October 2007 Volume 32 Number 5

Total Page:16

File Type:pdf, Size:1020Kb

October 2007 Volume 32 Number 5 OCTOBER 2007 VOLUME 32 NUMBER 5 THE USENIX MAGAZINE OPINION Musings RIK FARROW OSES Why Some Dead OSes Still Matter ANDREY MIRTCHOVSKI AND LATCHESAR IONKOV SECURITY (Digital) Identity 2.0 CAT OKITA LAW Hardening Your Systems Against Litigation ALEXANDER MUENTZ SYSADMIN An Introduction to Logical Domains, Part 2 OCTAVE ORGERON VOIP IP Telephony HEMANT SENGAR COLUMNS Practical Perl Tools: Let Me Draw You a Picture DAVID BLANK-EDELMAN iVoyeur: Opaque Brews DAVID JOSEPHSEN /dev/random ROBERT G. FERRELL STANDARDS Whither C++? NICHOLAS M. STOUGHTON BOOK REVIEWS Book Reviews ELIZABETH ZWICKY ET AL. USENIX NOTES Creating the EVT Workshop DAN WALLACH 2008 USENIX Nominating Committee ELLIE YOUNG Letters to the Editor CONFERENCES 2007 USENIX Annual Technical Conference Linux Symposium 2007 The Advanced Computing Systems Association Upcoming Events INTERNET MEASUREMENT CONFERENCE 2007 1ST USENIX W ORKSHOP ON LARGE -S CALE (IMC 2007 ) EXPLOITS AND EMERGENT THREATS (LEET ’08) Sponsored by ACM SIGCOMM in cooperation with USENIX Co-located with NSDI ’08 OCTOBER 24–26 , 2007, SAN DIEGO , CA, USA APRIL 15, 2008, SAN FRANCISCO , CA, USA http://www.imconf.net/imc-2007/ 5TH USENIX S YMPOSIUM ON NETWORKED 21 ST LARGE INSTALLATION SYSTEM SYSTEMS DESIGN AND IMPLEMENTATION ADMINISTRATION CONFERENCE (LISA ’07 ) (NSDI ’08) Sponsored by USENIX and SAGE Sponsored by USENIX in cooperation with ACM SIGCOMM and ACM SIGOPS NOVEMBER 11–16 , 2007, DALLAS , TX , USA http://www.usenix.org/lisa07 APRIL 16–18, 2008, SAN FRANCISCO , CA, USA http://www.usenix.org/nsdi08 ACM/IFIP/USENIX 8 TH INTERNATIONAL Paper titles and abstracts due: October 2, 2007 MIDDLEWARE CONFERENCE (MIDDLEWARE 2007 ) 2008 USENIX A NNUAL TECHNICAL CONFERENCE NOVEMBER 26 –30 , 2007, NEWPORT BEACH , CA, USA JUNE 22–27 , 2008, BOSTON, MA , USA http://middleware2007.ics.uci.edu/ http://www.usenix.org/usenix08 Paper submissions due: January 7, 2008 2008 L INUX STORAGE & F ILESYSTEM WORKSHOP (LSF ’08) 2008 USENIX/ACCURATE E LECTRONIC Co-located with FAST ’08 VOTING TECHNOLOGY WORKSHOP (EVT ’08) FEBRUARY 25–26 , 2008, SAN JOSE , CA, USA Co-located with USENIX Security ’08 JULY 28 –29, 2008, SAN JOSE, CA , USA 6TH USENIX C ONFERENCE ON FILE AND STORAGE TECHNOLOGIES (FAST ’08) 3RD USENIX W ORKSHOP ON HOT TOPICS IN Sponsored by USENIX in cooperation with ACM SIGOPS, IEEE SECURITY (H OT SEC ’08) Mass Storage Systems Technical Committee (MSSTC), and IEEE TCOS Co-located with USENIX Security ’08 FEBRUARY 26–29 , 2008, SAN JOSE , CA, USA JULY 29, 2008, SAN JOSE, CA , USA http://www.usenix.org/fast08 17 TH USENIX S ECURITY S YMPOSIUM (USENIX 2008 ACM I NTERNATIONAL CONFERENCE ON SECURITY ’08) VIRTUAL EXECUTION ENVIRONMENTS (VEE ’08) JULY 28 –AUGUST 1, 2008, SAN JOSE, CA , USA Sponsored by ACM SIGPLAN in cooperation with USENIX 8TH USENIX S YMPOSIUM ON OPERATING SYS - MARCH 5–7 , 2008, SEATTLE , WA, USA http://vee08.cs.tcd.ie TEMS DESIGN AND IMPLEMENTATION (OSDI ’08) DECEMBER 8–10 , 2008, SAN DIEGO , CA , USA USABLE SECURITY 2008 (USEC ’08) Co-located with NSDI ’08 APRIL 14, 2008, SAN FRANCISCO , CA, USA For a complete list of all USENIX & USENIX co-sponsored events, see http://www.usenix.org/events. OPINION 2 Musings RIK FARROW OPERATING SYSTEMS 5 Why Some Dead OSes Still Matter ANDREY MIRTCHOVSKI AND LATCHESAR IONKOV SECURITY 13 (Digital) Identity 2.0 contents CAT OKITA LAW 21 Hardening Your Systems Against Litigation ALEXANDER MUENTZ SYSADMIN 26 An Introduction to Logical Domains, Part 2 OCTAVE ORGERON VOIP 35 IP Telephony HEMANT SENGAR COLUMNS 43 Practical Perl Tools: Let Me Draw You a Picture DAVID BLANK-EDELMAN 50 iVoyeur: Opaque Brews DAVID JOSEPHSEN VOL. 32, #5, OCTOBER 2007 55 /dev/random EDITOR ;login: is the official ROBERT G. FERRELL Rik Farrow magazine of the [email protected] USENIX Association. STANDARDS MANAGING EDITOR ;login: (ISSN 1044-6397) is 58 Whither C++? Jane-Ellen Long published bi-monthly by the [email protected] USENIX Association, 2560 NICHOLAS M. STOUGHTON COPY EDITOR Ninth Street, Suite 215, David Couzens Berkeley, CA 94710. BOOK REVIEWS [email protected] $85 of each member’s annual 63 Book Reviews dues is for an annual sub - PRODUCTION ELIZABETH ZWICKY ET AL. Casey Henderson scription to ;login: . Subscrip - Jane-Ellen Long tions for nonmembers are $120 per year. USENIX NOTES TYPESETTER Star Type Periodicals postage paid at 67 Creating the EVT Workshop [email protected] Berkeley, CA, and additional DAN WALLACH offices. USENIX ASSOCIATION 68 2008 USENIX Nominating Committee 2560 Ninth Street, POSTMASTER: Send address ELLIE YOUNG Suite 215, Berkeley, changes to ;login: , California 94710 USENIX Association, 68 Letters to the Editor Phone: (510) 528-8649 2560 Ninth Street, FAX: (510) 548-5738 Suite 215, Berkeley, CA 94710. CONFERENCE REPORTS http://www.usenix.org http://www.sage.org ©2007 USENIX Association 70 2007 USENIX Annual Technical Conference USENIX is a registered trade - 93 Linux Symposium 2007 mark of the USENIX Associa - tion. Many of the designa - tions used by manufacturers and sellers to distinguish their products are claimed as trade - marks. USENIX acknowl - edges all trademarks herein. Where those designations ap - pear in this publication and USENIX is aware of a trade - mark claim, the designations have been printed in caps or initial caps. WHEN I FIRST READ ONE OF THIS issue’s articles, I found myself suggesting to RIK FARROW the author that he not use the term IT. I wrote back to him, saying that many of the readers of ;login: are system administrators and that they don’t consider themselves part of IT. musings Having said that, I wondered how true that is. I also pondered over my own aversion to being con - [email protected] sidered part of IT. The definition of IT appears be - nign (see sidebar). It even appears to match, in very broad terms, what it is that system, network, and security professionals do. The Priesthood Information technology, IT—the branch of engineering that deals with the use of computers My earliest vision of IT came with my first visit to a and telecommunications to retrieve and store and transmit information. computer room, sometime about 1961. I had vol - —wordnet.princeton.edu unteered to work with some “computer” people (no “IT” people back then) and write a program in assembly language that would run on a mainframe. The mainframe itself, in Rockville, MD, was tremendously impressive, with its many large, humming cabinets, the washing machine –sized disks with the intriguingly labeled (in red) “Write Protect” push buttons, and the CPU itself. I liked the flashing lights that showed memory addresses and data values, and it was sort of cool when the IT guy got the mainframe to play a song through the console speaker (poorly). But I was just as im - pressed by the spectacular air conditioning system, as the air inside the computer room was mar - velously filtered, cool, and dry. In 1969, I spent a summer working as an intern for GE in Bethesda, MD. I was the “software librarian,” and the only really cool part of my job is that I got total use of the mainframe, during lunchtime, about once a week. I learned to boot the main - frame, starting with binary cards, then a larger deck of Hollerith-encoded punch cards, then boot - strapped the terminal concentrator, and finally got the tape drive, which contained the master copy of the OS and utilities, going. Once the system was up, I installed patches, from other nine-track tapes or from paper tapes, then dumped the patches to new nine-track tapes for shipment to the other 18 mainframes like this one around the world. I took every CS course I could at the University of Maryland, which didn’t even have a CS degree in those days. Using punch cards, and submitting jobs that you would not see the results of for at least 4 hours, and sometimes 20, really helped with 2 ;LOGIN: VOL. 32, NO. 5 typing discipline, as a single typo was tremendously painful. You would hand your card deck over to the priesthood who managed the CS depart - ment’s mainframe, and they would load your deck into the card reader and then write it to nine-track tapes. The tapes, containing card images, got loaded on the mainframe, and the jobs would run one at a time. I later learned that there was some time-sharing going on, but most students were forced to run batch jobs. (With some 25,000 students and a single computer, we were fortunate that most were not doing anything with the computer.) None of these experiences should have left me with negative feelings toward being part of IT. I did not work with computers my first several years out of college, because most jobs went to people with experience, and the Vietnam War had provided large groups of people with real experience, seriously im - pacting the market for those, like myself, who got college degrees instead of traumatizing experiences. When I did get back into computers, it was because the microprocessor had started appearing in small systems. During the intervening years, DEC had been producing minicomputers, smaller, cheaper, and much less complex systems than their mainframe relatives, but even these were scarce. Micro - computers promised to change all that, making real computers available to everyone. I could see this clearly in 1978, and I quickly became a part of the early PC boom in the Bay Area. Perhaps my aversion to IT came later, when I was working as a sysadmin consultant. I would have experiences where I would learn about some prob - lem an IT staff was having and offer to take a look at it. For example, one company needed to migrate its database from a homebrew version to In - formix.
Recommended publications
  • Analysis of Cell-Based Rnai Screens Comment Michael Boutros*, Lígia P Brás†‡ and Wolfgang Huber†
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Open Access Software2006BoutrosetVolume al. 7, Issue 7, Article R66 Analysis of cell-based RNAi screens comment Michael Boutros*, Lígia P Brás†‡ and Wolfgang Huber† Addresses: *Signaling and Functional Genomics, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany. †EMBL - European Bioinformatics Institute, Cambridge CB10 1SD, UK. ‡Centre for Chemical and Biological Engineering, IST, Technical University of Lisbon, Av. Rovisco Pais, P-1049-001 Lisbon, Portugal. Correspondence: Michael Boutros. Email: [email protected]. Wolfgang Huber. Email: [email protected] reviews Published: 25 July 2006 Received: 27 March 2006 Revised: 7 June 2006 Genome Biology 2006, 7:R66 (doi:10.1186/gb-2006-7-7-r66) Accepted: 25 July 2006 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2006/7/7/R66 © 2006 Boutros et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. reports Analysis<p>cellHTS of cell-based is a new method RNAi screens for the analysis and documentation of RNAi screens.</p> Abstract RNA interference (RNAi) screening is a powerful technology for functional characterization of deposited research biological pathways. Interpretation of RNAi screens requires computational and statistical analysis techniques. We describe a method that integrates all steps to generate a scored phenotype list from raw data.
    [Show full text]
  • Modeling Language Evolution and Feature Dynamics in a Realistic Geographic Environment
    Modeling language evolution and feature dynamics in a realistic geographic environment Rhea Kapur Phillip Rogers The Pingry School Department of Linguistics [email protected] The University of California, Santa Barbara [email protected] Abstract Recent, innovative efforts to understand the uneven distribution of languages and linguistic fea- ture values in time and space attest to both the challenge these issues pose and the value in solving them. In this paper, we introduce a model for simulating languages and their features over time in a realistic geographic environment. At its core is a model of language phylogeny and migration whose parameters are chosen to reproduce known language family sizes and geographic disper- sions. This foundation in turn is used to explore the dynamics of linguistic features. Languages are assigned feature values that can change randomly or under the influence of nearby languages according to predetermined probabilities. We assess the effects of these settings on resulting geographic and genealogical patterns using homogeneity measures defined in the literature. The resulting model is both flexible and realistic, and it can be employed to answer a wide range of related questions.1 1 Introduction The distribution of linguistic feature values across time and space is uneven. The overall frequencies of particular feature values can be skewed with some highly frequent and others vanishingly rare, and many feature values have been observed to cluster geographically or within particular language families. Such patterns are most commonly explained in terms of the competing influences of inheritance, diffusion, universal tendencies of language drift, and chance. Understanding these dynamics has long been a goal of linguists, and it has important implications for historical linguistics, areal linguistics, and linguistic ty- pology.
    [Show full text]
  • Pipenightdreams Osgcal-Doc Mumudvb Mpg123-Alsa Tbb
    pipenightdreams osgcal-doc mumudvb mpg123-alsa tbb-examples libgammu4-dbg gcc-4.1-doc snort-rules-default davical cutmp3 libevolution5.0-cil aspell-am python-gobject-doc openoffice.org-l10n-mn libc6-xen xserver-xorg trophy-data t38modem pioneers-console libnb-platform10-java libgtkglext1-ruby libboost-wave1.39-dev drgenius bfbtester libchromexvmcpro1 isdnutils-xtools ubuntuone-client openoffice.org2-math openoffice.org-l10n-lt lsb-cxx-ia32 kdeartwork-emoticons-kde4 wmpuzzle trafshow python-plplot lx-gdb link-monitor-applet libscm-dev liblog-agent-logger-perl libccrtp-doc libclass-throwable-perl kde-i18n-csb jack-jconv hamradio-menus coinor-libvol-doc msx-emulator bitbake nabi language-pack-gnome-zh libpaperg popularity-contest xracer-tools xfont-nexus opendrim-lmp-baseserver libvorbisfile-ruby liblinebreak-doc libgfcui-2.0-0c2a-dbg libblacs-mpi-dev dict-freedict-spa-eng blender-ogrexml aspell-da x11-apps openoffice.org-l10n-lv openoffice.org-l10n-nl pnmtopng libodbcinstq1 libhsqldb-java-doc libmono-addins-gui0.2-cil sg3-utils linux-backports-modules-alsa-2.6.31-19-generic yorick-yeti-gsl python-pymssql plasma-widget-cpuload mcpp gpsim-lcd cl-csv libhtml-clean-perl asterisk-dbg apt-dater-dbg libgnome-mag1-dev language-pack-gnome-yo python-crypto svn-autoreleasedeb sugar-terminal-activity mii-diag maria-doc libplexus-component-api-java-doc libhugs-hgl-bundled libchipcard-libgwenhywfar47-plugins libghc6-random-dev freefem3d ezmlm cakephp-scripts aspell-ar ara-byte not+sparc openoffice.org-l10n-nn linux-backports-modules-karmic-generic-pae
    [Show full text]
  • 3.1 What Is the Restaurant Game?
    Learning Plan Networks in Conversational Video Games by Jeffrey David Orkin B.S., Tufts University (1995) M.S., University of Washington (2003) Submitted-to the Program in Media Arts and Sciences in partial fulfillment of the requirements for the degree of Master of Science at the MASSACHUSETTS INSTITUTE OF TECHNOLOGY August 2007 © Massachusetts Institute of Technology 2007. All rights reserved. A uthor ........................... .............. Program in Media Arts and Sciences August 13, 2007 C ertified by ...................................... Associate Professor Thesis Supervisor Accepted by................................... Deb Roy 1 6lsimnhairperson, Departmental Committee on Graduate Students QF TECHNOLOGY SEP 14 2007 ROTCH LIBRARIES 2 Learning Plan Networks in Conversational Video Games by Jeffrey David Orkin Submitted to the Program in Media Arts and Sciences on August 13, 2007, in partial fulfillment of the requirements for the degree of Master of Science Abstract We look forward to a future where robots collaborate with humans in the home and workplace, and virtual agents collaborate with humans in games and training simulations. A representation of common ground for everyday scenarios is essential for these agents if they are to be effective collaborators and communicators. Effective collaborators can infer a partner's goals and predict future actions. Effective communicators can infer the meaning of utterances based on semantic context. This thesis introduces a computational cognitive model of common ground called a Plan Network. A Plan Network is a statistical model that provides representations of social roles, object affordances, and expected patterns of behavior and language. I describe a methodology for unsupervised learning of a Plan Network using a multiplayer video game, visualization of this network, and evaluation of the learned model with respect to human judgment of typical behavior.
    [Show full text]
  • Annexes : Installation Du Logiciel R Et Des Packages R
    Annexes : Installation du logiciel R et des packages R Pr´e-requis et objectif • Aucun pr´e-requis n’est n´ecessaire.La lecture du chapitre 1 pourrait tou- tefois se r´ev´eler int´eressante. • Ce chapitre d´ecritcomment installer le logiciel R, dans sa version x (rem- placer partout dans le reste de ce document x par le num´ero de la derni`ere version disponible), sous le syst`emed’exploitation Microsoft Windows et aussi comment ajouter des packages suppl´ementaires sous Windows ou sous Linux. SECTION C.1 Installation de R sous Microsoft Windows Commencez par t´el´echarger le logiciel R (fichier R-x-win.exe o`u x est le nu- m´ero de la derni`ereversion disponible) `a l’aide de votre navigateur web usuel `a l’adresse suivante : http://cran.r-project.org/bin/windows/base/ Enregistrez ensuite ce fichier ex´ecutable sur le bureau de Windows puis double- cliquez sur le fichier R-x-win.exe dont voici l’icˆone : . Le logiciel s’installe alors et vous n’avez plus qu’`a suivre les instructions qui s’affichent et `a conserver les options propos´ees par d´efaut. Lorsque l’icˆone est ajout´ee sur le bureau, l’installation peut ˆetre consi- d´er´ee comme termin´ee. 574 Le logiciel R SECTION C.2 Installation de packages suppl´ementaires De nombreux modules (packages ou librairies) suppl´ementaires sont dispo- nibles sur le site internet : http://cran.r-project.org/web/packages/available_packages_by_name. html, ou bien encore ici : http://cran.r-project.org/bin/windows/contrib/, dans le dossier corres- pondant au num´ero x de votre version de R.
    [Show full text]
  • Determinants of Risk Perception Related to Exposure to Endocrine Disruptors During Pregnancy: a Qualitative and Quantitative Study on French Women
    Article Determinants of Risk Perception Related to Exposure to Endocrine Disruptors during Pregnancy: A Qualitative and Quantitative Study on French Women Steeve Rouillon 1,2,3, Houria El Ouazzani 1,2,3, Sylvie Rabouan 1,2, Virginie Migeot 1,2,3 and Marion Albouy-Llaty 1,2,3,* 1 INSERM, University Hospital of Poitiers, University of Poitiers, Clinical Investigation Center 1402, 2 rue de la Milétrie, 86021 Poitiers CEDEX, France; [email protected] (S.Ro.); [email protected] (H.E.O.); [email protected] (S.Ra.); [email protected] (V.M.) 2 Faculty of Medicine and Pharmacy, University of Poitiers, 6 rue de la Milétrie, 86000 Poitiers, France 3 Department of Public Health, BioSPharm Pole, University Hospital of Poitiers, 2 rue de la Milétrie, 86021 Poitiers CEDEX, France * Correspondence: [email protected]; Tel.: +33-549-443-323 Received: 27 August 2018; Accepted: 5 October 2018; Published: 11 October 2018 Abstract: Endocrine disruptors (EDCs) are known as environmental exposure factors. However, they are rarely reported by health professionals in clinical practice, particularly during pregnancy, even though they are associated with many deleterious consequences. The objectives of this study were to estimate the risk perception of pregnant women related to EDC exposure and to evaluate its determinants. A qualitative study based on the Health Belief Model was carried out through interviews of pregnant women and focus group with perinatal, environmental health and prevention professionals in 2015 in the city of Poitiers, France. Then, determinants of risk perception were included in a questionnaire administered to 300 women in the perinatal period through a quantitative study.
    [Show full text]
  • Linux Information Sheet Linux Information Sheet
    Linux Information Sheet Linux Information Sheet Table of Contents Linux Information Sheet....................................................................................................................................1 Michael K. Johnson <[email protected]>.......................................................................................1 1.Introduction to Linux............................................................................................................................1 2.Linux Features......................................................................................................................................1 3.Hardware Issues....................................................................................................................................1 4.An Incomplete List of Ported Programs and Other Software...............................................................1 5.Who uses Linux?...................................................................................................................................1 6.Getting Linux........................................................................................................................................1 7.Legal Status of Linux............................................................................................................................2 8.News About Linux................................................................................................................................2 9.The Future.............................................................................................................................................2
    [Show full text]
  • December 2016, Volume 34 No.2
    ISSN 0735-1348 Department of Physics, East Carolina University, 1000 East 5th Street, Greenville, NC 27858, USA http://www.ecu.edu/cs-cas/physics/ancient-timeline/ December 2016, Volume 34 No.2 IRSL dating of fast-fading sanidine feldspars from Sulawesi, Indonesia 1 Bo Li, Richard G. Roberts, Adam Brumm, Yu-Jie Guo, Budianto Hakim, Muhammad Ramli, Maxime Aubert, Rainer Grün, Jian-xin Zhao, E. Wahyu Saptomo Bayesian statistics in luminescence dating: The ‘baSAR’-model and its 14 implementation in the R package ‘Luminescence’ Norbert Mercier, Sebastian Kreutzer, Claire Christophe, Guillaume Guérin, Pierre Guibert, Christelle Lahaye, Philippe Lanos, Anne Philippe, and Chantal Tribolo RLumShiny - A graphical user interface for the R Package ‘Luminescence’ 22 Christoph Burow, Sebastian Kreutzer, Michael Dietze, Margret C. Fuchs, Manfred Fischer, Christoph Schmidt, Helmut Brückner Thesis abstracts 33 Bibliography 36 Ancient TL Started by the late David Zimmerman in 1977 EDITOR Regina DeWitt, Department of Physics, East Carolina University, Howell Science Complex, 1000 E. 5th Street Greenville, NC 27858, USA; Tel: +252-328-4980; Fax: +252-328-0753 ([email protected]) EDITORIAL BOARD Ian K. Bailiff, Luminescence Dating Laboratory, Univ. of Durham, Durham, UK ([email protected]) Geoff A.T. Duller, Institute of Geography and Earth Sciences, Aberystwyth University, Ceredigion, Wales, UK ([email protected]) Sheng-Hua Li, Department of Earth Sciences, The University of Hong Kong, Hong Kong, China ([email protected]) Shannon Mahan, U.S. Geological Survey, Denver Federal Center, Denver, CO, USA ([email protected]) Richard G. Roberts, School of Earth and Environmental Sciences, University of Wollongong, Australia ([email protected]) REVIEWERS PANEL Richard M.
    [Show full text]
  • Download Vim Tutorial (PDF Version)
    Vim About the Tutorial Vi IMproved (henceforth referred to as Vim) editor is one of the popular text editors. It is clone of Vi editor and written by Bram Moolenaar. It is cross platform editor and available on most popular platforms like Windows, Linux, Mac and other UNIX variants. It is command-centric editor, so beginners might find it difficult to work with it. But once you master it, you can solve many complex text-related tasks with few Vim commands. After completing this tutorial, readers should be able to use Vim fluently. Audience This tutorial is targeted for both beginners and intermediate users. After completing this tutorial, beginners will be able to use Vim effectively whereas intermediate users will take their knowledge to the next level. Prerequisites This tutorial assumes that reader has basic knowledge of computer system. Additionally, reader should be able to install, uninstall and configure software packages on given system. Conventions Following conventions are followed in entire tutorial: $ command execute this command in terminal as a non-root user 10j execute this command in Vim’s command mode :set nu execute this command in Vim’s command line mode Copyright & Disclaimer Copyright 2018 by Tutorials Point (I) Pvt. Ltd. All the content and graphics published in this e-book are the property of Tutorials Point (I) Pvt. Ltd. The user of this e-book is prohibited to reuse, retain, copy, distribute or republish any contents or a part of contents of this e-book in any manner without written consent of the publisher. We strive to update the contents of our website and tutorials as timely and as precisely as possible, however, the contents may contain inaccuracies or errors.
    [Show full text]
  • Rhea: a Transparent and Modular R Pipeline for Microbial Profiling Based on 16S Rrna Gene Amplicons
    Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons Ilias Lagkouvardos, Sandra Fischer, Neeraj Kumar and Thomas Clavel ZIEL—Core Facility Microbiome/NGS, Technical University of Munich, Freising, Germany ABSTRACT The importance of 16S rRNA gene amplicon profiles for understanding the influence of microbes in a variety of environments coupled with the steep reduction in sequencing costs led to a surge of microbial sequencing projects. The expanding crowd of scientists and clinicians wanting to make use of sequencing datasets can choose among a range of multipurpose software platforms, the use of which can be intimidating for non-expert users. Among available pipeline options for high-throughput 16S rRNA gene analysis, the R programming language and software environment for statistical computing stands out for its power and increased flexibility, and the possibility to adhere to most recent best practices and to adjust to individual project needs. Here we present the Rhea pipeline, a set of R scripts that encode a series of well- documented choices for the downstream analysis of Operational Taxonomic Units (OTUs) tables, including normalization steps, alpha- and beta-diversity analysis, taxonomic composition, statistical comparisons, and calculation of correlations. Rhea is primarily a straightforward starting point for beginners, but can also be a framework for advanced users who can modify and expand the tool. As the community standards evolve, Rhea will adapt to always represent the current state-of-the-art in microbial profiles analysis in the clear and comprehensive way allowed by the R language. Rhea scripts and documentation are freely available at https://lagkouvardos.github.io/Rhea.
    [Show full text]
  • Universal Ctags Documentation Release 0.3.0
    Universal Ctags Documentation Release 0.3.0 Universal Ctags Team 22 September 2021 Contents 1 Building ctags 2 1.1 Building with configure (*nix including GNU/Linux)........................2 1.2 Building/hacking/using on MS-Windows..............................4 1.3 Building on Mac OS.........................................7 2 Man pages 9 2.1 ctags.................................................9 2.2 tags.................................................. 33 2.3 ctags-optlib.............................................. 40 2.4 ctags-client-tools........................................... 46 2.5 ctags-incompatibilities........................................ 53 2.6 ctags-faq............................................... 56 2.7 ctags-lang-inko............................................ 62 2.8 ctags-lang-iPythonCell........................................ 62 2.9 ctags-lang-julia............................................ 63 2.10 ctags-lang-python.......................................... 65 2.11 ctags-lang-r.............................................. 69 2.12 ctags-lang-sql............................................. 70 2.13 ctags-lang-tcl............................................. 72 2.14 ctags-lang-verilog.......................................... 73 2.15 readtags................................................ 76 3 Parsers 81 3.1 Asm parser.............................................. 81 3.2 CMake parser............................................. 81 3.3 The new C/C++ parser........................................ 82 3.4 The
    [Show full text]
  • Supplementation of a Lacto-Fermented Rapeseed-Seaweed Blend Promotes
    Hui et al. Journal of Animal Science and Biotechnology (2021) 12:85 https://doi.org/10.1186/s40104-021-00601-2 RESEARCH Open Access Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets Yan Hui1, Paulina Tamez-Hidalgo2, Tomasz Cieplak1, Gizaw Dabessa Satessa3, Witold Kot4, Søren Kjærulff2, Mette Olaf Nielsen5, Dennis Sandris Nielsen1 and Lukasz Krych1* Abstract Background: The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. Results: This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria.
    [Show full text]