The Bioinformatics Playground
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FLOSS Final Report – Part 3 Free/Libre Open Source Software: Survey and Study
FLOSS Final Report – Part 3 Free/Libre Open Source Software: Survey and Study Basics of Open Source Software Markets and Business Models Berlin, July 2002 3 BERLECON RESEARCH GmbH Oranienburger Str. 32 10117 Berlin Tel.: +49 30 285296-0 Fax: +49 30 285296-29 Web: http://www.berlecon.de Email: [email protected] Acknowledgements: This work was prepared by Dorit Spiller and Thorsten Wichmann from Berlecon Research. It is part of the final report for the project „FLOSS – Free/Libre Open Source Software: Survey and Study“, which was financed under the European Com- mission‘s IST programme, key action 4 as accompanying measure (IST-2000-4.1.1). Disclaimer: The views expressed in this report are those of the authors and do not necessarily re- flect those of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of the following information. Nothing in this report implies or expresses a warranty of any kind. Results from this report should only be used as guidelines as part of an overall strategy. For detailed ad- vice on corporate planning, business processes and management, technology integra- tion and legal or tax issues, the services of a professional should be obtained. Names and trademarks mentioned in the report are the property of their respective owners. © 2002 by Berlecon Research GmbH. 4 V 1.1 - 020905 © 2002 by Berlecon Research GmbH. 5 Table of contents 1 Introduction....................................................................................................... 9 2 Software and the Open Source phenomenon.................................................... 11 2.1 The Open Source phenomenon ................................................................. -
Redhawk Linux User's Guide
Linux® User’s Guide 0898004-510 May 2006 Copyright 2006 by Concurrent Computer Corporation. All rights reserved. This publication or any part thereof is intended for use with Concurrent products by Concurrent personnel, customers, and end–users. It may not be reproduced in any form without the written permission of the publisher. The information contained in this document is believed to be correct at the time of publication. It is subject to change without notice. Concurrent makes no warranties, expressed or implied, concerning the information contained in this document. To report an error or comment on a specific portion of the manual, photocopy the page in question and mark the correction or comment on the copy. Mail the copy (and any additional comments) to Concurrent Computer Corporation, 2881 Gateway Drive, Pompano Beach, Florida, 33069. Mark the envelope “Attention: Publications Department.” This publication may not be reproduced for any other reason in any form without written permission of the publisher. RedHawk, iHawk, NightStar, NightTrace, NightSim, NightProbe and NightView are trademarks of Concurrent Computer Corporation. Linux is used pursuant to a sublicense from the Linux Mark Institute. Red Hat is a registered trademark of Red Hat, Inc. POSIX is a registered trademark of the Institute of Electrical and Electronics Engineers, Inc. AMD Opteron and AMD64 are trademarks of Advanced Micro Devices, Inc. The X Window System is a trademark of The Open Group. OSF/Motif is a registered trademark of the Open Software Foundation, Inc. Ethernet is a trademark of the Xerox Corporation. NFS is a trademark of Sun Microsystems, Inc. HyperTransport is a licensed trademark of the HyperTransport Technology Consortium. -
Linux Distributions for Bioinformatics
EMBnet. news 15.3 REVIEWS 35 run as a virtual machine, in parallel with the host Linux distributions for operating system, a feature which has the ad- vantage of giving occasional users or students bioinformatics: the possibility to use their usual environments while becoming familiar with a new operating an update system. This is reflected in the Linux distributions for bioinformatics that we have reviewed in this article. A trend that has been noticed in respect with the review we made in 2007 is the tenden- cy to use Ubuntu as base distribution which is in fact replacing Knoppix and to provide the bio- informatics bench environment also as a virtual machine which can be run inside the popular VMWare environment in parallel with the host op- erating system. While reviewing the distributions in this article we have paid particular attention to 1 Antonia Rana and Fabrizio Foscarini their user friendliness and ease of use. Joint Research Centre, European Commission Bio-Linux Bio-Linux [4], developed and distributed by the NERC Environmental Bioinformatics Centre, has Introduction evolved since our review in 2007, its home page The article provides an updated view on the has also changed. Its developers describe it as world of Linux distributions tailored for bioinformat- “…a fully featured, powerful, configurable and ics analysis. The main driver for producing these easy to maintain bioinformatics workstation ” and distributions is to provide an easy-to-use, user in fact it is rich with applications and documen- friendly environment for non IT specialised users tation. In its current versions, 5.0, the most nota- without strong requirements on the knowledge ble new features are the possibility to boot it from of the technology. -
Debian \ Amber \ Arco-Debian \ Arc-Live \ Aslinux \ Beatrix
Debian \ Amber \ Arco-Debian \ Arc-Live \ ASLinux \ BeatriX \ BlackRhino \ BlankON \ Bluewall \ BOSS \ Canaima \ Clonezilla Live \ Conducit \ Corel \ Xandros \ DeadCD \ Olive \ DeMuDi \ \ 64Studio (64 Studio) \ DoudouLinux \ DRBL \ Elive \ Epidemic \ Estrella Roja \ Euronode \ GALPon MiniNo \ Gibraltar \ GNUGuitarINUX \ gnuLiNex \ \ Lihuen \ grml \ Guadalinex \ Impi \ Inquisitor \ Linux Mint Debian \ LliureX \ K-DEMar \ kademar \ Knoppix \ \ B2D \ \ Bioknoppix \ \ Damn Small Linux \ \ \ Hikarunix \ \ \ DSL-N \ \ \ Damn Vulnerable Linux \ \ Danix \ \ Feather \ \ INSERT \ \ Joatha \ \ Kaella \ \ Kanotix \ \ \ Auditor Security Linux \ \ \ Backtrack \ \ \ Parsix \ \ Kurumin \ \ \ Dizinha \ \ \ \ NeoDizinha \ \ \ \ Patinho Faminto \ \ \ Kalango \ \ \ Poseidon \ \ MAX \ \ Medialinux \ \ Mediainlinux \ \ ArtistX \ \ Morphix \ \ \ Aquamorph \ \ \ Dreamlinux \ \ \ Hiwix \ \ \ Hiweed \ \ \ \ Deepin \ \ \ ZoneCD \ \ Musix \ \ ParallelKnoppix \ \ Quantian \ \ Shabdix \ \ Symphony OS \ \ Whoppix \ \ WHAX \ LEAF \ Libranet \ Librassoc \ Lindows \ Linspire \ \ Freespire \ Liquid Lemur \ Matriux \ MEPIS \ SimplyMEPIS \ \ antiX \ \ \ Swift \ Metamorphose \ miniwoody \ Bonzai \ MoLinux \ \ Tirwal \ NepaLinux \ Nova \ Omoikane (Arma) \ OpenMediaVault \ OS2005 \ Maemo \ Meego Harmattan \ PelicanHPC \ Progeny \ Progress \ Proxmox \ PureOS \ Red Ribbon \ Resulinux \ Rxart \ SalineOS \ Semplice \ sidux \ aptosid \ \ siduction \ Skolelinux \ Snowlinux \ srvRX live \ Storm \ Tails \ ThinClientOS \ Trisquel \ Tuquito \ Ubuntu \ \ A/V \ \ AV \ \ Airinux \ \ Arabian -
Lin1 3.2.0-4-Amd64 #1 SMP Debian 3.2.60-1+Deb7u3 X86 64 GNU/Linux :~$ Uname -R 3.2.0-4-Amd64 Kernel Verwendet Module Z.B
Vorbereitung auf LPIC-1 Georg Schönberger XORTEX eBusiness GmbH Version 30. März 2016 Kurz über mich... Studium Computer- und Mediensicherheit Gitter-basierende Kryptosysteme Studium Sichere Informationssysteme Auslagerung der IPSec- Verschlüsselung auf Grafikkarten Jobs F&E in Hagenberg Thomas-Krenn.AG XORTEX Autor (IT-Admin, LinuxUser) 2 LPIC-1 LVA Meine Tätigkeiten Betreuung Server-Infrastruktur Ceph Cluster Ansible Betreuung DRBD-Cluster mit LXC-Container Entwicklung von Monitoring-Plugins Entwicklung von Performance-Tests http://git.thomas-krenn.com Verbesserung der internen/externen Sicherheit Zertifizierungen Network+, Server+, Linux Essentials, LPIC-1, LPIC-2 3 LPIC-1 LVA Die LVA Vorbereitung auf LPIC-1 Version 4 Exam 101 und Exam 102 Themen LPIC-1 Objectives V4 (wiki.lpi.org) Guides Achtung – Version 3: Learn Linux, 101: A roadmap for LPIC-1 (ibm.com) GNU/Linux Administration Manuals (nongnu.org) Bücher LPIC-1: Sicher zur erfolgreichen Linux-Zertifizierung (Harald Maaßen) Achtung – Version 3: LPIC-1. Vorbereitung auf die Prüfung des Linux Professional Institute (Peer Heinlein) 4 LPIC-1 LVA Objectives: Exam 101 5 LPIC-1 LVA Topic 101: System Architecture Peripherie Module Virtuelle Dateisysteme (sysfs, procfs) Boot-Vorgang Runlevel 6 LPIC-1 LVA 101.1 Determine and configure hardware settings Kernel Module /proc /sys 7 LPIC-1 LVA Kernel Module Welchen Kernel verwende ich gerade? :~$ uname -a Linux lin1 3.2.0-4-amd64 #1 SMP Debian 3.2.60-1+deb7u3 x86_64 GNU/Linux :~$ uname -r 3.2.0-4-amd64 Kernel verwendet Module Z.B. als ladbare -
An Integrated Live Linux Distribution for the Bioinformatics Community Guangchuang Yu1†, Li-Gen Wang2,3†, Xiao-Hua Meng3 and Qing-Yu He1*
Yu et al. BMC Research Notes 2012, 5:360 http://www.biomedcentral.com/1756-0500/5/360 TECHNICAL NOTE Open Access LXtoo: an integrated live Linux distribution for the bioinformatics community Guangchuang Yu1†, Li-Gen Wang2,3†, Xiao-Hua Meng3 and Qing-Yu He1* Abstract Background: Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings: Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions: LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. Keywords: Bioinformatics, Software, Linux, Operating system Findings bioinformatics expertise, and thus often face data ana- The completion of the human genome project [1] lysis bottleneck, leading to the slow progress of bio- fuelled the spark of many post-omics technologies such logical research. as massively parallel sequencing, genotyping and proteo- Building tailored computing solutions requires specia- mics. These technologies dramatically increase biological lized knowledge. While this challenge can be overcome data generation, and the biological data throughput has by using free and open source software (FOSS) [4], the been increasing at a rate exceeding Moore’s Law [2]. -
Webserver WEBSER Shell-Zugriff Via Webbrowser Debian 6.0 S
COMMUNITY-EDITION Frei kopieren und beliebig weiter verteilen ! 04.2011 04.2011 APACHE-ALTERNATIVEN: WEBSITES AUFSETZEN UND PFLEGEN VER WEBSERVER WEBSER Shell-Zugriff via Webbrowser Debian 6.0 S. 6 Live- und Install-DVDs So verwalten Sie mit PHP Shell und Shell in a Box für 32- und 64-Bit-PCs den Webserver über die Kommandozeile S. 33, DVD Analyse-Tools für die Website Server-Logs grafisch aufbereiten und Benutzerzugriffe detailliert auswerten mit Webalizer und Piwik S. 38, 42, DVD Fünf Apache-Alternativen für alle Fälle S. 20, 28, DVD Profi-Server Nginx, hochsicherer Hiawatha, Allrounder Lighttpd, Minimalist Thttpd, schneller Einstieg mit Monkey HTTP Daemon MoonOS 4 S. 12 Schicke Mac-Optik für Ubuntu „Maverick“ Laptop-Schnäppchen Aspire 5253 Acers neuer 15,6-Zöller auf AMD-Fusion-Basis mit satter Grafik-Leistung und langer Laufzeit S. 80 Texterkennung in Platzfresser von Profi-Qualität S. 48, DVD der Platte putzen S. 70 Unity 2010.2 S. 8 Cuneiform: multilinguale OCR Dateileichen und Altlasten Maßgeschneiderte mit intuitiver Oberfläche aufspüren mit JDiskReport Distro auf Knopfdruck MythTV-Export Geballtes Wissen auf Knopfdruck S. 66 stets zur Hand S. 82, DVD Aufnahmen unkompliziert Goldendict vereint On- und wandeln, streamen, brennen Offline-Lexika in einer GUI ATI FIREPRO 3D • GOLDENDICT LOUT LUCIDOR MYTHTV OCR ATI 4 196067 008502 04 www.linux-user.de EDITORIAL Klare Ansage Sehr geehrte Leserinnen und Leser, im Vorfeld von Ubuntu 11.04 Wohlgemerkt: Die MIT-Lizenz des statt Lizenzgebühren zu verlan- sorgte Canonical immer wieder für Banshee-Projekts hätte jegliche gen. Diesem Geschäftsmodell fol- Schlagzeilen – zuletzt im Zusam- Änderungen auch ganz ohne Nach- gend, werde man grundsätzlich wo menhang mit der Ablösung des frage erlaubt, formaljuristisch war immer möglich aus der Software bisherigen Mediaplayers Rhythm- Canonicals Ansinnen völlig in der freien Upstream-Projekte Ge- box durch Banshee: Der nämlich Ordnung. -
Coase's Penguin, Or, Linux and the Nature of the Firm
Articles Coase's Penguin, or, Linux and The Nature of the Firm Yochai Benklert CONTENTS INTRODUCTION........... ......... ........ .................... 371 I. PEER PRODUCTIONALL AROUND ...................................................... 381 A. Content......................................................................................... 384 B. Relevance/Accreditation...........................................................390 C. Value-AddedDistribution ............................................................396 D. Summ ary ......................................................................................399 t Professorof Law, New York UniversitySchool of Law. Researchfor this Article was partlysupported by a grantfrom the FilomenD'Agostino and Max E. GreenbergResearch Fund at the New York UniversitySchool of Law. I owe thanksto many for commentson this and earlierdrafts, including: Bruce Ackerman, Ed Baker,Elazar Barkan, Jamie Boyle, Dan Burk,Ben Damstedt,Bob Ellickson,Terry Fisher, Natalie Jeremijenko,David Johnson,Dan Kahan,Niva Elkin Koren,Tara Lemmey, Larry Lessig, Doug Lichtman,Jerry Mashaw, Eben Moglen, Mark Nadel,Helen Nissenbaum, George Priest, Peggy Radin,Carol Rose, ChuckSabel, Alan Schwartz, Clay Shirky,Richard Stallman, and Kenji Yoshino.I owe special thanksto Steve Snyderfor his invaluableresearch assistance on the peerproduction enterprises described here. I have gotten many questionsabout the "Coase'sPenguin" portion of the title. It turnsout that the geek culturethat easily recognizes"Coase" doesn't recognizethe -
Sag Doch Mal Hi
Sag doch mal Hi Beitrag von „medProfiler“ vom 6. April 2015, 00:13 Hallo liebe Community Hier werde ich mich kurz vorstellen und wenn es mir jemand gleich tun möchte, dann hat er hier seine Bühne. Geboren und aufgewachsen bin ich in Thüringen. Ob ich ein Wunschkind war weiß ich nicht. Meine Eltern fahren jedenfalls noch heute jedes Jahr in den Zoo und bewerfen die Störche mit Steinen. Momentan lebe ich in Bayern und habe eine kleine Familie und einen Job. Bald geht es aber wieder zurück nach Mitteldeutschland. Leben im Kurzdurchlauf: Schule - Ausbildung zum medizinischen Masseur - 4 Jahre Bundeswehr Mittenwald - Rettungsdienst - Fachinformatiker. Hauptsächlich beschäftige ich mich mit den Fachbereichen Security, Verschlüsselung, Datenschutz und den Themen Privatsphäre sowie Netzneutralität. Es gibt sicher viele weitere Gebiete in denen man auch aktivistisch unterwegs sein und sich für einsetzen kann aber, sind wir realistisch, die schiere Masse politischer und gesellschaftlicher Scheiße ist alleine nicht mehr zu bewältigen. Da muss man sich zusammentun und aufteilen. Nein, das ist kein Widerspruch. Seit ein paar Jahren nutze ich ausschließlich Linux. Daheim überall Arch Linux und alle Server laufen mit Debian 7 und 8. Ich habe wenig Berührungsangst mit diversen Programmiersprachen, bin aber in Hardware und Netzwerk daheim. Als Hacker würde ich mich schon bezeichnen, allerdings beschränke ich mich auch hier auf Hardware. Seit geraumer Zeit unterstütze ich Anonymous und mag den Gedanken hinter der Bewegung. Leider sind viele gute Aktivisten inhaftiert oder unter massiven Druck gesetzt worden und es https://jollausers.de/thread/16-sag-doch-mal-hi/ 1 wurde schon eine Weile nichts Großes mehr auf die Beine gestellt. -
KNOPPIX/Math
KNOPPIX/Math: Portable and distributable collection of mathematical software and free documents Tatsuyoshi Hamada (Fukuoka University) Kuniyasu Suzaki (AIST) Kengo Iijima (AIST) Arimitsu Shikoda (Tohoku Gakuin University) ICMS2006 in Castro Urdiales 2006.09.02 1960s DEC PDF-7 http://research.microsoft.com/~gbell/Digital/timeline/1964-3.htm 1970s DECstation PDP-8 http://research.microsoft.com/~gbell/Digital/timeline/1977-2.htm A prototype of the Apple personal computer http://www.150.si.edu/chap9/9ap_le.htm 1980s IBM PC 5150 http://www-03.ibm.com/ibm/history/exhibits/pc/pc_1.html Apple IIe http://www.old-computers.com/museum/computer.asp?st=1&c=83 1990s Apple SE/30 http://www.apple-history.com/?page=gallery&model=se30 IBM ThinkPad 700C http://www-06.ibm.com/jp/event/museum/rekishi/92_tp.html 1995.08.24 1991.08.25 Microsoft Windows 95 Linus's first announcement 1991.10.05 Linux 0.0.2 Recently Panasonic Toughbook eLite W4 with Microsoft Windows XP Professional 12.1" XGA Color LCD Display, built-in DVD/CD-RW, only 2.8 lbs (1270g). http://www.lenovo.com/us/en/ http://www.sharp.co.jp/products/slc760/index.html Mathematicians need TeX system for writing papers. Mathematical software for calculating and visualization http://www.lg.fukuoka-u.ac.jp/~ynagata/latex/texlion.html Dynagraph Mathematicians need to communicate other mathematicians for deepening our investigations for getting new ideas Conferences and Workshops held in foreign countries Laptop computers become a ubiquitous parts We want to read and write e-mail messages in our native language. We have to set up and configure the desktop environment on our laptops. -
PAIPIX@ : from Desktop to Data Servers
PAIPIX@ : From Desktop to Data Servers http://www.paipix.org ●Old PAIPIX Live - “One of those Knoppix things” ● present usage at IM and the plan ● infrastructure at IM ● Updated Requirements and Developments ● New hardware systems at IM ●Present PAIPIX Installer/Live ● Debian distribution ● Debian installer and live ● PAIPIX packages and repositories ● The support for the meteorology tools ●Conclusions A. & L. Amorim ECMWF 11th Workshop on Meteorological Operational Systems - 16/11/2007 What was PAIPIX? Started as live Linux for scientific appl.: in 2004 -“one of those Knoppix like stuff” ● End 2004 – Complete system en,pt,es,fr,de,it version 3.7 - 2 GB live image used until today at IM ... ● End 2005 – Version 5 to support update of the installed system changed to be built from “Kanotix” ... ●2006 – Transition version 6. Shortcomings: ● Debian based but packed by a very small community ● The installer was a bit unstable (application specific) ● PAIPIX was “remastered” - depended on initial image A. & L. Amorim ECMWF 11th Workshop on Meteorological Operational Systems - 16/11/2007 Some evaluation of “old” PAIPIX news 20.06.2005 http://www.heise.de/english/newsticker/news/60800 “Moreover, in Version 4.0 a number of expansions have been integrated that have flowed back to Knoppix from the Knoppix-based distributions Kanotix, Quantian, Paipix and Freeduc. With, for example, the Kanotix hardware support for ISDN and DSL adapters from AVM, an improved hard disk installer, scientific software from Quantian and Paipix and learning software for children from Freeduc among them.” http://distrowatch.com/index.php?distribution=paipix http://quebecos.com/index.php? option=com_content&task=view&id=511&Itemid=2 Meteo. -
GNU/Linux Distro Timeline LEAF Version 10.9 Skolelinux Lindows Linspire Authors: A
1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 Libranet Omoikane (Arma) Gibraltar GNU/Linux distro timeline LEAF Version 10.9 Skolelinux Lindows Linspire Authors: A. Lundqvist, D. Rodic - futurist.se/gldt Freespire Published under the GNU Free Documentation License MEPIS SimplyMEPIS Impi Guadalinex Clonezilla Live Edubuntu Xubuntu gNewSense Geubuntu OpenGEU Fluxbuntu Eeebuntu Aurora OS Zebuntu ZevenOS Maryan Qimo wattOS Element Jolicloud Ubuntu Netrunner Ylmf Lubuntu eBox Zentyal Ubuntu eee Easy Peasy CrunchBang gOS Kiwi Ubuntulite U-lite Linux Mint nUbuntu Kubuntu Ulteo MoLinux BlankOn Elive OS2005 Maemo Epidemic sidux PelicanHPC Inquisitor Canaima Debian Metamorphose Estrella Roja BOSS PureOS NepaLinux Tuquito Trisquel Resulinux BeatriX grml DeadCD Olive Bluewall ASLinux gnuLiNex DeMuDi Progeny Quantian DSL-N Damn Small Linux Hikarunix Damn Vulnerable Linux Danix Parsix Kanotix Auditor Security Linux Backtrack Bioknoppix Whoppix WHAX Symphony OS Knoppix Musix ParallelKnoppix Kaella Shabdix Feather KnoppMyth Aquamorph Dreamlinux Morphix ZoneCD Hiwix Hiweed Deepin Kalango Kurumin Poseidon Dizinha NeoDizinha Patinho Faminto Finnix Storm Corel Xandros Moblin MeeGo Bogus Trans-Ameritech Android Mini Monkey Tinfoil Hat Tiny Core Yggdrasil Linux Universe Midori Quirky TAMU DILINUX DOSLINUX Mamona Craftworks BluePoint Yoper MCC Interim Pardus Xdenu EnGarde Puppy Macpup SmoothWall GPL SmoothWall Express IPCop IPFire Beehive Paldo Source Mage Sorcerer Lunar eIT easyLinux GoboLinux GeeXboX Dragora