) and PBRM1 (n = 24) were the most common mutations. BAP1 mutation was associated with ill-defined margin and presence of calcification (p = 0.02 and 0.002, respectively, Pearson's χ (2) test); MUC4 mutation was associated with an exophytic growth pattern (p = 0.002, Mann-Whitney U test). BAP1 mutation was associated with ill-defined tumor margins and presence of calcification; MUC4 mutation was associated with exophytic growth. Given the known prognostic implications of BAP1 and MUC4 mutations, these results support using radiogenomics to aid in prognostication and management.

  11. Tracking and flavour-tagging performance for HV-CMOS sensors in the context of the ATLAS ITK pixel simulation program

    Science.gov (United States)

    Calandri, A.; Vacavant, L.; Barbero, M.; Rozanov, A.; Djama, F.

    2016-12-01

    The HV-CMOS (High Voltage - Complementary Metal-Oxide Semiconductor) pixel technology has recently risen interest for the upgrade of the pixel detector of the ATLAS experiment towards the High Luminosity phase of the Large Hadron Collider (LHC) . HV-CMOS sensors can be employed in the pixel outer layers (R >15 cm), where the radiation hardness requirements are less stringent, as they could instrument large areas at a relatively low cost. In addition, smaller pixel granularity can be achieved by exploiting sub-pixel encoding technology. Therefore, the largest impact on physics performance, tracking and flavour tagging, could be reached if exploited in the innermost layer (in place of the current IBL) or in the next-to-innermost layer. This proceeding will present studies on tracking and flavour-tagging performance in presence of HV-CMOS sensors in the innermost layer of the ATLAS detector.

  12. ATLAS Large Scale Thin Gap Chambers

    Energy Technology Data Exchange (ETDEWEB)

    Soha, Aria [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)

    2014-04-29

    This is a technical scope of work (TSW) between the Fermi National Accelerator Laboratory (Fermilab) and the experimenters of the ATLAS sTGC New Small Wheel collaboration who have committed to participate in beam tests to be carried out during the FY2014 Fermilab Test Beam Facility program.

  13. North American Atlas - Sea Ice - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  14. North American Atlas - Populated Places - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  15. North American Atlas - Hydrography - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  16. North American Atlas - Political Boundaries - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  17. North American Atlas - Roads - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  18. North American Atlas - Glaciers - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  19. North American Atlas - Bathymetry - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  20. North American Atlas - Railroads - Direct Download

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — A joint venture involving the National Atlas programs in Canada (Natural Resources Canada), Mexico (Instituto Nacional de Estadística Geografía e Informática), and...

  1. Heavy ion physics with the ATLAS detector

    CERN Document Server

    Przybycien, Mariusz; The ATLAS collaboration

    2017-01-01

    The ATLAS experiment at the Large Hadron Collider has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This talk presents recent results on production of jet, electroweak bosons and quarkonium, electromagnetic processes in ultra-peripheral collisions, and bulk particle collectivity from Pb+Pb and p+Pb collisions.

  2. Recent Heavy Ion results from ATLAS experiment

    CERN Document Server

    Olszewski, Andrzej; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the Large Hadron Collider has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This talk presents recent results on production of jet, eletroweak bosons and quarkonium, electromagnetic processes in ultra-peripheral collisions, and bulk particle collectivity from PbPb and pPb collisions.

  3. Heavy Flavour Production at ATLAS and CMS

    CERN Document Server

    Barton, Adam Edward; The ATLAS collaboration

    2015-01-01

    Measurements of heavy-flavor properties are an important part of the physics program of the ATLAS and CMS experiments at LHC. They can potentionally expose physics beyond the standard model, constrain supersymmetry and advance hadron spectroscopy and test QCD. In the past years, the two experiments have published results in several different fields, such as rare decays, searches for new states, CP and P violation and quarkonia polarization. In this note, some of the most recent results from ATLAS and CMS are summarized.

  4. Jet Quenching Measurements with ATLAS at LHC

    CERN Document Server

    Brooks, W K; The ATLAS collaboration

    2009-01-01

    A broad program of measurements is planned for heavy ion collisions in ATLAS. With up to a factor of 30 increase in collision energy compared to existing data, significant new insights are anticipated to be obtained with the first data measured. Global features of the LHC collisions will be accessible with the early data and will set the stage for the precision measurements to follow. ATLAS is particularly well suited for exploration of "jet quenching," the extinction of energetic jets in the hot dense medium. Observations of heavy quark jet suppression will be possible with unprecedented energy reach and statistical precision, potentially yielding new insights into the basic mechanisms involved.

  5. The ATLAS Analysis Model

    CERN Multimedia

    Amir Farbin

    The ATLAS Analysis Model is a continually developing vision of how to reconcile physics analysis requirements with the ATLAS offline software and computing model constraints. In the past year this vision has influenced the evolution of the ATLAS Event Data Model, the Athena software framework, and physics analysis tools. These developments, along with the October Analysis Model Workshop and the planning for CSC analyses have led to a rapid refinement of the ATLAS Analysis Model in the past few months. This article introduces some of the relevant issues and presents the current vision of the future ATLAS Analysis Model. Event Data Model The ATLAS Event Data Model (EDM) consists of several levels of details, each targeted for a specific set of tasks. For example the Event Summary Data (ESD) stores calorimeter cells and tracking system hits thereby permitting many calibration and alignment tasks, but will be only accessible at particular computing sites with potentially large latency. In contrast, the Analysis...

  6. Physics with Tau Lepton Final States in ATLAS

    Directory of Open Access Journals (Sweden)

    Pingel Almut M.

    2013-05-01

    Full Text Available The ATLAS detector records collisions from two high-energetic proton beams circulating in the LHC. An integral part of the ATLAS physics program are analyses with tau leptons in the final state. Here an overview is given over the studies done in ATLAS with hadronically-decaying final state tau leptons: Standard Model cross-section measurements of Z → ττ, W → τν and tt̅ → bb̅ e/μν τhadν; τ polarization measurements in W → τν decays; Higgs searches and various searches for physics beyond the Standard Model.

  7. Development of the ATLAS Simulation Framework

    Institute of Scientific and Technical Information of China (English)

    A.DellAcqua; K.Amako; 等

    2001-01-01

    Object-oriented (OO) approach is the key technology to develop a software system in the LHC/ATLAS experiment.We developed a OO simulation framework based on the Geant4 general-purpose simulation toolkit.Because of complexity of simulation in ATLAS,we payed most attention to the scalability in its design.Although the first target to apply this framework is to implement the ATLAS full detector simulation program,there is no experiment-specific code in it,therefore it can be utilized for the development of any simulation package,not only for HEP experiments but also for various different research domains ,In this paper we discuss our approach of design and implementation of the framework.

  8. Tau identification using multivariate techniques in ATLAS

    CERN Document Server

    "O'Neil, D C; The ATLAS collaboration

    2011-01-01

    Tau leptons play an important role in the physics program of the LHC. They are being used in electroweak measurements, in detector related studies and in searches for new phenomena like the Higgs boson or Supersymmetry. Tau objects appear as collimated jets with low track multiplicity. Due to the background from QCD multijet processes, efficient tau identification techniques with large fake rejection are essential. Since single variable criteria are not enough to efficiently separate them from jets and electrons, modern multivariate techniques are used. In ATLAS, several advanced algorithms are applied to identify taus, including a projective likelihood estimator and boosted decision trees. All multivariate methods applied to the ATLAS simulated data perform better than the baseline cut analysis. Their performance is shown using high energy data collected at the ATLAS experiment. The strengths and weaknesses of each technique are also discussed.

  9. ATLAS Offline Software Performance Monitoring and Optimization

    CERN Document Server

    Chauhan, N; Kittelmann, T; Langenberg, R; Mandrysch , R; Salzburger, A; Seuster, R; Ritsch, E; Stewart, G; van Eldik, N; Vitillo, R

    2014-01-01

    In a complex multi-developer, multi-package software environment, such as the ATLAS offline Athena framework, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide optimisation. Code can be instrumented firstly using the PAPI tool, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles and instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event gives a good understanding of the whole algorithm level performance of ATLAS code. Further data can be obtained using pin, a dynamic binary instrumentation tool. Pintools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is...

  10. ATLAS Offline Software Performance Monitoring and Optimization

    CERN Document Server

    Chauhan, N; The ATLAS collaboration; Kittelmann, T; Langenberg, R; Mandrysch , R; Salzburger, A; Seuster, R; Ritsch, E; Stewart, G; van Eldik, N; Vitillo, R

    2013-01-01

    In a complex multi-developer, multi-package software environment, such as the ATLAS offline Athena framework, tracking the performance of the code can be a non-trivial task in itself. In this paper we describe improvements in the instrumentation of ATLAS offline software that have given considerable insight into the performance of the code and helped to guide optimisation. Code can be instrumented firstly using the PAPI tool, which is a programing interface for accessing hardware performance counters. PAPI events can count floating point operations, cycles and instructions and cache accesses. Triggering PAPI to start/stop counting for each algorithm and processed event gives a good understanding of the whole algorithm level performance of ATLAS code. Further data can be obtained using pin, a dynamic binary instrumentation tool. Pintools can be used to obtain similar statistics as PAPI, but advantageously without requiring recompilation of the code. Fine grained routine and instruction level instrumentation is...

  11. Book review: World atlas of mangroves

    Science.gov (United States)

    Krauss, Ken W.; Friess, Daniel A.

    2011-01-01

    Nearly 14 years have passed since the first atlas, World Mangrove Atlas (Spalding et al. 1997), was published. While scientists throughout the world have shared their insights about these ecosystems from a handful of “classic” mangrove ecology treatises, no book since has provided the same platform for understanding the global importance of mangroves by simply defining their distribution. The vast majority of mangrove research programs are modest in size and limited in funding. Nonetheless, much knowledge has been gained since the last atlas, including a potential role for mangroves in storm protection, proactive adjustment of soil surface elevation with sea-level rise, coastal water conservation, economic importance locally, etc. Furthermore, by documenting what can be lost, this book allows the reader to imagine what a world without mangroves might look like (see also Science 317, 41–42). If the first atlas established a mere image of an important wetland community type in peril, then this current edition paints a picture rivaling what an artist may have envisioned. The World Atlas of Mangroves is a comprehensive, well-written, ambitious, and artistic work that we can certainly recommend, and that should be part of any serious wetland library.

  12. Integrating genomics and proteomics data to predict drug effects using binary linear programming.

    Science.gov (United States)

    Ji, Zhiwei; Su, Jing; Liu, Chenglin; Wang, Hongyan; Huang, Deshuang; Zhou, Xiaobo

    2014-01-01

    The Library of Integrated Network-Based Cellular Signatures (LINCS) project aims to create a network-based understanding of biology by cataloging changes in gene expression and signal transduction that occur when cells are exposed to a variety of perturbations. It is helpful for understanding cell pathways and facilitating drug discovery. Here, we developed a novel approach to infer cell-specific pathways and identify a compound's effects using gene expression and phosphoproteomics data under treatments with different compounds. Gene expression data were employed to infer potential targets of compounds and create a generic pathway map. Binary linear programming (BLP) was then developed to optimize the generic pathway topology based on the mid-stage signaling response of phosphorylation. To demonstrate effectiveness of this approach, we built a generic pathway map for the MCF7 breast cancer cell line and inferred the cell-specific pathways by BLP. The first group of 11 compounds was utilized to optimize the generic pathways, and then 4 compounds were used to identify effects based on the inferred cell-specific pathways. Cross-validation indicated that the cell-specific pathways reliably predicted a compound's effects. Finally, we applied BLP to re-optimize the cell-specific pathways to predict the effects of 4 compounds (trichostatin A, MS-275, staurosporine, and digoxigenin) according to compound-induced topological alterations. Trichostatin A and MS-275 (both HDAC inhibitors) inhibited the downstream pathway of HDAC1 and caused cell growth arrest via activation of p53 and p21; the effects of digoxigenin were totally opposite. Staurosporine blocked the cell cycle via p53 and p21, but also promoted cell growth via activated HDAC1 and its downstream pathway. Our approach was also applied to the PC3 prostate cancer cell line, and the cross-validation analysis showed very good accuracy in predicting effects of 4 compounds. In summary, our computational model can be

  13. The Irish Wind Atlas

    Energy Technology Data Exchange (ETDEWEB)

    Watson, R. [Univ. College Dublin, Dept. of Electronic and Electrical Engineering, Dublin (Ireland); Landberg, L. [Risoe National Lab., Meteorology and Wind Energy Dept., Roskilde (Denmark)

    1999-03-01

    The development work on the Irish Wind Atlas is nearing completion. The Irish Wind Atlas is an updated improved version of the Irish section of the European Wind Atlas. A map of the irish wind resource based on a WA{sup s}P analysis of the measured data and station description of 27 measuring stations is presented. The results of previously presented WA{sup s}P/KAMM runs show good agreement with these results. (au)

  14. Future ATLAS Higgs Studies

    CERN Document Server

    Smart, Ben; The ATLAS collaboration

    2017-01-01

    The High-Luminosity LHC will prove a challenging environment to work in, with for example $=200$ expected. It will however also provide great opportunities for advancing studies of the Higgs boson. The ATLAS detector will be upgraded, and Higgs prospects analyses have been performed to assess the reach of ATLAS Higgs studies in the HL-LHC era. These analyses are presented, as are Run-2 ATLAS di-Higgs analyses for comparison.

  15. ATLAS inner detector performance

    CERN Document Server

    Gadomski, S

    2001-01-01

    The ATLAS Inner Detector consists of three subsystems using different tracking detector technologies: silicon pixels, silicon strips and straw tubes. The combination gives ATLAS a robust, hermetic and efficient tracking system, able to reconstruct tracks at the highest foreseen LHC luminosities. The inner detector provides vertex and momentum measurements, electron identification and some $K/\\pi$ separation. Since last year the beam pipe of ATLAS was changed, causing a redesign of the first tracking layer and a deterioration of the impact parameter resolutions.

  16. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  17. Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

    OpenAIRE

    Jaffe, David B.; Butler, Jonathan; Gnerre, Sante; Mauceli, Evan; Lindblad-Toh, Kerstin; Jill P. Mesirov; Michael C Zody; Lander, Eric S.

    2003-01-01

    We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rej...

  18. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S

    2005-01-01

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: Atlas Software Week Plenary 6-10 December 2004 North American ATLAS Physics Workshop (Tucson) 20-21 December 2004 (17 talks) Physics Analysis Tools Tutorial (Tucson) 19 December 2004 Full Chain Tutorial 21 September 2004 ATLAS Plenary Sessions, 17-18 February 2005 (17 talks) Coming soon: ATLAS Tutorial on Electroweak Physics, 14 Feb. 2005 Software Workshop, 21-22 February 2005 Click here to browse WLAP for all ATLAS lectures.

  19. "Dark Matter searches at ATLAS"

    CERN Document Server

    Gustavino, Giuliano; The ATLAS collaboration

    2016-01-01

    Although the existence of Dark Matter is a well-established hypothesis to explain a range of astrophysical and cosmological measurements, its nature and particle properties still remain one of the greatest unsolved puzzles of particle and astro-particle physics. The collider experiments have developed a comprehensive search program in this sector looking at a wide spectrum of channels in which a Dark Matter evidence can be traced. In this context the last results using the data sample collected at LHC at the new centre-of-mass energy of 13 TeV will be presented giving an outlook of the Dark Matter search status in the ATLAS experiment.

  20. Dark matter searches at ATLAS

    CERN Document Server

    Gustavino, Giuliano; The ATLAS collaboration

    2016-01-01

    Although the existence of Dark Matter is a well-established hypothesis to explain a range of astrophysical and cosmological measurements, its nature and particle properties still remain one of the greatest unsolved puzzles of particle and astro-particle physics. The collider experiments have developed a comprehensive search program in this sector looking at a wide spectrum of channels in which a Dark Matter evidence can be traced. In this context the last results using the data sample collected at LHC at the new centre-of-mass energy of 13 TeV will be presented giving an outlook of the Dark Matter search status in the ATLAS experiment.

  1. ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing

    Directory of Open Access Journals (Sweden)

    Kamatani Naoyuki

    2010-06-01

    Full Text Available Abstract Background The use of haplotype-based association tests can improve the power of genome-wide association studies. Since the observed genotypes are unordered pairs of alleles, haplotype phase must be inferred. However, estimating haplotype phase is time consuming. When millions of single-nucleotide polymorphisms (SNPs are analyzed in genome-wide association study, faster methods for haplotype estimation are required. Methods We developed a program package for parallel computation of haplotype estimation. Our program package, ParaHaplo 2.0, is intended for use in workstation clusters using the Intel Message Passing Interface (MPI. We compared the performance of our algorithm to that of the regular permutation test on both Japanese in Tokyo, Japan and Han Chinese in Beijing, China of the HapMap dataset. Results Parallel version of ParaHaplo 2.0 can estimate haplotypes 100 times faster than a non-parallel version of the ParaHaplo. Conclusion ParaHaplo 2.0 is an invaluable tool for conducting haplotype-based genome-wide association studies (GWAS. The need for fast haplotype estimation using parallel computing will become increasingly important as the data sizes of such projects continue to increase. The executable binaries and program sources of ParaHaplo are available at the following address: http://en.sourceforge.jp/projects/parallelgwas/releases/

  2. Generating information-rich high-throughput experimental materials genomes using functional clustering via multitree genetic programming and information theory.

    Science.gov (United States)

    Suram, Santosh K; Haber, Joel A; Jin, Jian; Gregoire, John M

    2015-04-13

    High-throughput experimental methodologies are capable of synthesizing, screening and characterizing vast arrays of combinatorial material libraries at a very rapid rate. These methodologies strategically employ tiered screening wherein the number of compositions screened decreases as the complexity, and very often the scientific information obtained from a screening experiment, increases. The algorithm used for down-selection of samples from higher throughput screening experiment to a lower throughput screening experiment is vital in achieving information-rich experimental materials genomes. The fundamental science of material discovery lies in the establishment of composition-structure-property relationships, motivating the development of advanced down-selection algorithms which consider the information value of the selected compositions, as opposed to simply selecting the best performing compositions from a high throughput experiment. Identification of property fields (composition regions with distinct composition-property relationships) in high throughput data enables down-selection algorithms to employ advanced selection strategies, such as the selection of representative compositions from each field or selection of compositions that span the composition space of the highest performing field. Such strategies would greatly enhance the generation of data-driven discoveries. We introduce an informatics-based clustering of composition-property functional relationships using a combination of information theory and multitree genetic programming concepts for identification of property fields in a composition library. We demonstrate our approach using a complex synthetic composition-property map for a 5 at. % step ternary library consisting of four distinct property fields and finally explore the application of this methodology for capturing relationships between composition and catalytic activity for the oxygen evolution reaction for 5429 catalyst compositions in a

  3. Web Service Based on GeoTools in The Atlas of Fire Protection

    Directory of Open Access Journals (Sweden)

    Jan Růžička

    2010-02-01

    Full Text Available The paper describes a simple way of a systems integration based on SOAP web services.  The systems integration described in the paper is covered by a system named The atlas of a fire protection. The atlas is a set of dynamically created maps published in WWW browser.  Technologies used for the solution are UMN MapServer, ArcIMS, PHP, GeoTools and Axis.  GeoTools and Axis are used for building platform and programming language independent component for the atlas. The paper describes a software architecture used for the atlas and a role of a web service in the integration.

  4. A Slice of ATLAS

    CERN Multimedia

    2004-01-01

    An entire section of the ATLAS detector is being assembled at Prévessin. Since May the components have been tested using a beam from the SPS, giving the ATLAS team valuable experience of operating the detector as well as an opportunity to debug the system.

  5. Higgs Measurement from ATLAS

    CERN Document Server

    Liu, Bo; The ATLAS collaboration

    2015-01-01

    Using run-I data record by ATLAS detector, many searches on the higgs decay modes have been done. Also some properties measurement of the Higgs Boson has been done. This talk will summarise the recent result of Higgs search and measurement from ATLAS.

  6. ATLAS Thesis Awards 2015

    CERN Multimedia

    Biondi, Silvia

    2016-01-01

    Winners of the ATLAS Thesis Award were presented with certificates and glass cubes during a ceremony on Thursday 25 February. The winners also presented their work in front of members of the ATLAS Collaboration. Winners: Javier Montejo Berlingen, Barcelona (Spain), Ruth Pöttgen, Mainz (Germany), Nils Ruthmann, Freiburg (Germany), and Steven Schramm, Toronto (Canada).

  7. ATLAS Colouring Book

    CERN Multimedia

    Anthony, Katarina

    2016-01-01

    The ATLAS Experiment Colouring Book is a free-to-download educational book, ideal for kids aged 5-9. It aims to introduce children to the field of High-Energy Physics, as well as the work being carried out by the ATLAS Collaboration.

  8. The ATLAS tile calorimeter

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Louis Rose-Dulcina, a technician from the ATLAS collaboration, works on the ATLAS tile calorimeter. Special manufacturing techniques were developed to mass produce the thousands of elements in this detector. Tile detectors are made in a sandwich-like structure where these scintillator tiles are placed between metal sheets.

  9. ATLAS people can run!

    CERN Multimedia

    Claudia Marcelloni de Oliveira; Pauline Gagnon

    It must be all the training we are getting every day, running around trying to get everything ready for the start of the LHC next year. This year, the ATLAS runners were in fine form and came in force. Nine ATLAS teams signed up for the 37th Annual CERN Relay Race with six runners per team. Under a blasting sun on Wednesday 23rd May 2007, each team covered the distances of 1000m, 800m, 800m, 500m, 500m and 300m taking the runners around the whole Meyrin site, hills included. A small reception took place in the ATLAS secretariat a week later to award the ATLAS Cup to the best ATLAS team. For the details on this complex calculation which takes into account the age of each runner, their gender and the color of their shoes, see the July 2006 issue of ATLAS e-news. The ATLAS Running Athena Team, the only all-women team enrolled this year, won the much coveted ATLAS Cup for the second year in a row. In fact, they are so good that Peter Schmid and Patrick Fassnacht are wondering about reducing the women's bonus in...

  10. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    Budker Nuclear Physics Institute, Novosibirsk Sequence 1 Shots of aircraft factory where machining for ATLAS is done Shots of aircraft Work on components for ATLAS big wheel Discussions between Tikhonov and Nordberg in workshop Sequence 2 Shots of downtown Novosibirsk, including little church which is mid-point of Russian Federation Sequence 3 Interview of Yuri Tikhonov by Andrew Millington

  11. ATLAS rewards industry

    CERN Multimedia

    Maximilien Brice

    2006-01-01

    For contributing vital pieces to the ATLAS puzzle, three industries were recognized on Friday 5 May during a supplier awards ceremony. After a welcome and overview of the ATLAS experiment by spokesperson Peter Jenni, CERN Secretary-General Maximilian Metzger stressed the importance of industry to CERN's scientific goals. Picture 30 : representatives of the three award-wining companies after the ceremony

  12. ATLAS brochure (Danish version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  13. ATLAS brochure (German version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  14. ATLAS brochure (Italian version)

    CERN Multimedia

    Lefevre, C

    2010-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  15. ATLAS brochure (French version)

    CERN Multimedia

    Lefevre, C

    2012-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  16. ATLAS Brochure (English version)

    CERN Multimedia

    Lefevre, Christiane

    2011-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  17. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    La Givrine near St Cergue Cross Country Skiing and Fondue at Basse Ruche with M Nordberg, P Jenni, M Nessi, F Gianotti and Co. ATLAS Management Fondu dinner, reviewing state of play of the experiment Many fun scenes from cross country skiing and after 41 minutes of the film starts the fondue dinner in a nice chalet with many persons working for ATLAS experiment

  18. ATLAS brochure (Spanish version)

    CERN Multimedia

    Lefevre, C

    2008-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  19. ATLAS brochure (Polish version)

    CERN Multimedia

    Lefevre, C

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  20. Higgs searches at ATLAS

    CERN Document Server

    Lafaye, R

    2002-01-01

    This proceeding is an overview of ATLAS capabilities on Higgs studies. After a short introduction on LEP and Tevatron searches on this subject, the ATLAS potential on a standard model and a supersymmetric Higgs discovery are summarized. Last, a section presents the Higgs parameters measurement that will be possible at LHC. (6 refs).

  1. Searches in ATLAS

    CERN Document Server

    Kondrashova, Nataliia; The ATLAS collaboration

    2017-01-01

    Many theories beyond the Standard Model predict new phenomena accessible by the LHC. Searches for new physics models are performed using the ATLAS experiment at the LHC. The results reported here use the pp collision data sample collected in 2015 and 2016 by the ATLAS detector at the LHC with a centre-of-mass energy of 13 TeV.

  2. ATLAS Brochure (english version)

    CERN Multimedia

    2004-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  3. ATLAS Brochure (german version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  4. ATLAS Brochure (english version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  5. ATLAS Brochure (french version)

    CERN Multimedia

    Marcastel, F

    2007-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  6. ATLAS brochure (Norwegian version)

    CERN Multimedia

    Lefevre, C

    2009-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter. Français

  7. ATLAS-Hadronic Calorimeter

    CERN Multimedia

    2003-01-01

    Hall 180 work on Hadronic Calorimeter The ATLAS hadronic tile calorimeter The Tile Calorimeter, which constitutes the central section of the ATLAS hadronic calorimeter, is a non-compensating sampling device made of iron and scintillating tiles. (IEEE Trans. Nucl. Sci. 53 (2006) 1275-81)

  8. ATLAS brochure (Catalan version)

    CERN Multimedia

    Lefevre, C

    2008-01-01

    ATLAS is the largest detector at the LHC, the most powerful particle accelerator in the world, which will start up in 2008. ATLAS is a multi-purpose detector, designed to throw light on fundamental questions such as the origin of mass and the nature of the Universe's dark matter.

  9. ATLAS Visitors Centre

    CERN Multimedia

    claudia Marcelloni

    2009-01-01

    ATLAS Visitors Centre has opened its shiny new doors to the public. Officially launched on Monday February 23rd, 2009, the permanent exhibition at Point 1 was conceived as a tour resource for ATLAS guides, and as a way to preserve the public’s opportunity to get a close-up look at the experiment in action when the cavern is sealed.

  10. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  11. Dear ATLAS colleagues,

    CERN Multimedia

    PH Department

    2008-01-01

    We are collecting old pairs of glasses to take out to Mali, where they can be re-used by people there. The price for a pair of glasses can often exceed 3 months salary, so they are prohibitively expensive for many people. If you have any old spectacles you can donate, please put them in the special box in the ATLAS secretariat, bldg.40-4-D01 before the Christmas closure on 19 December so we can take them with us when we leave for Africa at the end of the month. (more details in ATLAS e-news edition of 29 September 2008: http://atlas-service-enews.web.cern.ch/atlas-service-enews/news/news_mali.php) many thanks! Katharine Leney co-driver of the ATLAS car on the Charity Run to Mali

  12. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    Mortensen, Niels Gylling; Said Said, Usama; Badger, Jake

    2006-01-01

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  13. Wind Atlas for Egypt

    DEFF Research Database (Denmark)

    The results of a comprehensive, 8-year wind resource assessment programme in Egypt are presented. The objective has been to provide reliable and accurate wind atlas data sets for evaluating the potential wind power output from large electricityproducing wind turbine installations. The regional wind...... climates of Egypt have been determined by two independent methods: a traditional wind atlas based on observations from more than 30 stations all over Egypt, and a numerical wind atlas based on long-term reanalysis data and a mesoscale model (KAMM). The mean absolute error comparing the two methods is about...... 10% for two large-scale KAMM domains covering all of Egypt, and typically about 5% for several smaller-scale regional domains. The numerical wind atlas covers all of Egypt, whereas the meteorological stations are concentrated in six regions. The Wind Atlas for Egypt represents a significant step...

  14. ATLAS' major cooling project

    CERN Multimedia

    2005-01-01

    In 2005, a considerable effort has been put into commissioning the various units of ATLAS' complex cryogenic system. This is in preparation for the imminent cooling of some of the largest components of the detector in their final underground configuration. The liquid helium and nitrogen ATLAS refrigerators in USA 15. Cryogenics plays a vital role in operating massive detectors such as ATLAS. In many ways the liquefied argon, nitrogen and helium are the life-blood of the detector. ATLAS could not function without cryogens that will be constantly pumped via proximity systems to the superconducting magnets and subdetectors. In recent weeks compressors at the surface and underground refrigerators, dewars, pumps, linkages and all manner of other components related to the cryogenic system have been tested and commissioned. Fifty metres underground The helium and nitrogen refrigerators, installed inside the service cavern, are an important part of the ATLAS cryogenic system. Two independent helium refrigerators ...

  15. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  16. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  17. [Research on Atlas of Viscera].

    Science.gov (United States)

    Jin, S

    1994-01-01

    Chinese ancient visceral atlas, or anatomical illustrations were derived from Taoist and medical schools through observation in cadavers. During the period from Five-Dynasties to Song, there were several works on visceral atlas, including Yanluo illustration, Atlas of Ou Xifan's visceral atlas of fidelity, Li Jung's Atlas. Among them, there exist relations of transmission-heredity, with gradual improvement. It seems likely that the visceral illustrations in Japanese Wan'an Prescription is the extant illustration of Ou's. After the advent of Atlas of Fidelity visceral atlas was differentiated into 3 different kinds of illustrations, as the Inner Picture (Neijing) of Mingtang Atlas; Neizhao Picture in pulsological works and visceral picture in physical Shenxing picture. Chinese visceral atlas was transmitted to Japan, Korea, Persia, and Europe and exerted some influence on cosmopolitan medicine.

  18. Integrated genomic analyses of ovarian carcinoma

    NARCIS (Netherlands)

    Bell, D.; Berchuck, A.; Birrer, M.; Chien, J.; Dao, F.; Dhir, R.; DiSaia, P.; Gabra, H.; Glenn, P.; Godwin, A. K.; Gross, J.; Hartmann, L.; Huang, M.; Huntsman, D. G.; Iacocca, M.; Imielinski, M.; Kalloger, S.; Karlan, B. Y.; Levine, D. A.; Mills, G. B.; Morrison, C.; Mutch, D.; Olvera, N.; Orsulic, S.; Park, K.; Petrelli, N.; Rabeno, B.; Rader, J. S.; Sikic, B. I.; Smith-McCune, K.; Sood, A. K.; Bowtell, D.; Penny, R.; Testa, J. R.; Chang, K.; Dinh, H. H.; Drummond, J. A.; Fowler, G.; Gunaratne, P.; Hawes, A. C.; Kovar, C. L.; Lewis, L. R.; Morgan, M. B.; Newsham, I. F.; Santibanez, J.; Reid, J. G.; Trevino, L. R.; Wu, Y. -Q.; Wang, M.; Muzny, D. M.; Wheeler, D. A.; Gibbs, R. A.; Getz, G.; Lawrence, M. S.; Cibulskis, K.; Sivachenko, A. Y.; Sougnez, C.; Voet, D.; Wilkinson, J.; Bloom, T.; Ardlie, K.; Fennell, T.; Baldwin, J.; Gabriel, S.; Lander, E. S.; Ding, L.; Fulton, R. S.; Koboldt, D. C.; McLellan, M. D.; Wylie, T.; Walker, J.; O'Laughlin, M.; Dooling, D. J.; Fulton, L.; Abbott, R.; Dees, N. D.; Zhang, Q.; Kandoth, C.; Wendl, M.; Schierding, W.; Shen, D.; Harris, C. C.; Schmidt, H.; Kalicki, J.; Delehaunty, K. D.; Fronick, C. C.; Demeter, R.; Cook, L.; Wallis, J. W.; Lin, L.; Magrini, V. J.; Hodges, J. S.; Eldred, J. M.; Smith, S. M.; Pohl, C. S.; Vandin, F.; Raphael, B. J.; Weinstock, G. M.; Mardis, R.; Wilson, R. K.; Meyerson, M.; Winckler, W.; Getz, G.; Verhaak, R. G. W.; Carter, S. L.; Mermel, C. H.; Saksena, G.; Nguyen, H.; Onofrio, R. C.; Lawrence, M. S.; Hubbard, D.; Gupta, S.; Crenshaw, A.; Ramos, A. H.; Ardlie, K.; Chin, L.; Protopopov, A.; Zhang, Juinhua; Kim, T. M.; Perna, I.; Xiao, Y.; Zhang, H.; Ren, G.; Sathiamoorthy, N.; Park, R. W.; Lee, E.; Park, P. J.; Kucherlapati, R.; Absher, D. M.; Waite, L.; Sherlock, G.; Brooks, J. D.; Li, J. Z.; Xu, J.; Myers, R. M.; Laird, P. W.; Cope, L.; Herman, J. G.; Shen, H.; Weisenberger, D. J.; Noushmehr, H.; Pan, F.; Triche, T.; Berman, B. P.; Van den Berg, D. J.; Buckley, J.; Baylin, S. B.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Jakkula, L. R.; Durinck, S.; Han, J.; Dorton, S.; Marr, H.; Choi, Y. G.; Wang, V.; Wang, N. J.; Ngai, J.; Conboy, J. G.; Parvin, B.; Feiler, H. S.; Speed, T. P.; Gray, J. W.; Levine, D. A.; Socci, N. D.; Liang, Y.; Taylor, B. S.; Schultz, N.; Borsu, L.; Lash, A. E.; Brennan, C.; Viale, A.; Sander, C.; Ladanyi, M.; Hoadley, K. A.; Meng, S.; Du, Y.; Shi, Y.; Li, L.; Turman, Y. J.; Zang, D.; Helms, E. B.; Balu, S.; Zhou, X.; Wu, J.; Topal, M. D.; Hayes, D. N.; Perou, C. M.; Getz, G.; Voet, D.; Saksena, G.; Zhang, Junihua; Zhang, H.; Wu, C. J.; Shukla, S.; Cibulskis, K.; Lawrence, M. S.; Sivachenko, A.; Jing, R.; Park, R. W.; Liu, Y.; Park, P. J.; Noble, M.; Chin, L.; Carter, H.; Kim, D.; Karchin, R.; Spellman, P. T.; Purdom, E.; Neuvial, P.; Bengtsson, H.; Durinck, S.; Han, J.; Korkola, J. E.; Heiser, L. M.; Cho, R. J.; Hu, Z.; Parvin, B.; Speed, T. P.; Gray, J. W.; Schultz, N.; Cerami, E.; Taylor, B. S.; Olshen, A.; Reva, B.; Antipin, Y.; Shen, R.; Mankoo, P.; Sheridan, R.; Ciriello, G.; Chang, W. K.; Bernanke, J. A.; Borsu, L.; Levine, D. A.; Ladanyi, M.; Sander, C.; Haussler, D.; Benz, C. C.; Stuart, J. M.; Benz, S. C.; Sanborn, J. Z.; Vaske, C. J.; Zhu, J.; Szeto, C.; Scott, G. K.; Yau, C.; Hoadley, K. A.; Du, Y.; Balu, S.; Hayes, D. N.; Perou, C. M.; Wilkerson, M. D.; Zhang, N.; Akbani, R.; Baggerly, K. A.; Yung, W. K.; Mills, G. B.; Weinstein, J. N.; Penny, R.; Shelton, T.; Grimm, D.; Hatfield, M.; Morris, S.; Yena, P.; Rhodes, P.; Sherman, M.; Paulauskis, J.; Millis, S.; Kahn, A.; Greene, J. M.; Sfeir, R.; Jensen, M. A.; Chen, J.; Whitmore, J.; Alonso, S.; Jordan, J.; Chu, A.; Zhang, Jinghui; Barker, A.; Compton, C.; Eley, G.; Ferguson, M.; Fielding, P.; Gerhard, D. S.; Myles, R.; Schaefer, C.; Shaw, K. R. Mills; Vaught, J.; Vockley, J. B.; Good, P. J.; Guyer, M. S.; Ozenberger, B.; Peterson, J.; Thomson, E.; Cramer, D.W.

    2011-01-01

    A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade

  19. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  20. Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics – assessment and update

    Science.gov (United States)

    Freyhult, Eva; Edvardsson, Sverker; Tamas, Ivica; Moulton, Vincent; Poole, Anthony M

    2008-01-01

    Background The H/ACA family of small nucleolar RNAs (snoRNAs) plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA). In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program – Fisher – and previously presented several candidate snoRNAs based on our analysis [1]. Findings In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs [2] identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in [1], and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program [3]. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. Conclusion Our results confirm the validity of using minimum free energy (MFE) secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints. PMID:18710502

  1. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    Science.gov (United States)

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure.

  2. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

    Science.gov (United States)

    McKenna, Aaron; Hanna, Matthew; Banks, Eric; Sivachenko, Andrey; Cibulskis, Kristian; Kernytsky, Andrew; Garimella, Kiran; Altshuler, David; Gabriel, Stacey; Daly, Mark; DePristo, Mark A

    2010-09-01

    Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS--the 1000 Genome pilot alone includes nearly five terabases--make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.

  3. ATLAS: A Community Policing Response to Adverse Student Athlete Behavior

    Science.gov (United States)

    Williams, Robert

    2011-01-01

    The University at Albany Police and the University at Albany Athletics Department have teamed together to implement a ground breaking program aimed at identifying, addressing and managing negative behavior among student athletes. ATLAS stands for: Athletics, Team Building, Leadership Development, And Mentoring for Student Athletes. The program was…

  4. Full genome sequence of a Danish isolate of Mycobacterium avium subspecies paratuberculosis, strain Ejlskov2007

    DEFF Research Database (Denmark)

    Afzal, Mamuna; Abidi, Soad; Mikkelsen, Heidi

    , consisting of 4317 unique gene families. Comparison with M. avium paratuberculosis strain K10 revealed only 3436 genes in common (~70%). We have used GenomeAtlases to show conserved (and unique) regions along the Ejlskov2007 chromosome, compared to 2 other Mycobacterium avium sequenced genomes. Pan-genome...

  5. Ceremony for ATLAS cavern

    CERN Multimedia

    2003-01-01

    Wednesday 4 June will be a special day for CERN. The President of the Swiss Confederation, Pascal Couchepin, will officially inaugurate the huge ATLAS cavern now that the civil engineering works have ended. The inauguration ceremony will be held in the ATLAS surface building, with speeches by Pascal Couchepin and CERN, ATLAS and civil engineering personalities. This ceremony will be Webcast live. To access the Webcast on 4 June at 18h00 go to CERN Intranet home page or the following address : http://webcast.cern.ch/live.php

  6. Highlights from ATLAS

    CERN Document Server

    Charlton, D; The ATLAS collaboration

    2013-01-01

    Highlights of recent results from ATLAS were presented. The data collected to date, the detector and physics performance, and measurements of previously established Standard Model processes were reviewed briefly before summarising the latest ATLAS results in the Brout-Englert-Higgs sector, where big progress has been made in the year since the discovery. Finally, selected prospects for measurements including the data from the HL-LHC luminosity upgrade were presented, for both ATLAS and CMS. Many of the results mentioned are preliminary. These proceedings reflect only a brief summary of the material presented, and the status at the time of the conference is reported.

  7. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A

    2008-01-01

    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  8. EnviroAtlas - Des Moines, IA - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Des Moines, IA EnviroAtlas Community. It represents the outside edge of all the block groups included in the...

  9. EnviroAtlas - Cleveland, OH - Atlas Area Boundary

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundary of the Cleveland, OH EnviroAtlas Community. It represents the outside edge of all the block groups included in the...

  10. ATLAS-plus: Multimedia Instruction in Embryology, Gross Anatomy, and Histology

    Science.gov (United States)

    Chapman, CM; Miller, JG; Bush, LC; Bruenger, JA; Wysor, WJ; Meininger, ET; Wolf, FM; Fischer, TV; Beaudoin, AR; Burkel, WE; MacCallum, DK; Fisher, DL; Carlson, BM

    1992-01-01

    ATLAS-plus [Advanced Tools for Learning Anatomical Structure] is a multimedia program used to assist in the teaching of anatomy at the University of Michigan Medical School. ATLAS-plus contains three courses: Histology, Embryology, and Gross Anatomy. In addition to the three courses, a glossary containing terms from the three courses is available. All three courses and the glossary are accessible in the ATLAS-plus environment. The ATLAS-plus environment provides a consistent set of tools and options so that the user can navigate easily and intelligently in and between the various courses and modules in the ATLAS-plus world. The program is a collaboration between anatomy and cell biology faculty, medical students, graphic artists, systems analysts, and instructional designers. PMID:1482964

  11. The ATLAS Trigger Menu: Design and Performance

    CERN Document Server

    Bernius, C; The ATLAS collaboration

    2012-01-01

    The ATLAS trigger is a three-tiered system designed to select events of interest for the diverse ATLAS physics program such as Higgs Boson decays. At the same time the rate of events has to be reduced in order to stay within the limitations of available resources such as the output bandwidth, processing power and recording rate. At design capacity, the LHC has a bunch-crossing rate of 40 MHz whereas ATLAS detector has an average recording rate of about 300Hz. The decision to record an event is based on physics signatures found in the event such as energetic jets, leptons or large missing energy. The ATLAS trigger menu consists of several hundred trigger chains which are used during data taking. Each chain defines the selection criteria at each of the three trigger levels for a single physics signature. Additionally, the trigger menu specifies, depending on the physics purpose of the trigger, at which given rate the trigger is running. The continuously increasing luminosities together with optimisations of alg...

  12. ATLAS Event - First Splash of Particles in ATLAS

    CERN Multimedia

    ATLAS Outreach

    2008-01-01

    A simulated event. September 10, 2008 - The ATLAS detector lit up as a flood of particles traversed the detector when the beam was occasionally directed at a target near ATLAS. This allowed ATLAS physicists to study how well the various components of the detector were functioning in preparation for the forthcoming collisions. The first ATLAS data recorded on September 10, 2008 is seen here. Running time 24 seconds

  13. Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress.

    Science.gov (United States)

    Fernández, Jesús; Toro, Miguel Á; Sonesson, Anna K; Villanueva, Beatriz

    2014-01-01

    The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in the initial founders. Traditionally, base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and, therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during 10 generations of phenotypic selection applied in the subsequent breeding program.

  14. Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress

    Directory of Open Access Journals (Sweden)

    Jesús eFernández

    2014-11-01

    Full Text Available The success of an aquaculture breeding program critically depends on the way in which the base population of breeders is constructed since all the genetic variability for the traits included originally in the breeding goal as well as those to be included in the future is contained in those initial founders. Traditionally base populations were created from a number of wild strains by sampling equal numbers from each strain. However, for some aquaculture species improved strains are already available and therefore, mean phenotypic values for economically important traits can be used as a criterion to optimize the sampling when creating base populations. Also, the increasing availability of genome-wide genotype information in aquaculture species could help to refine the estimation of relationships within and between candidate strains and, thus, to optimize the percentage of individuals to be sampled from each strain. This study explores the advantages of using phenotypic and genome-wide information when constructing base populations for aquaculture breeding programs in terms of initial and subsequent trait performance and genetic diversity level. Results show that a compromise solution between diversity and performance can be found when creating base populations. Up to 6% higher levels of phenotypic performance can be achieved at the same level of global diversity in the base population by optimizing the selection of breeders instead of sampling equal numbers from each strain. The higher performance observed in the base population persisted during ten generations of phenotypic selection applied in the subsequent breeding program.

  15. Atlas Skills for Learning Rather than Learning Atlas Skills.

    Science.gov (United States)

    Carswell, R. J. B.

    1986-01-01

    Presents a model for visual learning and describes an approach to skills instruction which aids students in using atlases. Maintains that teachers must help students see atlases as tools capable of providing useful information rather than experiencing atlas learning as an empty exercise with little relevance to their lives. (JDH)

  16. Printed circuit for ATLAS

    CERN Multimedia

    Laurent Guiraud

    1999-01-01

    A printed circuit board made by scientists in the ATLAS collaboration for the transition radiaton tracker (TRT). This will read data produced when a high energy particle crosses the boundary between two materials with different electrical properties.

  17. ATLAS Cavern baseplate

    CERN Multimedia

    2002-01-01

    This video shows the incredible amounth of iron used for ATLAS cavern. Please look at the related links and also videos that are concerning the civil engineering where you can see even more detailed cavern excavation work.

  18. PeptideAtlas

    Data.gov (United States)

    U.S. Department of Health & Human Services — PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass...

  19. ATLAS TV PROJECT

    CERN Multimedia

    2006-01-01

    CERN, Building 40 Interview with theorist Mr. Philip Hinchliffe (Berkeley) as well an interview with his wife Mrs. Hinchliffe who is also Physics Department head at Berkeley. They are both working in ATLAS Experiment.

  20. Russian wind atlas

    Energy Technology Data Exchange (ETDEWEB)

    Starkov, A.N.; Bezroukikh, P.P.; Borisenko, M.M. (Russian Danish Institute of Energy Efficiency (RDIEE), Moscow (RU)); Landberg, L. (Risoe National Lab., Roskilde (DK))

    2000-07-01

    The Atlas provides the assessment of wind energy potential in the near-surface 200 metres of the atmospheric boundary layer. It is based on numerical modeling of wind flows according to hydrodynamic laws and takes into account the effects of roughness, orography and sheltering. The primary information is derived from long-term data series from 332 meteorological stations in Russia. The regional climatologies are calculated in the Atlas for five standard heights (10, 30, 50, 100, 200 m) and four roughness classes of flat and homogeneous terrain. Besides, the Atlas provides the maps of wind energy potential in Russia at 50 metres above ground level, the most important height for wind energy applications. The maps show mean wind speeds and mean wind power densities for any region and any of the five basic types of landscape. The Atlas gives recommendations and examples of wind energy resource assessment and siting of wind turbines. (LN)

  1. Vermont Natural Resources Atlas

    Data.gov (United States)

    Vermont Center for Geographic Information — The purpose of the Natural Resources Atlas is to provide geographic information about environmental features and sites that the Vermont Agency of Natural Resources...

  2. Lunar Sample Atlas

    Data.gov (United States)

    National Aeronautics and Space Administration — The Lunar Sample Atlas provides pictures of the Apollo samples taken in the Lunar Sample Laboratory, full-color views of the samples in microscopic thin-sections,...

  3. Overview of ATLAS results

    CERN Document Server

    Di Ciaccio, Anna; The ATLAS collaboration

    2012-01-01

    This talk presents recent ATLAS results on performances and physics concerning in particular: di-boson, single top cross-section measurements, Higgs measurement, SUSY and beyond Standard model searches.

  4. Higgs measurements with ATLAS

    CERN Document Server

    Queitsch-Maitland, Michaela; The ATLAS collaboration

    2017-01-01

    The final Run 1 and first Run 2 results with the ATLAS detector on the measurement of the cross sections, couplings and properties of the Higgs boson in individual final states and their combination are presented.

  5. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    ATLAS Physics Workshop at the University of Roma Tre held from Monday 06 June 2005 to Saturday 11 June 2005. Experts establishing workshop, poster, people milling Shots of Peter Jenni introduction Many audience shots Sequences from various talks

  6. ATLAS DAQ Configuration Databases

    Institute of Scientific and Technical Information of China (English)

    I.Alexandrov; A.Amorim; 等

    2001-01-01

    The configuration databases are an important part of the Trigger/DAQ system of the future ATLAS experiment .This paper describes their current status giving details of architecture,implementation,test results and plans for future work.

  7. The Latest from ATLAS

    CERN Multimedia

    2009-01-01

    Since November 2008, ATLAS has undertaken detailed maintenance, consolidation and repair work on the detector (see Bulletin of 20 July 2009). Today, the fraction of the detector that is operational has increased compared to last year: less than 1% of dead channels for most of the sub-systems. "We are going to start taking data this year with a detector which is even more efficient than it was last year," agrees ATLAS Spokesperson, Fabiola Gianotti. By mid-September the detector was fully closed again, and the cavern sealed. The magnet system has been operated at nominal current for extensive periods over recent months. Once the cavern was sealed, ATLAS began two weeks of combined running. Right now, subsystems are joining the run incrementally until the point where the whole detector is integrated and running as one. In the words of ATLAS Technical Coordinator, Marzio Nessi: "Now we really start physics." In parallel, the analysis ...

  8. California Ocean Uses Atlas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset is a result of the California Ocean Uses Atlas Project: a collaboration between NOAA's National Marine Protected Areas Center and Marine Conservation...

  9. The Research of VBA Programmed Modeling Based on Product Genome%基于产品基因组的VBA程序建模开发研究

    Institute of Scientific and Technical Information of China (English)

    陈煌; 陈锦昌

    2013-01-01

    In order to meet the market demand,improve the accuracy of establishing the digital model of product and meet the demand of the small batch production, the research has been proposed.Under the premise of sketching the whole product prototype,the product designer and the VBA programmers group leader divide the product into several different characteristic product genomes according to the product deconstructed rule which are based on genome,then the VBA program designers are responsible for the corresponding features genomes according to the distribution rule of product genome,with VBA programming language for constructing the parametric,programmed,exact and 3D digital modeling, which can exert the advantages of collaborative development and motivate the enthusiasm and innovative of team members.Therefore ,it can realize the organic union of perceptual product design and rational VBA program development, promoting the union of perceptual design and rational design.%为了适应市场需求,提高产品数字化建模的精确性和满足小批量生产,提出了在产品设计师手绘完成整个产品原型的前提下,依据基因组的产品解构规则把产品解构为若于个不同特征的产品基因组,再由VBA程序设计师们根据产品基因组的分配规则来负责对应的特征基因组,用VBA程序语言进行参数化、程序化与精确化的三维数字化建模,发挥协同开发的优势以及调动团队中各成员的热情与创新性,从而实现感性的产品设计与理性的VBA程序开发的有机结合,促进感性设计与理性设计的结合.

  10. Frontiers in cancer epidemiology: a challenge to the research community from the Epidemiology and Genomics Research Program at the National Cancer Institute.

    Science.gov (United States)

    Khoury, Muin J; Freedman, Andrew N; Gillanders, Elizabeth M; Harvey, Chinonye E; Kaefer, Christie; Reid, Britt C; Rogers, Scott; Schully, Sheri D; Seminara, Daniela; Verma, Mukesh

    2012-07-01

    The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is developing scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop in December 2012 to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies.

  11. Recent ATLAS Articles on WLAP

    CERN Multimedia

    Goldfarb, S.

    As reported in the September 2004 ATLAS eNews, the Web Lecture Archive Project is a system for the archiving and publishing of multimedia presentations, using the Web as medium. We list here newly available WLAP items relating to ATLAS: June ATLAS Plenary Meeting Tutorial on Physics EDM and Tools (June) Freiburg Overview Week Ketevi Assamagan's Tutorial on Analysis Tools Click here to browse WLAP for all ATLAS lectures.

  12. Recent results from ATLAS experiment

    CERN Document Server

    Smirnov, Sergei; The ATLAS collaboration

    2016-01-01

    The 2nd LHC run has started in 2015 with a pp centre-of-mass collision energy of 13 TeV and ATLAS has taken more than 20 fb-1 of data at the new energy by 2016 summer. In this talk, an overview is given on the ATLAS data taking and the improvements made to the ATLAS experiment during the 2-year shutdown 2013/2014. Selected new results from the recent data analysis from ATLAS is also presented.

  13. ATLAS physics results

    CERN Document Server

    AUTHOR|(CDS)2074312

    2015-01-01

    The ATLAS experiment at the Large Hadron Collider at CERN has been successfully taking data since the end of 2009 in proton-proton collisions at centre-of-mass energies of 7 and 8 TeV, and in heavy ion collisions. In these lectures, some of the most recent ATLAS results will be given on Standard Model measurements, the discovery of the Higgs boson, searches for supersymmetry and exotics and on heavy-ion results.

  14. ATLAS construction status

    CERN Document Server

    Jenni, P

    2006-01-01

    The ATLAS detector is being constructed at the LHC, in view of a data-taking start-up in 2007. This report concentrates on the progress and the technical challenges of the detector construction, and summarizes the status of the work as of August 2004. The project is on track to allow the highly motivated ATLAS collaboration to enter into a new exploratory domain of high-energy physics in 2007.

  15. ATLAS Transitional Radiation Tracker

    CERN Multimedia

    ATLAS Outreach

    2006-01-01

    This colorful 3D animation is an excerpt from the film "ATLAS-Episode II, The Particles Strike Back." Shot with a bug's eye view of the inside of the detector. The viewer is taken on a tour of the inner workings of the transitional radiation tracker within the ATLAS detector. Subjects covered include what the tracker is used to measure, its structure, what happens when particles pass through the tracker, how it distinguishes between different types of particles within it.

  16. The ATLAS electromagnetic calorimeter

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    Michel Mathieu, a technician for the ATLAS collaboration, is cabling the ATLAS electromagnetic calorimeter's first end-cap, before insertion into its cryostat. Millions of wires are connected to the electromagnetic calorimeter on this end-cap that must be carefully fed out from the detector so that data can be read out. Every element on the detector will be attached to one of these wires so that a full digital map of the end-cap can be recreated.

  17. Budker INP in ATLAS

    CERN Multimedia

    2001-01-01

    The Novosibirsk group has proposed a new design for the ATLAS liquid argon electromagnetic end-cap calorimeter with a constant thickness of absorber plates. This design has signifi- cant advantages compared to one in the Technical Proposal and it has been accepted by the ATLAS Collaboration. The Novosibirsk group is responsible for the fabrication of the precision aluminium structure for the e.m.end-cap calorimeter.

  18. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    1999-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are ever so busy to finish the different infrastructures for ATLAS. Real underground video. The film has original working sound.

  19. EnviroAtlas - Woodbine, IA - One Meter Resolution Urban Land Cover Data (2011)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Woodbine, IA land cover (LC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and near...

  20. EnviroAtlas - Woodbine, IA - Meter-Scale Urban Land Cover (MULC) Data (2011)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Woodbine, IA Meter-Scale Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red,...

  1. EnviroAtlas - Durham, NC - Meter-Scale Urban Land Cover (MULC) Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Durham, NC Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue...

  2. EnviroAtlas - Tampa, FL - Meter-Scale Urban Land Cover (MULC) Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Tampa, FL Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue...

  3. EnviroAtlas - Milwaukee, WI - Meter-Scale Urban Land Cover Data (MULC) Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Milwaukee, WI Meter Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green,...

  4. EnviroAtlas - Portland, ME - Meter-Scale Urban Land Cover (MULC) Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Portland, ME Meter-Scale Urban Land Cover (MULC) data was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green,...

  5. EnviroAtlas - Phoenix, AZ - Meter-Scale Urban Land Cover (MULC) Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Phoenix, AZ Meter-Scale Urban Land Cover (MULC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red,...

  6. EnviroAtlas - Portland, ME - One Meter Resolution Urban Land Cover (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Portland, ME land cover map was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and near infrared)...

  7. EnviroAtlas - Phoenix, AZ - One Meter Resolution Urban Land Cover Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Phoenix, AZ land cover (LC) data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and...

  8. EnviroAtlas -Tampa, FL- One Meter Resolution Urban Land Cover (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Tampa, FL land cover map was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and near infrared) aerial...

  9. EnviroAtlas -Durham, NC- One Meter Resolution Urban Area Land Cover Map (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Durham, NC land cover map was generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and near infrared) aerial...

  10. EnviroAtlas -Pittsburgh, PA- One Meter Resolution Urban Land Cover Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Pittsburgh, PA land cover map was generated from United States Department of Agriculture (USDA) National Agricultural Imagery Program (NAIP) four...

  11. EnviroAtlas -Milwaukee, WI- One Meter Resolution Urban Land Cover Data (2010)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The EnviroAtlas Milwaukee, WI land cover data and map were generated from USDA NAIP (National Agricultural Imagery Program) four band (red, green, blue and near...

  12. EnviroAtlas - Ecosystem Rarity Metrics by 12-digit HUC for the Conterminous United States

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset identifies rare ecosystems using base landcover data from the USGS GAP Analysis Program (Version 2, 2011) combined with landscape ecology...

  13. Image File - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available AT Atlas Image File Data detail Data name Image File Description of data contents Graphical abstracts (in PNG format) for the Technol...ogy Development projects of the Targeted Proteins Research Program (TPRP). One proj

  14. Automatic genomics: a user-friendly program for the automatic designing and plate loading of medium-throughput qPCR experiments.

    Science.gov (United States)

    Callejas, Sergio; Alvarez, Rebeca; Dopazo, Ana

    2011-01-01

    Quantitative PCR (qPCR) remains the method of choice for gene and microRNA (miRNA) expression studies. Many laboratories wish to automate some or all of the steps of medium-throughput qPCR experiments through the use of various types of liquid handling robots. However, it is not uncommon to find cases in which scripts provided by the robot supplier are too rigid for user-specific applications, do not include all the desired options, or are too complicated to be modified by a nonprofessional programmer. Here, we present Automatic Genomics, a program that allows users with a limited programming background to automate medium-throughput qPCR experiments by using commercially available liquid-handling robots. The user is able to optimize the plate design in terms of number of genes, number of samples, and controls.

  15. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  16. Five blood pressure loci identified by an updated genome-wide linkage scan: meta-analysis of the Family Blood Pressure Program.

    Science.gov (United States)

    Simino, Jeannette; Shi, Gang; Kume, Rezart; Schwander, Karen; Province, Michael A; Gu, C Charles; Kardia, Sharon; Chakravarti, Aravinda; Ehret, Georg; Olshen, Richard A; Turner, Stephen T; Ho, Low-Tone; Zhu, Xiaofeng; Jaquish, Cashell; Paltoo, Dina; Cooper, Richard S; Weder, Alan; Curb, J David; Boerwinkle, Eric; Hunt, Steven C; Rao, Dabeeru C

    2011-03-01

    A preliminary genome-wide linkage analysis of blood pressure in the Family Blood Pressure Program (FBPP) was reported previously. We harnessed the power and ethnic diversity of the final pooled FBPP dataset to identify novel loci for blood pressure thereby enhancing localization of genes containing less common variants with large effects on blood pressure levels and hypertension. We performed one overall and 4 race-specific meta-analyses of genome-wide blood pressure linkage scans using data on 4,226 African-American, 2,154 Asian, 4,229 Caucasian, and 2,435 Mexican-American participants (total N = 13,044). Variance components models were fit to measured (raw) blood pressure levels and two types of antihypertensive medication adjusted blood pressure phenotypes within each of 10 subgroups defined by race and network. A modified Fisher's method was used to combine the P values for each linkage marker across the 10 subgroups. Five quantitative trait loci (QTLs) were detected on chromosomes 6p22.3, 8q23.1, 20q13.12, 21q21.1, and 21q21.3 based on significant linkage evidence (defined by logarithm of odds (lod) score ≥3) in at least one meta-analysis and lod scores ≥1 in at least 2 subgroups defined by network and race. The chromosome 8q23.1 locus was supported by Asian-, Caucasian-, and Mexican-American-specific meta-analyses. The new QTLs reported justify new candidate gene studies. They may help support results from genome-wide association studies (GWAS) that fall in these QTL regions but fail to achieve the genome-wide significance.

  17. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  18. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  19. Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics – assessment and update

    Directory of Open Access Journals (Sweden)

    Tamas Ivica

    2008-07-01

    Full Text Available Abstract Background The H/ACA family of small nucleolar RNAs (snoRNAs plays a central role in guiding the pseudouridylation of ribosomal RNA (rRNA. In an effort to systematically identify the complete set of rRNA-modifying H/ACA snoRNAs from the genome sequence of the budding yeast, Saccharomyces cerevisiae, we developed a program – Fisher – and previously presented several candidate snoRNAs based on our analysis 1. Findings In this report, we provide a brief update of this work, which was aborted after the publication of experimentally-identified snoRNAs 2 identical to candidates we had identified bioinformatically using Fisher. Our motivation for revisiting this work is to report on the status of the candidate snoRNAs described in 1, and secondly, to report that a modified version of Fisher together with the available multiple yeast genome sequences was able to correctly identify several H/ACA snoRNAs for modification sites not identified by the snoGPS program 3. While we are no longer developing Fisher, we briefly consider the merits of the Fisher algorithm relative to snoGPS, which may be of use for workers considering pursuing a similar search strategy for the identification of small RNAs. The modified source code for Fisher is made available as supplementary material. Conclusion Our results confirm the validity of using minimum free energy (MFE secondary structure prediction to guide comparative genomic screening for RNA families with few sequence constraints.

  20. Program in Functional Genomics of Autoimmunity and Immunology of yhe University of Kentucky and the University of Alabama

    Energy Technology Data Exchange (ETDEWEB)

    Alan M Kaplan

    2012-10-12

    This grant will be used to augment the equipment infrastructure and core support at the University of Kentucky and the University of Alabama particularly in the areas of genomics/informatics, molecular analysis and cell separation. In addition, we will promote collaborative research interactions through scientific workshops and exchange of scientists, as well as joint exploration of the role of immune receptors as targets in autoimmunity and host defense, innate and adaptive immune responses, and mucosal immunity in host defense.

  1. EnviroAtlas - Metrics for Cleveland, OH

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). The layers in this web...

  2. EnviroAtlas - Metrics for Austin, TX

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). The layers in this web...

  3. EnviroAtlas Community Boundaries Web Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset shows the boundaries of all EnviroAtlas Communities. It represents the outside edge of all the block groups included in each EnviroAtlas...

  4. Virtual Visit to the ATLAS Control Room by the University of Bern

    CERN Multimedia

    ATLAS Experiment

    2012-01-01

    Fresher's day for potential future bachelor students Infotage für Studieninteressierte Bachelor Once a year the University of Bern organizes two information days for young potential future bachelor students. Young aspiring candidates interested in a career in physics will be shown the forefront of physics research, where a trip around the university physics laboratories, and a direct video link to the ATLAS Control room at CERN's Large Hadron Collider is part of the program. A physicist from Bern will present directly from the ATLAS control room for a direct and personal view into the physics at the LHC, the Higgs particle, the generation of mass, antimatter, the origin of the universe and the involvement of the Bern high-energy physics team in the ATLAS experiment. This also allows for fruitful discussions about their own perspectives of perhaps becoming a CERN physicist one day. http://atlas-live-virtual-visit.web.cern.ch/atlas-live-virtual-visit/2012/Bern-2012.html

  5. ATLAS Future Framework Requirements Group Report

    CERN Document Server

    The ATLAS collaboration

    2016-01-01

    The Future Frameworks Requirements Group was constituted in Summer 2013 to consider and summarise the framework requirements from trigger and offline for configuring, scheduling and monitoring the data processing software needed by the ATLAS experiment. The principal motivation for such a re-examination arises from the current and anticipated evolution of CPUs, where multiple cores, hyper-threading and wide vector registers require a shift to a concurrent programming model. Such a model requires extensive changes in the current Gaudi/Athena frameworks and offers the opportunity to consider how HLT and offline processing can be better accommodated within the ATLAS framework. This note contains the report of the Future Frameworks Requirements Group.

  6. The ATLAS Data Management Software Engineering Process

    CERN Document Server

    Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A; Molfetas, A

    2014-01-01

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

  7. The ATLAS Data Management Software Engineering Process

    CERN Document Server

    Lassnig, M; The ATLAS collaboration; Stewart, G A; Barisits, M; Beermann, T; Vigne, R; Serfon, C; Goossens, L; Nairz, A

    2013-01-01

    Rucio is the next-generation data management system of the ATLAS experiment. The software engineering process to develop Rucio is fundamentally different to existing software development approaches in the ATLAS distributed computing community. Based on a conceptual design document, development takes place using peer-reviewed code in a test-driven environment. The main objectives are to ensure that every engineer understands the details of the full project, even components usually not touched by them, that the design and architecture are coherent, that temporary contributors can be productive without delay, that programming mistakes are prevented before being committed to the source code, and that the source is always in a fully functioning state. This contribution will illustrate the workflows and products used, and demonstrate the typical development cycle of a component from inception to deployment within this software engineering process. Next to the technological advantages, this contribution will also hi...

  8. Distributed analysis in ATLAS

    CERN Document Server

    Legger, Federica; The ATLAS collaboration

    2015-01-01

    The ATLAS experiment accumulated more than 140 PB of data during the first run of the Large Hadron Collider (LHC) at CERN. The analysis of such an amount of data for the distributed physics community is a challenging task. The Distributed Analysis (DA) system of the ATLAS experiment is an established and stable component of the ATLAS distributed computing operations. About half a million user jobs are daily running on DA resources, submitted by more than 1500 ATLAS physicists. The reliability of the DA system during the first run of the LHC and the following shutdown period has been high thanks to the continuous automatic validation of the distributed analysis sites and the user support provided by a dedicated team of expert shifters. During the LHC shutdown, the ATLAS computing model has undergone several changes to improve the analysis workflows, including the re-design of the production system, a new analysis data format and event model, and the development of common reduction and analysis frameworks. We r...

  9. ATLAS: Exceeding all expectations

    CERN Multimedia

    CERN Bulletin

    2010-01-01

    “One year ago it would have been impossible for us to guess that the machine and the experiments could achieve so much so quickly”, says Fabiola Gianotti, ATLAS spokesperson. The whole chain – from collision to data analysis – has worked remarkably well in ATLAS.   The first LHC proton run undoubtedly exceeded expectations for the ATLAS experiment. “ATLAS has worked very well since the beginning. Its overall data-taking efficiency is greater than 90%”, says Fabiola Gianotti. “The quality and maturity of the reconstruction and simulation software turned out to be better than we expected for this initial stage of the experiment. The Grid is a great success, and right from the beginning it has allowed members of the collaboration all over the world to participate in the data analysis in an effective and timely manner, and to deliver physics results very quickly”. In just a few months of data taking, ATLAS has observed t...

  10. ATLAS Review Office

    CERN Multimedia

    Szeless, B

    The ATLAS internal reviews, be it the mandatory Production Readiness Reviews, the now newly installed Production Advancement Reviews, or the more and more requested different Design Reviews, have become a part of our ATLAS culture over the past years. The Activity Systems Status Overviews are, for the time being, a one in time event and should be held for each system as soon as possible to have some meaning. There seems to a consensus that the reviews have become a useful project tool for the ATLAS management but even more so for the sub-systems themselves making achievements as well as possible shortcomings visible. One other recognized byproduct is the increasing cross talk between the systems, a very important ingredient to make profit all the systems from the large collective knowledge we dispose of in ATLAS. In the last two months, the first two PARs were organized for the MDT End Caps and the TRT Barrel Modules, both part of the US contribution to the ATLAS Project. Furthermore several different design...

  11. OCCIPITALIZATION OF ATLAS

    Directory of Open Access Journals (Sweden)

    Sween Walia

    2014-12-01

    Full Text Available Occipitalization of atlas is an osseous anomaly of the craniovertebral junction which occurs at the base of the skull in the region of the foramen magnum. The knowledge of such a fusion is important because skeletal abnormalities at the craniocervical junction may result in sudden death. During bone cleaning procedure and routine undergraduate osteology teaching, three skulls with Occipitalization of atlas were encountered in the department of Anatomy at MMIMSR, Mullana, India. In one skull, both anterior and posterior arch were completely fused with occipital bone while the transverse process on the right side was not fused whereas left transverse process was fused with occipital bone. Both anterior and posterior arch were completely fused whereas transverse process on both sides were not fused in other skull. In another skull, partial and asymmetrical Occipitalization of atlas vertebra with occipital bone was found with bifid posterior arch of atlas at the level of posterior tubercle. Anterior arch was completely fused with basilar part of occipital bone but both the transverse processes were not fused. Reduced diameter of foramen magnum due to the atlanto-occipital fusion might cause neurological complications due to compression of spinal cord or medulla oblongata, vertebral vessels, 1st cervical nerve, thus, knowledge of occipitalization of the atlas may be of substantial importance to orthopaedicians, neurosurgeons, physicians and radiologists dealing with abnormalities of the cervical spine.

  12. Dark Matter searches with the ATLAS Detector

    CERN Document Server

    Cortes-Gonzalez, Arely; The ATLAS collaboration

    2017-01-01

    The presence of a non-baryonic dark matter component in the Universe is inferred from the observation of its gravitational interaction. If dark matter interacts weakly with the Standard Model it would be produced at the LHC, escaping the detector and leaving a large missing transverse momentum as their signature. The ATLAS detector has developed a broad and systematic search program for dark matter production in LHC collisions. The results of these searches on the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  13. Dark Matter Searches with the ATLAS detector

    CERN Document Server

    Elliot, Alison; The ATLAS collaboration

    2017-01-01

    The presence of a non-baryonic dark matter component in the Universe is inferred from the observation of its gravitational interaction. If dark matter interacts weakly with the Standard Model it would be produced at the LHC, escaping the detector and leaving a large missing transverse momentum as its signature. The ATLAS detector has developed a broad and systematic search program for dark matter production in LHC collisions. The results of these searches on the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  14. Dark matter searches with the ATLAS detector

    CERN Document Server

    Whalen, Kathleen; The ATLAS collaboration

    2017-01-01

    The presence of a non-baryonic dark matter component in the Universe is inferred from the observation of its gravitational interaction. If dark matter interacts weakly with the Standard Model it would be produced at the LHC, escaping the detector and leaving a large missing transverse momentum as its signature. The ATLAS detector has developed a broad and systematic search program for dark matter production in LHC collisions. The results of these searches using the first 13 TeV data, their interpretation, and the design and possible evolution of the search program will be presented.

  15. New format for ATLAS e-news

    CERN Document Server

    Pauline Gagnon

    ATLAS e-news got a new look! As of November 30, 2007, we have a new format for ATLAS e-news. Please go to: http://atlas-service-enews.web.cern.ch/atlas-service-enews/index.html . ATLAS e-news will now be published on a weekly basis. If you are not an ATLAS colaboration member but still want to know how the ATLAS experiment is doing, we will soon have a version of ATLAS e-news intended for the general public. Information will be sent out in due time.

  16. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribute...... to next generation. The main goal of this study was to see the potential of using genomic prediction in a commercial Barley breeding program. The data used in this study was from Nordic Seed company which is located in Denmark. Around 350 advanced lines were genotyped with 9K Barely chip from Illumina...

  17. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

    Directory of Open Access Journals (Sweden)

    Sophie S Abby

    Full Text Available Biologists often wish to use their knowledge on a few experimental models of a given molecular system to identify homologs in genomic data. We developed a generic tool for this purpose.Macromolecular System Finder (MacSyFinder provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include functional analogs, and the multiple uses of a same component by different systems. Models are used to search for molecular systems in complete genomes or in unstructured data like metagenomes. The components of the systems are searched by sequence similarity using Hidden Markov model (HMM protein profiles. The assignment of hits to a given system is decided based on compliance with the content and organization of the system model. A graphical interface, MacSyView, facilitates the analysis of the results by showing overviews of component content and genomic context. To exemplify the use of MacSyFinder we built models to detect and class CRISPR-Cas systems following a previously established classification. We show that MacSyFinder allows to easily define an accurate "Cas-finder" using publicly available protein profiles.MacSyFinder is a standalone application implemented in Python. It requires Python 2.7, Hmmer and makeblastdb (version 2.2.28 or higher. It is freely available with its source code under a GPLv3 license at https://github.com/gem-pasteur/macsyfinder. It is compatible with all platforms supporting Python and Hmmer/makeblastdb. The "Cas-finder" (models and HMM profiles is distributed as a compressed tarball archive as Supporting Information.

  18. Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases

    Directory of Open Access Journals (Sweden)

    Ilya eZaslavsky

    2014-09-01

    Full Text Available Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today’s data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI. A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS, a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML: XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POIs, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas

  19. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2014-01-01

    Physics processes involving tau leptons play a crucial role in understanding particle physics at the high energy frontier. The ability to efficiently trigger on events containing hadronic tau decays is therefore of particular importance to the ATLAS experiment. During the 2012 run, the Large Hadronic Collder (LHC) reached instantaneous luminosities of nearly $10^{34} cm^{-2}s^{-1}$ with bunch crossings occurring every $50 ns$. This resulted in a huge event rate and a high probability of overlapping interactions per bunch crossing (pile-up). With this in mind it was necessary to design an ATLAS tau trigger system that could reduce the event rate to a manageable level, while efficiently extracting the most interesting physics events in a pile-up robust manner. In this poster the ATLAS tau trigger is described, its performance during 2012 is presented, and the outlook for the LHC Run II is briefly summarized.

  20. Event visualization in ATLAS

    CERN Document Server

    Bianchi, Riccardo-Maria; The ATLAS collaboration

    2017-01-01

    At the beginning, HEP experiments made use of photographical images both to record and store experimental data and to illustrate their findings. Then the experiments evolved and needed to find ways to visualize their data. With the availability of computer graphics, software packages to display event data and the detector geometry started to be developed. Here, an overview of the usage of event display tools in HEP is presented. Then the case of the ATLAS experiment is considered in more detail and two widely used event display packages are presented, Atlantis and VP1, focusing on the software technologies they employ, as well as their strengths, differences and their usage in the experiment: from physics analysis to detector development, and from online monitoring to outreach and communication. Towards the end, the other ATLAS visualization tools will be briefly presented as well. Future development plans and improvements in the ATLAS event display packages will also be discussed.

  1. The Tomato Expression Atlas.

    Science.gov (United States)

    Fernandez-Pozo, Noe; Zheng, Yi; Snyder, Stephen I; Nicolas, Philippe; Shinozaki, Yoshihito; Fei, Zhangjun; Catala, Carmen; Giovannoni, James J; Rose, Jocelyn K C; Mueller, Lukas A

    2017-08-01

    With the development of new high-throughput DNA sequencing technologies and decreasing costs, large gene expression datasets are being generated at an accelerating rate, but can be complex to visualize. New, more interactive and intuitive tools are needed to visualize the spatiotemporal context of expression data and help elucidate gene function. Using tomato fruit as a model, we have developed the Tomato Expression Atlas to facilitate effective data analysis, allowing the simultaneous visualization of groups of genes at a cell/tissue level of resolution within an organ, enhancing hypothesis development and testing in addition to candidate gene identification. This atlas can be adapted to different types of expression data from diverse multicellular species. The Tomato Expression Atlas is available at http://tea.solgenomics.net/ . Source code is available at https://github.com/solgenomics/Tea . jr286@cornell.edu or lam87@cornell.edu. Supplementary data are available at Bioinformatics online.

  2. ATLAS rewards industry

    CERN Multimedia

    2006-01-01

    Showing excellence in mechanics, electronics and cryogenics, three industries are honoured for their contributions to the ATLAS experiment. Representatives of the three award-wining companies after the ceremony. For contributing vital pieces to the ATLAS puzzle, three industries were recognized on Friday 5 May during a supplier awards ceremony. After a welcome and overview of the ATLAS experiment by spokesperson Peter Jenni, CERN Secretary-General Maximilian Metzger stressed the importance of industry to CERN's scientific goals. Close interaction with CERN was a key factor in the selection of each rewarded company, in addition to the high-quality products they delivered to the experiment. Alu Menziken Industrie AG, of Switzerland, was honoured for the production of 380,000 aluminium tubes for the Monitored Drift Tube Chambers (MDT). As Giora Mikenberg, the Muon System Project Leader stressed, the aluminium tubes were delivered on time with an extraordinary quality and precision. Between October 2000 and Jan...

  3. ATLAS production system

    CERN Document Server

    Borodin, Mikhail; The ATLAS collaboration; De, Kaushik; Klimentov, Alexei; Golubkov, Dmitry; Maeno, Tadashi; Mashinistov, Ruslan; Wenaus, Torre; Padolski, Siarhei

    2016-01-01

    The second generation of the ATLAS production system called ProdSys2 is a distributed workload manager which used by thousands of physicists to analyze the data remotely, with the volume of processed data is beyond the exabyte scale, across a more than hundred heterogeneous sites. It achieves high utilization by combining dynamic job definition based on many criterias, such as input and output size, memory requirements and CPU consumption with manageable scheduling policies and by supporting different kind of computational resources, such as GRID, clouds, supercomputers and volunteering computers. Besides jobs definition Production System also includes flexible web user interface, which implements user-friendly environment for main ATLAS workflows, e.g. simple way of combining different data flows, and real-time monitoring, optimised for using with huge amount of information to present. We present an overview of the ATLAS Production System major components: job and task definition, workflow manager web user i...

  4. Two ATLAS suppliers honoured

    CERN Multimedia

    2007-01-01

    The ATLAS experiment has recognised the outstanding contribution of two firms to the pixel detector. Recipients of the supplier award with Peter Jenni, ATLAS spokesperson, and Maximilian Metzger, CERN Secretary-General.At a ceremony held at CERN on 28 November, the ATLAS collaboration presented awards to two of its suppliers that had produced sensor wafers for the pixel detector. The CiS Institut für Mikrosensorik of Erfurt in Germany has supplied 655 sensor wafers containing a total of 1652 sensor tiles and the firm ON Semiconductor has supplied 515 sensor wafers (1177 sensor tiles) from its foundry at Roznov in the Czech Republic. Both firms have successfully met the very demanding requirements. ATLAS’s huge pixel detector is very complicated, requiring expertise in highly specialised integrated microelectronics and precision mechanics. Pixel detector project leader Kevin Einsweiler admits that when the project was first propo...

  5. ATLAS TDAQ System Administration:

    CERN Document Server

    Lee, Christopher Jon; The ATLAS collaboration; Bogdanchikov, Alexander; Ballestrero, Sergio; Contescu, Alexandru Cristian; Dubrov, Sergei; Fazio, Daniel; Korol, Aleksandr; Scannicchio, Diana; Twomey, Matthew Shaun; Voronkov, Artem

    2015-01-01

    The ATLAS Trigger and Data Acquisition (TDAQ) system is responsible for the online processing of live data, streaming from the ATLAS experiment at the Large Hadron Collider (LHC) at CERN. The online farm is composed of ̃3000 servers, processing the data readout from ̃100 million detector channels through multiple trigger levels. During the two years of the first Long Shutdown (LS1) there has been a tremendous amount of work done by the ATLAS TDAQ System Administrators, implementing numerous new software applications, upgrading the OS and the hardware, changing some design philosophies and exploiting the High Level Trigger farm with different purposes. During the data taking only critical security updates are applied and broken hardware is replaced to ensure a stable operational environment. The LS1 provided an excellent opportunity to look into new technologies and applications that would help to improve and streamline the daily tasks of not only the System Administrators, but also of the scientists who wil...

  6. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  7. AtlasT4SS: A curated database for type IV secretion systems

    Directory of Open Access Journals (Sweden)

    Souza Rangel C

    2012-08-01

    Full Text Available Abstract Background The type IV secretion system (T4SS can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system. Description The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive, one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins. Conclusions In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and

  8. MBAT: A scalable informatics system for unifying digital atlasing workflows

    Directory of Open Access Journals (Sweden)

    Sane Nikhil

    2010-12-01

    Full Text Available Abstract Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context

  9. $b$-hadron production at ATLAS and CMS experiments

    CERN Document Server

    De La Cruz Burelo, Eduard

    2016-01-01

    We report on a selected number of studies performed by the ATLAS and the CMS collaborations on b -hadron production. Both experiments have a rich program on b -hadron physics exploiting the large cross section of b -hadrons at the high energies of the LHC.

  10. The numerical wind atlas - the KAMM/WAsP method

    DEFF Research Database (Denmark)

    Frank, H.P.; Rathmann, Ole; Mortensen, Niels Gylling

    2001-01-01

    The method of combining the Karlsruhe Atmospheric Mesoscale Model, KAMM, with the Wind Atlas Analysis and Application Program, WAsP, to make local predictions of the wind resource is presented. It combines the advantages of mesoscale modeling - overviewover a big region and use of global data bases...

  11. Recent Heavy Ion Results from The ATLAS Experiment

    CERN Document Server

    Olszewski, Andrzej; The ATLAS collaboration

    2017-01-01

    The ATLAS experiment at the Large Hadron Collider (LHC) has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This overview presents recent results on bulk particle collectivity and hard probes, the jets and heavy flavor production, measured in Pb+Pb, p+Pb and pp collisions at the LHC energies.

  12. Recent Heavy Ion Results from the ATLAS Experiment

    CERN Document Server

    Przybycien, Mariusz; The ATLAS collaboration

    2016-01-01

    The ATLAS experiment at the Large Hadron Collider has undertaken a broad physics program to probe and characterize the hot nuclear matter created in relativistic lead-lead collisions. This talk presents recent results on production of jet, electroweak bosons and quarkonium, electromagnetic processes in ultra-peripheral collisions, and bulk particle collectivity from PbPb and pPb collisions.

  13. The ATLAS Simulation Infrastructure

    CERN Document Server

    Aad, Georges; Abdallah, Jalal; Abdelalim, Ahmed Ali; Abdesselam, Abdelouahab; Abdinov, Ovsat; Abi, Babak; Abolins, Maris; Abramowicz, Halina; Abreu, Henso; Acharya, Bobby Samir; Adams, David; Addy, Tetteh; Adelman, Jahred; Adorisio, Cristina; Adragna, Paolo; Adye, Tim; Aefsky, Scott; Aguilar-Saavedra, Juan Antonio; Aharrouche, Mohamed; Ahlen, Steven; Ahles, Florian; Ahmad, Ashfaq; Ahmed, Hossain; Ahsan, Mahsana; Aielli, Giulio; Akdogan, Taylan; Åkesson, Torsten Paul Ake; Akimoto, Ginga; Akimov , Andrei; Aktas, Adil; Alam, Mohammad; Alam, Muhammad Aftab; Albrand, Solveig; Aleksa, Martin; Aleksandrov, Igor; Alexa, Calin; Alexander, Gideon; Alexandre, Gauthier; Alexopoulos, Theodoros; Alhroob, Muhammad; Aliev, Malik; Alimonti, Gianluca; Alison, John; Aliyev, Magsud; Allport, Phillip; Allwood-Spiers, Sarah; Almond, John; Aloisio, Alberto; Alon, Raz; Alonso, Alejandro; Alviggi, Mariagrazia; Amako, Katsuya; Amelung, Christoph; Amorim, Antonio; Amorós, Gabriel; Amram, Nir; Anastopoulos, Christos; Andeen, Timothy; Anders, Christoph Falk; Anderson, Kelby; Andreazza, Attilio; Andrei, George Victor; Anduaga, Xabier; Angerami, Aaron; Anghinolfi, Francis; Anjos, Nuno; Annovi, Alberto; Antonaki, Ariadni; Antonelli, Mario; Antonelli, Stefano; Antos, Jaroslav; Antunovic, Bijana; Anulli, Fabio; Aoun, Sahar; Arabidze, Giorgi; Aracena, Ignacio; Arai, Yasuo; Arce, Ayana; Archambault, John-Paul; Arfaoui, Samir; Arguin, Jean-Francois; Argyropoulos, Theodoros; Arik, Metin; Armbruster, Aaron James; Arnaez, Olivier; Arnault, Christian; Artamonov, Andrei; Arutinov, David; Asai, Makoto; Asai, Shoji; Silva, José; Asfandiyarov, Ruslan; Ask, Stefan; Åsman, Barbro; Asner, David; Asquith, Lily; Assamagan, Ketevi; Astbury, Alan; Astvatsatourov, Anatoli; Atoian, Grigor; Auerbach, Benjamin; Augsten, Kamil; Aurousseau, Mathieu; Austin, Nicholas; Avolio, Giuseppe; Avramidou, Rachel Maria; Axen, David; Ay, Cano; Azuelos, Georges; Azuma, Yuya; Baak, Max; Bach, Andre; Bachacou, Henri; Bachas, Konstantinos; Backes, Moritz; Badescu, Elisabeta; Bagnaia, Paolo; Bai, Yu; Bain, Travis; Baines, John; Baker, Mark; Baker, Oliver Keith; Baker, Sarah; Baltasar Dos Santos Pedrosa, Fernando; Banas, Elzbieta; Banerjee, Piyali; Banerjee, Swagato; Banfi, Danilo; Bangert, Andrea Michelle; Bansal, Vikas; Baranov, Sergey; Baranov, Sergei; Barashkou, Andrei; Barber, Tom; Barberio, Elisabetta Luigia; Barberis, Dario; Barbero, Marlon; Bardin, Dmitri; Barillari, Teresa; Barisonzi, Marcello; Barklow, Timothy; Barlow, Nick; Barnett, Bruce; Barnett, Michael; Baroncelli, Antonio; Barr, Alan; Barreiro, Fernando; Barreiro Guimarães da Costa, João; Barrillon, Pierre; Bartoldus, Rainer; Bartsch, Detlef; Bates, Richard; Batkova, Lucia; Batley, Richard; Battaglia, Andreas; Battistin, Michele; Bauer, Florian; Bawa, Harinder Singh; Bazalova, Magdalena; Beare, Brian; Beau, Tristan; Beauchemin, Pierre-Hugues; Beccherle, Roberto; Becerici, Neslihan; Bechtle, Philip; Beck, Graham; Beck, Hans Peter; Beckingham, Matthew; Becks, Karl-Heinz; Beddall, Ayda; Beddall, Andrew; Bednyakov, Vadim; Bee, Christopher; Begel, Michael; Behar Harpaz, Silvia; Behera, Prafulla; Beimforde, Michael; Belanger-Champagne, Camille; Bell, Paul; Bell, William; Bella, Gideon; Bellagamba, Lorenzo; Bellina, Francesco; Bellomo, Massimiliano; Belloni, Alberto; Belotskiy, Konstantin; Beltramello, Olga; Ben Ami, Sagi; Benary, Odette; Benchekroun, Driss; Bendel, Markus; Benedict, Brian Hugues; Benekos, Nektarios; Benhammou, Yan; Benincasa, Gianpaolo; Benjamin, Douglas; Benoit, Mathieu; Bensinger, James; Benslama, Kamal; Bentvelsen, Stan; Beretta, Matteo; Berge, David; Bergeaas Kuutmann, Elin; Berger, Nicolas; Berghaus, Frank; Berglund, Elina; Beringer, Jürg; Bernat, Pauline; Bernhard, Ralf; Bernius, Catrin; Berry, Tracey; Bertin, Antonio; Besana, Maria Ilaria; Besson, Nathalie; Bethke, Siegfried; Bianchi, Riccardo-Maria; Bianco, Michele; Biebel, Otmar; Biesiada, Jed; Biglietti, Michela; Bilokon, Halina; Bindi, Marcello; Binet, Sebastien; Bingul, Ahmet; Bini, Cesare; Biscarat, Catherine; Bitenc, Urban; Black, Kevin; Blair, Robert; Blanchard, Jean-Baptiste; Blanchot, Georges; Blocker, Craig; Blondel, Alain; Blum, Walter; Blumenschein, Ulrike; Bobbink, Gerjan; Bocci, Andrea; Boehler, Michael; Boek, Jennifer; Boelaert, Nele; Böser, Sebastian; Bogaerts, Joannes Andreas; Bogouch, Andrei; Bohm, Christian; Bohm, Jan; Boisvert, Veronique; Bold, Tomasz; Boldea, Venera; Bondarenko, Valery; Bondioli, Mario; Boonekamp, Maarten; Bordoni, Stefania; Borer, Claudia; Borisov, Anatoly; Borissov, Guennadi; Borjanovic, Iris; Borroni, Sara; Bos, Kors; Boscherini, Davide; Bosman, Martine; Boterenbrood, Hendrik; Bouchami, Jihene; Boudreau, Joseph; Bouhova-Thacker, Evelina Vassileva; Boulahouache, Chaouki; Bourdarios, Claire; Boveia, Antonio; Boyd, James; Boyko, Igor; Bozovic-Jelisavcic, Ivanka; Bracinik, Juraj; Braem, André; Branchini, Paolo; Brandenburg, George; Brandt, Andrew; Brandt, Gerhard; Brandt, Oleg; Bratzler, Uwe; Brau, Benjamin; Brau, James; Braun, Helmut; Brelier, Bertrand; Bremer, Johan; Brenner, Richard; Bressler, Shikma; Britton, Dave; Brochu, Frederic; Brock, Ian; Brock, Raymond; Brodet, Eyal; Bromberg, Carl; Brooijmans, Gustaaf; Brooks, William; Brown, Gareth; Bruckman de Renstrom, Pawel; Bruncko, Dusan; Bruneliere, Renaud; Brunet, Sylvie; Bruni, Alessia; Bruni, Graziano; Bruschi, Marco; Bucci, Francesca; Buchanan, James; Buchholz, Peter; Buckley, Andrew; Budagov, Ioulian; Budick, Burton; Büscher, Volker; Bugge, Lars; Bulekov, Oleg; Bunse, Moritz; Buran, Torleiv; Burckhart, Helfried; Burdin, Sergey; Burgess, Thomas; Burke, Stephen; Busato, Emmanuel; Bussey, Peter; Buszello, Claus-Peter; Butin, Françcois; Butler, Bart; Butler, John; Buttar, Craig; Butterworth, Jonathan; Byatt, Tom; Caballero, Jose; Cabrera Urbán, Susana; Caforio, Davide; Cakir, Orhan; Calafiura, Paolo; Calderini, Giovanni; Calfayan, Philippe; Calkins, Robert; Caloba, Luiz; Calvet, David; Camarri, Paolo; Cameron, David; Campana, Simone; Campanelli, Mario; Canale, Vincenzo; Canelli, Florencia; Canepa, Anadi; Cantero, Josu; Capasso, Luciano; Capeans Garrido, Maria Del Mar; Caprini, Irinel; Caprini, Mihai; Capua, Marcella; Caputo, Regina; Caramarcu, Costin; Cardarelli, Roberto; Carli, Tancredi; Carlino, Gianpaolo; Carminati, Leonardo; Caron, Bryan; Caron, Sascha; Carrillo Montoya, German D.; Carron Montero, Sebastian; Carter, Antony; Carter, Janet; Carvalho, João; Casadei, Diego; Casado, Maria Pilar; Cascella, Michele; Castaneda Hernandez, Alfredo Martin; Castaneda-Miranda, Elizabeth; Castillo Gimenez, Victoria; Castro, Nuno Filipe; Cataldi, Gabriella; Catinaccio, Andrea; Catmore, James; Cattai, Ariella; Cattani, Giordano; Caughron, Seth; Cauz, Diego; Cavalleri, Pietro; Cavalli, Donatella; Cavalli-Sforza, Matteo; Cavasinni, Vincenzo; Ceradini, Filippo; Cerqueira, Augusto Santiago; Cerri, Alessandro; Cerrito, Lucio; Cerutti, Fabio; Cetin, Serkant Ali; Chafaq, Aziz; Chakraborty, Dhiman; Chan, Kevin; Chapman, John Derek; Chapman, John Wehrley; Chareyre, Eve; Charlton, Dave; Chavda, Vikash; Cheatham, Susan; Chekanov, Sergei; Chekulaev, Sergey; Chelkov, Gueorgui; Chen, Hucheng; Chen, Shenjian; Chen, Xin; Cheplakov, Alexander; Chepurnov, Vladimir; Cherkaoui El Moursli, Rajaa; Tcherniatine, Valeri; Chesneanu, Daniela; Cheu, Elliott; Cheung, Sing-Leung; Chevalier, Laurent; Chevallier, Florent; Chiarella, Vitaliano; Chiefari, Giovanni; Chikovani, Leila; Childers, John Taylor; Chilingarov, Alexandre; Chiodini, Gabriele; Chizhov, Mihail; Choudalakis, Georgios; Chouridou, Sofia; Christidi, Illectra-Athanasia; Christov, Asen; Chromek-Burckhart, Doris; Chu, Ming-Lee; Chudoba, Jiri; Ciapetti, Guido; Ciftci, Abbas Kenan; Ciftci, Rena; Cinca, Diane; Cindro, Vladimir; Ciobotaru, Matei Dan; Ciocca, Claudia; Ciocio, Alessandra; Cirilli, Manuela; Citterio, Mauro; Clark, Allan G.; Clark, Philip James; Cleland, Bill; Clemens, Jean-Claude; Clement, Benoit; Clement, Christophe; Coadou, Yann; Cobal, Marina; Coccaro, Andrea; Cochran, James H.; Coggeshall, James; Cogneras, Eric; Colijn, Auke-Pieter; Collard, Caroline; Collins, Neil; Collins-Tooth, Christopher; Collot, Johann; Colon, German; Conde Muiño, Patricia; Coniavitis, Elias; Consonni, Michele; Constantinescu, Serban; Conta, Claudio; Conventi, Francesco; Cooke, Mark; Cooper, Ben; Cooper-Sarkar, Amanda; Cooper-Smith, Neil; Copic, Katherine; Cornelissen, Thijs; Corradi, Massimo; Corriveau, Francois; Corso-Radu, Alina; Cortes-Gonzalez, Arely; Cortiana, Giorgio; Costa, Giuseppe; Costa, María José; Costanzo, Davide; Costin, Tudor; Côté, David; Coura Torres, Rodrigo; Courneyea, Lorraine; Cowan, Glen; Cowden, Christopher; Cox, Brian; Cranmer, Kyle; Cranshaw, Jack; Cristinziani, Markus; Crosetti, Giovanni; Crupi, Roberto; Crépé-Renaudin, Sabine; Cuenca Almenar, Cristóbal; Cuhadar Donszelmann, Tulay; Curatolo, Maria; Curtis, Chris; Cwetanski, Peter; Czyczula, Zofia; D'Auria, Saverio; D'Onofrio, Monica; D'Orazio, Alessia; Da Via, Cinzia; Dabrowski, Wladyslaw; Dai, Tiesheng; Dallapiccola, Carlo; Dallison, Steve; Daly, Colin; Dam, Mogens; Danielsson, Hans Olof; Dannheim, Dominik; Dao, Valerio; Darbo, Giovanni; Darlea, Georgiana Lavinia; Davey, Will; Davidek, Tomas; Davidson, Nadia; Davidson, Ruth; Davies, Merlin; Davison, Adam; Dawson, Ian; Daya, Rozmin; De, Kaushik; de Asmundis, Riccardo; De Castro, Stefano; De Castro Faria Salgado, Pedro; De Cecco, Sandro; de Graat, Julien; De Groot, Nicolo; de Jong, Paul; De Mora, Lee; De Oliveira Branco, Miguel; De Pedis, Daniele; De Salvo, Alessandro; De Sanctis, Umberto; De Santo, Antonella; De Vivie De Regie, Jean-Baptiste; De Zorzi, Guido; Dean, Simon; Dedovich, Dmitri; Degenhardt, James; Dehchar, Mohamed; Del Papa, Carlo; Del Peso, Jose; Del Prete, Tarcisio; Dell'Acqua, Andrea; Dell'Asta, Lidia; Della Pietra, Massimo; della Volpe, Domenico; Delmastro, Marco; Delsart, Pierre-Antoine; Deluca, Carolina; Demers, Sarah; Demichev, Mikhail; Demirkoz, Bilge; Deng, Jianrong; Deng, Wensheng; Denisov, Sergey; Derkaoui, Jamal Eddine; Derue, Frederic; Dervan, Paul; Desch, Klaus Kurt; Deviveiros, Pier-Olivier; Dewhurst, Alastair; DeWilde, Burton; Dhaliwal, Saminder; Dhullipudi, Ramasudhakar; Di Ciaccio, Anna; Di Ciaccio, Lucia; Di Domenico, Antonio; Di Girolamo, Alessandro; Di Girolamo, Beniamino; Di Luise, Silvestro; Di Mattia, Alessandro; Di Nardo, Roberto; Di Simone, Andrea; Di Sipio, Riccardo; Diaz, Marco Aurelio; Diblen, Faruk; Diehl, Edward; Dietrich, Janet; Dietzsch, Thorsten; Diglio, Sara; Dindar Yagci, Kamile; Dingfelder, Jochen; Dionisi, Carlo; Dita, Petre; Dita, Sanda; Dittus, Fridolin; Djama, Fares; Djilkibaev, Rashid; Djobava, Tamar; do Vale, Maria Aline Barros; Do Valle Wemans, André; Doan, Thi Kieu Oanh; Dobos, Daniel; Dobson, Ellie; Dobson, Marc; Doglioni, Caterina; Doherty, Tom; Dolejsi, Jiri; Dolenc, Irena; Dolezal, Zdenek; Dolgoshein, Boris; Dohmae, Takeshi; Donega, Mauro; Donini, Julien; Dopke, Jens; Doria, Alessandra; Dos Anjos, Andre; Dotti, Andrea; Dova, Maria-Teresa; Doxiadis, Alexander; Doyle, Tony; Drasal, Zbynek; Dris, Manolis; Dubbert, Jörg; Duchovni, Ehud; Duckeck, Guenter; Dudarev, Alexey; Dudziak, Fanny; Dührssen , Michael; Duflot, Laurent; Dufour, Marc-Andre; Dunford, Monica; Duran Yildiz, Hatice; Dushkin, Andrei; Duxfield, Robert; Dwuznik, Michal; Düren, Michael; Ebenstein, William; Ebke, Johannes; Eckweiler, Sebastian; Edmonds, Keith; Edwards, Clive; Egorov, Kirill; Ehrenfeld, Wolfgang; Ehrich, Thies; Eifert, Till; Eigen, Gerald; Einsweiler, Kevin; Eisenhandler, Eric; Ekelof, Tord; El Kacimi, Mohamed; Ellert, Mattias; Elles, Sabine; Ellinghaus, Frank; Ellis, Katherine; Ellis, Nicolas; Elmsheuser, Johannes; Elsing, Markus; Emeliyanov, Dmitry; Engelmann, Roderich; Engl, Albert; Epp, Brigitte; Eppig, Andrew; Erdmann, Johannes; Ereditato, Antonio; Eriksson, Daniel; Ermoline, Iouri; Ernst, Jesse; Ernst, Michael; Ernwein, Jean; Errede, Deborah; Errede, Steven; Ertel, Eugen; Escalier, Marc; Escobar, Carlos; Espinal Curull, Xavier; Esposito, Bellisario; Etienvre, Anne-Isabelle; Etzion, Erez; Evans, Hal; Fabbri, Laura; Fabre, Caroline; Facius, Katrine; Fakhrutdinov, Rinat; Falciano, Speranza; Fang, Yaquan; Fanti, Marcello; Farbin, Amir; Farilla, Addolorata; Farley, Jason; Farooque, Trisha; Farrington, Sinead; Farthouat, Philippe; Fassnacht, Patrick; Fassouliotis, Dimitrios; Fatholahzadeh, Baharak; Fayard, Louis; Fayette, Florent; Febbraro, Renato; Federic, Pavol; Fedin, Oleg; Fedorko, Woiciech; Feligioni, Lorenzo; Felzmann, Ulrich; Feng, Cunfeng; Feng, Eric; Fenyuk, Alexander; Ferencei, Jozef; Ferland, Jonathan; Fernandes, Bruno; Fernando, Waruna; Ferrag, Samir; Ferrando, James; Ferrara, Valentina; Ferrari, Arnaud; Ferrari, Pamela; Ferrari, Roberto; Ferrer, Antonio; Ferrer, Maria Lorenza; Ferrere, Didier; Ferretti, Claudio; Fiascaris, Maria; Fiedler, Frank; Filipčič, Andrej; Filippas, Anastasios; Filthaut, Frank; Fincke-Keeler, Margret; Fiolhais, Miguel; Fiorini, Luca; Firan, Ana; Fischer, Gordon; Fisher, Matthew; Flechl, Martin; Fleck, Ivor; Fleckner, Johanna; Fleischmann, Philipp; Fleischmann, Sebastian; Flick, Tobias; Flores Castillo, Luis; Flowerdew, Michael; Fonseca Martin, Teresa; Formica, Andrea; Forti, Alessandra; Fortin, Dominique; Fournier, Daniel; Fowler, Andrew; Fowler, Ken; Fox, Harald; Francavilla, Paolo; Franchino, Silvia; Francis, David; Franklin, Melissa; Franz, Sebastien; Fraternali, Marco; Fratina, Sasa; Freestone, Julian; French, Sky; Froeschl, Robert; Froidevaux, Daniel; Frost, James; Fukunaga, Chikara; Fullana Torregrosa, Esteban; Fuster, Juan; Gabaldon, Carolina; Gabizon, Ofir; Gadfort, Thomas; Gadomski, Szymon; Gagliardi, Guido; Gagnon, Pauline; Galea, Cristina; Gallas, Elizabeth; Gallas, Manuel; Gallo, Valentina Santina; Gallop, Bruce; Gallus, Petr; Galyaev, Eugene; Gan, K K; Gao, Yongsheng; Gaponenko, Andrei; Garcia-Sciveres, Maurice; García, Carmen; García Navarro, José Enrique; Gardner, Robert; Garelli, Nicoletta; Garitaonandia, Hegoi; Garonne, Vincent; Gatti, Claudio; Gaudio, Gabriella; Gautard, Valerie; Gauzzi, Paolo; Gavrilenko, Igor; Gay, Colin; Gaycken, Goetz; Gazis, Evangelos; Ge, Peng; Gee, Norman; Geich-Gimbel, Christoph; Gellerstedt, Karl; Gemme, Claudia; Genest, Marie-Hélène; Gentile, Simonetta; Georgatos, Fotios; George, Simon; Gershon, Avi; Ghazlane, Hamid; Ghodbane, Nabil; Giacobbe, Benedetto; Giagu, Stefano; Giakoumopoulou, Victoria; Giangiobbe, Vincent; Gianotti, Fabiola; Gibbard, Bruce; Gibson, Adam; Gibson, Stephen; Gilbert, Laura; Gilchriese, Murdock; Gilewsky, Valentin; Gingrich, Douglas; Ginzburg, Jonatan; Giokaris, Nikos; Giordani, MarioPaolo; Giordano, Raffaele; Giorgi, Francesco Michelangelo; Giovannini, Paola; Giraud, Pierre-Francois; Girtler, Peter; Giugni, Danilo; Giusti, Paolo; Gjelsten, Børge Kile; Gladilin, Leonid; Glasman, Claudia; Glazov, Alexandre; Glitza, Karl-Walter; Glonti, George; Godfrey, Jennifer; Godlewski, Jan; Goebel, Martin; Göpfert, Thomas; Goeringer, Christian; Gössling, Claus; Göttfert, Tobias; Goggi, Virginio; Goldfarb, Steven; Goldin, Daniel; Golling, Tobias; Gomes, Agostinho; Gomez Fajardo, Luz Stella; Gonçcalo, Ricardo; Gonella, Laura; Gong, Chenwei; González de la Hoz, Santiago; Gonzalez Silva, Laura; Gonzalez-Sevilla, Sergio; Goodson, Jeremiah Jet; Goossens, Luc; Gordon, Howard; Gorelov, Igor; Gorfine, Grant; Gorini, Benedetto; Gorini, Edoardo; Gorišek, Andrej; Gornicki, Edward; Gosdzik, Bjoern; Gosselink, Martijn; Gostkin, Mikhail Ivanovitch; Gough Eschrich, Ivo; Gouighri, Mohamed; Goujdami, Driss; Goulette, Marc Phillippe; Goussiou, Anna; Goy, Corinne; Grabowska-Bold, Iwona; Grafström, Per; Grahn, Karl-Johan; Grancagnolo, Sergio; Grassi, Valerio; Gratchev, Vadim; Grau, Nathan; Gray, Heather; Gray, Julia Ann; Graziani, Enrico; Green, Barry; Greenshaw, Timothy; Greenwood, Zeno Dixon; Gregor, Ingrid-Maria; Grenier, Philippe; Griesmayer, Erich; Griffiths, Justin; Grigalashvili, Nugzar; Grillo, Alexander; Grimm, Kathryn; Grinstein, Sebastian; Grishkevich, Yaroslav; Groh, Manfred; Groll, Marius; Gross, Eilam; Grosse-Knetter, Joern; Groth-Jensen, Jacob; Grybel, Kai; Guicheney, Christophe; Guida, Angelo; Guillemin, Thibault; Guler, Hulya; Gunther, Jaroslav; Guo, Bin; Gupta, Ambreesh; Gusakov, Yury; Gutierrez, Andrea; Gutierrez, Phillip; Guttman, Nir; Gutzwiller, Olivier; Guyot, Claude; Gwenlan, Claire; Gwilliam, Carl; Haas, Andy; Haas, Stefan; Haber, Carl; Hadavand, Haleh Khani; Hadley, David; Haefner, Petra; Härtel, Roland; Hajduk, Zbigniew; Hakobyan, Hrachya; Haller, Johannes; Hamacher, Klaus; Hamilton, Andrew; Hamilton, Samuel; Han, Liang; Hanagaki, Kazunori; Hance, Michael; Handel, Carsten; Hanke, Paul; Hansen, Jørgen Beck; Hansen, Jorn Dines; Hansen, John Renner; Hansen, Peter Henrik; Hansl-Kozanecka, Traudl; Hansson, Per; Hara, Kazuhiko; Hare, Gabriel; Harenberg, Torsten; Harrington, Robert; Harris, Orin; Harrison, Karl; Hartert, Jochen; Hartjes, Fred; Harvey, Alex; Hasegawa, Satoshi; Hasegawa, Yoji; Hashemi, Kevan; Hassani, Samira; Haug, Sigve; Hauschild, Michael; Hauser, Reiner; Havranek, Miroslav; Hawkes, Christopher; Hawkings, Richard John; Hayakawa, Takashi; Hayward, Helen; Haywood, Stephen; Head, Simon; Hedberg, Vincent; Heelan, Louise; Heim, Sarah; Heinemann, Beate; Heisterkamp, Simon; Helary, Louis; Heller, Mathieu; Hellman, Sten; Helsens, Clement; Hemperek, Tomasz; Henderson, Robert; Henke, Michael; Henrichs, Anna; Henriques Correia, Ana Maria; Henrot-Versille, Sophie; Hensel, Carsten; Henß, Tobias; Hernández Jiménez, Yesenia; Hershenhorn, Alon David; Herten, Gregor; Hertenberger, Ralf; Hervas, Luis; Hessey, Nigel; Higón-Rodriguez, Emilio; Hill, John; Hiller, Karl Heinz; Hillert, Sonja; Hillier, Stephen; Hinchliffe, Ian; Hines, Elizabeth; Hirose, Minoru; Hirsch, Florian; Hirschbuehl, Dominic; Hobbs, John; Hod, Noam; Hodgkinson, Mark; Hodgson, Paul; Hoecker, Andreas; Hoeferkamp, Martin; Hoffman, Julia; Hoffmann, Dirk; Hohlfeld, Marc; Holy, Tomas; Holzbauer, Jenny; Homma, Yasuhiro; Horazdovsky, Tomas; Hori, Takuya; Horn, Claus; Horner, Stephan; Hostachy, Jean-Yves; Hou, Suen; Hoummada, Abdeslam; Howe, Travis; Hrivnac, Julius; Hryn'ova, Tetiana; Hsu, Pai-hsien Jennifer; Hsu, Shih-Chieh; Huang, Guang Shun; Hubacek, Zdenek; Hubaut, Fabrice; Huegging, Fabian; Hughes, Emlyn; Hughes, Gareth; Hurwitz, Martina; Husemann, Ulrich; Huseynov, Nazim; Huston, Joey; Huth, John; Iacobucci, Giuseppe; Iakovidis, Georgios; Ibragimov, Iskander; Iconomidou-Fayard, Lydia; Idarraga, John; Iengo, Paolo; Igonkina, Olga; Ikegami, Yoichi; Ikeno, Masahiro; Ilchenko, Yuri; Iliadis, Dimitrios; Ince, Tayfun; Ioannou, Pavlos; Iodice, Mauro; Irles Quiles, Adrian; Ishikawa, Akimasa; Ishino, Masaya; Ishmukhametov, Renat; Isobe, Tadaaki; Issakov, Vladimir; Issever, Cigdem; Istin, Serhat; Itoh, Yuki; Ivashin, Anton; Iwanski, Wieslaw; Iwasaki, Hiroyuki; Izen, Joseph; Izzo, Vincenzo; Jackson, Brett; Jackson, John; Jackson, Paul; Jaekel, Martin; Jain, Vivek; Jakobs, Karl; Jakobsen, Sune; Jakubek, Jan; Jana, Dilip; Jansen, Eric; Jantsch, Andreas; Janus, Michel; Jared, Richard; Jarlskog, Göran; Jeanty, Laura; Jen-La Plante, Imai; Jenni, Peter; Jež, Pavel; Jézéquel, Stéphane; Ji, Weina; Jia, Jiangyong; Jiang, Yi; Jimenez Belenguer, Marcos; Jin, Shan; Jinnouchi, Osamu; Joffe, David; Johansen, Marianne; Johansson, Erik; Johansson, Per; Johnert, Sebastian; Johns, Kenneth; Jon-And, Kerstin; Jones, Graham; Jones, Roger; Jones, Tim; Jorge, Pedro; Joseph, John; Juranek, Vojtech; Jussel, Patrick; Kabachenko, Vasily; Kaci, Mohammed; Kaczmarska, Anna; Kado, Marumi; Kagan, Harris; Kagan, Michael; Kaiser, Steffen; Kajomovitz, Enrique; Kalinin, Sergey; Kalinovskaya, Lidia; Kalinowski, Artur; Kama, Sami; Kanaya, Naoko; Kaneda, Michiru; Kantserov, Vadim; Kanzaki, Junichi; Kaplan, Benjamin; Kapliy, Anton; Kaplon, Jan; Kar, Deepak; Karagounis, Michael; Karagoz, Muge; Kartvelishvili, Vakhtang; Karyukhin, Andrey; Kashif, Lashkar; Kasmi, Azzedine; Kass, Richard; Kastanas, Alex; Kastoryano, Michael; Kataoka, Mayuko; Kataoka, Yousuke; Katsoufis, Elias; Katzy, Judith; Kaushik, Venkatesh; Kawagoe, Kiyotomo; Kawamoto, Tatsuo; Kawamura, Gen; Kayl, Manuel; Kayumov, Fred; Kazanin, Vassili; Kazarinov, Makhail; Keates, James Robert; Keeler, Richard; Keener, Paul; Kehoe, Robert; Keil, Markus; Kekelidze, George; Kelly, Marc; Kenyon, Mike; Kepka, Oldrich; Kerschen, Nicolas; Kerševan, Borut Paul; Kersten, Susanne; Kessoku, Kohei; Khakzad, Mohsen; Khalil-zada, Farkhad; Khandanyan, Hovhannes; Khanov, Alexander; Kharchenko, Dmitri; Khodinov, Alexander; Khomich, Andrei; Khoriauli, Gia; Khovanskiy, Nikolai; Khovanskiy, Valery; Khramov, Evgeniy; Khubua, Jemal; Kim, Hyeon Jin; Kim, Min Suk; Kim, Peter; Kim, Shinhong; Kind, Oliver; Kind, Peter; King, Barry; Kirk, Julie; Kirsch, Guillaume; Kirsch, Lawrence; Kiryunin, Andrey; Kisielewska, Danuta; Kittelmann, Thomas; Kiyamura, Hironori; Kladiva, Eduard; Klein, Max; Klein, Uta; Kleinknecht, Konrad; Klemetti, Miika; Klier, Amit; Klimentov, Alexei; Klingenberg, Reiner; Klinkby, Esben; Klioutchnikova, Tatiana; Klok, Peter; Klous, Sander; Kluge, Eike-Erik; Kluge, Thomas; Kluit, Peter; Klute, Markus; Kluth, Stefan; Knecht, Neil; Kneringer, Emmerich; Ko, Byeong Rok; Kobayashi, Tomio; Kobel, Michael; Koblitz, Birger; Kocian, Martin; Kocnar, Antonin; Kodys, Peter; Köneke, Karsten; König, Adriaan; Koenig, Sebastian; Köpke, Lutz; Koetsveld, Folkert; Koevesarki, Peter; Koffas, Thomas; Koffeman, Els; Kohn, Fabian; Kohout, Zdenek; Kohriki, Takashi; Kolanoski, Hermann; Kolesnikov, Vladimir; Koletsou, Iro; Koll, James; Kollar, Daniel; Kolos, Serguei; Kolya, Scott; Komar, Aston; Komaragiri, Jyothsna Rani; Kondo, Takahiko; Kono, Takanori; Konoplich, Rostislav; Konovalov, Serguei; Konstantinidis, Nikolaos; Koperny, Stefan; Korcyl, Krzysztof; Kordas, Kostantinos; Korn, Andreas; Korolkov, Ilya; Korolkova, Elena; Korotkov, Vladislav; Kortner, Oliver; Kortner, Sandra; Kostka, Peter; Kostyukhin, Vadim; Kotov, Serguei; Kotov, Vladislav; Kotov, Konstantin; Kourkoumelis, Christine; Koutsman, Alex; Kowalewski, Robert Victor; Kowalski, Henri; Kowalski, Tadeusz; Kozanecki, Witold; Kozhin, Anatoly; Kral, Vlastimil; Kramarenko, Viktor; Kramberger, Gregor; Krasny, Mieczyslaw Witold; Krasznahorkay, Attila; Kreisel, Arik; Krejci, Frantisek; Kretzschmar, Jan; Krieger, Nina; Krieger, Peter; Kroeninger, Kevin; Kroha, Hubert; Kroll, Joe; Kroseberg, Juergen; Krstic, Jelena; Kruchonak, Uladzimir; Krüger, Hans; Krumshteyn, Zinovii; Kubota, Takashi; Kuehn, Susanne; Kugel, Andreas; Kuhl, Thorsten; Kuhn, Dietmar; Kukhtin, Victor; Kulchitsky, Yuri; Kuleshov, Sergey; Kummer, Christian; Kuna, Marine; Kunkle, Joshua; Kupco, Alexander; Kurashige, Hisaya; Kurata, Masakazu; Kurchaninov, Leonid; Kurochkin, Yurii; Kus, Vlastimil; Kwee, Regina; La Rotonda, Laura; Labbe, Julien; Lacasta, Carlos; Lacava, Francesco; Lacker, Heiko; Lacour, Didier; Lacuesta, Vicente Ramón; Ladygin, Evgueni; Lafaye, Rémi; Laforge, Bertrand; Lagouri, Theodota; Lai, Stanley; Lamanna, Massimo; Lampen, Caleb; Lampl, Walter; Lancon, Eric; Landgraf, Ulrich; Landon, Murrough; Lane, Jenna; Lankford, Andrew; Lanni, Francesco; Lantzsch, Kerstin; Lanza, Agostino; Laplace, Sandrine; Lapoire, Cecile; Laporte, Jean-Francois; Lari, Tommaso; Larner, Aimee; Lassnig, Mario; Laurelli, Paolo; Lavrijsen, Wim; Laycock, Paul; Lazarev, Alexandre; Lazzaro, Alfio; Le Dortz, Olivier; Le Guirriec, Emmanuel; Le Menedeu, Eve; Le Vine, Micheal; Lebedev, Alexander; Lebel, Céline; LeCompte, Thomas; Ledroit-Guillon, Fabienne Agnes Marie; Lee, Hurng-Chun; Lee, Jason; Lee, Shih-Chang; Lefebvre, Michel; Legendre, Marie; LeGeyt, Benjamin; Legger, Federica; Leggett, Charles; Lehmacher, Marc; Lehmann Miotto, Giovanna; Lei, Xiaowen; Leitner, Rupert; Lellouch, Daniel; Lellouch, Jeremie; Lendermann, Victor; Leney, Katharine; Lenz, Tatiana; Lenzen, Georg; Lenzi, Bruno; Leonhardt, Kathrin; Leroy, Claude; Lessard, Jean-Raphael; Lester, Christopher; Leung Fook Cheong, Annabelle; Levêque, Jessica; Levin, Daniel; Levinson, Lorne; Leyton, Michael; Li, Haifeng; Li, Shumin; Li, Xuefei; Liang, Zhihua; Liang, Zhijun; Liberti, Barbara; Lichard, Peter; Lichtnecker, Markus; Lie, Ki; Liebig, Wolfgang; Lilley, Joseph; Lim, Heuijin; Limosani, Antonio; Limper, Maaike; Lin, Simon; Linnemann, James; Lipeles, Elliot; Lipinsky, Lukas; Lipniacka, Anna; Liss, Tony; Lissauer, David; Lister, Alison; Litke, Alan; Liu, Chuanlei; Liu, Dong; Liu, Hao; Liu, Jianbei; Liu, Minghui; Liu, Tiankuan; Liu, Yanwen; Livan, Michele; Lleres, Annick; Lloyd, Stephen; Lobodzinska, Ewelina; Loch, Peter; Lockman, William; Lockwitz, Sarah; Loddenkoetter, Thomas; Loebinger, Fred; Loginov, Andrey; Loh, Chang Wei; Lohse, Thomas; Lohwasser, Kristin; Lokajicek, Milos; Long, Robin Eamonn; Lopes, Lourenco; Lopez Mateos, David; Losada, Marta; Loscutoff, Peter; Lou, Xinchou; Lounis, Abdenour; Loureiro, Karina; Lovas, Lubomir; Love, Jeremy; Love, Peter; Lowe, Andrew; Lu, Feng; Lubatti, Henry; Luci, Claudio; Lucotte, Arnaud; Ludwig, Andreas; Ludwig, Dörthe; Ludwig, Inga; Luehring, Frederick; Luisa, Luca; Lumb, Debra; Luminari, Lamberto; Lund, Esben; Lund-Jensen, Bengt; Lundberg, Björn; Lundberg, Johan; Lundquist, Johan; Lynn, David; Lys, Jeremy; Lytken, Else; Ma, Hong; Ma, Lian Liang; Macana Goia, Jorge Andres; Maccarrone, Giovanni; Macchiolo, Anna; Maček, Boštjan; Machado Miguens, Joana; Mackeprang, Rasmus; Madaras, Ronald; Mader, Wolfgang; Maenner, Reinhard; Maeno, Tadashi; Mättig, Peter; Mättig, Stefan; Magalhaes Martins, Paulo Jorge; Magradze, Erekle; Mahalalel, Yair; Mahboubi, Kambiz; Mahmood, A.; Maiani, Camilla; Maidantchik, Carmen; Maio, Amélia; Majewski, Stephanie; Makida, Yasuhiro; Makouski, Mikhail; Makovec, Nikola; Malecki, Piotr; Malecki, Pawel; Maleev, Victor; Malek, Fairouz; Mallik, Usha; Malon, David; Maltezos, Stavros; Malyshev, Vladimir; Malyukov, Sergei; Mambelli, Marco; Mameghani, Raphael; Mamuzic, Judita; Mandelli, Luciano; Mandić, Igor; Mandrysch, Rocco; Maneira, José; Mangeard, Pierre-Simon; Manjavidze, Ioseb; Manning, Peter; Manousakis-Katsikakis, Arkadios; Mansoulie, Bruno; Mapelli, Alessandro; Mapelli, Livio; March , Luis; Marchand, Jean-Francois; Marchese, Fabrizio; Marchiori, Giovanni; Marcisovsky, Michal; Marino, Christopher; Marroquim, Fernando; Marshall, Zach; Marti-Garcia, Salvador; Martin, Alex; Martin, Andrew; Martin, Brian; Martin, Brian; Martin, Franck Francois; Martin, Jean-Pierre; Martin, Tim; Martin dit Latour, Bertrand; Martinez, Mario; Martinez Outschoorn, Verena; Martini, Agnese; Martyniuk, Alex; Marzano, Francesco; Marzin, Antoine; Masetti, Lucia; Mashimo, Tetsuro; Mashinistov, Ruslan; Masik, Jiri; Maslennikov, Alexey; Massa, Ignazio; Massol, Nicolas; Mastroberardino, Anna; Masubuchi, Tatsuya; Matricon, Pierre; Matsunaga, Hiroyuki; Matsushita, Takashi; Mattravers, Carly; Maxfield, Stephen; Mayne, Anna; Mazini, Rachid; Mazur, Michael; Mazzanti, Marcello; Mc Donald, Jeffrey; Mc Kee, Shawn Patrick; McCarn, Allison; McCarthy, Robert; McCubbin, Norman; McFarlane, Kenneth; McGlone, Helen; Mchedlidze, Gvantsa; McMahon, Steve; McPherson, Robert; Meade, Andrew; Mechnich, Joerg; Mechtel, Markus; Medinnis, Mike; Meera-Lebbai, Razzak; Meguro, Tatsuma; Mehlhase, Sascha; Mehta, Andrew; Meier, Karlheinz; Meirose, Bernhard; Melachrinos, Constantinos; Mellado Garcia, Bruce Rafael; Mendoza Navas, Luis; Meng, Zhaoxia; Menke, Sven; Meoni, Evelin; Mermod, Philippe; Merola, Leonardo; Meroni, Chiara; Merritt, Frank; Messina, Andrea; Metcalfe, Jessica; Mete, Alaettin Serhan; Meyer, Jean-Pierre; Meyer, Jochen; Meyer, Joerg; Meyer, Thomas Christian; Meyer, W. Thomas; Miao, Jiayuan; Michal, Sebastien; Micu, Liliana; Middleton, Robin; Migas, Sylwia; Mijović, Liza; Mikenberg, Giora; Mikestikova, Marcela; Mikuž, Marko; Miller, David; Mills, Corrinne; Mills, Bill; Milov, Alexander; Milstead, David; Milstein, Dmitry; Minaenko, Andrey; Miñano, Mercedes; Minashvili, Irakli; Mincer, Allen; Mindur, Bartosz; Mineev, Mikhail; Ming, Yao; Mir, Lluisa-Maria; Mirabelli, Giovanni; Misawa, Shigeki; Miscetti, Stefano; Misiejuk, Andrzej; Mitrevski, Jovan; Mitsou, Vasiliki A.; Miyagawa, Paul; Mjörnmark, Jan-Ulf; Mladenov, Dimitar; Moa, Torbjoern; Moed, Shulamit; Moeller, Victoria; Mönig, Klaus; Möser, Nicolas; Mohr, Wolfgang; Mohrdieck-Möck, Susanne; Moles-Valls, Regina; Molina-Perez, Jorge; Monk, James; Monnier, Emmanuel; Montesano, Simone; Monticelli, Fernando; Moore, Roger; Mora Herrera, Clemencia; Moraes, Arthur; Morais, Antonio; Morel, Julien; Morello, Gianfranco; Moreno, Deywis; Moreno Llácer, María; Morettini, Paolo; Morii, Masahiro; Morley, Anthony Keith; Mornacchi, Giuseppe; Morozov, Sergey; Morris, John; Moser, Hans-Guenther; Mosidze, Maia; Moss, Josh; Mount, Richard; Mountricha, Eleni; Mouraviev, Sergei; Moyse, Edward; Mudrinic, Mihajlo; Mueller, Felix; Mueller, James; Mueller, Klemens; Müller, Thomas; Muenstermann, Daniel; Muir, Alex; Munwes, Yonathan; Murillo Garcia, Raul; Murray, Bill; Mussche, Ido; Musto, Elisa; Myagkov, Alexey; Myska, Miroslav; Nadal, Jordi; Nagai, Koichi; Nagano, Kunihiro; Nagasaka, Yasushi; Nairz, Armin Michael; Nakamura, Koji; Nakano, Itsuo; Nakatsuka, Hiroki; Nanava, Gizo; Napier, Austin; Nash, Michael; Nation, Nigel; Nattermann, Till; Naumann, Thomas; Navarro, Gabriela; Nderitu, Simon Kirichu; Neal, Homer; Nebot, Eduardo; Nechaeva, Polina; Negri, Andrea; Negri, Guido; Nelson, Andrew; Nelson, Timothy Knight; Nemecek, Stanislav; Nemethy, Peter; Nepomuceno, Andre Asevedo; Nessi, Marzio; Neubauer, Mark; Neusiedl, Andrea; Neves, Ricardo; Nevski, Pavel; Newcomer, Mitchel; Nickerson, Richard; Nicolaidou, Rosy; Nicolas, Ludovic; Nicoletti, Giovanni; Nicquevert, Bertrand; Niedercorn, Francois; Nielsen, Jason; Nikiforov, Andriy; Nikolaev, Kirill; Nikolic-Audit, Irena; Nikolopoulos, Konstantinos; Nilsen, Henrik; Nilsson, Paul; Nisati, Aleandro; Nishiyama, Tomonori; Nisius, Richard; Nodulman, Lawrence; Nomachi, Masaharu; Nomidis, Ioannis; Nordberg, Markus; Nordkvist, Bjoern; Notz, Dieter; Novakova, Jana; Nozaki, Mitsuaki; Nožička, Miroslav; Nugent, Ian Michael; Nuncio-Quiroz, Adriana-Elizabeth; Nunes Hanninger, Guilherme; Nunnemann, Thomas; Nurse, Emily; O'Neil, Dugan; O'Shea, Val; Oakham, Gerald; Oberlack, Horst; Ochi, Atsuhiko; Oda, Susumu; Odaka, Shigeru; Odier, Jerome; Ogren, Harold; Oh, Alexander; Oh, Seog; Ohm, Christian; Ohshima, Takayoshi; Ohshita, Hidetoshi; Ohsugi, Takashi; Okada, Shogo; Okawa, Hideki; Okumura, Yasuyuki; Okuyama, Toyonobu; Olchevski, Alexander; Oliveira, Miguel Alfonso; Oliveira Damazio, Denis; Oliver, John; Oliver Garcia, Elena; Olivito, Dominick; Olszewski, Andrzej; Olszowska, Jolanta; Omachi, Chihiro; Onofre, António; Onyisi, Peter; Oram, Christopher; Oreglia, Mark; Oren, Yona; Orestano, Domizia; Orlov, Iliya; Oropeza Barrera, Cristina; Orr, Robert; Ortega, Eduardo; Osculati, Bianca; Ospanov, Rustem; Osuna, Carlos; Ottersbach, John; Ould-Saada, Farid; Ouraou, Ahmimed; Ouyang, Qun; Owen, Mark; Owen, Simon; Oyarzun, Alejandro; Ozcan, Veysi Erkcan; Ozone, Kenji; Ozturk, Nurcan; Pacheco Pages, Andres; Padilla Aranda, Cristobal; Paganis, Efstathios; Pahl, Christoph; Paige, Frank; Pajchel, Katarina; Palestini, Sandro; Pallin, Dominique; Palma, Alberto; Palmer, Jody; Pan, Yibin; Panagiotopoulou, Evgenia; Panes, Boris; Panikashvili, Natalia; Panitkin, Sergey; Pantea, Dan; Panuskova, Monika; Paolone, Vittorio; Papadopoulou, Theodora; Park, Su-Jung; Park, Woochun; Parker, Andy; Parker, Sherwood; Parodi, Fabrizio; Parsons, John; Parzefall, Ulrich; Pasqualucci, Enrico; Passeri, Antonio; Pastore, Fernanda; Pastore, Francesca; Pásztor , Gabriella; Pataraia, Sophio; Pater, Joleen; Patricelli, Sergio; Patwa, Abid; Pauly, Thilo; Peak, Lawrence; Pecsy, Martin; Pedraza Morales, Maria Isabel; Peleganchuk, Sergey; Peng, Haiping; Penson, Alexander; Penwell, John; Perantoni, Marcelo; Perez, Kerstin; Perez Codina, Estel; Pérez García-Estañ, María Teresa; Perez Reale, Valeria; Perini, Laura; Pernegger, Heinz; Perrino, Roberto; Persembe, Seda; Perus, Antoine; Peshekhonov, Vladimir; Petersen, Brian; Petersen, Troels; Petit, Elisabeth; Petridou, Chariclia; Petrolo, Emilio; Petrucci, Fabrizio; Petschull, Dennis; Petteni, Michele; Pezoa, Raquel; Phan, Anna; Phillips, Alan; Piacquadio, Giacinto; Piccinini, Maurizio; Piegaia, Ricardo; Pilcher, James; Pilkington, Andrew; Pina, João Antonio; Pinamonti, Michele; Pinfold, James; Pinto, Belmiro; Pizio, Caterina; Placakyte, Ringaile; Plamondon, Mathieu; Pleier, Marc-Andre; Poblaguev, Andrei; Poddar, Sahill; Podlyski, Fabrice; Poffenberger, Paul; Poggioli, Luc; Pohl, Martin; Polci, Francesco; Polesello, Giacomo; Policicchio, Antonio; Polini, Alessandro; Poll, James; Polychronakos, Venetios; Pomeroy, Daniel; Pommès, Kathy; Ponsot, Patrick; Pontecorvo, Ludovico; Pope, Bernard; Popeneciu, Gabriel Alexandru; Popovic, Dragan; Poppleton, Alan; Popule, Jiri; Portell Bueso, Xavier; Porter, Robert; Pospelov, Guennady; Pospisil, Stanislav; Potekhin, Maxim; Potrap, Igor; Potter, Christina; Potter, Christopher; Potter, Keith; Poulard, Gilbert; Poveda, Joaquin; Prabhu, Robindra; Pralavorio, Pascal; Prasad, Srivas; Pravahan, Rishiraj; Pribyl, Lukas; Price, Darren; Price, Lawrence; Prichard, Paul; Prieur, Damien; Primavera, Margherita; Prokofiev, Kirill; Prokoshin, Fedor; Protopopescu, Serban; Proudfoot, James; Prudent, Xavier; Przysiezniak, Helenka; Psoroulas, Serena; Ptacek, Elizabeth; Puigdengoles, Carles; Purdham, John; Purohit, Milind; Puzo, Patrick; Pylypchenko, Yuriy; Qi, Ming; Qian, Jianming; Qian, Weiming; Qin, Zhonghua; Quadt, Arnulf; Quarrie, David; Quayle, William; Quinonez, Fernando; Raas, Marcel; Radeka, Veljko; Radescu, Voica; Radics, Balint; Rador, Tonguc; Ragusa, Francesco; Rahal, Ghita; Rahimi, Amir; Rajagopalan, Srinivasan; Rammensee, Michael; Rammes, Marcus; Rauscher, Felix; Rauter, Emanuel; Raymond, Michel; Read, Alexander Lincoln; Rebuzzi, Daniela; Redelbach, Andreas; Redlinger, George; Reece, Ryan; Reeves, Kendall; Reinherz-Aronis, Erez; Reinsch, Andreas; Reisinger, Ingo; Reljic, Dusan; Rembser, Christoph; Ren, Zhongliang; Renkel, Peter; Rescia, Sergio; Rescigno, Marco; Resconi, Silvia; Resende, Bernardo; Reznicek, Pavel; Rezvani, Reyhaneh; Richards, Alexander; Richards, Ronald; Richter, Robert; Richter-Was, Elzbieta; Ridel, Melissa; Rijpstra, Manouk; Rijssenbeek, Michael; Rimoldi, Adele; Rinaldi, Lorenzo; Rios, Ryan Randy; Riu, Imma; Rizatdinova, Flera; Rizvi, Eram; Roa Romero, Diego Alejandro; Robertson, Steven; Robichaud-Veronneau, Andree; Robinson, Dave; Robinson, James; Robinson, Mary; Robson, Aidan; Rocha de Lima, Jose Guilherme; Roda, Chiara; Roda Dos Santos, Denis; Rodriguez, Diego; Rodriguez Garcia, Yohany; Roe, Shaun; Røhne, Ole; Rojo, Victoria; Rolli, Simona; Romaniouk, Anatoli; Romanov, Victor; Romeo, Gaston; Romero Maltrana, Diego; Roos, Lydia; Ros, Eduardo; Rosati, Stefano; Rosenbaum, Gabriel; Rosselet, Laurent; Rossetti, Valerio; Rossi, Leonardo Paolo; Rotaru, Marina; Rothberg, Joseph; Rousseau, David; Royon, Christophe; Rozanov, Alexander; Rozen, Yoram; Ruan, Xifeng; Ruckert, Benjamin; Ruckstuhl, Nicole; Rud, Viacheslav; Rudolph, Gerald; Rühr, Frederik; Ruggieri, Federico; Ruiz-Martinez, Aranzazu; Rumyantsev, Leonid; Rurikova, Zuzana; Rusakovich, Nikolai; Rutherfoord, John; Ruwiedel, Christoph; Ruzicka, Pavel; Ryabov, Yury; Ryan, Patrick; Rybkin, Grigori; Rzaeva, Sevda; Saavedra, Aldo; Sadrozinski, Hartmut; Sadykov, Renat; Sakamoto, Hiroshi; Salamanna, Giuseppe; Salamon, Andrea; Saleem, Muhammad; Salihagic, Denis; Salnikov, Andrei; Salt, José; Salvachua Ferrando, Belén; Salvatore, Daniela; Salvatore, Pasquale Fabrizio; Salvucci, Antonio; Salzburger, Andreas; Sampsonidis, Dimitrios; Samset, Björn Hallvard; Sandaker, Heidi; Sander, Heinz Georg; Sanders, Michiel; Sandhoff, Marisa; Sandhu, Pawan; Sandstroem, Rikard; Sandvoss, Stephan; Sankey, Dave; Sanny, Bernd; Sansoni, Andrea; Santamarina Rios, Cibran; Santoni, Claudio; Santonico, Rinaldo; Saraiva, João; Sarangi, Tapas; Sarkisyan-Grinbaum, Edward; Sarri, Francesca; Sasaki, Osamu; Sasao, Noboru; Satsounkevitch, Igor; Sauvage, Gilles; Savard, Pierre; Savine, Alexandre; Savinov, Vladimir; Sawyer, Lee; Saxon, David; Says, Louis-Pierre; Sbarra, Carla; Sbrizzi, Antonio; Scannicchio, Diana; Schaarschmidt, Jana; Schacht, Peter; Schäfer, Uli; Schaetzel, Sebastian; Schaffer, Arthur; Schaile, Dorothee; Schamberger, R.~Dean; Schamov, Andrey; Schegelsky, Valery; Scheirich, Daniel; Schernau, Michael; Scherzer, Max; Schiavi, Carlo; Schieck, Jochen; Schioppa, Marco; Schlenker, Stefan; Schmidt, Evelyn; Schmieden, Kristof; Schmitt, Christian; Schmitz, Martin; Schott, Matthias; Schouten, Doug; Schovancova, Jaroslava; Schram, Malachi; Schreiner, Alexander; Schroeder, Christian; Schroer, Nicolai; Schroers, Marcel; Schultes, Joachim; Schultz-Coulon, Hans-Christian; Schumacher, Jan; Schumacher, Markus; Schumm, Bruce; Schune, Philippe; Schwanenberger, Christian; Schwartzman, Ariel; Schwemling, Philippe; Schwienhorst, Reinhard; Schwierz, Rainer; Schwindling, Jerome; Scott, Bill; Searcy, Jacob; Sedykh, Evgeny; Segura, Ester; Seidel, Sally; Seiden, Abraham; Seifert, Frank; Seixas, José; Sekhniaidze, Givi; Seliverstov, Dmitry; Sellden, Bjoern; Semprini-Cesari, Nicola; Serfon, Cedric; Serin, Laurent; Seuster, Rolf; Severini, Horst; Sevior, Martin; Sfyrla, Anna; Shabalina, Elizaveta; Shamim, Mansoora; Shan, Lianyou; Shank, James; Shao, Qi Tao; Shapiro, Marjorie; Shatalov, Pavel; Shaw, Kate; Sherman, Daniel; Sherwood, Peter; Shibata, Akira; Shimojima, Makoto; Shin, Taeksu; Shmeleva, Alevtina; Shochet, Mel; Shupe, Michael; Sicho, Petr; Sidoti, Antonio; Siegert, Frank; Siegrist, James; Sijacki, Djordje; Silbert, Ohad; Silver, Yiftah; Silverstein, Daniel; Silverstein, Samuel; Simak, Vladislav; Simic, Ljiljana; Simion, Stefan; Simmons, Brinick; Simonyan, Margar; Sinervo, Pekka; Sinev, Nikolai; Sipica, Valentin; Siragusa, Giovanni; Sisakyan, Alexei; Sivoklokov, Serguei; Sjölin, Jörgen; Sjursen, Therese; Skovpen, Kirill; Skubic, Patrick; Slater, Mark; Slavicek, Tomas; Sliwa, Krzysztof; Sloper, John erik; Sluka, Tomas; Smakhtin, Vladimir; Smirnov, Sergei; Smirnov, Yuri; Smirnova, Lidia; Smirnova, Oxana; Smith, Ben Campbell; Smith, Douglas; Smith, Kenway; Smizanska, Maria; Smolek, Karel; Snesarev, Andrei; Snow, Steve; Snow, Joel; Snuverink, Jochem; Snyder, Scott; Soares, Mara; Sobie, Randall; Sodomka, Jaromir; Soffer, Abner; Solans, Carlos; Solar, Michael; Solc, Jaroslav; Solfaroli Camillocci, Elena; Solodkov, Alexander; Solovyanov, Oleg; Soluk, Richard; Sondericker, John; Sopko, Vit; Sopko, Bruno; Sosebee, Mark; Soukharev, Andrey; Spagnolo, Stefania; Spanò, Francesco; Spencer, Edwin; Spighi, Roberto; Spigo, Giancarlo; Spila, Federico; Spiwoks, Ralf; Spousta, Martin; Spreitzer, Teresa; Spurlock, Barry; St. Denis, Richard Dante; Stahl, Thorsten; Stahlman, Jonathan; Stamen, Rainer; Stancu, Stefan Nicolae; Stanecka, Ewa; Stanek, Robert; Stanescu, Cristian; Stapnes, Steinar; Starchenko, Evgeny; Stark, Jan; Staroba, Pavel; Starovoitov, Pavel; Stastny, Jan; Stavina, Pavel; Stavropoulos, Georgios; Steele, Genevieve; Steinbach, Peter; Steinberg, Peter; Stekl, Ivan; Stelzer, Bernd; Stelzer, Harald Joerg; Stelzer-Chilton, Oliver; Stenzel, Hasko; Stevenson, Kyle; Stewart, Graeme; Stockton, Mark; Stoerig, Kathrin; Stoicea, Gabriel; Stonjek, Stefan; Strachota, Pavel; Stradling, Alden; Straessner, Arno; Strandberg, Jonas; Strandberg, Sara; Strandlie, Are; Strauss, Michael; Strizenec, Pavol; Ströhmer, Raimund; Strom, David; Stroynowski, Ryszard; Strube, Jan; Stugu, Bjarne; Su, Dong; Soh, Dart-yin; Sugaya, Yorihito; Sugimoto, Takuya; Suhr, Chad; Suk, Michal; Sulin, Vladimir; Sultansoy, Saleh; Sumida, Toshi; Sun, Xiaohu; Sundermann, Jan Erik; Suruliz, Kerim; Sushkov, Serge; Susinno, Giancarlo; Sutton, Mark; Suzuki, Takuya; Suzuki, Yu; Sykora, Ivan; Sykora, Tomas; Szymocha, Tadeusz; Sánchez, Javier; Ta, Duc; Tackmann, Kerstin; Taffard, Anyes; Tafirout, Reda; Taga, Adrian; Takahashi, Yuta; Takai, Helio; Takashima, Ryuichi; Takeda, Hiroshi; Takeshita, Tohru; Talby, Mossadek; Talyshev, Alexey; Tamsett, Matthew; Tanaka, Junichi; Tanaka, Reisaburo; Tanaka, Satoshi; Tanaka, Shuji; Tapprogge, Stefan; Tardif, Dominique; Tarem, Shlomit; Tarrade, Fabien; Tartarelli, Giuseppe Francesco; Tas, Petr; Tasevsky, Marek; Tassi, Enrico; Tatarkhanov, Mous; Taylor, Christopher; Taylor, Frank; Taylor, Geoffrey; Taylor, Ryan P.; Taylor, Wendy; Teixeira-Dias, Pedro; Ten Kate, Herman; Teng, Ping-Kun; Tennenbaum-Katan, Yaniv-David; Terada, Susumu; Terashi, Koji; Terron, Juan; Terwort, Mark; Testa, Marianna; Teuscher, Richard; Thioye, Moustapha; Thoma, Sascha; Thomas, Juergen; Thompson, Stan; Thompson, Emily; Thompson, Peter; Thompson, Paul; Thompson, Ray; Thomson, Evelyn; Thun, Rudolf; Tic, Tomas; Tikhomirov, Vladimir; Tikhonov, Yury; Tipton, Paul; Tique Aires Viegas, Florbela De Jes; Tisserant, Sylvain; Toczek, Barbara; Todorov, Theodore; Todorova-Nova, Sharka; Toggerson, Brokk; Tojo, Junji; Tokár, Stanislav; Tokushuku, Katsuo; Tollefson, Kirsten; Tomasek, Lukas; Tomasek, Michal; Tomoto, Makoto; Tompkins, Lauren; Toms, Konstantin; Tonoyan, Arshak; Topfel, Cyril; Topilin, Nikolai; Torrence, Eric; Torró Pastor, Emma; Toth, Jozsef; Touchard, Francois; Tovey, Daniel; Trefzger, Thomas; Tremblet, Louis; Tricoli, Alesandro; Trigger, Isabel Marian; Trincaz-Duvoid, Sophie; Trinh, Thi Nguyet; Tripiana, Martin; Triplett, Nathan; Trischuk, William; Trivedi, Arjun; Trocmé, Benjamin; Troncon, Clara; Trzupek, Adam; Tsarouchas, Charilaos; Tseng, Jeffrey; Tsiakiris, Menelaos; Tsiareshka, Pavel; Tsionou, Dimitra; Tsipolitis, Georgios; Tsiskaridze, Vakhtang; Tskhadadze, Edisher; Tsukerman, Ilya; Tsulaia, Vakhtang; Tsung, Jieh-Wen; Tsuno, Soshi; Tsybychev, Dmitri; Tuggle, Joseph; Turecek, Daniel; Turk Cakir, Ilkay; Turlay, Emmanuel; Tuts, Michael; Twomey, Matthew Shaun; Tylmad, Maja; Tyndel, Mike; Uchida, Kirika; Ueda, Ikuo; Ugland, Maren; Uhlenbrock, Mathias; Uhrmacher, Michael; Ukegawa, Fumihiko; Unal, Guillaume; Undrus, Alexander; Unel, Gokhan; Unno, Yoshinobu; Urbaniec, Dustin; Urkovsky, Evgeny; Urquijo, Phillip; Urrejola, Pedro; Usai, Giulio; Uslenghi, Massimiliano; Vacavant, Laurent; Vacek, Vaclav; Vachon, Brigitte; Vahsen, Sven; Valente, Paolo; Valentinetti, Sara; Valkar, Stefan; Valladolid Gallego, Eva; Vallecorsa, Sofia; Valls Ferrer, Juan Antonio; Van Berg, Richard; van der Graaf, Harry; van der Kraaij, Erik; van der Poel, Egge; van der Ster, Daniel; van Eldik, Niels; van Gemmeren, Peter; van Kesteren, Zdenko; van Vulpen, Ivo; Vandelli, Wainer; Vaniachine, Alexandre; Vankov, Peter; Vannucci, Francois; Vari, Riccardo; Varnes, Erich; Varouchas, Dimitris; Vartapetian, Armen; Varvell, Kevin; Vasilyeva, Lidia; Vassilakopoulos, Vassilios; Vazeille, Francois; Vellidis, Constantine; Veloso, Filipe; Veneziano, Stefano; Ventura, Andrea; Ventura, Daniel; Venturi, Manuela; Venturi, Nicola; Vercesi, Valerio; Verducci, Monica; Verkerke, Wouter; Vermeulen, Jos; Vetterli, Michel; Vichou, Irene; Vickey, Trevor; Viehhauser, Georg; Villa, Mauro; Villani, Giulio; Villaplana Perez, Miguel; Vilucchi, Elisabetta; Vincter, Manuella; Vinek, Elisabeth; Vinogradov, Vladimir; Viret, Sébastien; Virzi, Joseph; Vitale , Antonio; Vitells, Ofer; Vivarelli, Iacopo; Vives Vaque, Francesc; Vlachos, Sotirios; Vlasak, Michal; Vlasov, Nikolai; Vogel, Adrian; Vokac, Petr; Volpi, Matteo; von der Schmitt, Hans; von Loeben, Joerg; von Radziewski, Holger; von Toerne, Eckhard; Vorobel, Vit; Vorwerk, Volker; Vos, Marcel; Voss, Rudiger; Voss, Thorsten Tobias; Vossebeld, Joost; Vranjes, Nenad; Vranjes Milosavljevic, Marija; Vrba, Vaclav; Vreeswijk, Marcel; Vu Anh, Tuan; Vudragovic, Dusan; Vuillermet, Raphael; Vukotic, Ilija; Wagner, Peter; Walbersloh, Jorg; Walder, James; Walker, Rodney; Walkowiak, Wolfgang; Wall, Richard; Wang, Chiho; Wang, Haichen; Wang, Jin; Wang, Song-Ming; Warburton, Andreas; Ward, Patricia; Warsinsky, Markus; Wastie, Roy; Watkins, Peter; Watson, Alan; Watson, Miriam; Watts, Gordon; Watts, Stephen; Waugh, Anthony; Waugh, Ben; Weber, Marc; Weber, Manuel; Weber, Michele; Weber, Pavel; Weidberg, Anthony; Weingarten, Jens; Weiser, Christian; Wellenstein, Hermann; Wells, Phillippa; Wen, Mei; Wenaus, Torre; Wendler, Shanti; Wengler, Thorsten; Wenig, Siegfried; Wermes, Norbert; Werner, Matthias; Werner, Per; Werth, Michael; Werthenbach, Ulrich; Wessels, Martin; Whalen, Kathleen; White, Andrew; White, Martin; White, Sebastian; Whitehead, Samuel Robert; Whiteson, Daniel; Whittington, Denver; Wicek, Francois; Wicke, Daniel; Wickens, Fred; Wiedenmann, Werner; Wielers, Monika; Wienemann, Peter; Wiglesworth, Craig; Wiik, Liv Antje Mari; Wildauer, Andreas; Wildt, Martin Andre; Wilkens, Henric George; Williams, Eric; Williams, Hugh; Willocq, Stephane; Wilson, John; Wilson, Michael Galante; Wilson, Alan; Wingerter-Seez, Isabelle; Winklmeier, Frank; Wittgen, Matthias; Wolter, Marcin Wladyslaw; Wolters, Helmut; Wosiek, Barbara; Wotschack, Jorg; Woudstra, Martin; Wraight, Kenneth; Wright, Catherine; Wright, Dennis; Wrona, Bozydar; Wu, Sau Lan; Wu, Xin; Wulf, Evan; Wynne, Benjamin; Xaplanteris, Leonidas; Xella, Stefania; Xie, Song; Xu, Da; Xu, Neng; Yamada, Miho; Yamamoto, Akira; Yamamoto, Kyoko; Yamamoto, Shimpei; Yamamura, Taiki; Yamaoka, Jared; Yamazaki, Takayuki; Yamazaki, Yuji; Yan, Zhen; Yang, Haijun; Yang, Un-Ki; Yang, Zhaoyu; Yao, Weiming; Yao, Yushu; Yasu, Yoshiji; Ye, Jingbo; Ye, Shuwei; Yilmaz, Metin; Yoosoofmiya, Reza; Yorita, Kohei; Yoshida, Riktura; Young, Charles; Youssef, Saul; Yu, Dantong; Yu, Jaehoon; Yuan, Li; Yurkewicz, Adam; Zaidan, Remi; Zaitsev, Alexander; Zajacova, Zuzana; Zambrano, Valentina; Zanello, Lucia; Zaytsev, Alexander; Zeitnitz, Christian; Zeller, Michael; Zemla, Andrzej; Zendler, Carolin; Zenin, Oleg; Ženiš, Tibor; Zenonos, Zenonas; Zenz, Seth; Zerwas, Dirk; Zevi della Porta, Giovanni; Zhan, Zhichao; Zhang, Huaqiao; Zhang, Jinlong; Zhang, Qizhi; Zhang, Xueyao; Zhao, Long; Zhao, Tianchi; Zhao, Zhengguo; Zhemchugov, Alexey; Zhong, Jiahang; Zhou, Bing; Zhou, Ning; Zhou, Yue; Zhu, Cheng Guang; Zhu, Hongbo; Zhu, Yingchun; Zhuang, Xuai; Zhuravlov, Vadym; Zimmermann, Robert; Zimmermann, Simone; Zimmermann, Stephanie; Ziolkowski, Michael; Živković, Lidija; Zobernig, Georg; Zoccoli, Antonio; zur Nedden, Martin; Zutshi, Vishnu

    2010-01-01

    The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.

  14. ATLAS SCT Commissioning

    CERN Document Server

    Limper, Maaike

    2007-01-01

    The Barrel and End-Cap SCT detectors are installed in the ATLAS cavern. This paper will focus on the assembly, installation and first tests of the SCT in-situ. The thermal, electrical and optical services were tested and the results will be reviewed. Problems with the cooling have led to a modification for the heaters on the cooling return lines. The first tests of the SCT in-situ will be described using the calibration scans. The performance of the SCT, in particular the fraction of working channels and the noise performance, is well within the ATLAS specification.

  15. The ATLAS Detector Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Clark, P.J. [University of Edinburgh, School of Physics and Astronomy, James Clerk Maxwell Building, The Kings Buildings, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom)

    2011-06-15

    We present the simulation software for the ATLAS experiment [G. Aad et al., The ATLAS Experiment at the CERN Large Hadron Collider, JINST 3 (2008), S08003] at the Large Hadron Collider [L. Evans and P. Bryant, LHC Machine, JINST 3 (2008), S08001]. The overall infrastructure and some selected features are discussed. In particular, the detector description, the interface to Geant4, event generator support, magnetic field integration improvements, pile-up and digitisation of overlapping events and fast simulation. Also described are performance studies, large scale production and the validation of the simulated output against recent data.

  16. ATLAS TV PROJECT

    CERN Multimedia

    2005-01-01

    CAMERA ON TOROID The ATLAS barrel toroid system consists of eight coils, each of axial length 25.3 m, assembled radially and symmetrically around the beam axis. The coils are of a flat racetrack type with two double-pancake windings made of 20.5 kA aluminium-stabilized niobium-titanium superconductor. The video is about the slow lowering of the toroid down to the cavern of ATLAS. It is very demanding task. The camera is placed on top of the toroid.

  17. ATLAS fast physics monitoring

    Indian Academy of Sciences (India)

    Karsten Köneke; on behalf of the ATLAS Collaboration

    2012-11-01

    The ATLAS experiment at the Large Hadron Collider is recording data from proton–proton collisions at a centre-of-mass energy of 7 TeV since the spring of 2010. The integrated luminosity has grown nearly exponentially since then and continues to rise fast. The ATLAS Collaboration has set up a framework to automatically process the rapidly growing dataset and produce performance and physics plots for the most interesting analyses. The system is designed to give fast feedback. The histograms are produced within hours of data reconstruction (2–3 days after data taking). Hints of potentially interesting physics signals obtained this way are followed up by physics groups.

  18. Improving ATLAS reprocessing software

    CERN Document Server

    Novak, Tadej

    2014-01-01

    For my CERN Summer Student programme I have been working with ATLAS reprocessing group. Data taken at ATLAS experiment is not only processed after being taken, but is also reprocessed multiple times afterwards. This allows applying new alignments, calibration of detector and using improved or faster algorithms. Reprocessing is usually done in campaigns for different periods of data or for different interest groups. The idea of my project was to simplify the definition of tasks and monitoring of their progress. I created a LIST configuration files generator script in Python and a monitoring webpage for tracking current reprocessing tasks.

  19. Jet Physics in ATLAS

    CERN Document Server

    Sandoval, C; The ATLAS collaboration

    2012-01-01

    Measurements of hadronic jets provide tests of strong interactions which are interesting both in their own right and as backgrounds to many New Physics searches. It is also through tests of Quantum Chromodynamics that new physics may be discovered. The extensive dataset recorded with the ATLAS detector throughout the 7 TeV centre-of-mass LHC operation period allows QCD to be probed at distances never reached before. We present a review of selected ATLAS jet physics measurements. These measurements constitute precision tests of QCD in a new energy regime, and show sensitivity to the parton densities in the proton and to the value of the strong coupling, alpha_s.

  20. ATLAS/CMS Upgrades

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00370685; The ATLAS collaboration

    2016-01-01

    Precision studies of the Standard Model (SM) and the searches of the physics beyond the SM are ongoing at the ATLAS and CMS experiments at the Large Hadron Collider (LHC). A luminosity upgrade of LHC is planned, which provides a significant challenge for the experiments. In this report, the plans of the ATLAS and CMS upgrades are introduced. Physics prospects for selected topics, including Higgs coupling measurements, Bs,d -> mumu decays, and top quark decays through flavor changing neutral current, are also shown.

  1. The ATLAS Simulation Infrastructure

    Science.gov (United States)

    Aad, G.; Abbott, B.; Abdallah, J.; Abdelalim, A. A.; Abdesselam, A.; Abdinov, O.; Abi, B.; Abolins, M.; Abramowicz, H.; Abreu, H.; Acharya, B. S.; Adams, D. L.; Addy, T. N.; Adelman, J.; Adorisio, C.; Adragna, P.; Adye, T.; Aefsky, S.; Aguilar-Saavedra, J. A.; Aharrouche, M.; Ahlen, S. P.; Ahles, F.; Ahmad, A.; Ahmed, H.; Ahsan, M.; Aielli, G.; Akdogan, T.; Åkesson, T. P. A.; Akimoto, G.; Akimov, A. V.; Aktas, A.; Alam, M. S.; Alam, M. A.; Albrand, S.; Aleksa, M.; Aleksandrov, I. N.; Alexa, C.; Alexander, G.; Alexandre, G.; Alexopoulos, T.; Alhroob, M.; Aliev, M.; Alimonti, G.; Alison, J.; Aliyev, M.; Allport, P. P.; Allwood-Spiers, S. E.; Almond, J.; Aloisio, A.; Alon, R.; Alonso, A.; Alviggi, M. G.; Amako, K.; Amelung, C.; Amorim, A.; Amorós, G.; Amram, N.; Anastopoulos, C.; Andeen, T.; Anders, C. F.; Anderson, K. J.; Andreazza, A.; Andrei, V.; Anduaga, X. S.; Angerami, A.; Anghinolfi, F.; Anjos, N.; Annovi, A.; Antonaki, A.; Antonelli, M.; Antonelli, S.; Antos, J.; Antunovic, B.; Anulli, F.; Aoun, S.; Arabidze, G.; Aracena, I.; Arai, Y.; Arce, A. T. H.; Archambault, J. P.; Arfaoui, S.; Arguin, J.-F.; Argyropoulos, T.; Arik, M.; Armbruster, A. J.; Arnaez, O.; Arnault, C.; Artamonov, A.; Arutinov, D.; Asai, M.; Asai, S.; Asfandiyarov, R.; Ask, S.; Åsman, B.; Asner, D.; Asquith, L.; Assamagan, K.; Astbury, A.; Astvatsatourov, A.; Atoian, G.; Auerbach, B.; Augsten, K.; Aurousseau, M.; Austin, N.; Avolio, G.; Avramidou, R.; Axen, D.; Ay, C.; Azuelos, G.; Azuma, Y.; Baak, M. A.; Bach, A. M.; Bachacou, H.; Bachas, K.; Backes, M.; Badescu, E.; Bagnaia, P.; Bai, Y.; Bain, T.; Baines, J. T.; Baker, O. K.; Baker, M. D.; Baker, S.; Baltasar Dos Santos Pedrosa, F.; Banas, E.; Banerjee, P.; Banerjee, S.; Banfi, D.; Bangert, A.; Bansal, V.; Baranov, S. P.; Baranov, S.; Barashkou, A.; Barber, T.; Barberio, E. L.; Barberis, D.; Barbero, M.; Bardin, D. Y.; Barillari, T.; Barisonzi, M.; Barklow, T.; Barlow, N.; Barnett, B. M.; Barnett, R. M.; Baroncelli, A.; Barr, A. J.; Barreiro, F.; Barreiro Guimarães da Costa, J.; Barrillon, P.; Bartoldus, R.; Bartsch, D.; Bates, R. L.; Batkova, L.; Batley, J. R.; Battaglia, A.; Battistin, M.; Bauer, F.; Bawa, H. S.; Bazalova, M.; Beare, B.; Beau, T.; Beauchemin, P. H.; Beccherle, R.; Becerici, N.; Bechtle, P.; Beck, G. A.; Beck, H. P.; Beckingham, M.; Becks, K. H.; Beddall, A. J.; Beddall, A.; Bednyakov, V. A.; Bee, C.; Begel, M.; Behar Harpaz, S.; Behera, P. K.; Beimforde, M.; Belanger-Champagne, C.; Bell, P. J.; Bell, W. H.; Bella, G.; Bellagamba, L.; Bellina, F.; Bellomo, M.; Belloni, A.; Belotskiy, K.; Beltramello, O.; Ben Ami, S.; Benary, O.; Benchekroun, D.; Bendel, M.; Benedict, B. H.; Benekos, N.; Benhammou, Y.; Benincasa, G. P.; Benjamin, D. P.; Benoit, M.; Bensinger, J. R.; Benslama, K.; Bentvelsen, S.; Beretta, M.; Berge, D.; Bergeaas Kuutmann, E.; Berger, N.; Berghaus, F.; Berglund, E.; Beringer, J.; Bernat, P.; Bernhard, R.; Bernius, C.; Berry, T.; Bertin, A.; Besana, M. I.; Besson, N.; Bethke, S.; Bianchi, R. M.; Bianco, M.; Biebel, O.; Biesiada, J.; Biglietti, M.; Bilokon, H.; Bindi, M.; Binet, S.; Bingul, A.; Bini, C.; Biscarat, C.; Bitenc, U.; Black, K. M.; Blair, R. E.; Blanchard, J.-B.; Blanchot, G.; Blocker, C.; Blondel, A.; Blum, W.; Blumenschein, U.; Bobbink, G. J.; Bocci, A.; Boehler, M.; Boek, J.; Boelaert, N.; Böser, S.; Bogaerts, J. A.; Bogouch, A.; Bohm, C.; Bohm, J.; Boisvert, V.; Bold, T.; Boldea, V.; Bondarenko, V. G.; Bondioli, M.; Boonekamp, M.; Bordoni, S.; Borer, C.; Borisov, A.; Borissov, G.; Borjanovic, I.; Borroni, S.; Bos, K.; Boscherini, D.; Bosman, M.; Boterenbrood, H.; Bouchami, J.; Boudreau, J.; Bouhova-Thacker, E. V.; Boulahouache, C.; Bourdarios, C.; Boveia, A.; Boyd, J.; Boyko, I. R.; Bozovic-Jelisavcic, I.; Bracinik, J.; Braem, A.; Branchini, P.; Brandenburg, G. W.; Brandt, A.; Brandt, G.; Brandt, O.; Bratzler, U.; Brau, B.; Brau, J. E.; Braun, H. M.; Brelier, B.; Bremer, J.; Brenner, R.; Bressler, S.; Britton, D.; Brochu, F. M.; Brock, I.; Brock, R.; Brodet, E.; Bromberg, C.; Brooijmans, G.; Brooks, W. K.; Brown, G.; Bruckman de Renstrom, P. A.; Bruncko, D.; Bruneliere, R.; Brunet, S.; Bruni, A.; Bruni, G.; Bruschi, M.; Bucci, F.; Buchanan, J.; Buchholz, P.; Buckley, A. G.; Budagov, I. A.; Budick, B.; Büscher, V.; Bugge, L.; Bulekov, O.; Bunse, M.; Buran, T.; Burckhart, H.; Burdin, S.; Burgess, T.; Burke, S.; Busato, E.; Bussey, P.; Buszello, C. P.; Butin, F.; Butler, B.; Butler, J. M.; Buttar, C. M.; Butterworth, J. M.; Byatt, T.; Caballero, J.; Cabrera Urbán, S.; Caforio, D.; Cakir, O.; Calafiura, P.; Calderini, G.; Calfayan, P.; Calkins, R.; Caloba, L. 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F.; Cherkaoui El Moursli, R.; Tcherniatine, V.; Chesneanu, D.; Cheu, E.; Cheung, S. L.; Chevalier, L.; Chevallier, F.; Chiarella, V.; Chiefari, G.; Chikovani, L.; Childers, J. T.; Chilingarov, A.; Chiodini, G.; Chizhov, V.; Choudalakis, G.; Chouridou, S.; Christidi, I. A.; Christov, A.; Chromek-Burckhart, D.; Chu, M. L.; Chudoba, J.; Ciapetti, G.; Ciftci, A. K.; Ciftci, R.; Cinca, D.; Cindro, V.; Ciobotaru, M. D.; Ciocca, C.; Ciocio, A.; Cirilli, M.; Citterio, M.; Clark, A.; Clark, P. J.; Cleland, W.; Clemens, J. C.; Clement, B.; Clement, C.; Coadou, Y.; Cobal, M.; Coccaro, A.; Cochran, J.; Coggeshall, J.; Cogneras, E.; Colijn, A. P.; Collard, C.; Collins, N. J.; Collins-Tooth, C.; Collot, J.; Colon, G.; Conde Muiño, P.; Coniavitis, E.; Consonni, M.; Constantinescu, S.; Conta, C.; Conventi, F.; Cooke, M.; Cooper, B. D.; Cooper-Sarkar, A. M.; Cooper-Smith, N. 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B.; de Zorzi, G.; Dean, S.; Dedovich, D. V.; Degenhardt, J.; Dehchar, M.; Del Papa, C.; Del Peso, J.; Del Prete, T.; Dell'Acqua, A.; Dell'Asta, L.; Della Pietra, M.; Della Volpe, D.; Delmastro, M.; Delsart, P. A.; Deluca, C.; Demers, S.; Demichev, M.; Demirkoz, B.; Deng, J.; Deng, W.; Denisov, S. P.; Derkaoui, J. E.; Derue, F.; Dervan, P.; Desch, K.; Deviveiros, P. O.; Dewhurst, A.; Dewilde, B.; Dhaliwal, S.; Dhullipudi, R.; di Ciaccio, A.; di Ciaccio, L.; di Domenico, A.; di Girolamo, A.; di Girolamo, B.; di Luise, S.; di Mattia, A.; di Nardo, R.; di Simone, A.; di Sipio, R.; Diaz, M. A.; Diblen, F.; Diehl, E. B.; Dietrich, J.; Dietzsch, T. A.; Diglio, S.; Dindar Yagci, K.; Dingfelder, J.; Dionisi, C.; Dita, P.; Dita, S.; Dittus, F.; Djama, F.; Djilkibaev, R.; Djobava, T.; Do Vale, M. A. B.; Do Valle Wemans, A.; Doan, T. K. O.; Dobos, D.; Dobson, E.; Dobson, M.; Doglioni, C.; Doherty, T.; Dolejsi, J.; Dolenc, I.; Dolezal, Z.; Dolgoshein, B. A.; Dohmae, T.; Donega, M.; Donini, J.; Dopke, J.; Doria, A.; Dos Anjos, A.; Dotti, A.; Dova, M. T.; Doxiadis, A.; Doyle, A. T.; Drasal, Z.; Dris, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Dudarev, A.; Dudziak, F.; Dührssen, M.; Duflot, L.; Dufour, M.-A.; Dunford, M.; Duran Yildiz, H.; Dushkin, A.; Duxfield, R.; Dwuznik, M.; Düren, M.; Ebenstein, W. L.; Ebke, J.; Eckweiler, S.; Edmonds, K.; Edwards, C. A.; Egorov, K.; Ehrenfeld, W.; Ehrich, T.; Eifert, T.; Eigen, G.; Einsweiler, K.; Eisenhandler, E.; Ekelof, T.; El Kacimi, M.; Ellert, M.; Elles, S.; Ellinghaus, F.; Ellis, K.; Ellis, N.; Elmsheuser, J.; Elsing, M.; Emeliyanov, D.; Engelmann, R.; Engl, A.; Epp, B.; Eppig, A.; Erdmann, J.; Ereditato, A.; Eriksson, D.; Ermoline, I.; Ernst, J.; Ernst, M.; Ernwein, J.; Errede, D.; Errede, S.; Ertel, E.; Escalier, M.; Escobar, C.; Espinal Curull, X.; Esposito, B.; Etienvre, A. I.; Etzion, E.; Evans, H.; Fabbri, L.; Fabre, C.; Facius, K.; Fakhrutdinov, R. M.; Falciano, S.; Fang, Y.; Fanti, M.; Farbin, A.; Farilla, A.; Farley, J.; Farooque, T.; Farrington, S. M.; Farthouat, P.; Fassnacht, P.; Fassouliotis, D.; Fatholahzadeh, B.; Fayard, L.; Fayette, F.; Febbraro, R.; Federic, P.; Fedin, O. L.; Fedorko, W.; Feligioni, L.; Felzmann, C. U.; Feng, C.; Feng, E. J.; Fenyuk, A. B.; Ferencei, J.; Ferland, J.; Fernandes, B.; Fernando, W.; Ferrag, S.; Ferrando, J.; Ferrara, V.; Ferrari, A.; Ferrari, P.; Ferrari, R.; Ferrer, A.; Ferrer, M. L.; Ferrere, D.; Ferretti, C.; Fiascaris, M.; Fiedler, F.; Filipčič, A.; Filippas, A.; Filthaut, F.; Fincke-Keeler, M.; Fiolhais, M. C. N.; Fiorini, L.; Firan, A.; Fischer, G.; Fisher, M. J.; Flechl, M.; Fleck, I.; Fleckner, J.; Fleischmann, P.; Fleischmann, S.; Flick, T.; Flores Castillo, L. R.; Flowerdew, M. J.; Fonseca Martin, T.; Formica, A.; Forti, A.; Fortin, D.; Fournier, D.; Fowler, A. J.; Fowler, K.; Fox, H.; Francavilla, P.; Franchino, S.; Francis, D.; Franklin, M.; Franz, S.; Fraternali, M.; Fratina, S.; Freestone, J.; French, S. T.; Froeschl, R.; Froidevaux, D.; Frost, J. A.; Fukunaga, C.; Fullana Torregrosa, E.; Fuster, J.; Gabaldon, C.; Gabizon, O.; Gadfort, T.; Gadomski, S.; Gagliardi, G.; Gagnon, P.; Galea, C.; Gallas, E. J.; Gallas, M. V.; Gallo, V.; Gallop, B. J.; Gallus, P.; Galyaev, E.; Gan, K. K.; Gao, Y. S.; Gaponenko, A.; Garcia-Sciveres, M.; García, C.; García Navarro, J. E.; Gardner, R. W.; Garelli, N.; Garitaonandia, H.; Garonne, V.; Gatti, C.; Gaudio, G.; Gautard, V.; Gauzzi, P.; Gavrilenko, I. L.; Gay, C.; Gaycken, G.; Gazis, E. N.; Ge, P.; Gee, C. N. P.; Geich-Gimbel, Ch.; Gellerstedt, K.; Gemme, C.; Genest, M. H.; Gentile, S.; Georgatos, F.; George, S.; Gershon, A.; Ghazlane, H.; Ghodbane, N.; Giacobbe, B.; Giagu, S.; Giakoumopoulou, V.; Giangiobbe, V.; Gianotti, F.; Gibbard, B.; Gibson, A.; Gibson, S. M.; Gilbert, L. M.; Gilchriese, M.; Gilewsky, V.; Gingrich, D. M.; Ginzburg, J.; Giokaris, N.; Giordani, M. P.; Giordano, R.; Giorgi, F. M.; Giovannini, P.; Giraud, P. F.; Girtler, P.; Giugni, D.; Giusti, P.; Gjelsten, B. K.; Gladilin, L. K.; Glasman, C.; Glazov, A.; Glitza, K. W.; Glonti, G. L.; Godfrey, J.; Godlewski, J.; Goebel, M.; Göpfert, T.; Goeringer, C.; Gössling, C.; Göttfert, T.; Goggi, V.; Goldfarb, S.; Goldin, D.; Golling, T.; Gomes, A.; Gomez Fajardo, L. S.; Gonçalo, R.; Gonella, L.; Gong, C.; González de La Hoz, S.; Gonzalez Silva, M. L.; Gonzalez-Sevilla, S.; Goodson, J. J.; Goossens, L.; Gordon, H. A.; Gorelov, I.; Gorfine, G.; Gorini, B.; Gorini, E.; Gorišek, A.; Gornicki, E.; Gosdzik, B.; Gosselink, M.; Gostkin, M. I.; Gough Eschrich, I.; Gouighri, M.; Goujdami, D.; Goulette, M. P.; Goussiou, A. G.; Goy, C.; Grabowska-Bold, I.; Grafström, P.; Grahn, K.-J.; Grancagnolo, S.; Grassi, V.; Gratchev, V.; Grau, N.; Gray, H. M.; Gray, J. A.; Graziani, E.; Green, B.; Greenshaw, T.; Greenwood, Z. D.; Gregor, I. M.; Grenier, P.; Griesmayer, E.; Griffiths, J.; Grigalashvili, N.; Grillo, A. A.; Grimm, K.; Grinstein, S.; Grishkevich, Y. V.; Groh, M.; Groll, M.; Gross, E.; Grosse-Knetter, J.; Groth-Jensen, J.; Grybel, K.; Guicheney, C.; Guida, A.; Guillemin, T.; Guler, H.; Gunther, J.; Guo, B.; Gupta, A.; Gusakov, Y.; Gutierrez, A.; Gutierrez, P.; Guttman, N.; Gutzwiller, O.; Guyot, C.; Gwenlan, C.; Gwilliam, C. B.; Haas, A.; Haas, S.; Haber, C.; Hadavand, H. K.; Hadley, D. R.; Haefner, P.; Härtel, R.; Hajduk, Z.; Hakobyan, H.; Haller, J.; Hamacher, K.; Hamilton, A.; Hamilton, S.; Han, L.; Hanagaki, K.; Hance, M.; Handel, C.; Hanke, P.; Hansen, J. R.; Hansen, J. B.; Hansen, J. D.; Hansen, P. H.; Hansl-Kozanecka, T.; Hansson, P.; Hara, K.; Hare, G. A.; Harenberg, T.; Harrington, R. D.; Harris, O. M.; Harrison, K.; Hartert, J.; Hartjes, F.; Harvey, A.; Hasegawa, S.; Hasegawa, Y.; Hashemi, K.; Hassani, S.; Haug, S.; Hauschild, M.; Hauser, R.; Havranek, M.; Hawkes, C. M.; Hawkings, R. J.; Hayakawa, T.; Hayward, H. S.; Haywood, S. J.; Head, S. J.; Hedberg, V.; Heelan, L.; Heim, S.; Heinemann, B.; Heisterkamp, S.; Helary, L.; Heller, M.; Hellman, S.; Helsens, C.; Hemperek, T.; Henderson, R. C. W.; Henke, M.; Henrichs, A.; Henriques Correia, A. M.; Henrot-Versille, S.; Hensel, C.; Henß, T.; Hernández Jiménez, Y.; Hershenhorn, A. D.; Herten, G.; Hertenberger, R.; Hervas, L.; Hessey, N. P.; Higón-Rodriguez, E.; Hill, J. C.; Hiller, K. H.; Hillert, S.; Hillier, S. J.; Hinchliffe, I.; Hines, E.; Hirose, M.; Hirsch, F.; Hirschbuehl, D.; Hobbs, J.; Hod, N.; Hodgkinson, M. C.; Hodgson, P.; Hoecker, A.; Hoeferkamp, M. R.; Hoffman, J.; Hoffmann, D.; Hohlfeld, M.; Holy, T.; Holzbauer, J. L.; Homma, Y.; Horazdovsky, T.; Hori, T.; Horn, C.; Horner, S.; Horvat, S.; Hostachy, J.-Y.; Hou, S.; Hoummada, A.; Howe, T.; Hrivnac, J.; Hryn'ova, T.; Hsu, P. J.; Hsu, S.-C.; Huang, G. S.; Hubacek, Z.; Hubaut, F.; Huegging, F.; Hughes, E. W.; Hughes, G.; Hurwitz, M.; Husemann, U.; Huseynov, N.; Huston, J.; Huth, J.; Iacobucci, G.; Iakovidis, G.; Ibragimov, I.; Iconomidou-Fayard, L.; Idarraga, J.; Iengo, P.; Igonkina, O.; Ikegami, Y.; Ikeno, M.; Ilchenko, Y.; Iliadis, D.; Ince, T.; Ioannou, P.; Iodice, M.; Irles Quiles, A.; Ishikawa, A.; Ishino, M.; Ishmukhametov, R.; Isobe, T.; Issakov, V.; Issever, C.; Istin, S.; Itoh, Y.; Ivashin, A. V.; Iwanski, W.; Iwasaki, H.; Izen, J. M.; Izzo, V.; Jackson, B.; Jackson, J. N.; Jackson, P.; Jaekel, M. R.; Jain, V.; Jakobs, K.; Jakobsen, S.; Jakubek, J.; Jana, D. K.; Jansen, E.; Jantsch, A.; Janus, M.; Jared, R. C.; Jarlskog, G.; Jeanty, L.; Jen-La Plante, I.; Jenni, P.; Jez, P.; Jézéquel, S.; Ji, W.; Jia, J.; Jiang, Y.; Jimenez Belenguer, M.; Jin, S.; Jinnouchi, O.; Joffe, D.; Johansen, M.; Johansson, K. E.; Johansson, P.; Johnert, S.; Johns, K. A.; Jon-And, K.; Jones, G.; Jones, R. W. L.; Jones, T. J.; Jorge, P. M.; Joseph, J.; Juranek, V.; Jussel, P.; Kabachenko, V. V.; Kaci, M.; Kaczmarska, A.; Kado, M.; Kagan, H.; Kagan, M.; Kaiser, S.; Kajomovitz, E.; Kalinin, S.; Kalinovskaya, L. V.; Kalinowski, A.; Kama, S.; Kanaya, N.; Kaneda, M.; Kantserov, V. A.; Kanzaki, J.; Kaplan, B.; Kapliy, A.; Kaplon, J.; Kar, D.; Karagounis, M.; Karagoz Unel, M.; Kartvelishvili, V.; Karyukhin, A. N.; Kashif, L.; Kasmi, A.; Kass, R. D.; Kastanas, A.; Kastoryano, M.; Kataoka, M.; Kataoka, Y.; Katsoufis, E.; Katzy, J.; Kaushik, V.; Kawagoe, K.; Kawamoto, T.; Kawamura, G.; Kayl, M. S.; Kayumov, F.; Kazanin, V. A.; Kazarinov, M. Y.; Keates, J. R.; Keeler, R.; Keener, P. T.; Kehoe, R.; Keil, M.; Kekelidze, G. D.; Kelly, M.; Kenyon, M.; Kepka, O.; Kerschen, N.; Kerševan, B. P.; Kersten, S.; Kessoku, K.; Khakzad, M.; Khalil-Zada, F.; Khandanyan, H.; Khanov, A.; Kharchenko, D.; Khodinov, A.; Khomich, A.; Khoriauli, G.; Khovanskiy, N.; Khovanskiy, V.; Khramov, E.; Khubua, J.; Kim, H.; Kim, M. S.; Kim, P. C.; Kim, S. H.; Kind, O.; Kind, P.; King, B. T.; Kirk, J.; Kirsch, G. P.; Kirsch, L. E.; Kiryunin, A. E.; Kisielewska, D.; Kittelmann, T.; Kiyamura, H.; Kladiva, E.; Klein, M.; Klein, U.; Kleinknecht, K.; Klemetti, M.; Klier, A.; Klimentov, A.; Klingenberg, R.; Klinkby, E. B.; Klioutchnikova, T.; Klok, P. F.; Klous, S.; Kluge, E.-E.; Kluge, T.; Kluit, P.; Klute, M.; Kluth, S.; Knecht, N. S.; Kneringer, E.; Ko, B. R.; Kobayashi, T.; Kobel, M.; Koblitz, B.; Kocian, M.; Kocnar, A.; Kodys, P.; Köneke, K.; König, A. C.; Koenig, S.; Köpke, L.; Koetsveld, F.; Koevesarki, P.; Koffas, T.; Koffeman, E.; Kohn, F.; Kohout, Z.; Kohriki, T.; Kolanoski, H.; Kolesnikov, V.; Koletsou, I.; Koll, J.; Kollar, D.; Kolos, S.; Kolya, S. D.; Komar, A. A.; Komaragiri, J. R.; Kondo, T.; Kono, T.; Konoplich, R.; Konovalov, S. P.; Konstantinidis, N.; Koperny, S.; Korcyl, K.; Kordas, K.; Korn, A.; Korolkov, I.; Korolkova, E. V.; Korotkov, V. A.; Kortner, O.; Kostka, P.; Kostyukhin, V. V.; Kotov, S.; Kotov, V. M.; Kotov, K. Y.; Kourkoumelis, C.; Koutsman, A.; Kowalewski, R.; Kowalski, H.; Kowalski, T. Z.; Kozanecki, W.; Kozhin, A. S.; Kral, V.; Kramarenko, V. A.; Kramberger, G.; Krasny, M. W.; Krasznahorkay, A.; Kreisel, A.; Krejci, F.; Kretzschmar, J.; Krieger, N.; Krieger, P.; Kroeninger, K.; Kroha, H.; Kroll, J.; Kroseberg, J.; Krstic, J.; Kruchonak, U.; Krüger, H.; Krumshteyn, Z. V.; Kubota, T.; Kuehn, S.; Kugel, A.; Kuhl, T.; Kuhn, D.; Kukhtin, V.; Kulchitsky, Y.; Kuleshov, S.; Kummer, C.; Kuna, M.; Kunkle, J.; Kupco, A.; Kurashige, H.; Kurata, M.; Kurchaninov, L. L.; Kurochkin, Y. A.; Kus, V.; Kwee, R.; La Rotonda, L.; Labbe, J.; Lacasta, C.; Lacava, F.; Lacker, H.; Lacour, D.; Lacuesta, V. R.; Ladygin, E.; Lafaye, R.; Laforge, B.; Lagouri, T.; Lai, S.; Lamanna, M.; Lampen, C. L.; Lampl, W.; Lancon, E.; Landgraf, U.; Landon, M. P. J.; Lane, J. L.; Lankford, A. J.; Lanni, F.; Lantzsch, K.; Lanza, A.; Laplace, S.; Lapoire, C.; Laporte, J. F.; Lari, T.; Larner, A.; Lassnig, M.; Laurelli, P.; Lavrijsen, W.; Laycock, P.; Lazarev, A. B.; Lazzaro, A.; Le Dortz, O.; Le Guirriec, E.; Le Menedeu, E.; Le Vine, M.; Lebedev, A.; Lebel, C.; Lecompte, T.; Ledroit-Guillon, F.; Lee, H.; Lee, J. S. H.; Lee, S. C.; Lefebvre, M.; Legendre, M.; Legeyt, B. C.; Legger, F.; Leggett, C.; Lehmacher, M.; Lehmann Miotto, G.; Lei, X.; Leitner, R.; Lellouch, D.; Lellouch, J.; Lendermann, V.; Leney, K. J. C.; Lenz, T.; Lenzen, G.; Lenzi, B.; Leonhardt, K.; Leroy, C.; Lessard, J.-R.; Lester, C. G.; Leung Fook Cheong, A.; Levêque, J.; Levin, D.; Levinson, L. J.; Leyton, M.; Li, H.; Li, S.; Li, X.; Liang, Z.; Liang, Z.; Liberti, B.; Lichard, P.; Lichtnecker, M.; Lie, K.; Liebig, W.; Lilley, J. N.; Lim, H.; Limosani, A.; Limper, M.; Lin, S. C.; Linnemann, J. T.; Lipeles, E.; Lipinsky, L.; Lipniacka, A.; Liss, T. M.; Lissauer, D.; Lister, A.; Litke, A. M.; Liu, C.; Liu, D.; Liu, H.; Liu, J. B.; Liu, M.; Liu, T.; Liu, Y.; Livan, M.; Lleres, A.; Lloyd, S. L.; Lobodzinska, E.; Loch, P.; Lockman, W. S.; Lockwitz, S.; Loddenkoetter, T.; Loebinger, F. K.; Loginov, A.; Loh, C. W.; Lohse, T.; Lohwasser, K.; Lokajicek, M.; Long, R. E.; Lopes, L.; Lopez Mateos, D.; Losada, M.; Loscutoff, P.; Lou, X.; Lounis, A.; Loureiro, K. F.; Lovas, L.; Love, J.; Love, P. A.; Lowe, A. J.; Lu, F.; Lubatti, H. J.; Luci, C.; Lucotte, A.; Ludwig, A.; Ludwig, D.; Ludwig, I.; Luehring, F.; Luisa, L.; Lumb, D.; Luminari, L.; Lund, E.; Lund-Jensen, B.; Lundberg, B.; Lundberg, J.; Lundquist, J.; Lynn, D.; Lys, J.; Lytken, E.; Ma, H.; Ma, L. L.; Macana Goia, J. A.; Maccarrone, G.; Macchiolo, A.; Maček, B.; Machado Miguens, J.; Mackeprang, R.; Madaras, R. J.; Mader, W. F.; Maenner, R.; Maeno, T.; Mättig, P.; Mättig, S.; Magalhaes Martins, P. J.; Magradze, E.; Mahalalel, Y.; Mahboubi, K.; Mahmood, A.; Maiani, C.; Maidantchik, C.; Maio, A.; Majewski, S.; Makida, Y.; Makouski, M.; Makovec, N.; Malecki, Pa.; Malecki, P.; Maleev, V. P.; Malek, F.; Mallik, U.; Malon, D.; Maltezos, S.; Malyshev, V.; Malyukov, S.; Mambelli, M.; Mameghani, R.; Mamuzic, J.; Mandelli, L.; Mandić, I.; Mandrysch, R.; Maneira, J.; Mangeard, P. S.; Manjavidze, I. D.; Manning, P. M.; Manousakis-Katsikakis, A.; Mansoulie, B.; Mapelli, A.; Mapelli, L.; March, L.; Marchand, J. F.; Marchese, F.; Marchiori, G.; Marcisovsky, M.; Marino, C. P.; Marroquim, F.; Marshall, Z.; Marti-Garcia, S.; Martin, A. J.; Martin, A. J.; Martin, B.; Martin, B.; Martin, F. F.; Martin, J. P.; Martin, T. A.; Martin Dit Latour, B.; Martinez, M.; Martinez Outschoorn, V.; Martini, A.; Martyniuk, A. C.; Marzano, F.; Marzin, A.; Masetti, L.; Mashimo, T.; Mashinistov, R.; Masik, J.; Maslennikov, A. L.; Massa, I.; Massol, N.; Mastroberardino, A.; Masubuchi, T.; Matricon, P.; Matsunaga, H.; Matsushita, T.; Mattravers, C.; Maxfield, S. J.; Mayne, A.; Mazini, R.; Mazur, M.; Mazzanti, M.; McDonald, J.; McKee, S. P.; McCarn, A.; McCarthy, R. L.; McCubbin, N. A.; McFarlane, K. W.; McGlone, H.; McHedlidze, G.; McMahon, S. J.; McPherson, R. A.; Meade, A.; Mechnich, J.; Mechtel, M.; Medinnis, M.; Meera-Lebbai, R.; Meguro, T. M.; Mehlhase, S.; Mehta, A.; Meier, K.; Meirose, B.; Melachrinos, C.; Mellado Garcia, B. R.; Mendoza Navas, L.; Meng, Z.; Menke, S.; Meoni, E.; Mermod, P.; Merola, L.; Meroni, C.; Merritt, F. S.; Messina, A. M.; Metcalfe, J.; Mete, A. S.; Meyer, J.-P.; Meyer, J.; Meyer, J.; Meyer, T. C.; Meyer, W. T.; Miao, J.; Michal, S.; Micu, L.; Middleton, R. P.; Migas, S.; Mijović, L.; Mikenberg, G.; Mikestikova, M.; Mikuž, M.; Miller, D. W.; Mills, W. J.; Mills, C. M.; Milov, A.; Milstead, D. A.; Milstein, D.; Minaenko, A. A.; Miñano, M.; Minashvili, I. A.; Mincer, A. I.; Mindur, B.; Mineev, M.; Ming, Y.; Mir, L. M.; Mirabelli, G.; Misawa, S.; Miscetti, S.; Misiejuk, A.; Mitrevski, J.; Mitsou, V. A.; Miyagawa, P. S.; Mjörnmark, J. U.; Mladenov, D.; Moa, T.; Moed, S.; Moeller, V.; Mönig, K.; Möser, N.; Mohr, W.; Mohrdieck-Möck, S.; Moles-Valls, R.; Molina-Perez, J.; Monk, J.; Monnier, E.; Montesano, S.; Monticelli, F.; Moore, R. W.; Mora Herrera, C.; Moraes, A.; Morais, A.; Morel, J.; Morello, G.; Moreno, D.; Moreno Llácer, M.; Morettini, P.; Morii, M.; Morley, A. K.; Mornacchi, G.; Morozov, S. V.; Morris, J. D.; Moser, H. G.; Mosidze, M.; Moss, J.; Mount, R.; Mountricha, E.; Mouraviev, S. V.; Moyse, E. J. W.; Mudrinic, M.; Mueller, F.; Mueller, J.; Mueller, K.; Müller, T. A.; Muenstermann, D.; Muir, A.; Munwes, Y.; Murillo Garcia, R.; Murray, W. J.; Mussche, I.; Musto, E.; Myagkov, A. G.; Myska, M.; Nadal, J.; Nagai, K.; Nagano, K.; Nagasaka, Y.; Nairz, A. M.; Nakamura, K.; Nakano, I.; Nakatsuka, H.; Nanava, G.; Napier, A.; Nash, M.; Nation, N. R.; Nattermann, T.; Naumann, T.; Navarro, G.; Nderitu, S. K.; Neal, H. A.; Nebot, E.; Nechaeva, P.; Negri, A.; Negri, G.; Nelson, A.; Nelson, T. K.; Nemecek, S.; Nemethy, P.; Nepomuceno, A. A.; Nessi, M.; Neubauer, M. S.; Neusiedl, A.; Neves, R. M.; Nevski, P.; Newcomer, F. M.; Nickerson, R. B.; Nicolaidou, R.; Nicolas, L.; Nicoletti, G.; Nicquevert, B.; Niedercorn, F.; Nielsen, J.; Nikiforov, A.; Nikolaev, K.; Nikolic-Audit, I.; Nikolopoulos, K.; Nilsen, H.; Nilsson, P.; Nisati, A.; Nishiyama, T.; Nisius, R.; Nodulman, L.; Nomachi, M.; Nomidis, I.; Nordberg, M.; Nordkvist, B.; Notz, D.; Novakova, J.; Nozaki, M.; Nožička, M.; Nugent, I. M.; Nuncio-Quiroz, A.-E.; Nunes Hanninger, G.; Nunnemann, T.; Nurse, E.; O'Neil, D. C.; O'Shea, V.; Oakham, F. G.; Oberlack, H.; Ochi, A.; Oda, S.; Odaka, S.; Odier, J.; Ogren, H.; Oh, A.; Oh, S. H.; Ohm, C. C.; Ohshima, T.; Ohshita, H.; Ohsugi, T.; Okada, S.; Okawa, H.; Okumura, Y.; Okuyama, T.; Olchevski, A. G.; Oliveira, M.; Oliveira Damazio, D.; Oliver, J.; Oliveira Garcia, E.; Olivito, D.; Olszewski, A.; Olszowska, J.; Omachi, C.; Onofre, A.; Onyisi, P. U. E.; Oram, C. J.; Oreglia, M. J.; Oren, Y.; Orestano, D.; Orlov, I.; Oropeza Barrera, C.; Orr, R. S.; Ortega, E. O.; Osculati, B.; Ospanov, R.; Osuna, C.; Ottersbach, J. P.; Ould-Saada, F.; Ouraou, A.; Ouyang, Q.; Owen, M.; Owen, S.; Oyarzun, A.; Ozcan, V. E.; Ozone, K.; Ozturk, N.; Pacheco Pages, A.; Padilla Aranda, C.; Paganis, E.; Pahl, C.; Paige, F.; Pajchel, K.; Palestini, S.; Pallin, D.; Palma, A.; Palmer, J. D.; Pan, Y. B.; Panagiotopoulou, E.; Panes, B.; Panikashvili, N.; Panitkin, S.; Pantea, D.; Panuskova, M.; Paolone, V.; Papadopoulou, Th. D.; Park, S. J.; Park, W.; Parker, M. A.; Parker, S. I.; Parodi, F.; Parsons, J. A.; Parzefall, U.; Pasqualucci, E.; Passeri, A.; Pastore, F.; Pastore, Fr.; Pásztor, G.; Pataraia, S.; Pater, J. R.; Patricelli, S.; Patwa, A.; Pauly, T.; Peak, L. S.; Pecsy, M.; Pedraza Morales, M. I.; Peleganchuk, S. V.; Peng, H.; Penson, A.; Penwell, J.; Perantoni, M.; Perez, K.; Perez Codina, E.; Pérez García-Estañ, M. T.; Perez Reale, V.; Perini, L.; Pernegger, H.; Perrino, R.; Persembe, S.; Perus, P.; Peshekhonov, V. D.; Petersen, B. A.; Petersen, T. C.; Petit, E.; Petridou, C.; Petrolo, E.; Petrucci, F.; Petschull, D.; Petteni, M.; Pezoa, R.; Phan, A.; Phillips, A. W.; Piacquadio, G.; Piccinini, M.; Piegaia, R.; Pilcher, J. E.; Pilkington, A. D.; Pina, J.; Pinamonti, M.; Pinfold, J. L.; Pinto, B.; Pizio, C.; Placakyte, R.; Plamondon, M.; Pleier, M.-A.; Poblaguev, A.; Poddar, S.; Podlyski, F.; Poffenberger, P.; Poggioli, L.; Pohl, M.; Polci, F.; Polesello, G.; Policicchio, A.; Polini, A.; Poll, J.; Polychronakos, V.; Pomeroy, D.; Pommès, K.; Ponsot, P.; Pontecorvo, L.; Pope, B. G.; Popeneciu, G. A.; Popovic, D. S.; Poppleton, A.; Popule, J.; Portell Bueso, X.; Porter, R.; Pospelov, G. E.; Pospisil, S.; Potekhin, M.; Potrap, I. N.; Potter, C. J.; Potter, C. T.; Potter, K. P.; Poulard, G.; Poveda, J.; Prabhu, R.; Pralavorio, P.; Prasad, S.; Pravahan, R.; Pribyl, L.; Price, D.; Price, L. E.; Prichard, P. M.; Prieur, D.; Primavera, M.; Prokofiev, K.; Prokoshin, F.; Protopopescu, S.; Proudfoot, J.; Prudent, X.; Przysiezniak, H.; Psoroulas, S.; Ptacek, E.; Puigdengoles, C.; Purdham, J.; Purohit, M.; Puzo, P.; Pylypchenko, Y.; Qi, M.; Qian, J.; Qian, W.; Qin, Z.; Quadt, A.; Quarrie, D. R.; Quayle, W. B.; Quinonez, F.; Raas, M.; Radeka, V.; Radescu, V.; Radics, B.; Rador, T.; Ragusa, F.; Rahal, G.; Rahimi, A. M.; Rajagopalan, S.; Rammensee, M.; Rammes, M.; Rauscher, F.; Rauter, E.; Raymond, M.; Read, A. L.; Rebuzzi, D. M.; Redelbach, A.; Redlinger, G.; Reece, R.; Reeves, K.; Reinherz-Aronis, E.; Reinsch, A.; Reisinger, I.; Reljic, D.; Rembser, C.; Ren, Z. L.; Renkel, P.; Rescia, S.; Rescigno, M.; Resconi, S.; Resende, B.; Reznicek, P.; Rezvani, R.; Richards, A.; Richards, R. A.; Richter, R.; Richter-Was, E.; Ridel, M.; Rijpstra, M.; Rijssenbeek, M.; Rimoldi, A.; Rinaldi, L.; Rios, R. R.; Riu, I.; Rizatdinova, F.; Rizvi, E.; Roa Romero, D. A.; Robertson, S. H.; Robichaud-Veronneau, A.; Robinson, D.; Robinson, J. E. M.; Robinson, M.; Robson, A.; Rocha de Lima, J. G.; Roda, C.; Roda Dos Santos, D.; Rodriguez, D.; Rodriguez Garcia, Y.; Roe, S.; Røhne, O.; Rojo, V.; Rolli, S.; Romaniouk, A.; Romanov, V. M.; Romeo, G.; Romero Maltrana, D.; Roos, L.; Ros, E.; Rosati, S.; Rosenbaum, G. A.; Rosselet, L.; Rossetti, V.; Rossi, L. P.; Rotaru, M.; Rothberg, J.; Rousseau, D.; Royon, C. R.; Rozanov, A.; Rozen, Y.; Ruan, X.; Ruckert, B.; Ruckstuhl, N.; Rud, V. I.; Rudolph, G.; Rühr, F.; Ruggieri, F.; Ruiz-Martinez, A.; Rumyantsev, L.; Rurikova, Z.; Rusakovich, N. A.; Rutherfoord, J. P.; Ruwiedel, C.; Ruzicka, P.; Ryabov, Y. F.; Ryan, P.; Rybkin, G.; Rzaeva, S.; Saavedra, A. F.; Sadrozinski, H. F.-W.; Sadykov, R.; Sakamoto, H.; Salamanna, G.; Salamon, A.; Saleem, M. S.; Salihagic, D.; Salnikov, A.; Salt, J.; Salvachua Ferrando, B. M.; Salvatore, D.; Salvatore, F.; Salvucci, A.; Salzburger, A.; Sampsonidis, D.; Samset, B. H.; Sandaker, H.; Sander, H. G.; Sanders, M. P.; Sandhoff, M.; Sandhu, P.; Sandstroem, R.; Sandvoss, S.; Sankey, D. P. C.; Sanny, B.; Sansoni, A.; Santamarina Rios, C.; Santoni, C.; Santonico, R.; Saraiva, J. G.; Sarangi, T.; Sarkisyan-Grinbaum, E.; Sarri, F.; Sasaki, O.; Sasao, N.; Satsounkevitch, I.; Sauvage, G.; Savard, P.; Savine, A. Y.; Savinov, V.; Sawyer, L.; Saxon, D. H.; Says, L. P.; Sbarra, C.; Sbrizzi, A.; Scannicchio, D. A.; Schaarschmidt, J.; Schacht, P.; Schäfer, U.; Schaetzel, S.; Schaffer, A. C.; Schaile, D.; Schamberger, R. D.; Schamov, A. G.; Schegelsky, V. A.; Scheirich, D.; Schernau, M.; Scherzer, M. I.; Schiavi, C.; Schieck, J.; Schioppa, M.; Schlenker, S.; Schmidt, E.; Schmieden, K.; Schmitt, C.; Schmitz, M.; Schott, M.; Schouten, D.; Schovancova, J.; Schram, M.; Schreiner, A.; Schroeder, C.; Schroer, N.; Schroers, M.; Schultes, J.; Schultz-Coulon, H.-C.; Schumacher, J. W.; Schumacher, M.; Schumm, B. A.; Schune, Ph.; Schwanenberger, C.; Schwartzman, A.; Schwemling, Ph.; Schwienhorst, R.; Schwierz, R.; Schwindling, J.; Scott, W. G.; Searcy, J.; Sedykh, E.; Segura, E.; Seidel, S. C.; Seiden, A.; Seifert, F.; Seixas, J. M.; Sekhniaidze, G.; Seliverstov, D. M.; Sellden, B.; Semprini-Cesari, N.; Serfon, C.; Serin, L.; Seuster, R.; Severini, H.; Sevior, M. E.; Sfyrla, A.; Shabalina, E.; Shamim, M.; Shan, L. Y.; Shank, J. T.; Shao, Q. T.; Shapiro, M.; Shatalov, P. B.; Shaw, K.; Sherman, D.; Sherwood, P.; Shibata, A.; Shimojima, M.; Shin, T.; Shmeleva, A.; Shochet, M. J.; Shupe, M. A.; Sicho, P.; Sidoti, A.; Siegert, F.; Siegrist, J.; Sijacki, Dj.; Silbert, O.; Silva, J.; Silver, Y.; Silverstein, D.; Silverstein, S. B.; Simak, V.; Simic, Lj.; Simion, S.; Simmons, B.; Simonyan, M.; Sinervo, P.; Sinev, N. B.; Sipica, V.; Siragusa, G.; Sisakyan, A. N.; Sivoklokov, S. Yu.; Sjoelin, J.; Sjursen, T. B.; Skovpen, K.; Skubic, P.; Slater, M.; Slavicek, T.; Sliwa, K.; Sloper, J.; Sluka, T.; Smakhtin, V.; Smirnov, S. Yu.; Smirnov, Y.; Smirnova, L. N.; Smirnova, O.; Smith, B. C.; Smith, D.; Smith, K. M.; Smizanska, M.; Smolek, K.; Snesarev, A. A.; Snow, S. W.; Snow, J.; Snuverink, J.; Snyder, S.; Soares, M.; Sobie, R.; Sodomka, J.; Soffer, A.; Solans, C. A.; Solar, M.; Solc, J.; Solfaroli Camillocci, E.; Solodkov, A. A.; Solovyanov, O. V.; Soluk, R.; Sondericker, J.; Sopko, V.; Sopko, B.; Sosebee, M.; Soukharev, A.; Spagnolo, S.; Spanò, F.; Spencer, E.; Spighi, R.; Spigo, G.; Spila, F.; Spiwoks, R.; Spousta, M.; Spreitzer, T.; Spurlock, B.; Denis, R. D. St.; Stahl, T.; Stahlman, J.; Stamen, R.; Stancu, S. N.; Stanecka, E.; Stanek, R. W.; Stanescu, C.; Stapnes, S.; Starchenko, E. A.; Stark, J.; Staroba, P.; Starovoitov, P.; Stastny, J.; Stavina, P.; Stavropoulos, G.; Steele, G.; Steinbach, P.; Steinberg, P.; Stekl, I.; Stelzer, B.; Stelzer, H. J.; Stelzer-Chilton, O.; Stenzel, H.; Stevenson, K.; Stewart, G. A.; Stockton, M. C.; Stoerig, K.; Stoicea, G.; Stonjek, S.; Strachota, P.; Stradling, A. R.; Straessner, A.; Strandberg, J.; Strandberg, S.; Strandlie, A.; Strauss, M.; Strizenec, P.; Ströhmer, R.; Strom, D. M.; Stroynowski, R.; Strube, J.; Stugu, B.; Soh, D. A.; Su, D.; Sugaya, Y.; Sugimoto, T.; Suhr, C.; Suk, M.; Sulin, V. V.; Sultansoy, S.; Sumida, T.; Sun, X. H.; Sundermann, J. E.; Suruliz, K.; Sushkov, S.; Susinno, G.; Sutton, M. R.; Suzuki, T.; Suzuki, Y.; Sykora, I.; Sykora, T.; Szymocha, T.; Sánchez, J.; Ta, D.; Tackmann, K.; Taffard, A.; Tafirout, R.; Taga, A.; Takahashi, Y.; Takai, H.; Takashima, R.; Takeda, H.; Takeshita, T.; Talby, M.; Talyshev, A.; Tamsett, M. C.; Tanaka, J.; Tanaka, R.; Tanaka, S.; Tanaka, S.; Tapprogge, S.; Tardif, D.; Tarem, S.; Tarrade, F.; Tartarelli, G. F.; Tas, P.; Tasevsky, M.; Tassi, E.; Tatarkhanov, M.; Taylor, C.; Taylor, F. E.; Taylor, G. N.; Taylor, R. P.; Taylor, W.; Teixeira-Dias, P.; Ten Kate, H.; Teng, P. K.; Tennenbaum-Katan, Y. D.; Terada, S.; Terashi, K.; Terron, J.; Terwort, M.; Testa, M.; Teuscher, R. J.; Thioye, M.; Thoma, S.; Thomas, J. P.; Thompson, E. N.; Thompson, P. D.; Thompson, P. D.; Thompson, R. J.; Thompson, A. S.; Thomson, E.; Thun, R. P.; Tic, T.; Tikhomirov, V. O.; Tikhonov, Y. A.; Tipton, P.; Tique Aires Viegas, F. J.; Tisserant, S.; Toczek, B.; Todorov, T.; Todorova-Nova, S.; Toggerson, B.; Tojo, J.; Tokár, S.; Tokushuku, K.; Tollefson, K.; Tomasek, L.; Tomasek, M.; Tomoto, M.; Tompkins, L.; Toms, K.; Tonoyan, A.; Topfel, C.; Topilin, N. D.; Torrence, E.; Torró Pastor, E.; Toth, J.; Touchard, F.; Tovey, D. R.; Trefzger, T.; Tremblet, L.; Tricoli, A.; Trigger, I. M.; Trincaz-Duvoid, S.; Trinh, T. N.; Tripiana, M. F.; Triplett, N.; Trischuk, W.; Trivedi, A.; Trocmé, B.; Troncon, C.; Trzupek, A.; Tsarouchas, C.; Tseng, J. C.-L.; Tsiakiris, M.; Tsiareshka, P. V.; Tsionou, D.; Tsipolitis, G.; Tsiskaridze, V.; Tskhadadze, E. G.; Tsukerman, I. I.; Tsulaia, V.; Tsung, J.-W.; Tsuno, S.; Tsybychev, D.; Tuggle, J. M.; Turecek, D.; Turk Cakir, I.; Turlay, E.; Tuts, P. M.; Twomey, M. S.; Tylmad, M.; Tyndel, M.; Uchida, K.; Ueda, I.; Ugland, M.; Uhlenbrock, M.; Uhrmacher, M.; Ukegawa, F.; Unal, G.; Undrus, A.; Unel, G.; Unno, Y.; Urbaniec, D.; Urkovsky, E.; Urquijo, P.; Urrejola, P.; Usai, G.; Uslenghi, M.; Vacavant, L.; Vacek, V.; Vachon, B.; Vahsen, S.; Valente, P.; Valentinetti, S.; Valkar, S.; Valladolid Gallego, E.; Vallecorsa, S.; Valls Ferrer, J. A.; van Berg, R.; van der Graaf, H.; van der Kraaij, E.; van der Poel, E.; van der Ster, D.; van Eldik, N.; van Gemmeren, P.; van Kesteren, Z.; van Vulpen, I.; Vandelli, W.; Vaniachine, A.; Vankov, P.; Vannucci, F.; Vari, R.; Varnes, E. W.; Varouchas, D.; Vartapetian, A.; Varvell, K. E.; Vasilyeva, L.; Vassilakopoulos, V. I.; Vazeille, F.; Vellidis, C.; Veloso, F.; Veneziano, S.; Ventura, A.; Ventura, D.; Venturi, M.; Venturi, N.; Vercesi, V.; Verducci, M.; Verkerke, W.; Vermeulen, J. C.; Vetterli, M. C.; Vichou, I.; Vickey, T.; Viehhauser, G. H. A.; Villa, M.; Villani, E. G.; Villaplana Perez, M.; Vilucchi, E.; Vincter, M. G.; Vinek, E.; Vinogradov, V. B.; Viret, S.; Virzi, J.; Vitale, A.; Vitells, O.; Vivarelli, I.; Vives Vaque, F.; Vlachos, S.; Vlasak, M.; Vlasov, N.; Vogel, A.; Vokac, P.; Volpi, M.; von der Schmitt, H.; von Loeben, J.; von Radziewski, H.; von Toerne, E.; Vorobel, V.; Vorwerk, V.; Vos, M.; Voss, R.; Voss, T. T.; Vossebeld, J. H.; Vranjes, N.; Vranjes Milosavljevic, M.; Vrba, V.; Vreeswijk, M.; Vu Anh, T.; Vudragovic, D.; Vuillermet, R.; Vukotic, I.; Wagner, P.; Walbersloh, J.; Walder, J.; Walker, R.; Walkowiak, W.; Wall, R.; Wang, C.; Wang, H.; Wang, J.; Wang, S. M.; Warburton, A.; Ward, C. P.; Warsinsky, M.; Wastie, R.; Watkins, P. M.; Watson, A. T.; Watson, M. F.; Watts, G.; Watts, S.; Waugh, A. T.; Waugh, B. M.; Weber, M. D.; Weber, M.; Weber, M. S.; Weber, P.; Weidberg, A. R.; Weingarten, J.; Weiser, C.; Wellenstein, H.; Wells, P. S.; Wen, M.; Wenaus, T.; Wendler, S.; Wengler, T.; Wenig, S.; Wermes, N.; Werner, M.; Werner, P.; Werth, M.; Werthenbach, U.; Wessels, M.; Whalen, K.; White, A.; White, M. J.; White, S.; Whitehead, S. R.; Whiteson, D.; Whittington, D.; Wicek, F.; Wicke, D.; Wickens, F. J.; Wiedenmann, W.; Wielers, M.; Wienemann, P.; Wiglesworth, C.; Wiik, L. A. M.; Wildauer, A.; Wildt, M. A.; Wilkens, H. G.; Williams, E.; Williams, H. H.; Willocq, S.; Wilson, J. A.; Wilson, M. G.; Wilson, A.; Wingerter-Seez, I.; Winklmeier, F.; Wittgen, M.; Wolter, M. W.; Wolters, H.; Wosiek, B. K.; Wotschack, J.; Woudstra, M. J.; Wraight, K.; Wright, C.; Wright, D.; Wrona, B.; Wu, S. L.; Wu, X.; Wulf, E.; Wynne, B. M.; Xaplanteris, L.; Xella, S.; Xie, S.; Xu, D.; Xu, N.; Yamada, M.; Yamamoto, A.; Yamamoto, K.; Yamamoto, S.; Yamamura, T.; Yamaoka, J.; Yamazaki, T.; Yamazaki, Y.; Yan, Z.; Yang, H.; Yang, U. K.; Yang, Z.; Yao, W.-M.; Yao, Y.; Yasu, Y.; Ye, J.; Ye, S.; Yilmaz, M.; Yoosoofmiya, R.; Yorita, K.; Yoshida, R.; Young, C.; Youssef, S. P.; Yu, D.; Yu, J.; Yuan, L.; Yurkewicz, A.; Zaidan, R.; Zaitsev, A. M.; Zajacova, Z.; Zambrano, V.; Zanello, L.; Zaytsev, A.; Zeitnitz, C.; Zeller, M.; Zemla, A.; Zendler, C.; Zenin, O.; Zenis, T.; Zenonos, Z.; Zenz, S.; Zerwas, D.; Zevi Della Porta, G.; Zhan, Z.; Zhang, H.; Zhang, J.; Zhang, Q.; Zhang, X.; Zhao, L.; Zhao, T.; Zhao, Z.; Zhemchugov, A.; Zhong, J.; Zhou, B.; Zhou, N.; Zhou, Y.; Zhu, C. G.; Zhu, H.; Zhu, Y.; Zhuang, X.; Zhuravlov, V.; Zimmermann, R.; Zimmermann, S.; Zimmermann, S.; Ziolkowski, M.; Živković, L.; Zobernig, G.; Zoccoli, A.; Zur Nedden, M.; Zutshi, V.

    2010-12-01

    The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.

  2. ParaHaplo 3.0: A program package for imputation and a haplotype-based whole-genome association study using hybrid parallel computing

    Directory of Open Access Journals (Sweden)

    Kamatani Naoyuki

    2011-05-01

    Full Text Available Abstract Background Use of missing genotype imputations and haplotype reconstructions are valuable in genome-wide association studies (GWASs. By modeling the patterns of linkage disequilibrium in a reference panel, genotypes not directly measured in the study samples can be imputed and used for GWASs. Since millions of single nucleotide polymorphisms need to be imputed in a GWAS, faster methods for genotype imputation and haplotype reconstruction are required. Results We developed a program package for parallel computation of genotype imputation and haplotype reconstruction. Our program package, ParaHaplo 3.0, is intended for use in workstation clusters using the Intel Message Passing Interface. We compared the performance of ParaHaplo 3.0 on the Japanese in Tokyo, Japan and Han Chinese in Beijing, and Chinese in the HapMap dataset. A parallel version of ParaHaplo 3.0 can conduct genotype imputation 20 times faster than a non-parallel version of ParaHaplo. Conclusions ParaHaplo 3.0 is an invaluable tool for conducting haplotype-based GWASs. The need for faster genotype imputation and haplotype reconstruction using parallel computing will become increasingly important as the data sizes of such projects continue to increase. ParaHaplo executable binaries and program sources are available at http://en.sourceforge.jp/projects/parallelgwas/releases/.

  3. Genomes to Life''Center for Molecular and Cellular Systems'': A research program for identification and characterization of protein complexes.

    Energy Technology Data Exchange (ETDEWEB)

    Buchanan, M V.; Larimer, Frank; Wiley, H S.; Kennel, S J.; Squier, Thomas C.; Ramsey, John M.; Rodland, Karin D.; Hurst, G B.; Smith, Richard D.; Xu, Ying; Dixon, David A.; Doktycz, M J.; Colson, Steve D.; Gesteland, R; Giometti, Carol S.; Young, Mark E.; Giddings, Ralph M.

    2002-02-01

    Goal 1 of Department of Energy's Genomes to Life (GTL) program seeks to identify and characterize the complete set of protein complexes within a cell. Goal 1 forms the foundation necessary to accomplish the other objectives of the GTL program, which focus on gene regulatory networks and molecular level characterization of interactions in microbial communities. Together this information would allow cells and their components to be understood in sufficient detail to predict, test, and understand the responses of a biological system to its environment. The Center for Molecular and Cellular Systems has been established to identify and characterize protein complexes using high through-put analytical technologies. A dynamic research program is being developed that supports the goals of the Center by focusing on the development of new capabilities for sample preparation and complex separations, molecular level identification of the protein complexes by mass spectrometry, characterization of the complexes in living cells by imaging techniques, and bioinformatics and computational tools for the collection and interpretation of data and formation of databases and tools to allow the data to be shared by the biological community.

  4. Local atlas selection for discrete multi-atlas segmentation

    OpenAIRE

    Alchatzidis, Stavros; Sotiras, Aristeidis; Paragios, Nikos

    2015-01-01

    International audience; Multi-atlas segmentation is commonly performed in two separate steps: i) multiple pairwise registrations, and ii) fusion of the deformed segmentation masks towards labeling objects of interest. In this paper we propose an approach for integrated volume segmentation through multi-atlas registration. To tackle this problem, we opt for a graphical model where registration and segmentation nodes are coupled. The aim is to recover simultaneously all atlas deformations along...

  5. Diffraction and Forward Physics in ATLAS: results and perspectives

    CERN Document Server

    Bruschi, M; The ATLAS collaboration

    2014-01-01

    The present and future potential of ATLAS for diffraction and forward physics is presented. As recent results the rapidity gap cross section and elastic and total pp cross sections are reported. The phase 1 upgrade project AFP is presented and it is shown how it will complement the ALFA acceptance for diffractive physics in measurements taken with beta*=90m. Moreover, the AFP detector will guarantee good acceptance on diffractive events also with normal running conditions optics allowing not only to improve the ATLAS detector performances, but also being fundamental for potential discoveries (for instance, extra dimensions) in case the high luminosity program will be feasible.

  6. Diffraction and Forward Physics in ATLAS: results and perspectives

    CERN Document Server

    Bruschi, Marco; The ATLAS collaboration

    2015-01-01

    The present and future potential of ATLAS for diffraction and forward physics is presented. As recent results the rapidity gap cross section and elastic and total pp cross sections are reported. The upgrade project AFP is presented and it is shown how it will complement the ALFA acceptance for diffractive physics in measurements taken with \\(\\beta^{*}\\)=90 m LHC\\ beam optics. Moreover, the AFP detector will guarantee good acceptance on diffractive events also with normal running conditions optics allowing not only to improve the ATLAS detector performances, but also being fundamental for potential discoveries (for instance, extra dimensions) in case the high luminosity program will be feasible.

  7. Preparation of Northern Mid-Continent Petroleum Atlas

    Energy Technology Data Exchange (ETDEWEB)

    Lee C. Gerhard; Timothy R. Carr; W. Lynn Watney

    1998-05-01

    As proposed, the third year program will continue and expand upon the Kansas elements of the original program, and provide improved on-line access to the prototype atlas. The third year of the program will result in a digital atlas sufficient to provide a permanent improvement in data access to Kansas operators. The ultimate goal of providing an interactive history-matching interface with a regional data base will be demonstrated as the program covers more geographic territory and the data base expands. The atlas will expand to include significant reservoirs representing the major plays in Kansas, and North Dakota. Primary products of the third year prototype atlas will be on-line accessible digital data bases and technical publications covering two additional petroleum plays in Kansas and one in North Dakota. Regional databases will be supplemented with geological field studies of selected fields in each play. Digital imagery, digital mapping, relational data queries, and geographical information systems will be integral to the field studies and regional data sets. Data sets will have relational links to provide opportunity for history-matching, feasibility, and risk analysis tests on contemplated exploration and development projects. The flexible "web-like" design of the atlas provides ready access to data, and technology at a variety of scales from regional, to field, to lease, and finally to the individual well bore. The digital structure of the atlas permits the operator to access comprehensive reservoir data and customize the interpretative products (e.g., maps and cross-sections) to their needs. The atlas will be accessible in digital form on-line using a World-Wide-Web browser as the graphical user interface. Regional data sets and field studies will be free-standing entities that will be made available on-line through the Internet to users as they are completed. Technology transfer activities will be ongoing from the earliest part of this project

  8. Luminosity Measurement Using Cherenkov Integrating Detector (LUCID) in ATLAS

    CERN Document Server

    Caforio, D

    2008-01-01

    LUCID (LUminosity measurement using Cherenkov Integrating Detector) is a Cherenkov counter designed to monitor the luminosity in the ATLAS experiment. Since the final accuracy of the measurement of some crucial physical quantities in the LHC program will depend on the precision of the luminosity measurement, it is mandatory to push the latter to its best. This in turn implies the need to monitor the beam conditions. In this paper an overview of LUCID is given. After a description of the detector, an insight into the luminosity measurement strategy in ATLAS is given, as well as a description of the calibration strategy of LUCID.

  9. Genome-wide Functional Analysis of CREB/Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs

    Science.gov (United States)

    Lakhina, Vanisha; Arey, Rachel N.; Kaletsky, Rachel; Kauffman, Amanda; Stein, Geneva; Keyes, William; Xu, Daniel; Murphy, Coleen T.

    2014-01-01

    SUMMARY Induced CREB activity is a hallmark of long-term memory, but the full repertoire of CREB transcriptional targets required specifically for memory is not known in any system. To obtain a more complete picture of the mechanisms involved in memory, we combined memory training with genome-wide transcriptional analysis of C. elegans CREB mutants. This approach identified 757 significant CREB/memory-induced targets and confirmed the involvement of known memory genes from other organisms, but also suggested new mechanisms and novel components that may be conserved through mammals. CREB mediates distinct basal and memory transcriptional programs at least partially through spatial restriction of CREB activity: basal targets are regulated primarily in nonneuronal tissues, while memory targets are enriched for neuronal expression, emanating from CREB activity in AIM neurons. This suite of novel memory-associated genes will provide a platform for the discovery of orthologous mammalian long-term memory components. PMID:25611510

  10. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs.

    Science.gov (United States)

    Lakhina, Vanisha; Arey, Rachel N; Kaletsky, Rachel; Kauffman, Amanda; Stein, Geneva; Keyes, William; Xu, Daniel; Murphy, Coleen T

    2015-01-21

    Induced CREB activity is a hallmark of long-term memory, but the full repertoire of CREB transcriptional targets required specifically for memory is not known in any system. To obtain a more complete picture of the mechanisms involved in memory, we combined memory training with genome-wide transcriptional analysis of C. elegans CREB mutants. This approach identified 757 significant CREB/memory-induced targets and confirmed the involvement of known memory genes from other organisms, but also suggested new mechanisms and novel components that may be conserved through mammals. CREB mediates distinct basal and memory transcriptional programs at least partially through spatial restriction of CREB activity: basal targets are regulated primarily in nonneuronal tissues, while memory targets are enriched for neuronal expression, emanating from CREB activity in AIM neurons. This suite of novel memory-associated genes will provide a platform for the discovery of orthologous mammalian long-term memory components.

  11. Genome-wide ChIP-seq profiling of PPARγ/RXR target sites and gene program during adipogenesis

    DEFF Research Database (Denmark)

    Nielsen, Ronni; Pedersen, Thomas Åskov; Hagenbeek, Dik

    Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors which bind to DNA as heterodimers with members of the retinoid X receptor family. PPARγ is an important regulator of adipocyte differentiation and function. In addition to driving the adipogenic process, PPARγ activates...... directly a large number of genes involved in lipid metabolism. Using ChIP combined with deep sequencing we have generated a genome-wide map of PPARγ-RXR binding to chromatin as well as the activation of associated target genes during differentiation of murine 3T3-L1 adipocytes. Our analysis shows...... that target sites/genes attain RXR and PPARγ occupancy at different time points and that sites are often co-occupied by C/EBP factors. Coupling this analysis with RNAPII occupancy throughout adipogenesis revealed that PPARg:RXR is specifically associated with induced genes involved in diverse processes...

  12. The UCSC Cancer Genomics Browser: update 2011.

    Science.gov (United States)

    Sanborn, J Zachary; Benz, Stephen C; Craft, Brian; Szeto, Christopher; Kober, Kord M; Meyer, Laurence; Vaske, Charles J; Goldman, Mary; Smith, Kayla E; Kuhn, Robert M; Karolchik, Donna; Kent, W James; Stuart, Joshua M; Haussler, David; Zhu, Jingchun

    2011-01-01

    The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for multiple samples alongside their associated clinical information. Multiple data sets can be viewed simultaneously as coordinated 'heatmap tracks' to compare across studies or different data modalities. Users can order, filter, aggregate, classify and display data interactively based on any given feature set including clinical features, annotated biological pathways and user-contributed collections of genes. Integrated standard statistical tools provide dynamic quantitative analysis within all available data sets. The browser hosts a growing body of publicly available cancer genomics data from a variety of cancer types, including data generated from the Cancer Genome Atlas project. Multiple consortiums use the browser on confidential prepublication data enabled by private installations. Many new features have been added, including the hgMicroscope tumor image viewer, hgSignature for real-time genomic signature evaluation on any browser track, and 'PARADIGM' pathway tracks to display integrative pathway activities. The browser is integrated with the UCSC Genome Browser; thus inheriting and integrating the Genome Browser's rich set of human biology and genetics data that enhances the interpretability of the cancer genomics data.

  13. ATLAS Future Plans: Upgrade and the Physics with High Luminosity

    CERN Document Server

    Rajagopalan, Srini; The ATLAS collaboration

    2012-01-01

    ATLAS is planning a series of detector upgrades to cope with increasing instantaneous luminosity and multiple interactions per crossing to ensure that acceptance to new physics and precision measurements are preserved. During the next several years, LHC is expected to collide protons on protons at a center of mass energy up to 14 TeV with luminosities reaching 1 to 2 x 1034 cm^-2 s^-1, accumulating ~100 fb^-1 per year following a Phase 1 Upgrade (2018). The detector upgrades focus on precision tracking and improved trigger capabilities to sustain higher rates. Subsequently, the LHC plans calls for a five-fold increase in instantaneous luminosity, thereby increasing the delivered luminosity to ~3000 fb^-1 by 2030. The increased luminosity will significantly increase the physics reach of ATLAS building on the recent discovery of the Higgs-like boson. The planned detector upgrades and the impact on the ATLAS physics program will be discussed.

  14. ATLAS Future Plans: Upgrade and the Physics with High Luminosity

    Directory of Open Access Journals (Sweden)

    Rajagopalan S.

    2013-05-01

    Full Text Available The ATLAS experiment is planning a series of detector upgrades to cope with the planned increases in instantaneous luminosity and multiple interactions per crossing to maintain its physics capabilities. During the coming decade, the Large Hadron Collider will collide protons on protons at a center of mass energy up to 14 TeV with luminosities steadily increasing in a phased approach to over 5 × 1034 cm−2s−1. The resulting large data sets will significantly enhance the physics reach of the ATLAS detector building on the recent discovery of the Higgs-like boson. The planned detector upgrades being designed to cope with the increasing luminosity and its impact on the ATLAS physics program will be discussed.

  15. Object Oriented Reconstruction and Particle Identification in the ATLAS Calorimeter

    Institute of Scientific and Technical Information of China (English)

    B.Caron; J.Collot; 等

    2001-01-01

    The reconstruction and subsequent particle identification is a challenge in a complex and a high luminosity environment such as those expected in the ATLAS detector at the LHC.The ATLAS software has chosen the object oriented paradigm and has recently migrated much of its software components developed earlier using procedural programming languages.The new software,which emphasizes on the separation between algorthms and data objects,has been successfully integrated in the broader ATLAS framework.We will present a status report of the reconstruction software summarizing the experiences gained in the migration of several software components.We will examine some of the components of the calorimeter software design,which include simulation of real-time detector effects and online environment,and strategies deployed for identification of particles.

  16. Online Monitoring software framework in the ATLAS experiment

    CERN Document Server

    Barczyk, M.; Caprini, M.; Da Silva Conceicao, J.; Dobson, M.; Flammer, J.; Jones, R.; Kazarov, A.; Kolos, S.; Liko, D.; Lucio, L.; Mapelli, L.; Soloviev, I.; Hart, R.; Amorim, A.; Klose, D.; Lima, J.; Pedro, L.; Wolters, H.; Badescu, E.; Alexandrov, I.; Kotov, V.; Mineev, M.; Ryabov, Yu.; CHEP 2003 Computing in High Energy Physics; Ryabov, Yu.

    2003-01-01

    A fast, efficient and comprehensive monitoring system is a vital part of any HEP experiment. This paper describes the software framework that will be used during ATLAS data taking to monitor the state of the data acquisition and the quality of physics data in the experiment. The framework has been implemented by the Online Software group of the ATLAS Trigger&Data Acquisition (TDAQ) project and has already been used for several years in the ATLAS test beams at CERN. The inter-process communication in the framework is implemented via CORBA, which provides portability between different operating systems and programming languages. This paper will describe the design and the most important aspects of the online monitoring framework implementation. It will also show some test results, which indicate the performance and scalability of the current implementation.

  17. Data Federation Strategies for ATLAS using XRootD

    CERN Document Server

    Gardner, R; The ATLAS collaboration; Duckeck, G; Elmsheuser, J; Hanushevski, A; Hönig, F; Iven, J; Legger, F; Vukotic, I; Yang, W

    2014-01-01

    In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the w...

  18. Data Federation Strategies for ATLAS using XRootD

    CERN Document Server

    Gardner, R; The ATLAS collaboration; Duckeck, G; Elmsheuser, J; Hanushevski, A; Hönig, F; Iven, J; Legger, F; Vukotic, I; Yang, W

    2013-01-01

    In the past year the ATLAS Collaboration accelerated its program to federate data storage resources using an architecture based on XRootD with its attendant redirection and storage integration services. The main goal of the federation is an improvement in the data access experience for the end user while allowing more efficient and intelligent use of computing resources. Along with these advances come integration with existing ATLAS production services (PanDA and its pilot services) and data management services (DQ2, and in the next generation, Rucio). Functional testing of the federation has been integrated into the standard ATLAS and WLCG monitoring frameworks and a dedicated set of tools provides high granularity information on its current and historical usage. We use a federation topology designed to search from the site's local storage outward to its region and to globally distributed storage resources. We describe programmatic testing of various federation access modes including direct access over the w...

  19. Integration of Titan supercomputer at OLCF with ATLAS Production System

    CERN Document Server

    Barreiro Megino, Fernando Harald; The ATLAS collaboration

    2017-01-01

    The PanDA (Production and Distributed Analysis) workload management system was developed to meet the scale and complexity of distributed computing for the ATLAS ex- periment. PanDA managed resources are distributed worldwide, on hundreds of computing sites, with thousands of physicists accessing hundreds of Petabytes of data and the rate of data processing already exceeds Exabyte per year. While PanDA currently uses more than 200,000 cores at well over 100 Grid sites, future LHC data taking runs will require more resources than Grid computing can possibly provide. Additional computing and storage resources are required. Therefore ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. In this talk we will describe a project aimed at integration of ATLAS Production System with Titan supercom- puter at Oak Ridge Leadership Computing Facility (OLCF). Current approach utilizes modi ed PanDA Pilot framework for ...

  20. Physics potential of ATLAS upgrades at HL-LHC

    CERN Document Server

    Testa, Marianna; The ATLAS collaboration

    2017-01-01

    The High Luminosity-Large Hadron Collider (HL-LHC) is expected to start in 2026 and to pro- vide an integrated luminosity of 3000 fb−1 in ten years, a factor 10 more than what will be collected by 2023. This high statistics will allow ATLAS to perform precise measurements in the Higgs sector and improve searches for new physics at the TeV scale. The luminosity needed is L ∼ 7.51034 cm−2 s−1, corresponding to ∼200 additional proton-proton pile- up interactions. To face such harsh environment some sub-detectors of the ATLAS experiment will be upgraded or completely substituted. The performances of the new or upgraded ATLAS sub-detectors are presented, focusing in particular on the new inner tracker and a proposed high granularity time device. The impact of those upgrades on crucial physics measurements for HL-LHC program is also shown.

  1. Energy calibration of the electromagnetic calorimeter in ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Hanisch, Stefanie [CERN (Switzerland); TU Dresden (Germany); Aleksa, Martin [CERN (Switzerland); Straessner, Arno [TU Dresden (Germany)

    2016-07-01

    The liquid Argon calorimeter of the ATLAS detector is the essential detector system for precise energy measurement of electrons and photons. Hence, its performance is crucial for a wide range of the ATLAS physics program. To achieve an excellent performance an outstanding calibration is required. This talk discusses the general strategy for the current calibration scheme of the EM energy scale and its improvement with respect to run-I, its validation and the recommendations for physics analyses. The MVA techniques used to achieve the calibration at the per-mille level are presented. Studies to validate their performance using various fit models in single particle and Z→ee simulations as well as a selection of Z→ee events in data recorded with the ATLAS detector in 2015 are outlined. Further, a discussion of the systematic uncertainties derived from Z→ee data events is given.

  2. Integration of Titan supercomputer at OLCF with ATLAS production system

    CERN Document Server

    Panitkin, Sergey; The ATLAS collaboration

    2016-01-01

    The PanDA (Production and Distributed Analysis) workload management system was developed to meet the scale and complexity of distributed computing for the ATLAS experiment. PanDA managed resources are distributed worldwide, on hundreds of computing sites, with thousands of physicists accessing hundreds of Petabytes of data and the rate of data processing already exceeds Exabyte per year. While PanDA currently uses more than 200,000 cores at well over 100 Grid sites, future LHC data taking runs will require more resources than Grid computing can possibly provide. Additional computing and storage resources are required. Therefore ATLAS is engaged in an ambitious program to expand the current computing model to include additional resources such as the opportunistic use of supercomputers. In this talk we will describe a project aimed at integration of ATLAS Production System with Titan supercomputer at Oak Ridge Leadership Computing Facility (OLCF). Current approach utilizes modified PanDA Pilot framework for job...

  3. Metadata aided run selection at ATLAS

    Science.gov (United States)

    Buckingham, R. M.; Gallas, E. J.; C-L Tseng, J.; Viegas, F.; Vinek, E.; ATLAS Collaboration

    2011-12-01

    Management of the large volume of data collected by any large scale scientific experiment requires the collection of coherent metadata quantities, which can be used by reconstruction or analysis programs and/or user interfaces, to pinpoint collections of data needed for specific purposes. In the ATLAS experiment at the LHC, we have collected metadata from systems storing non-event-wise data (Conditions) into a relational database. The Conditions metadata (COMA) database tables not only contain conditions known at the time of event recording, but also allow for the addition of conditions data collected as a result of later analysis of the data (such as improved measurements of beam conditions or assessments of data quality). A new web based interface called "runBrowser" makes these Conditions Metadata available as a Run based selection service. runBrowser, based on PHP and JavaScript, uses jQuery to present selection criteria and report results. It not only facilitates data selection by conditions attributes, but also gives the user information at each stage about the relationship between the conditions chosen and the remaining conditions criteria available. When a set of COMA selections are complete, runBrowser produces a human readable report as well as an XML file in a standardized ATLAS format. This XML can be saved for later use or refinement in a future runBrowser session, shared with physics/detector groups, or used as input to ELSSI (event level Metadata browser) or other ATLAS run or event processing services.

  4. Tau identification using multivariate techniques in ATLAS

    Science.gov (United States)

    O'Neil, D. C.; ATLAS Collaboration

    2012-06-01

    Tau leptons play an important role in the physics program of the LHC. They are being used in electroweak measurements, in detector related studies and in searches for new phenomena like the Higgs boson or Supersymmetry. In the detector, tau leptons are reconstructed as collimated jets with low track multiplicity. Due to the background from QCD multijet processes, efficient tau identification techniques with large fake rejection are essential. Since single variable criteria are not enough to efficiently separate them from jets and electrons, modern multivariate techniques are used. In ATLAS, several advanced algorithms are applied to identify taus, including a projective likelihood estimator and boosted decision trees. All multivariate methods applied to the ATLAS simulated data perform better than the baseline cut analysis. Their performance is shown using high energy data collected at the ATLAS experiment. The improvement ranges from a factor of 2 to 5 in rejection for the same efficiency, depending on the selected efficiency operating point and the number of prongs in the tau decay. The strengths and weaknesses of each technique are also discussed.

  5. The ATLAS Trigger algorithms upgrade and performance in Run 2

    CERN Document Server

    Bernius, Catrin; The ATLAS collaboration

    2017-01-01

    Title: The ATLAS Trigger algorithms upgrade and performance in Run 2 (TDAQ) The ATLAS trigger has been used very successfully for the online event selection during the first part of the second LHC run (Run-2) in 2015/16 at a center-of-mass energy of 13 TeV. The trigger system is composed of a hardware Level-1 trigger and a software-based high-level trigger; it reduces the event rate from the bunch-crossing rate of 40 MHz to an average recording rate of about 1 kHz. The excellent performance of the ATLAS trigger has been vital for the ATLAS physics program of Run-2, selecting interesting collision events for wide variety of physics signatures with high efficiency. The trigger selection capabilities of ATLAS during Run-2 have been significantly improved compared to Run-1, in order to cope with the higher event rates and pile-up which are the result of the almost doubling of the center-of-mass collision energy and the increase in the instantaneous luminosity of the LHC. At the Level-1 trigger the undertaken impr...

  6. ATLAS Civil Engineering Point 1

    CERN Multimedia

    Jean-Claude Vialis

    2000-01-01

    Different phases of realisation to Point 1 : zone of the ATLAS experiment The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are ever so busy to finish the different infrastructures for ATLAS. Real underground video. When passing throw the walls the succeeding can be heard and seen. The film has original working sound.

  7. A Review on Genomics APIs

    Directory of Open Access Journals (Sweden)

    Rajeswari Swaminathan

    2016-01-01

    Full Text Available The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a Google Genomics, b SMART Genomics, and c 23andMe. The functionalities, reference implementations (if available and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

  8. An integrated expression atlas of miRNAs and their promoters in human and mouse

    DEFF Research Database (Denmark)

    de Rie, Derek; Abugessaisa, Imad; Alam, Tanvir

    2017-01-01

    MicroRNAs (miRNAs) are short non-coding RNAs with key roles in cellular regulation. As part of the fifth edition of the Functional Annotation of Mammalian Genome (FANTOM5) project, we created an integrated expression atlas of miRNAs and their promoters by deep-sequencing 492 short RNA (sRNA) libr...

  9. ATLAS Detector Upgrade Prospects

    Science.gov (United States)

    Dobre, M.; ATLAS Collaboration

    2017-01-01

    After the successful operation at the centre-of-mass energies of 7 and 8 TeV in 2010-2012, the LHC was ramped up and successfully took data at the centre-of-mass energies of 13 TeV in 2015 and 2016. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, which will deliver of the order of five times the LHC nominal instantaneous luminosity along with luminosity levelling. The ultimate goal is to extend the dataset from about few hundred fb ‑1 expected for LHC running by the end of 2018 to 3000 fb ‑1 by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of extensions to larger pseudorapidity, particularly in tracking and muon systems. This report summarizes various improvements to the ATLAS detector required to cope with the anticipated evolution of the LHC luminosity during this decade and the next. A brief overview is also given on physics prospects with a pp centre-of-mass energy of 14 TeV.

  10. ATLAS Supersymmetry Searches

    CERN Document Server

    Ughetto, Michael; The ATLAS collaboration

    2016-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles, with focus on those obtained using proton-proton collisions at a centre of mass energy of 13 TeV.

  11. HWW in ATLAS

    CERN Document Server

    Rados, Pere; The ATLAS collaboration

    2016-01-01

    The H-->WW channel plays an important role in Higgs boson property measurements, searches for rare decay modes, and searches for possible extended Higgs sectors. In this talk the latest H-->WW results from ATLAS will be briefly summarised.

  12. Prime wires for ATLAS

    CERN Multimedia

    2003-01-01

    In an award ceremony on 3 September, ATLAS honoured the French company Axon Cable for its special coaxial cables, which were purpose-built for the Liquid Argon calorimeter modules. Working for CERN since the 1970s, Axon' Cable received the ATLAS supplier award last week for its contribution to the liquid argon calorimeter cables of ATLAS (LAL/Orsay, France and University of Victoria, Canada), started in 1996. Its two sets of minicoaxial cables, called harnesses "A" and "B", are designed to function in the harsh conditions in the liquid argon (at 90 Kelvin or -183°C) and under extreme radiation (up to several Mrads). The cables are mainly used for the readout of the calorimeters, and are connected to the outside world by 114 signal feedthroughs with 1920 channels each. The signal from the detectors is transmitted directly without any amplification, which imposes tight restrictions on the impedance and on the signal propagation time of the cables. Peter Jenni, ATLAS spokesperson, gives the award for best s...

  13. ATLAS starts moving in

    CERN Multimedia

    2004-01-01

    The first large active detector component was lowered into the ATLAS cavern on 1 March. It consisted of the 8 modules forming the lower part of the central barrel of the tile hadronic calorimeter. The work of assembling the barrel, which comprises 64 modules, started the following day.

  14. Hard Probes at ATLAS

    CERN Document Server

    Citron, Z; The ATLAS collaboration

    2014-01-01

    The ATLAS collaboration has measured several hard probe observables in Pb+Pb and p+Pb collisions at the LHC. These measurements include jets which show modification in the hot dense medium of heavy ion collisions as well as color neutral electro-weak bosons. Together, they elucidate the nature of heavy ion collisions.

  15. The observer's sky atlas

    CERN Document Server

    Karkoschka, E

    2007-01-01

    This title includes a short introduction to observing, a thorough description of the star charts and tables, a glossary and much more. It is perfect for both the beginner and seasoned observer. It is fully revised edition of a best-selling and highly-praised sky atlas.

  16. A thermosiphon for ATLAS

    CERN Multimedia

    Rosaria Marraffino

    2013-01-01

    A new thermosiphon cooling system, designed for the ATLAS silicon detectors by CERN’s EN-CV team in collaboration with the experiment, will replace the current system in the next LHC run in 2015. Using the basic properties of density difference and making gravity do the hard work, the thermosiphon promises to be a very reliable solution that will ensure the long-term stability of the whole system.   Former compressor-based cooling system of the ATLAS inner detectors. The system is currently being replaced by the innovative thermosiphon. (Photo courtesy of Olivier Crespo-Lopez). Reliability is the major issue for the present cooling system of the ATLAS silicon detectors. The system was designed 13 years ago using a compressor-based cooling cycle. “The current cooling system uses oil-free compressors to avoid fluid pollution in the delicate parts of the silicon detectors,” says Michele Battistin, EN-CV-PJ section leader and project leader of the ATLAS thermosiphon....

  17. ATLAS solenoid operates underground

    CERN Document Server

    2006-01-01

    A new phase for the ATLAS collaboration started with the first operation of a completed sub-system: the Central Solenoid. Teams monitoring the cooling and powering of the ATLAS solenoid in the control room. The solenoid was cooled down to 4.5 K from 17 to 23 May. The first current was established the same evening that the solenoid became cold and superconductive. 'This makes the ATLAS Central Solenoid the very first cold and superconducting magnet to be operated in the LHC underground areas!', said Takahiko Kondo, professor at KEK. Though the current was limited to 1 kA, the cool-down and powering of the solenoid was a major milestone for all of the control, cryogenic, power and vacuum systems-a milestone reached by the hard work and many long evenings invested by various teams from ATLAS, all of CERN's departments and several large and small companies. Since the Central Solenoid and the barrel liquid argon (LAr) calorimeter share the same cryostat vacuum vessel, this achievement was only possible in perfe...

  18. Higgs searches with ATLAS

    CERN Document Server

    Price, J D; The ATLAS collaboration

    2013-01-01

    Summary of the ATLAS analyses for the rarer SM Higgs decay channels, and the limits of the SM Higgs invisible decay width. Analyses included are the VH->Vbb, H->tautau, VH->VWW, H->Zy, H->mumu, ttH->ttyy and ZH->ll+inv.

  19. Tema-atlas

    DEFF Research Database (Denmark)

    Jensen, Ole Michael; Olsen, S.

    I dette tema-atlas viser forskere på By og Byg, hvordan registre over befolkning, bygninger og forbrug kan overføres til kort ved hjælp af GIS-teknologi. Atlasset er samtidig en illustration af de muligheder, som tegner sig i kommunerne for at udnytte eksisterende registre i forbindelse med...

  20. Prototype ATLAS straw tracker

    CERN Multimedia

    Laurent Guiraud

    1998-01-01

    This is an early prototype of the straw tracking device for the ATLAS detector at CERN. This detector will be part of the LHC project, scheduled to start operation in 2008. The straw tracker will consist of thousands of gas-filled straws, each containing a wire, allowing the tracks of particles to be followed.

  1. ATLAS Experiment Brochure

    CERN Multimedia

    AUTHOR|(INSPIRE)INSPIRE-00085461

    2016-01-01

    ATLAS is one of the four major experiments at the Large Hadron Collider at CERN. It is a general-purpose particle physics experiment run by an international collaboration, and is designed to exploit the full discovery potential and the huge range of physics opportunities that the LHC provides.

  2. Exotic searches at ATLAS

    CERN Document Server

    Turra, Ruggero; The ATLAS collaboration

    2016-01-01

    The ATLAS detector has collected 3.2 fb^-1 of proton-proton collisions at 13 TeV centre of mass energy during the 2015 LHC run. A selected review of the recent result are presented in the context of the direct search for BSM, not SUSY, not BSM Higgs.

  3. Atlas of NATO.

    Science.gov (United States)

    Young, Harry F.

    This atlas provides basic information about the North Atlantic Treaty Organization (NATO). Formed in response to growing concern for the security of Western Europe after World War II, NATO is a vehicle for Western efforts to reduce East-West tensions and the level of armaments. NATO promotes political and economic collaboration as well as military…

  4. Taking ATLAS to new heights

    CERN Multimedia

    Abha Eli Phoboo, ATLAS experiment

    2013-01-01

    Earlier this month, 51 members of the ATLAS collaboration trekked up to the highest peak in the Atlas Mountains, Mt. Toubkal (4,167m), in North Africa.    The physicists were in Marrakech, Morocco, attending the ATLAS Overview Week (7 - 11 October), which was held for the first time on the African continent. Around 300 members of the collaboration met to discuss the status of the LS1 upgrades and plans for the next run of the LHC. Besides the trek, 42 ATLAS members explored the Saharan sand dunes of Morocco on camels.  Photos courtesy of Patrick Jussel.

  5. ATLAS Virtual Visit-Hue-05-08-2014

    CERN Multimedia

    2014-01-01

    Hue University of Sciences (HUSC) is a multidisciplinary education and training institution including graduate and undergraduate education programs, and research activities conducted in the fields of Natural Science, Engineering, Social Science and Humanity. On 5th August, HUSC in collaboration with the ICTP Physics without Frontiers program organized a particle physics masterclass for selected physics students. The goal of this program is to give young physics students the opportunity to learn about the experiments at CERN, in particular performing an analysis with real LHC data, and to motivate and inspire the students to continue onto phyiscs master and PhD programs. Physics without Frontiers: Vietnam is organised by Kate Shaw (ICTP), Loan Truong (SISSA-ICTP), Phuong Dang (Freiburg) and Lan Tran (DESY). - See more at: http://atlas-live-virtual-visit.web.cern.ch/atlas-live-virtual-visit/2014/Hue-2014.html#sthash.4FIZzsgh.dpuf

  6. 17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

    CERN Multimedia

    Mona Schweizer

    2008-01-01

    17 April 2008 - Head of Internal Audit Network meeting visiting the ATLAS experimental area with CERN ATLAS Team Leader P. Fassnacht, ATLAS Technical Coordinator M. Nessi and ATLAS Resources Manager M. Nordberg.

  7. Integrative bioinformatics analysis of genomic and proteomic approaches to understand the transcriptional regulatory program in coronary artery disease pathways.

    Directory of Open Access Journals (Sweden)

    Rajani Kanth Vangala

    Full Text Available Patients with cardiovascular disease show a panel of differentially regulated serum biomarkers indicative of modulation of several pathways from disease onset to progression. Few of these biomarkers have been proposed for multimarker risk prediction methods. However, the underlying mechanism of the expression changes and modulation of the pathways is not yet addressed in entirety. Our present work focuses on understanding the regulatory mechanisms at transcriptional level by identifying the core and specific transcription factors that regulate the coronary artery disease associated pathways. Using the principles of systems biology we integrated the genomics and proteomics data with computational tools. We selected biomarkers from 7 different pathways based on their association with the disease and assayed 24 biomarkers along with gene expression studies and built network modules which are highly regulated by 5 core regulators PPARG, EGR1, ETV1, KLF7 and ESRRA. These network modules in turn comprise of biomarkers from different pathways showing that the core regulatory transcription factors may work together in differential regulation of several pathways potentially leading to the disease. This kind of analysis can enhance the elucidation of mechanisms in the disease and give better strategies of developing multimarker module based risk predictions.

  8. Integrative bioinformatics analysis of genomic and proteomic approaches to understand the transcriptional regulatory program in coronary artery disease pathways.

    Science.gov (United States)

    Vangala, Rajani Kanth; Ravindran, Vandana; Ghatge, Madan; Shanker, Jayashree; Arvind, Prathima; Bindu, Hima; Shekar, Meghala; Rao, Veena S

    2013-01-01

    Patients with cardiovascular disease show a panel of differentially regulated serum biomarkers indicative of modulation of several pathways from disease onset to progression. Few of these biomarkers have been proposed for multimarker risk prediction methods. However, the underlying mechanism of the expression changes and modulation of the pathways is not yet addressed in entirety. Our present work focuses on understanding the regulatory mechanisms at transcriptional level by identifying the core and specific transcription factors that regulate the coronary artery disease associated pathways. Using the principles of systems biology we integrated the genomics and proteomics data with computational tools. We selected biomarkers from 7 different pathways based on their association with the disease and assayed 24 biomarkers along with gene expression studies and built network modules which are highly regulated by 5 core regulators PPARG, EGR1, ETV1, KLF7 and ESRRA. These network modules in turn comprise of biomarkers from different pathways showing that the core regulatory transcription factors may work together in differential regulation of several pathways potentially leading to the disease. This kind of analysis can enhance the elucidation of mechanisms in the disease and give better strategies of developing multimarker module based risk predictions.

  9. Genomic Expression Program Involving the Haa1p-Regulon in Saccharomyces cerevisiae Response to Acetic Acid

    Science.gov (United States)

    Becker, Jorg D.; Sá-Correia, Isabel

    2010-01-01

    Abstract The alterations occurring in yeast genomic expression during early response to acetic acid and the involvement of the transcription factor Haa1p in this transcriptional reprogramming are described in this study. Haa1p was found to regulate, directly or indirectly, the transcription of approximately 80% of the acetic acid-activated genes, suggesting that Haa1p is the main player in the control of yeast response to this weak acid. The genes identified in this work as being activated in response to acetic acid in a Haa1p-dependent manner include protein kinases, multidrug resistance transporters, proteins involved in lipid metabolism, in nucleic acid processing, and proteins of unknown function. Among these genes, the expression of SAP30 and HRK1 provided the strongest protective effect toward acetic acid. SAP30 encode a subunit of a histone deacetylase complex and HRK1 encode a protein kinase belonging to a family of protein kinases dedicated to the regulation of plasma membrane transporters activity. The deletion of the HRK1 gene was found to lead to the increase of the accumulation of labeled acetic acid into acid-stressed yeast cells, suggesting that the role of both HAA1 and HRK1 in providing protection against acetic acid is, at least partially, related with their involvement in the reduction of intracellular acetate concentration. PMID:20955010

  10. EnviroAtlas - Ecosystem Service Market and Project Locations, U.S., 2015, Forest Trends' Ecosystem Marketplace

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset contains points depicting the location of market-based programs, referred to herein as markets, and projects addressing ecosystem services...

  11. EnviroAtlas - Ecosystem Service Market and Project Areas, U.S., 2015, Forest Trends' Ecosystem Marketplace

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting the geographic areas of market-based programs, referred to herein as markets, and projects addressing ecosystem...

  12. EnviroAtlas - Number of Water Markets per HUC8 Watershed, U.S., 2015, Forest Trends' Ecosystem Marketplace

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting the number of watershed-level market-based programs, referred to herein as markets, in operation per 8-digit HUC...

  13. EnviroAtlas - Ecosystem Service Market and Project Enabling Conditions, U.S., 2016, Forest Trends' Ecosystem Marketplace

    Data.gov (United States)

    U.S. Environmental Protection Agency — This EnviroAtlas dataset contains polygons depicting conditions enabling market-based programs, referred to herein as markets, and projects addressing ecosystem...

  14. Atlas of genetics and cytogenetics in oncology and haematology in 2013.

    Science.gov (United States)

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians.

  15. Atlas of Genetics and Cytogenetics in Oncology and Haematology in 2013

    Science.gov (United States)

    Huret, Jean-Loup; Ahmad, Mohammad; Arsaban, Mélanie; Bernheim, Alain; Cigna, Jérémy; Desangles, François; Guignard, Jean-Christophe; Jacquemot-Perbal, Marie-Christine; Labarussias, Maureen; Leberre, Vanessa; Malo, Anne; Morel-Pair, Catherine; Mossafa, Hossein; Potier, Jean-Claude; Texier, Guillaume; Viguié, Franck; Yau Chun Wan-Senon, Sylvie; Zasadzinski, Alain; Dessen, Philippe

    2013-01-01

    The Atlas of Genetics and Cytogenetics in Oncology and Haematology (http://AtlasGeneticsOncology.org) is a peer-reviewed internet journal/encyclopaedia/database focused on genes implicated in cancer, cytogenetics and clinical entities in cancer and cancer-prone hereditary diseases. The main goal of the Atlas is to provide review articles that describe complementary topics, namely, genes, genetic abnormalities, histopathology, clinical diagnoses and a large iconography. This description, which was historically based on karyotypic abnormalities and in situ hybridization (fluorescence in situ hybridization) techniques, now benefits from comparative genomic hybridization and massive sequencing, uncovering a tremendous amount of genetic rearrangements. As the Atlas combines different types of information (genes, genetic abnormalities, histopathology, clinical diagnoses and external links), its content is currently unique. The Atlas is a cognitive tool for fundamental and clinical research and has developed into an encyclopaedic work. In clinical practice, it contributes to the cytogenetic diagnosis and may guide treatment decision making, particularly regarding rare diseases (because they are numerous and are frequently encountered). Readers as well as the authors of the Atlas are researchers and/or clinicians. PMID:23161685

  16. Improving atlas methodology

    Science.gov (United States)

    Robbins, C.S.; Dowell, B.A.; O'Brien, J.

    1987-01-01

    We are studying a sample of Maryland (2 %) and New Hampshire (4 %) Atlas blocks and a small sample in Maine. These three States used different sampling methods and block sizes. We compare sampling techniques, roadside with off-road coverage, our coverage with that of the volunteers, and different methods of quantifying Atlas results. The 7 1/2' (12-km) blocks used in the Maine Atlas are satisfactory for coarse mapping, but are too large to enable changes to be detected in the future. Most states are subdividing the standard 7 1/2' maps into six 5-km blocks. The random 1/6 sample of 5-km blocks used in New Hampshire, Vermont (published 1985), and many other states has the advantage of permitting detection of some changes in the future, but the disadvantage of leaving important habitats unsampled. The Maryland system of atlasing all 1,200 5-km blocks and covering one out of each six by quarterblocks (2 1/2-km) is far superior if enough observers can be found. A good compromise, not yet attempted, would be to Atlas a 1/6 random sample of 5-km blocks and also one other carefully selected (non-random) block on the same 7 1/2' map--the block that would include the best sample of habitats or elevations not in the random block. In our sample the second block raised the percentage of birds found from 86% of the birds recorded in the 7 1/2' quadrangle to 93%. It was helpful to list the expected species in each block and to revise this list annually. We estimate that 90-100 species could be found with intensive effort in most Maryland blocks; perhaps 95-105 in New Hampshire. It was also helpful to know which species were under-sampled so we could make a special effort to search for these. A total of 75 species per block (or 75% of the expected species in blocks with very restricted habitat diversity) is considered a practical and adequate goal in these States. When fewer than 60 species are found per block, a high proportion of the rarer species are missed, as well as some of

  17. HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors.

    Science.gov (United States)

    Pocock, Ginger M; Becker, Jordan T; Swanson, Chad M; Ahlquist, Paul; Sherer, Nathan M

    2016-04-01

    Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent "burst-like" transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm.

  18. Tau Lepton Reconstruction and Identification at ATLAS

    Directory of Open Access Journals (Sweden)

    Friedrich Felix

    2012-07-01

    Full Text Available Tau leptons play an important role in the physics program at the LHC. They are used in searches for new phenomena like the Higgs boson or Supersymmetry and in electroweak measurements. Identifying hadronically decaying tau leptons with good performance is an essential part of these analyses. We present the current status of the tau reconstruction and identification at the LHC with the ATLAS detector. The tau identification efficiencies and their systematic uncertainties are measured using W → τv and Z → ττ events, and compared with the predictions from Monte Carlo simulations.

  19. Physics performance of the ATLAS pixel detector

    Science.gov (United States)

    Tsuno, S.

    2017-01-01

    In preparation for LHC Run-2 the ATLAS detector introduced a new pixel detector, the Insertable B-Layer (IBL). This detector is located between the beampipe and what was the innermost pixel layer. The tracking and vertex reconstruction are significantly improved and good performance is expected in high level objects such a b-quark jet tagging. This in turn, leads to better physics results. This note summarizes the impact of the IBL detector on physics results, especially focusing on the analyses using b-quark jets throughout 2016 summer physics program.

  20. Astrophysics experiments with radioactive beams at ATLAS

    Directory of Open Access Journals (Sweden)

    B. B. Back

    2014-02-01

    Full Text Available Reactions involving short-lived nuclei play an important role in nuclear astrophysics, especially in explosive scenarios which occur in novae, supernovae or X-ray bursts. This article describes the nuclear astrophysics program with radioactive ion beams at the ATLAS accelerator at Argonne National Laboratory. The CARIBU facility as well as recent improvements for the in-flight technique are discussed. New detectors which are important for studies of the rapid proton or the rapid neutron-capture processes are described. At the end we briefly mention plans for future upgrades to enhance the intensity, purity and the range of in-flight and CARIBU beams.

  1. Single Top Physics at ATLAS and CMS

    CERN Document Server

    zur Nedden, Martin; The ATLAS collaboration

    2016-01-01

    A summary over the single top analyses in the ATLAS and CMS experiments is given. In this talk, the measurements of the single top cross sections in the t-channel, the Wt-channel and the s-channel are shown as the basis for a rich physics program with single top quarks. After discussing also the differential and fiducial cross sections and the V_tb properties, the single-top analyses are used as the bases for searches for physics beyond the Standard Model. Searches for Mono-tops, Flavour Changing Neutral Currents and anomalous couplings are discussed.

  2. Physics performance of the ATLAS Pixel Detector

    CERN Document Server

    Tsuno, Soshi; The ATLAS collaboration

    2016-01-01

    One noticeable upgrade from Run-1 to Run-2 with ATLAS detector in proton-proton collisions at LHC is the introduction of the new pixel detector, IBL, located on the beam pipe as the extra innermost pixel layer. The tracking and vertex reconstruction are significantly improved and good performance is expected in high level object such a $b$-quark jet tagging, in turn, it leads the better physics results. This note summarizes what is the impact on the IBL detector to the physics results especially focusing on the analyses using the $b$-quark jets throughout 2016 summer physics program.

  3. ATLAS: civil engineering Point 1

    CERN Multimedia

    2000-01-01

    The ATLAS experimental area is located in Point 1, just across the main CERN entrance, in the commune of Meyrin. There people are busy to finish the different infrastructures for ATLAS. Real underground video. Nice view from the surface to the cavern from the pit side - all the big machines looked very small. The film has original working sound.

  4. ATLAS recognises its best suppliers

    CERN Multimedia

    2002-01-01

    The ATLAS Collaboration has recently rewarded two of its suppliers in the construction of very major detector components, fabricated in Japan. The ATLAS Supplier Award in recognition of excellent supplier performance has just been attributed to Kawasaki Heavy Industries, while Toshiba Corporation received the award two months ago at their headquarters in Japan.

  5. Lowering the first ATLAS toroid

    CERN Multimedia

    Maximilien Brice

    2004-01-01

    The ATLAS detector on the LHC at CERN will consist of eight toroid magnets, the first of which was lowered into the cavern in these images on 26 October 2004. The coils are supported on platforms where they will be attached to form a giant torus. The platforms will hold about 300 tonnes of ATLAS' muon chambers and will envelop the inner detectors.

  6. ATLAS Award for Difficult Task

    CERN Multimedia

    2004-01-01

    Two Russian companies were honoured with an ATLAS Award, for supply of the ATLAS Inner Detector barrel support structure elements, last week. On 23 March the Russian company ORPE Technologiya and its subcontractor, RSP Khrunitchev, were jointly presented with an ATLAS Supplier Award. Since 1998, ORPE Technologiya has been actively involved in the development of the carbon-fibre reinforced plastic elements of the ATLAS Inner Detector barrel support structure. After three years of joint research and development, CERN and ORPE Technologiya launched the manufacturing contract. It had a tight delivery schedule and very demanding specifications in terms of mechanical tolerance and stability. The contract was successfully completed with the arrival of the last element of the structure at CERN on 8 January 2004. The delivery of this key component of the Inner Detector deserves an ATLAS Award given the difficulty of manufacturing the end-frames, which very few companies in the world would have been able to do at an ...

  7. Jet substructure in ATLAS

    CERN Document Server

    Miller, David W

    2011-01-01

    Measurements are presented of the jet invariant mass and substructure in proton-proton collisions at $\\sqrt{s} = 7$ TeV with the ATLAS detector using an integrated luminosity of 37 pb$^{-1}$. These results exercise the tools for distinguishing the signatures of new boosted massive particles in the hadronic final state. Two "fat" jet algorithms are used, along with the filtering jet grooming technique that was pioneered in ATLAS. New jet substructure observables are compared for the first time to data at the LHC. Finally, a sample of candidate boosted top quark events collected in the 2010 data is analyzed in detail for the jet substructure properties of hadronic "top-jets" in the final state. These measurements demonstrate not only our excellent understanding of QCD in a new energy regime but open the path to using complex jet substructure observables in the search for new physics.

  8. ATLAS Transition Radiation Tracker

    CERN Multimedia

    2006-01-01

    The ATLAS transition radiation tracker is made of 300'000 straw tubes, up to 144cm long. Filled with a gas mixture and threaded with a wire, each straw is a complete mini-detector in its own right. An electric field is applied between the wire and the outside wall of the straw. As particles pass through, they collide with atoms in the gas, knocking out electrons. The avalanche of electrons is detected as an electrical signal on the wire in the centre. The tracker plays two important roles. Firstly, it makes more position measurements, giving more dots for the computers to join up to recreate the particle tracks. Also, together with the ATLAS calorimeters, it distinguishes between different types of particles depending on whether they emit radiation as they make the transition from the surrounding foil into the straws.

  9. ATLAS IBL operational experience

    CERN Document Server

    Takubo, Yosuke; The ATLAS collaboration

    2016-01-01

    The Insertable B-Layer (IBL) is the inner most pixel layer in the ATLAS experiment, which was installed at 3.3 cm radius from the beam axis in 2014 to improve the tracking performance. To cope with the high radiation and hit occupancy due to proximity to the interaction point, a new read-out chip and two different silicon sensor technologies (planar and 3D) have been developed for the IBL. After the long shut-down period over 2013 and 2014, the ATLAS experiment started data-taking in May 2015 for Run-2 of the Large Hadron Collider (LHC). The IBL has been operated successfully since the beginning of Run-2 and shows excellent performance with the low dead module fraction, high data-taking efficiency and improved tracking capability. The experience and challenges in the operation of the IBL is described as well as its performance.

  10. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    The tau lepton plays a crucial role in understanding particle physics at the Tera scale. One of the most promising probes of the Higgs boson coupling to fermions is with detector signatures involving taus. In addition, many theories beyond the Standard Model, such as supersymmetry and exotic particles (Wʹ′ and Zʹ′), predict new physics with large couplings to taus. The ability to trigger on hadronic tau decays is therefore critical to achieving the physics goals of the ATLAS experiment. The higher instantaneous luminosities of proton-proton collisions achieved by the Large Hadron Collider (LHC) in 2012 resulted in a larger probability of overlap (pile-up) between bunch crossings, and so it was critical for ATLAS to have an effective tau trigger strategy. The details of this strategy are summarized in this poster, and the latest performance measurements are presented.

  11. The ATLAS Tau Trigger

    CERN Document Server

    Rados, PK; The ATLAS collaboration

    2013-01-01

    The tau lepton plays a crucial role in understanding particle physics at the Tera scale. One of the most promising probes of the Higgs boson coupling to fermions is with detector signatures involving taus. In addition, many theories beyond the Standard Model, such as supersymmetry and exotic particles (Wʹ and Zʹ), predict new physics with large couplings to taus. The ability to trigger on hadronic tau decays is therefore critical to achieving the physics goals of the ATLAS experiment. The higher instantaneous luminosities of proton-proton collisions achieved by the Large Hadron Collider (LHC) in 2012 resulted in a larger probability of overlap (pile-up) between bunch crossings, and so it was critical for ATLAS to have an effective tau trigger strategy. The details of this strategy are summarized in this paper, and the results of the latest performance measurements are presented.

  12. ATLAS software packaging

    CERN Document Server

    Rybkin, G

    2012-01-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages - platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis pro...

  13. Jet Physics in ATLAS

    CERN Document Server

    Sandoval, C; The ATLAS collaboration

    2012-01-01

    Measurements of hadronic jets provide tests of strong interactions which are interesting both in their own right and as backgrounds to many New Physics searches. It is also through tests of Quantum Chromodynamics that new physics may be discovered. The extensive dataset recorded with the ATLAS detector throughout the 7 TeV and 8 TeV centre-of-mass LHC operation periods allows QCD to be probed at distances never reached before. We present a review of selected ATLAS jet physics measurements. These measurements constitute precision tests of QCD in a new energy regime, and show sensitivity to the parton densities in the proton and to the value of the strong coupling, alpha_s.

  14. Supersymmetry searches in ATLAS

    CERN Document Server

    Torro Pastor, Emma; The ATLAS collaboration

    2016-01-01

    Weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  15. SUSY searches in ATLAS

    CERN Document Server

    ATLAS, C; The ATLAS collaboration

    2014-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  16. Supersymmetry Searches in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00237280; The ATLAS collaboration

    2015-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  17. SUSY Searches in ATLAS

    CERN Document Server

    Zhuang, Xuai; The ATLAS collaboration

    2016-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles, with focus on those obtained using proton-proton collisions at a centre of mass energy of 13 TeV using 2015+2016 data. The searches with final states including jets, missing transverse momentum, light leptons will be presented.

  18. Supersymmetry Searches with ATLAS

    CERN Document Server

    Hill, Ewan; The ATLAS collaboration

    2015-01-01

    Supersymmetry is one of the best motivated and studied theories of physics beyond the Standard Model. This talk summarises recent ATLAS results on searches for supersymmetric particles. Weak and strong production Supersymmetry scenarios are considered, along with direct production of third generation supersymmtric particles. The searches involve final states including jets, missing transverse momentum, leptons, and long lived particles. Sensitivity projections for the 13 TeV data are also presented.

  19. ATLAS reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bartsch, R.R.

    1995-09-01

    Key elements of the 36 MJ ATLAS capacitor bank have been evaluated for individual probabilities of failure. These have been combined to estimate system reliability which is to be greater than 95% on each experimental shot. This analysis utilizes Weibull or Weibull-like distributions with increasing probability of failure with the number of shots. For transmission line insulation, a minimum thickness is obtained and for the railgaps, a method for obtaining a maintenance interval from forthcoming life tests is suggested.

  20. ATLAS support rails

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    These supports will hold the 7000 tonne ATLAS detector in its cavern at the LHC. The huge toroid will be assembled from eight coils that will house some of the muon chambers. Supported within the toroid will be the inner detector, containing tracking devices, as well as devices to measure the energies of the particles produced in the 14 TeV proton-proton collisions at the LHC.

  1. The ATLAS Experiment Movie

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  2. Top physics at ATLAS

    CERN Document Server

    Romano, M

    2016-01-01

    This paper is an overview of recent results on top-quark physics obtained by the ATLAS Collaboration from the analysis of pp collisions at $\\sqrt s$= 7 and 8TeV at the Large Hadron Collider. Total and differential top-quark pair (t$\\overline t$), single top and t$\\overline t$+$\\gamma$ cross-sections and top properties measurements are presented.

  3. Hybrid Atlas Models

    CERN Document Server

    Ichiba, Tomoyuki; Banner, Adrian; Karatzas, Ioannis; Fernholz, Robert

    2009-01-01

    We study Atlas-type models of equity markets with local characteristics that depend on both name and rank, and in ways that induce a stability of the capital distribution. Ergodic properties and rankings of processes are examined with reference to the theory of reflected Brownian motions in polyhedral domains. In the context of such models, we discuss properties of various investment strategies, including the so-called growth-optimal and universal portfolios.

  4. Higgs results from ATLAS

    Directory of Open Access Journals (Sweden)

    Chen Xin

    2016-01-01

    Full Text Available The updated Higgs measurements in various search channels with ATLAS Run 1 data are reviewed. Both the Standard Model (SM Higgs results, such as H → γγ, ZZ, WW, ττ, μμ, bb̄, and Beyond Standard Model (BSM results, such as the charged Higgs, Higgs invisible decay and tensor couplings, are summarized. Prospects for future Higgs searches are briefly discussed.

  5. El experimento ATLAS

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  6. L'esperimento ATLAS

    CERN Multimedia

    ATLAS Outreach Committee

    2000-01-01

    This award winning film gives a glimpse behind the scenes of building the ATLAS detector. This film asks: Why are so many physicists anxious to build this apparatus? Will they be able to answer fundamental questions such as: Where does mass come from? Why does the Universe have so little antimatter? Are there extra dimensions of space that are hidden from our view? Is there an underlying theory to find? Major surprises are likely in this unknown part of physics.

  7. ATLAS Upgrade Plans

    CERN Document Server

    Hopkins, W; The ATLAS collaboration

    2014-01-01

    After the successful LHC operation at the center-of-mass energies of 7 and 8 TeV in 2010-2012, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity leveling. The final goal is to extend the dataset from about few hundred fb−1 expected for LHC running to 3000/fb by around 2035 for ATLAS and CMS. In parallel, the experiments need to be keep lockstep with the accelerator to accommodate running beyond the nominal luminosity this decade. Current planning in ATLAS envisions significant upgrades to the detector during the consolidation of the LHC to reach full LHC energy and further upgrades. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new...

  8. ATLAS Detector Upgrade Prospects

    CERN Document Server

    Dobre, Monica; The ATLAS collaboration

    2016-01-01

    After the successful operation at the centre-of-mass energies of 7 and 8 TeV in 2010-2012, the LHC is ramped up and successfully took data at the centre-of-mass energies of 13 TeV in 2015. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity levelling. The ultimate goal is to extend the dataset from about few hundred f b −1 expected for LHC running to 3000 f b −1 by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of ext...

  9. ATLAS Job Transforms

    CERN Document Server

    Stewart, G A; The ATLAS collaboration; Maddocks, H J; Harenberg, T; Sandhoff, M; Sarrazin, B

    2013-01-01

    The need to run complex workflows for a high energy physics experiment such as ATLAS has always been present. However, as computing resources have become even more constrained, compared to the wealth of data generated by the LHC, the need to use resources efficiently and manage complex workflows within a single grid job have increased. In ATLAS, a new Job Transform framework has been developed that we describe in this paper. This framework manages the multiple execution steps needed to `transform' one data type into another (e.g., RAW data to ESD to AOD to final ntuple) and also provides a consistent interface for the ATLAS production system. The new framework uses a data driven workflow definition which is both easy to manage and powerful. After a transform is defined, jobs are expressed simply by specifying the input data and the desired output data. The transform infrastructure then executes only the necessary substeps to produce the final data products. The global execution cost of running the job is mini...

  10. ATLAS Job Transforms

    CERN Document Server

    Stewart, G A; The ATLAS collaboration; Maddocks, H J; Harenberg, T; Sandhoff, M; Sarrazin, B

    2013-01-01

    The need to run complex workflows for a high energy physics experiment such as ATLAS has always been present. However, as computing resources have become even more constrained, compared to the wealth of data generated by the LHC, the need to use resources efficiently and manage complex workflows within a single grid job have increased. In ATLAS, a new Job Transform framework has been developed that we describe in this paper. This framework manages the multiple execution steps needed to 'transform' one data type into another (e.g., RAW data to ESD to AOD to final ntuple) and also provides a consistent interface for the ATLAS production system. The new framework uses a data driven workflow definition which is both easy to manage and powerful. After a transform is defined, jobs are expressed simply by specifying the input data and the desired output data. The transform infrastructure then executes only the necessary substeps to produce the final data products. The global execution cost of running the job is mini...

  11. Atlas du Liban

    Directory of Open Access Journals (Sweden)

    Ramez Philippe Maalouf

    2008-11-01

    Full Text Available Compte-rendu de l’ouvrage Atlas du Liban: territoires et société, sous la direction d’Éric Verdeil, Ghaleb Faour et Sébastien Velut, édition franco-libanaise de l’IFPO (Institut Français du Proche-Orient et du CNRS Liban (Conseil National de la Recherche Scientifique – Liban, Beyrouth 2007.Resenha do livro Atlas du Liban: territoires et société, sob a direção de Éric Verdeil, Ghaleb Faour e Sébastien Velut, editado por iniciativa franco-libanesa do IFPO (Institut Français du Proche-Orient e pelo CNRS Liban (Conseil National de la Recherche Scientifique – Liban, Beirute, 2007.Review of Atlas du Liban: territoires et société, edited by Éric Verdeil, Ghaleb Faour and Sébastien Velut, french-lebanese edition by IFPO (Institut Français du Proche-Orient and CNRS Liban (Conseil National de la Recherche Scientifique – Liban Beirut, 2007.

  12. Clean tracks for ATLAS

    CERN Multimedia

    2006-01-01

    First cosmic ray tracks in the integrated ATLAS barrel SCT and TRT tracking detectors. A snap-shot of a cosmic ray event seen in the different layers of both the SCT and TRT detectors. The ATLAS Inner Detector Integration Team celebrated a major success recently, when clean tracks of cosmic rays were detected in the completed semiconductor tracker (SCT) and transition radiation tracker (TRT) barrels. These tracking tests come just months after the successful insertion of the SCT into the TRT (See Bulletin 09/2006). The cosmic ray test is important for the experiment because, after 15 years of hard work, it is the last test performed on the fully assembled barrel before lowering it into the ATLAS cavern. The two trackers work together to provide millions of channels so that particles' tracks can be identified and measured with great accuracy. According to the team, the preliminary results were very encouraging. After first checks of noise levels in the final detectors, a critical goal was to study their re...

  13. ATLAS overview week highlights

    CERN Multimedia

    D. Froidevaux

    2005-01-01

    A warm and early October afternoon saw the beginning of the 2005 ATLAS overview week, which took place Rue de La Montagne Sainte-Geneviève in the heart of the Quartier Latin in Paris. All visitors had been warned many times by the ATLAS management and the organisers that the premises would be the subject of strict security clearance because of the "plan Vigipirate", which remains at some level of alert in all public buildings across France. The public building in question is now part of the Ministère de La Recherche, but used to host one of the so-called French "Grandes Ecoles", called l'Ecole Polytechnique (in France there is only one Ecole Polytechnique, whereas there are two in Switzerland) until the end of the seventies, a little while after it opened its doors also to women. In fact, the setting chosen for this ATLAS overview week by our hosts from LPNHE Paris has turned out to be ideal and the security was never an ordeal. For those seeing Paris for the first time, there we...

  14. ATLAS Detector Upgrade Prospects

    CERN Document Server

    Dobre, Monica; The ATLAS collaboration

    2016-01-01

    After the successful operation at the center-of-mass energies of 7 and 8 TeV in 2010 - 2012, the LHC is ramped up and successfully took data at the center-of-mass energies of 13 TeV in 2015. Meanwhile, plans are actively advancing for a series of upgrades of the accelerator, culminating roughly ten years from now in the high-luminosity LHC (HL-LHC) project, delivering of the order of five times the LHC nominal instantaneous luminosity along with luminosity leveling. The ultimate goal is to extend the dataset from about few hundred fb−1 expected for LHC running to 3000 fb−1 by around 2035 for ATLAS and CMS. The challenge of coping with the HL-LHC instantaneous and integrated luminosity, along with the associated radiation levels, requires further major changes to the ATLAS detector. The designs are developing rapidly for a new all-silicon tracker, significant upgrades of the calorimeter and muon systems, as well as improved triggers and data acquisition. ATLAS is also examining potential benefits of extens...

  15. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  16. DESIGN AND COMPILATION OF AGRICULTURAL ELECTRONIC ATLAS AT COUNTY-LEVEL

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    With the rapid development and application of new techniques, cartography has enteredthe 21st centumono-medium, static into 3-D, multi-media, dynamic and network (including intemet), and gradually is developing towards 4-D (time, space). There appeared digital map, electronic map, soft map, hard map, interactive map, mingle map etc. Agricultural map needs to include much more contents in 3-D, multi-media than other types of map. Only electronic map can represent completely these contents. Compiling agricultural electronic atlas at county-level aims to reflect scientifiAgricultural electronic atlas at county-level should take "sustainable development" as the theme; systematically reflect the natural resources and natural environment in a county; the spatial and temporal distribution and changing law of agricultural resources (including climate, soil and water). In the paper the authors introduce the concrete contents of agricultural electronic atlas, their compilation process, and corresponding software and hardware as well as an example. In agricultural electronic atlas design the most advanced multi-media techniques must be used. The procedure of agricultural electronic atlas includesthe study on compilation aim, content selection analysis, overall framework and data organization, determining compilation program. Agriculture includes many contents; each county has its own emphasis. In designing we set upa county's theme according to its concrete situation, the atlas contents are selected around the theme. For example, the main problems faced by the agriculture of Da'an City in Jilin Province is land desertification, so land desertification and its control are the theme of agricultural electronic atlas of Da'an City. When we compile other county's agricultural electronic atlas, only changing theme contents, can we get another county's agricultural electronic atlas.

  17. Bisprimer--a program for the design of primers for bisulfite-based genomic sequencing of both plant and Mammalian DNA samples.

    Science.gov (United States)

    Kovacova, Viera; Janousek, Bohuslav

    2012-01-01

    Plants and animals differ in the sequence context of the methylated sites in DNA. Plants exhibit cytosine methylation in CG, CHG, and CHH sites, whereas CG methylation is the only form present in mammals (with an exception of the early embryonic development). This fact must be taken into account in the design of primers for bisulfite-based genomic sequencing because CHG and CHH sites can remain unmodified. Surprisingly, no user-friendly primer design program is publicly available that could be used to design primers in plants and to simultaneously check the properties of primers such as the potential for primer-dimer formation. For studies concentrating on particular DNA loci, the correct design of primers is crucial. The program, called BisPrimer, includes 2 different subprograms for the primer design, the first one for mammals and the second one for angiosperm plants. Each subprogram is divided into 2 variants. The first variant serves to design primers that preferentially bind to the bisulfite-modified primer-binding sites (C to U conversion). This type of primer preferentially amplifies the bisulfite-converted DNA strands. This feature can help to avoid problems connected with an incomplete bisulfite modification that can sometimes occur for technical reasons. The second variant is intended for the analysis of samples that are supposed to consist of a mixture of DNA molecules that have different levels of cytosine methylation (e.g., pollen DNA). In this case, the aim is to minimize the selection in favor of either less methylated or more methylated molecules.

  18. Evolution of the ATLAS Distributed Computing during the LHC long shutdown

    CERN Document Server

    Campana, S; The ATLAS collaboration

    2013-01-01

    The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the WLCG distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileu...

  19. Evolution of the ATLAS Distributed Computing system during the LHC Long shutdown

    CERN Document Server

    Campana, S; The ATLAS collaboration

    2014-01-01

    The ATLAS Distributed Computing project (ADC) was established in 2007 to develop and operate a framework, following the ATLAS computing model, to enable data storage, processing and bookkeeping on top of the WLCG distributed infrastructure. ADC development has always been driven by operations and this contributed to its success. The system has fulfilled the demanding requirements of ATLAS, daily consolidating worldwide up to 1PB of data and running more than 1.5 million payloads distributed globally, supporting almost one thousand concurrent distributed analysis users. Comprehensive automation and monitoring minimized the operational manpower required. The flexibility of the system to adjust to operational needs has been important to the success of the ATLAS physics program. The LHC shutdown in 2013-2015 affords an opportunity to improve the system in light of operational experience and scale it to cope with the demanding requirements of 2015 and beyond, most notably a much higher trigger rate and event pileu...

  20. JAtlasView: a Java atlas-viewer for browsing biomedical 3D images and atlases

    Directory of Open Access Journals (Sweden)

    Scott Mark

    2005-03-01

    Full Text Available Abstract Background Many three-dimensional (3D images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are available for viewing this data ranging from commercial visualization packages to freely available, typically system architecture dependent, solutions. Here we discuss an atlas viewer implemented to run on any workstation using the architecture neutral Java programming language. Results We report the development of a freely available Java based viewer for 3D image data, descibe the structure and functionality of the viewer and how automated tools can be developed to manage the Java Native Interface code. The viewer allows arbitrary re-sectioning of the data and interactive browsing through the volume. With appropriately formatted data, for example as provided for the Electronic Atlas of the Developing Human Brain, a 3D surface view and anatomical browsing is available. The interface is developed in Java with Java3D providing the 3D rendering. For efficiency the image data is manipulated using the Woolz image-processing library provided as a dynamically linked module for each machine architecture. Conclusion We conclude that Java provides an appropriate environment for efficient development of these tools and techniques exist to allow computationally efficient image-processing libraries to be integrated relatively easily.