Coassembly and binning of a twenty-year metagenomic time-series from Lake Mendota.

Autor: Oliver T; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. toliver4@spelman.edu.; Department of Biology, Spelman College, Atlanta, GA, 30314, USA. toliver4@spelman.edu., Varghese N; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Roux S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Schulz F; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Huntemann M; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Clum A; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Foster B; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Foster B; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Riley R; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., LaButti K; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Egan R; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Hajek P; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Mukherjee S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Ovchinnikova G; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Reddy TBK; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Calhoun S; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Hayes RD; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Rohwer RR; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA., Zhou Z; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA., Daum C; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Copeland A; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Chen IA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Ivanova NN; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Kyrpides NC; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Mouncey NJ; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Del Rio TG; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Grigoriev IV; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA., Hofmeyr S; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Oliker L; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA., Yelick K; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Electrical Engineering and Computer Sciences Department, University of California Berkeley, Berkeley, CA, 94720, USA., Anantharaman K; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA., McMahon KD; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.; Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA., Woyke T; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA., Eloe-Fadrosh EA; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. eaeloefadrosh@lbl.gov.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. eaeloefadrosh@lbl.gov.

Publikováno v: Scientific data [Sci Data] 2024 Sep 04; Vol. 11 (1), pp. 966. Date of Electronic Publication: 2024 Sep 04.

Terabase-Scale Coassembly of a Tropical Soil Microbiome.

Autor: Riley R; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Bowers RM; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Camargo AP; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Campbell A; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA., Egan R; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Eloe-Fadrosh EA; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Foster B; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Hofmeyr S; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Huntemann M; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Kellom M; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Kimbrel JA; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA., Oliker L; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA., Yelick K; Applied Math and Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.; Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA., Pett-Ridge J; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA.; Life & Environmental Sciences Department, University of California Merced, Merced, California, USA., Salamov A; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Varghese NJ; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA., Clum A; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley California, USA.

Publikováno v: Microbiology spectrum [Microbiol Spectr] 2023 Aug 17; Vol. 11 (4), pp. e0020023. Date of Electronic Publication: 2023 Jun 13.

Performance Analysis of GPU Programming Models Using the Roofline Scaling Trajectories

Autor: Ibrahim, KZ, Williams, S, Oliker, L

Performance analysis is a daunting job, especially for the rapid-evolving accelerator technologies. The Roofline Scaling Trajectories technique aims at diagnosing various performance bottlenecks for GPU programming models through the visually intuiti

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https://escholarship.org/uc/item/5nv5d9b2

Critical Assessment of Metagenome Interpretation: the second round of challenges.

Autor: Meyer F; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Fritz A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Deng ZL; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany., Koslicki D; Pennsylvania State University, State College, PA, USA., Lesker TR; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany.; Helmholtz Centre for Infection Research, Braunschweig, Germany., Gurevich A; Saint Petersburg State University, Saint Petersburg, Russia., Robertson G; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany., Alser M; Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland., Antipov D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Beghini F; Department CIBIO, University of Trento, Trento, Italy., Bertrand D; Genome Institute of Singapore, Singapore, Singapore., Brito JJ; University of Southern California, Los Angeles, CA, USA., Brown CT; University of California, Davis, Davis, CA, USA., Buchmann J; Institute for Biological Data Science, Heinrich-Heine-University, Düsseldorf, Germany., Buluç A; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chen B; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Chikhi R; Institut Pasteur, Paris, France., Clausen PTLC; National Food Institute, Division of Global Surveillance, Technical University of Denmark, Lyngby, Denmark., Cristian A; Drexel University, Philadelphia, PA, USA.; Google Inc., Philadelphia, PA, USA., Dabrowski PW; Robert Koch-Institut, Berlin, Germany.; Hochschule für Technik und Wirtschaft Berlin, Berlin, Germany., Darling AE; University of Technology Sydney, Sydney, Australia., Egan R; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Eskin E; University of California, Los Angeles, Los Angeles, CA, USA., Georganas E; Intel Corporation, Santa Clara, CA, USA., Goltsman E; DOE Joint Genome Institute, Berkeley, CA, USA.; Lawrence Berkeley National Laboratories, Berkeley, CA, USA., Gray MA; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA., Hansen LH; University of Copenhagen, Department of Plant and Environmental Science, Frederiksberg, Denmark., Hofmeyr S; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Huang P; School of Computer Science, Fudan University, Shanghai, China., Irber L; University of California, Davis, Davis, CA, USA., Jia H; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Jørgensen TS; Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark.; Aarhus University, Department of Environmental Science, Roskilde, Denmark., Kieser SD; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Swiss Institute of Bioinformatics, Geneva, Switzerland., Klemetsen T; The Arctic University of Norway, Tromsø, Norway., Kola A; Charité-Universitätsmedizin Berlin, Berlin, Germany., Kolmogorov M; Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA., Korobeynikov A; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia.; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, Russia., Kwan J; University of Wisconsin-Madison, Madison, WI, USA., LaPierre N; University of California, Los Angeles, Los Angeles, CA, USA., Lemaitre C; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Li C; Genome Institute of Singapore, Singapore, Singapore., Limasset A; Université Lille, CNRS, CRIStAL, Lille, France., Malcher-Miranda F; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Mangul S; University of Southern California, Los Angeles, CA, USA., Marcelino VR; Sydney Medical School, The University of Sydney, Sydney, Australia.; Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia., Marchet C; Université Lille, CNRS, CRIStAL, Lille, France., Marijon P; Department of Computer Science, Inria, University of Lille, CNRS, Lille, France., Meleshko D; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, Russia., Mende DR; Amsterdam University Medical Center, Amsterdam, the Netherlands., Milanese A; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Nagarajan N; Genome Institute of Singapore, A*STAR, Singapore, Singapore.; National University of Singapore, Singapore, Singapore., Nissen J; DTU Health Tech, Kongens, Lyngby, Denmark., Nurk S; Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA., Oliker L; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., Paoli L; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Peterlongo P; Univ. Rennes, Inria, CNRS, IRISA, Rennes, France., Piro VC; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany., Porter JS; University of Virginia, Charlottesville, VA, USA., Rasmussen S; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Rees ER; University of Wisconsin-Madison, Madison, WI, USA., Reinert K; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Renard B; Hasso Plattner Institute, Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.; Bioinformatics Unit (MF1), Robert Koch Institute, Berlin, Germany., Robertsen EM; The Arctic University of Norway, Tromsø, Norway., Rosen GL; Drexel University, Philadelphia, PA, USA.; Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Philadelphia, PA, USA.; Center for Biological Discovery from Big Data, Philadelphia, PA, USA., Ruscheweyh HJ; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sarwal V; University of California, Los Angeles, Los Angeles, CA, USA., Segata N; Department CIBIO, University of Trento, Trento, Italy., Seiler E; Institute for Bioinformatics, FU Berlin, Berlin, Germany., Shi L; Florida Polytechnic University, Lakeland, FL, USA., Sun F; Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA, USA., Sunagawa S; Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland., Sørensen SJ; University of Copenhagen, Copenhagen, Denmark., Thomas A; DOE Joint Genome Institute, Berkeley, CA, USA.; University of British Columbia, Vancouver, British Columbia, Canada., Tong C; Genome Institute of Singapore, Singapore, Singapore., Trajkovski M; Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.; Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland., Tremblay J; Energy, Mining and Environment, National Research Council Canada, Montreal, Quebec, Canada., Uritskiy G; Phase Genomics, Seattle, WA, USA., Vicedomini R; Institut Pasteur, Paris, France., Wang Z; School of Computer Science, Fudan University, Shanghai, China., Wang Z; School of Mathematical Sciences, Fudan University, Shanghai, China., Wang Z; Department of Energy Joint Genome Institute, Berkeley, CA, USA.; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; School of Natural Sciences, University of California at Merced, Merced, CA, USA., Warren A; University of Virginia, Charlottesville, VA, USA., Willassen NP; The Arctic University of Norway, Tromsø, Norway., Yelick K; Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; University of California, Berkeley, Berkeley, CA, USA., You R; School of Computer Science, Fudan University, Shanghai, China., Zeller G; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany., Zhao Z; Drexel University, Philadelphia, PA, USA., Zhu S; Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China., Zhu J; BGI-Shenzhen, Shenzhen, China.; Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, China., Garrido-Oter R; Max Planck Institute for Plant Breeding Research, Köln, Germany., Gastmeier P; Charité-Universitätsmedizin Berlin, Berlin, Germany., Hacquard S; Max Planck Institute for Plant Breeding Research, Köln, Germany., Häußler S; Helmholtz Centre for Infection Research, Braunschweig, Germany., Khaledi A; Helmholtz Centre for Infection Research, Braunschweig, Germany., Maechler F; Charité-Universitätsmedizin Berlin, Berlin, Germany., Mesny F; Max Planck Institute for Plant Breeding Research, Köln, Germany., Radutoiu S; Aarhus University, Aarhus, Denmark., Schulze-Lefert P; Max Planck Institute for Plant Breeding Research, Köln, Germany., Smit N; Helmholtz Centre for Infection Research, Braunschweig, Germany., Strowig T; Helmholtz Centre for Infection Research, Braunschweig, Germany., Bremges A; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany., Sczyrba A; Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany., McHardy AC; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany. amc14@helmholtz-hzi.de.; German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Braunschweig, Germany. amc14@helmholtz-hzi.de.; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany. amc14@helmholtz-hzi.de.

Publikováno v: Nature methods [Nat Methods] 2022 Apr; Vol. 19 (4), pp. 429-440. Date of Electronic Publication: 2022 Apr 08.

Exploiting Thread Parallelism for Ocean Modeling on Cray XC Supercomputers

Autor: Sarje, A, Jacobsen, D, Williams, S, Ringler, T, Oliker, L

Publikováno v: Sarje, A; Jacobsen, D; Williams, S; Ringler, T; & Oliker, L. (2016). Exploiting Thread Parallelism for Ocean Modeling on Cray XC Supercomputers. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/1kd706h2

The incorporation of increasing core counts in modern processors used to build state-of-the-art supercomputers is driving application development towards exploitation of thread parallelism, in addition to distributed memory parallelism, with the goal

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::1f1bb217301c5f18fb039cdcc36747c6
https://escholarship.org/uc/item/1kd706h2