Sesión sobre GNU Linux - Introduction and Administration. Dentro de curso de postgrado "Data Science. Aplicaciones a la Biologia y a la Medicina con Python y R". Universidad de Barcelona. 2020
Brief introduction to GNU/Linux OS. Introduction of basic concepts, commands, And a few tips for administration tasks.
With the context of a course in Data Science: Applications to Biology and Medicine with Python and R (2020 edition). Postgraduate course at University of Barcelona.
This document provides an overview of Ubuntu, an open-source operating system based on Debian Linux. It discusses Ubuntu's history and philosophy, how it differs from Windows, exploring the Ubuntu desktop environment, examples of Ubuntu in government and enterprise use, and answers common questions about Ubuntu. The presentation encourages users to try Ubuntu and explore the benefits of open-source software.
Introduction to GNU/Linux, Free/Libre Open Source Software, comparing the OS with Mac OSX and Microsoft Windows, and a few other infos and pointers.
Content partially reused from a Masters Degree at VHIR where I had to tech that introduction prior to using GNU/Linux tools for Bioinformatics in that master of traslational medicine: https://www.vhir.org
This document discusses how information and communication technologies (ICT), specifically free and open source software (FOSS), can help people's organizations in their work and struggles for social change. It provides examples of FOSS tools like Ubuntu, Mozilla Firefox, OpenOffice that can improve efficiency, data collection/analysis, and advocacy. While FOSS provides advantages over proprietary software in terms of cost, customization and community support, there are also challenges to adoption like technical skills requirements and lack of alternatives for some proprietary applications. Case studies show how human rights groups have successfully used FOSS for documentation, data analysis and advocacy work.
Sesión sobre GNU Linux - Introduction and Administration. Dentro de curso de postgrado "Data Science. Aplicaciones a la Biologia y a la Medicina con Python y R". Universidad de Barcelona. 2020
Brief introduction to GNU/Linux OS. Introduction of basic concepts, commands, And a few tips for administration tasks.
With the context of a course in Data Science: Applications to Biology and Medicine with Python and R (2020 edition). Postgraduate course at University of Barcelona.
This document provides an overview of Ubuntu, an open-source operating system based on Debian Linux. It discusses Ubuntu's history and philosophy, how it differs from Windows, exploring the Ubuntu desktop environment, examples of Ubuntu in government and enterprise use, and answers common questions about Ubuntu. The presentation encourages users to try Ubuntu and explore the benefits of open-source software.
Introduction to GNU/Linux, Free/Libre Open Source Software, comparing the OS with Mac OSX and Microsoft Windows, and a few other infos and pointers.
Content partially reused from a Masters Degree at VHIR where I had to tech that introduction prior to using GNU/Linux tools for Bioinformatics in that master of traslational medicine: https://www.vhir.org
This document discusses how information and communication technologies (ICT), specifically free and open source software (FOSS), can help people's organizations in their work and struggles for social change. It provides examples of FOSS tools like Ubuntu, Mozilla Firefox, OpenOffice that can improve efficiency, data collection/analysis, and advocacy. While FOSS provides advantages over proprietary software in terms of cost, customization and community support, there are also challenges to adoption like technical skills requirements and lack of alternatives for some proprietary applications. Case studies show how human rights groups have successfully used FOSS for documentation, data analysis and advocacy work.
This document outlines the content of a Linux system and network administration course taught over 15 lectures and labs. The course covers topics such as Linux installation, desktop environments, file systems, user administration, networking configuration including DHCP, NIS, NFS, DNS, mail servers and firewalls. It also covers troubleshooting, system monitoring and installing additional software packages. The course is graded based on two exams and a lab component, and requires a minimum of 80% attendance and 60% marks to pass.
This document provides an overview of the history and development of the Linux operating system. It discusses how Linux originated from earlier operating systems like Unix and was completed using software from the GNU project. Key advantages of Linux mentioned include low cost, stability, performance, flexibility and security. The document also describes the file hierarchy and culture of free software in Linux. It provides examples of commands used in Linux and explains the use of sudo for privilege escalation.
OpenAIRE at the 8th e-Infrastructure Concetration Meeting Nov 5, 2010 CERN -...OpenAIRE
By Iryna Kuchma (EIFL), Birgit Schmidt (Goettingen State and University Library) presented at the 8th e-Infrastructure Concetration Meeting Nov 5, 2010 CERN - Geneva
This document provides an agenda for a session on installing the LAMP stack on Ubuntu Desktop. The agenda includes discussing Windows vs Linux, the Linux kernel, Linux distributions, installing Linux, Linux commands and shortcuts, the Mauritius Linux User Group, and LAMP (Linux, Apache, MySQL, PHP). Links are provided for further information on each topic.
This document provides an introduction to free and open source software (FOSS) including its history and key concepts. It discusses how the GNU project and Linux kernel led to the development of GNU/Linux distributions. It also lists some popular FOSS alternatives to proprietary software and provides demonstrations of educational FOSS tools.
[MM2023] Ducho: A Unified Framework for the Extraction of Multimodal Features...Daniele Malitesta
Slides for the paper "Ducho: A Unified Framework for the Extraction of Multimodal Features in Recommendation", accepted and presented at the 31st ACM International Conference on Multimedia (MM'23).
Paper: https://dl.acm.org/doi/10.1145/3581783.3613458
Code: https://github.com/sisinflab/Ducho
Raspbian is an optimized version of the Debian operating system designed specifically for the Raspberry Pi. It inherits most traits from Debian Jessie, but is modified and optimized to run on Raspberry Pi hardware. Originally a port of the Debian 'armhf' port for ARM-based systems, Raspbian aims to put a full desktop computer experience on Raspberry Pi devices to promote access to computing for education.
This 1st presentation in the training "Introduction to linux for bioinformatics" gives an introduction to Linux, and the concepts by which Linux operates.
BITS: Introduction to linux, distributions and installationBITS
This slide is part of the BITS training session: "Introduction to linux for life sciences."
See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203890%3Abioperl-additional-material&catid=84&Itemid=284
An introduction to the linux kernel and device drivers (NTU CSIE 2016.03)William Liang
This lecture is for a 3-hours class -- Open Source System Software & Practice -- in Dept. Computer Science and Information Engineering of National Taiwan University, organized and hosted by Prof. Shih-Hao Hung.
The slides give an introductory overview on the Linux kernel and device drivers. It covers introductions and references for the Linux kernel, boot process overview, basics for system integration, character device drivers, and preliminary description and in-class issue discussion about memory management, multitask and concurrency control, interrupt handling, and waiting queue control, etc.
Andhra pradesh workshop user manual october 2016OERindia
Subject Teacher Forum workshop for Andhra Pradesh Maths and Science teachers.
This is the handout or the workshop, created by IT for change Resouce center Bengaluru.
The document provides an introduction to free and open source software. It discusses the history of the movement from the early days of freely shared software to the current GNU/Linux system. It explains Richard Stallman's founding of the Free Software Foundation in response to the rise of proprietary software. It outlines the four essential freedoms that define free software.
Michael Weber - Rechenkraft.net - From Volunteers to ScientistsCitizenCyberlab
Michael Weber presenting Rechenkraft.net - From Volunteers to Scientists, at the Citizen Cyberlab Summit, 17-18 September 2015, University of Geneva (UNIGE).
The document discusses open source software options for operating systems, session management tools, desktop applications, and additional resources that can be used to set up public workstations in libraries. It provides lists of recommended open source operating systems like Ubuntu and Groovix, session management software like libKi, productivity and multimedia applications, and websites for additional support. Finally, it lists some vendors that provide open source-based systems and hardware designed for public library workstations.
The document discusses Docker containers and their architecture. It begins by explaining that Docker originated as a tool called Docker created by dotCloud to manage customer applications in the cloud. It became very popular with developers and dotCloud changed its name to Docker, Inc. and focused its business on Docker. The document then discusses how Docker uses Linux kernel features like control groups (cgroups) and namespaces to isolate containers and their resources. It explains that Docker architecture includes a client, daemon, containers running applications, and an optional distributed data store. Finally, it provides an example of basic Docker commands to check the Docker version and run a test container.
LoCloud - D2.5: Lightweight Digital Library Prototype (LoCloud Collections Se...locloud
This report presents the prototype of LoCloud Collections system. The main aim of LoCloud Collections (initially named Lightweight Digital Library) is to
provide small cultural institutions with the possibility to host their digitized collections (metadata as well as content) very easily in the cloud, and make that data widely available on the internet, and in particular to Europeana.
The developed service prototype is available on-line at https://locloudhosting.net/ and can be used by anyone to create new digital library in just a few minutes.
The document provides an overview of Linux operating systems, distributions of Linux like Ubuntu, and how to get and install Ubuntu. It discusses what Linux is, popular Linux distributions like Ubuntu, desktop environments like GNOME and KDE, and how Ubuntu can be installed using options like a live CD, WUBI, or USB drive. It also touches on reasons for using Ubuntu like its large community support and emphasis on usability.
This document provides an overview of a 2 hour Linux workshop. It will cover the history and architecture of Linux, the file system, basic commands, and software management. No prior Linux experience is necessary. The workshop will focus on Ubuntu but discuss other Linux flavors. It will start with the history of UNIX and the GNU project. It will then cover the Linux kernel, open source software, Ubuntu releases, filesystems like ext3 and ext4, files and directories, basic commands, and installing, removing, and upgrading software using tools like apt, Synaptic, and command line commands.
The document provides an introduction to the Linux operating system, discussing its origins from the collaborative efforts of many programmers to create a free and open source alternative to commercial UNIX systems. It describes how Linus Torvalds created the initial Linux kernel in 1991 and how it has since been refined by numerous contributors. The summary concludes that Linux has grown from humble beginnings to become a widely used and respected operating system available across many computing platforms.
"SEMINAR: Análisis de Big data con Tidyverse y Spark: uso en estadística pública"
By Xavier de Pedro Puente, Ph.D.
Senior Technician at the Barcelona City Council.
Wednesday, March 29th, 2023. 16h-19:00h + questions
Within the context of the postgraduate course on
"Data Science. Applications to Biology and Medicine with Python and R"
at University of Barcelona (IL3). 2023.
Taller Allibera el teu ordinador amb Linux en catalaXavier de Pedro
DIMECRES 25/05/2022 a les 18:30h - CÀPSULA FORMATIVA: ALLIBERA EL TEU ORDINADOR
Casal de Barri Can Carol
http://cancarolvallcarca.cat
Aquesta càpsula tindrà una part introductòria on es repassaran els principals problemes que hi sol haver en emprar ordinadors amb sistemes operatius privatius de
llibertats. Es mostraran, pas a pas, formes d’instal·lar un sistema operatiu lliure, i en català, actualitzat (i actualitzable fàcilment per xarxa de forma periòdica).
Durant la sessió es farà una instal·lació d’un sistema operatiu lliure en un ordinador al costat del sistema operatiu que ja hi té instal·lat (sense malmetre’l). També es mostrarà un altre ordinador similar ja enllestit.
Es recomana portar l’ordinador propi.
Más contenido relacionado
Similar a GNU Linux - Introduction and Administration
This document outlines the content of a Linux system and network administration course taught over 15 lectures and labs. The course covers topics such as Linux installation, desktop environments, file systems, user administration, networking configuration including DHCP, NIS, NFS, DNS, mail servers and firewalls. It also covers troubleshooting, system monitoring and installing additional software packages. The course is graded based on two exams and a lab component, and requires a minimum of 80% attendance and 60% marks to pass.
This document provides an overview of the history and development of the Linux operating system. It discusses how Linux originated from earlier operating systems like Unix and was completed using software from the GNU project. Key advantages of Linux mentioned include low cost, stability, performance, flexibility and security. The document also describes the file hierarchy and culture of free software in Linux. It provides examples of commands used in Linux and explains the use of sudo for privilege escalation.
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Slides for the paper "Ducho: A Unified Framework for the Extraction of Multimodal Features in Recommendation", accepted and presented at the 31st ACM International Conference on Multimedia (MM'23).
Paper: https://dl.acm.org/doi/10.1145/3581783.3613458
Code: https://github.com/sisinflab/Ducho
Raspbian is an optimized version of the Debian operating system designed specifically for the Raspberry Pi. It inherits most traits from Debian Jessie, but is modified and optimized to run on Raspberry Pi hardware. Originally a port of the Debian 'armhf' port for ARM-based systems, Raspbian aims to put a full desktop computer experience on Raspberry Pi devices to promote access to computing for education.
This 1st presentation in the training "Introduction to linux for bioinformatics" gives an introduction to Linux, and the concepts by which Linux operates.
BITS: Introduction to linux, distributions and installationBITS
This slide is part of the BITS training session: "Introduction to linux for life sciences."
See http://www.bits.vib.be/index.php?option=com_content&view=article&id=17203890%3Abioperl-additional-material&catid=84&Itemid=284
An introduction to the linux kernel and device drivers (NTU CSIE 2016.03)William Liang
This lecture is for a 3-hours class -- Open Source System Software & Practice -- in Dept. Computer Science and Information Engineering of National Taiwan University, organized and hosted by Prof. Shih-Hao Hung.
The slides give an introductory overview on the Linux kernel and device drivers. It covers introductions and references for the Linux kernel, boot process overview, basics for system integration, character device drivers, and preliminary description and in-class issue discussion about memory management, multitask and concurrency control, interrupt handling, and waiting queue control, etc.
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The document discusses open source software options for operating systems, session management tools, desktop applications, and additional resources that can be used to set up public workstations in libraries. It provides lists of recommended open source operating systems like Ubuntu and Groovix, session management software like libKi, productivity and multimedia applications, and websites for additional support. Finally, it lists some vendors that provide open source-based systems and hardware designed for public library workstations.
The document discusses Docker containers and their architecture. It begins by explaining that Docker originated as a tool called Docker created by dotCloud to manage customer applications in the cloud. It became very popular with developers and dotCloud changed its name to Docker, Inc. and focused its business on Docker. The document then discusses how Docker uses Linux kernel features like control groups (cgroups) and namespaces to isolate containers and their resources. It explains that Docker architecture includes a client, daemon, containers running applications, and an optional distributed data store. Finally, it provides an example of basic Docker commands to check the Docker version and run a test container.
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provide small cultural institutions with the possibility to host their digitized collections (metadata as well as content) very easily in the cloud, and make that data widely available on the internet, and in particular to Europeana.
The developed service prototype is available on-line at https://locloudhosting.net/ and can be used by anyone to create new digital library in just a few minutes.
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This document provides an overview of a 2 hour Linux workshop. It will cover the history and architecture of Linux, the file system, basic commands, and software management. No prior Linux experience is necessary. The workshop will focus on Ubuntu but discuss other Linux flavors. It will start with the history of UNIX and the GNU project. It will then cover the Linux kernel, open source software, Ubuntu releases, filesystems like ext3 and ext4, files and directories, basic commands, and installing, removing, and upgrading software using tools like apt, Synaptic, and command line commands.
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"SEMINAR: Análisis de Big data con Tidyverse y Spark: uso en estadística pública"
By Xavier de Pedro Puente, Ph.D.
Senior Technician at the Barcelona City Council.
Wednesday, March 29th, 2023. 16h-19:00h + questions
Within the context of the postgraduate course on
"Data Science. Applications to Biology and Medicine with Python and R"
at University of Barcelona (IL3). 2023.
Taller Allibera el teu ordinador amb Linux en catalaXavier de Pedro
DIMECRES 25/05/2022 a les 18:30h - CÀPSULA FORMATIVA: ALLIBERA EL TEU ORDINADOR
Casal de Barri Can Carol
http://cancarolvallcarca.cat
Aquesta càpsula tindrà una part introductòria on es repassaran els principals problemes que hi sol haver en emprar ordinadors amb sistemes operatius privatius de
llibertats. Es mostraran, pas a pas, formes d’instal·lar un sistema operatiu lliure, i en català, actualitzat (i actualitzable fàcilment per xarxa de forma periòdica).
Durant la sessió es farà una instal·lació d’un sistema operatiu lliure en un ordinador al costat del sistema operatiu que ja hi té instal·lat (sense malmetre’l). També es mostrarà un altre ordinador similar ja enllestit.
Es recomana portar l’ordinador propi.
Seminario "Análisis de Big Data con Tidyverse y Spark: uso en estadística pública". Dentro de curso de postgrado: "Data Science. Applications to Biology and Medicine with Python and R". Universidad de Barcelona. 2020
Challenges and opportunities in Artificial IntelligenceXavier de Pedro
Short Talk in a Workshop to discuss use of Artificial Intelligence among cities, universities and other partners for potential projects in this area. Held at the Barcelona Supercomputing Center.
The document summarizes Barcelona's Digital City Plan for 2017-2020, which includes several government measures related to open data and digitization. The plan focuses on 5 strategic areas: data sovereignty, ethical data management, developing a city-wide data infrastructure called CityOS, using data to drive internal innovation, and sharing data through a data commons. It will be implemented according to a scheduled timeline and coordinated by a board for transversal data coordination alongside the Municipal Data Office.
Enhance your Team Work with Distributed Version Control Systems - DVCSXavier de Pedro
Distributed revision control takes a peer-to-peer approach to version control, as opposed to the client-server approach of centralized systems. Rather than a single, central repository on which clients synchronize, each peer's working copy of the co<x>debase is a complete repository. Distributed revision control synchronizes repositories by exchanging patches (sets of changes) from peer to peer. This results in some important differences from a centralized system:
No canonical, reference copy of the co<x>debase exists by default; only working copies.
Common operations (such as commits, viewing history, and reverting changes) are fast, because there is no need to communicate with a central server.
Communication is only necessary when sharing changes among other peers.
Each working copy effectively functions as a remote backup of the co<x>debase and of its change-history, protecting against data loss.
Other differences include:
Multiple "central" repositories.
Code from disparate repositories are merged based on a web of trust, i.e., historical merit or quality of changes.
Numerous different development models are possible, such as development / release branches or a Commander / Lieutenant model, allowing for efficient delegation of topical developments in very large projects.[3] Lieutenants are project members who have the power to dynamically decide which branches to merge.
Network is not involved for common operations.
A separate set of "sync" operations are available for committing or receiving changes with remote repositories.
DVCS proponents point to several advantages of distributed version control systems over the traditional centralised model:
Allows users to work productively when not connected to a network.
Makes most operations much faster.
Allows participation in projects without requiring permissions from project authorities, and thus arguably better fosters culture of meritocracy instead of requiring "committer" status.
Allows private work, so users can use their changes even for early drafts they do not want to publish.
Avoids relying on one physical machine as a single point of failure.
Permits centralized control of the "release version" of the project
On FLOSS software projects it is much easier to create a project fork from a project that is stalled because of leadership conflicts or design disagreements.
Enhance your Team Work with Distributed Version Control Systems - DVCSXavier de Pedro
Distributed revision control takes a peer-to-peer approach to version control, as opposed to the client-server approach of centralized systems. Rather than a single, central repository on which clients synchronize, each peer's working copy of the co<x>debase is a complete repository. Distributed revision control synchronizes repositories by exchanging patches (sets of changes) from peer to peer. This results in some important differences from a centralized system:
No canonical, reference copy of the co<x>debase exists by default; only working copies.
Common operations (such as commits, viewing history, and reverting changes) are fast, because there is no need to communicate with a central server.
Communication is only necessary when sharing changes among other peers.
Each working copy effectively functions as a remote backup of the co<x>debase and of its change-history, protecting against data loss.
Other differences include:
Multiple "central" repositories.
Code from disparate repositories are merged based on a web of trust, i.e., historical merit or quality of changes.
Numerous different development models are possible, such as development / release branches or a Commander / Lieutenant model, allowing for efficient delegation of topical developments in very large projects.[3] Lieutenants are project members who have the power to dynamically decide which branches to merge.
Network is not involved for common operations.
A separate set of "sync" operations are available for committing or receiving changes with remote repositories.
DVCS proponents point to several advantages of distributed version control systems over the traditional centralised model:
Allows users to work productively when not connected to a network.
Makes most operations much faster.
Allows participation in projects without requiring permissions from project authorities, and thus arguably better fosters culture of meritocracy instead of requiring "committer" status.
Allows private work, so users can use their changes even for early drafts they do not want to publish.
Avoids relying on one physical machine as a single point of failure.
Permits centralized control of the "release version" of the project
On FLOSS software projects it is much easier to create a project fork from a project that is stalled because of leadership conflicts or design disagreements.
150511 programari lliure_i_taller_de_linux_v2Xavier de Pedro
Seminari sobre Programari Lliure i GNU/Linux, amb taller guiat per a instal·lar-te Ubuntu al teu ordinador de forma dual amb el teu altre sistema operatiu.
Hack-tivisme amb eines i continguts alliberats: beneficia-te'n!Xavier de Pedro
Xerrada al Fòrum Social Català 2014. http://2014.forumsocialcatala.cat/item11
En el taller es reflexionarà sobre els avantatges d'emprar coneixement lliure i alliberar el coneixement generat per nosaltres. S'explicarà com s'ha de fer per a garantir que les generacions futures puguin emprar i continuar millorant el coneixement que hem generat de forma individual o col·lectiva.
En el taller separarem el coneixement en tres tipus:
1. informació en si mateixa, com poden ser documents escrits, plànols de construcció d'objectes/cases/màquines, o també vídeos, documentals, música o altres documents en formats àudio (contes explicats per a nens, etc).
2. programes informàtics (d'ordinador, tauleta, telèfon intel·ligent, però també del cotxe, electrodomèstics, drons, etc)
3. eines físiques (impressores 3D, telèfons, tractors, tallers per fabricar maons per a la construcció, forns, etc)
El tipus de llicència de copyright escollida és important, i determina que haguem protegit legalment que altres persones puguin emprar i modificar, si volem, el nostre coneixement, i també ens protegeix de que altres persones no pugui apoderar-se en exclusiva del nostre coneixement sense demanar-nos permís previ per arribar a algun acord que ens satisfaci.
Podem posar un exemple, en el cas dels programes informàtics. La majoria de persones empren els programes que venien amb l'ordinador, i els que “els hi han passat” amics o familiars per a instal·lar-se. En la majoria de casos això vol dir emprar i piratejar programari (software) propietari: MS Windows, MS Office, Photoshop, Ilustrator, ... Això és il·legal i poc ètic, i ens fa deixar d'aprofitar la fantàstica oportunitat d'emprar programari lliure per a les mateixes tasques. Aquest programari és diu lliure per que porta associades unes llibertats legals del que pots fer amb el programa. L'objectiu d'aquest taller és introduir la reflexió sobre quin programari solem emprar per tradició i comoditat, quina alternativa tenim, i les conseqüències positives que té per a nosaltres, i per a la Comunitat, d'escollir programari lliure per davant del programari propietari sempre que n'existeixin alternatives prou madures com ja existeixen en molts àmbits.
Al taller s'exposaran exemples reals de l'àmbit de la documentació, elaboració de plànols de edificacions, construcció del necessari per a sostenir una civilització, fotos i vídeos (quins sí i quins no), programes d'ordinador/tauleta i telèfon mòbil, i de quina manera ens en podem beneficiar de forma individual i col·lectiva del seu ús.
Hack-tivisme amb continguts i eines alliberades: beneficia-te'n!Xavier de Pedro
Xerrada sobre com l'ètica hacker ens pot ajudar en el nostre activisme per un món millor si emprem continguts lliures (amb copyleft, llicències de copyright de tipus "Creative Commons") i eines lliures, com són el programari lliure (eines immaterials) i el maquinari lliure (eines materials). S'indica també com ens poden beneficiar d'aquestes pràctiques, tant de forma individual com col·lectivament.
Xerrada feta el 5 d'Abril de 2014 emmarcada dins les Jornades de Cultura Lliure al Centre Civic Can Basté de Nou Barris de Barcelona (Catalunya, Espanya).
Més informació (i diapositives amb enllaços clicables, etc):
http://llavorspac.org/CanBaste
V Jornadas de Software Libre - UPC: TikiWiki en contextos educativos (I) y (II)Xavier de Pedro
V Jornades de Programari Lliure
ETSEIB (UPC), del 5 al 8 de juliol de 2006
http://jornadespl.org
Aquesta obra està sota una Llicència de Creative Commons Atribució - CompartirPerIgual 2.5. Espanya.
De Pedro, X. y Reyes, J. 2006a. “TikiWiki en contextos educativos (I): las comunidades abiertas de aprendizaje cooperativo y reflexivo”. V Jornadas de Software Libre, Universidad Politécnica de Cataluña. Texto completo: http://www.ub.edu/gclub/dl52 (530 Kb).
De Pedro, X. y Reyes, J. 2006b. “TikiWiki en contextos educativos (II): los sistemas de evaluación de los aprendizajes”. V Jornadas de Software Libre, Universidad Politécnica de Cataluña. Texto completo: http://www.ub.edu/gclub/dl53 (698 Kb)
Empleo de isótopos estables en cadenas tróficasXavier de Pedro
Este documento presenta los conceptos generales y resultados del uso de isótopos estables 13C, 15N y 34S para estudiar las cadenas tróficas en el ecosistema marino de la Bahía de Alfacs en el Mediterráneo noroccidental. Se introducen los conceptos básicos de fraccionamiento isotópico y se describen los ciclos biogeoquímicos del carbono, nitrógeno y azufre en la bahía. Los resultados muestran un enriquecimiento de aproximadamente 1.5‰ en δ13C y 3.5
II jornadas de Usuarios R: Usando de forma segura R vía web con TikiXavier de Pedro
Usando de forma segura R vía web con Tiki.
Xavier de Pedro*, Àlex Sanchez
Departamento de Estadística
Universitdad de Barcelona
http://estbioinfo.stat.ub.es
Xavier.dePedro@ub.edu
1) Nuestras necesidades
2) GUI's Web para R
3) Tiki y el nuevo PluginR
4) Ejemplos y casos de uso
5) Trabajo futuro
A menudo el personal docente e investigador (PDI) de los centros de investigación utiliza software propietario para la gestión de su contenido en páginas web y facilitar la colaboración con otros (departamento, grupo de investigación, proyecto, colegas extranjeros...). Se suelen buscar aplicaciones del estilo Web 2.0, por lo que si antes se solía usar herramientas como bscw, o MS Sharepoint, ahora no es raro ver el uso de Google sites, Google Docs, Wikispaces, .... El software usado no suele ser lo bastante completo o versátil como para permitir configurar el escenario de uso deseado según las necesidades que se tienen en cada caso. Y por tanto, es frecuente que se acaben usando multitud de programas diferentes, con sus respectivos nombres de usuario y contraseña, para todas y cada una de sus necesidades de publicación y colaboración on-line (noticias, archivos, foros, wiki, hojas de cálculo, trackers o bases de datos, ...). En muchos casos, además, se suele perder el control de los datos al estar en empresas externas que imponen sus propias condiciones de uso.
Actualmente existen diversas aplicaciones web 2.0 de software libre que, en teoría, podrían facilitar dichos escenarios de uso (Tiki, Plone, Drupal, Joomla, Twiki, ...). En esta comunicación se aborda el caso de la recientemente liberada versión 3.0 de Tiki (Tikiwiki CMS/Groupware - http://tikiwiki.org). Se hará un análisis de las múltiples prestaciones de qué dispone ya funcionales en cuanto se instala la aplicación [motor wiki potente y translingüístico (CLWE), edición visual (Wysiwyg) o rápida (Wiki), foros, blogs, trackers, folksonomia / marcas libres, mapas y GIS libre, web semántica, múltiples plugins ya instalados para funcionalidades avanzadas, webservices, sistema granular de permisos y categorización jerárquica de contenido, búsqueda sensible a permisos de lectura...]. Por otra parte, se citarán casos concretos de uso en universidades catalanas, y se ilustrará con una breve demostración de instalación y configuración a la estética de la Universidad de Barcelona en unos pocos clics.
Casos de uso a gran escala:
* Sitio internacional de soporte de Mozilla Firefox (http://support.mozilla.com),
* Wiki de KDE (http://wiki.kde.org).
La comunicación está destinada a alumnado y profesorado que no conozca prácticamente Tiki 3.0, y esté buscando un sistema unificado y actualizado de herramientas web para facilitar la colaboración con sus colegas sin recurrir a software propietario ni a multitud de aplicaciones sueltas.
Colaboración entre PDI (2): Gestión bibliográfica con BibusXavier de Pedro
Este documento presenta Bibus, un programa de código abierto para la gestión bibliográfica que es una alternativa libre a programas propietarios como Endnote o Reference Manager. Bibus permite crear bibliografías compartidas en MySQL y es compatible con formatos como BibTeX y RIS. También se puede exportar un currículum en formato BibTeX para su gestión bibliográfica local o en la web. El documento menciona otras alternativas libres como JabRef, Zotero, Wikindx y Refbase, así como opciones propietarias como Endnote Web y Refworks.
Colaboración entre PDI (1): Estadística y Gráficos Científicos con R.Xavier de Pedro
A menudo el personal docente e investigador (PDI) de los centros de investigación utiliza software propietario para sus modelos, cálculos estadísticos y visualización de datos científicos (Matlab, Mathematica, Statistica, SPSS...). A medio o largo plazo a menudo se acaba buscando la colaboración con otros docentes e investgadores en areas de trabajo afines, o el alumnado necesita realizar cálculos estadísticos y gráficos fuera del aula o una vez acabada la carrera, lo que suele suponer que se tengan que comprar licencias de software (¿o se pirateen, a veces?) para poder usarlo. Una de las alternativas libres con enormes ventajas a medio y largo plazo, así como con un enorme potencial y crecimiento en la última década ha sido el software R (http://www.r-project.org).
Así, en esta comunicación se abordan brevemente algunas ventajas e inconvenientes del uso de R para facilitar la colaboración entre PDI (actual y futuro), a partir de la experiencia concreta del autor de la comunicación. Se muestran algunas aplicaciones gráficas para interaccionar con R, y se citan algunas de las alternativas actuales libres. La comunicaicón está destinada a alumnado y profesorado que no conozca practicamente R aún, y que use alternativas propietarias para sus tareas de investigación y docencia.
Más en http://www.ub.edu/gclub/jornadespl2009
0903 Resum del Miquel sobre les Jornades Internacionals sobre Organismes Modi...Xavier de Pedro
6 i 7 de Març de 2009. Resum de les Jornades Internacionals sobre Organismes Modificats Genèticament. A la residència d'Investigadors del CSIC, a Barcelona.
Ponents:
Dr. Marcello Buiatti, Catedràtic de Genètica de la Universitat de Florència (Itàlia), “a
quí beneficien els ogm?”
Dr. Brian John, Doctor en Geografia, "GM Free Cymru" (Escòcia lliure de transgènics).
Dr. Armin Spök, Doctor en Genètica Molecular. Professor a les universitats de Graz i Klagenfurt (Àustria). Membre dels grups d'experts de l'Autoritat Europea de Seguretat Alimentària (EFSA) i de l'OCDE ., “què ha fet Àustria en aquest tema”.
Dr. Henk Hobbelink, Grain,”OMG,
crisi alimentària i canvi climàtic”.
Fabio Boscareli, Toscana lliure de transgènics, “les regions lliures i un cas concret”.
Dr. Giles-Eric Séralini, Catedràtic de Biologia Molecular de la Universitat de Caen
(França), President del Consell Científic de CRIIGEN, “els OGM i la salud”.
Dra. Ricarda A. Steinbrecher, “els impactes dels OGM a l'agriculttura i al medi ambient”
Taula rodona.
Presentació del Curs d'Introducció al Programari de Fonts Obertes (Software de Fuentes Abiertas), organitzat per la CENATIC (http://www.cenatic.es), la Conferència de Rectors de les Universitats
Espanyoles (CRUE) i el gclUB (http://gclub.ub.es) a la Universitat de Barcelona, el 6 de Març de 2009
II Jornades Internet Social - Citilab Cornellà - FTIC - STSIXavier de Pedro
II Jornades Internet Social - al Citilab de Cornellà - de les subvencions FTIC - STSI. Elaborat per Joan Sabaté, director del CETEI - Fundació Joan XXIII. Av. M.D. Bellvitge 100. 08907 L'Hospitalet de Llobregat (Barcelona). Amb llicència Creative Commons, Atribució - Compartir per igual segons els autors.
Immersive Learning That Works: Research Grounding and Paths ForwardLeonel Morgado
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
Discovery of An Apparent Red, High-Velocity Type Ia Supernova at 𝐳 = 2.9 wi...Sérgio Sacani
We present the JWST discovery of SN 2023adsy, a transient object located in a host galaxy JADES-GS
+
53.13485
−
27.82088
with a host spectroscopic redshift of
2.903
±
0.007
. The transient was identified in deep James Webb Space Telescope (JWST)/NIRCam imaging from the JWST Advanced Deep Extragalactic Survey (JADES) program. Photometric and spectroscopic followup with NIRCam and NIRSpec, respectively, confirm the redshift and yield UV-NIR light-curve, NIR color, and spectroscopic information all consistent with a Type Ia classification. Despite its classification as a likely SN Ia, SN 2023adsy is both fairly red (
�
(
�
−
�
)
∼
0.9
) despite a host galaxy with low-extinction and has a high Ca II velocity (
19
,
000
±
2
,
000
km/s) compared to the general population of SNe Ia. While these characteristics are consistent with some Ca-rich SNe Ia, particularly SN 2016hnk, SN 2023adsy is intrinsically brighter than the low-
�
Ca-rich population. Although such an object is too red for any low-
�
cosmological sample, we apply a fiducial standardization approach to SN 2023adsy and find that the SN 2023adsy luminosity distance measurement is in excellent agreement (
≲
1
�
) with
Λ
CDM. Therefore unlike low-
�
Ca-rich SNe Ia, SN 2023adsy is standardizable and gives no indication that SN Ia standardized luminosities change significantly with redshift. A larger sample of distant SNe Ia is required to determine if SN Ia population characteristics at high-
�
truly diverge from their low-
�
counterparts, and to confirm that standardized luminosities nevertheless remain constant with redshift.
SDSS1335+0728: The awakening of a ∼ 106M⊙ black hole⋆Sérgio Sacani
Context. The early-type galaxy SDSS J133519.91+072807.4 (hereafter SDSS1335+0728), which had exhibited no prior optical variations during the preceding two decades, began showing significant nuclear variability in the Zwicky Transient Facility (ZTF) alert stream from December 2019 (as ZTF19acnskyy). This variability behaviour, coupled with the host-galaxy properties, suggests that SDSS1335+0728 hosts a ∼ 106M⊙ black hole (BH) that is currently in the process of ‘turning on’. Aims. We present a multi-wavelength photometric analysis and spectroscopic follow-up performed with the aim of better understanding the origin of the nuclear variations detected in SDSS1335+0728. Methods. We used archival photometry (from WISE, 2MASS, SDSS, GALEX, eROSITA) and spectroscopic data (from SDSS and LAMOST) to study the state of SDSS1335+0728 prior to December 2019, and new observations from Swift, SOAR/Goodman, VLT/X-shooter, and Keck/LRIS taken after its turn-on to characterise its current state. We analysed the variability of SDSS1335+0728 in the X-ray/UV/optical/mid-infrared range, modelled its spectral energy distribution prior to and after December 2019, and studied the evolution of its UV/optical spectra. Results. From our multi-wavelength photometric analysis, we find that: (a) since 2021, the UV flux (from Swift/UVOT observations) is four times brighter than the flux reported by GALEX in 2004; (b) since June 2022, the mid-infrared flux has risen more than two times, and the W1−W2 WISE colour has become redder; and (c) since February 2024, the source has begun showing X-ray emission. From our spectroscopic follow-up, we see that (i) the narrow emission line ratios are now consistent with a more energetic ionising continuum; (ii) broad emission lines are not detected; and (iii) the [OIII] line increased its flux ∼ 3.6 years after the first ZTF alert, which implies a relatively compact narrow-line-emitting region. Conclusions. We conclude that the variations observed in SDSS1335+0728 could be either explained by a ∼ 106M⊙ AGN that is just turning on or by an exotic tidal disruption event (TDE). If the former is true, SDSS1335+0728 is one of the strongest cases of an AGNobserved in the process of activating. If the latter were found to be the case, it would correspond to the longest and faintest TDE ever observed (or another class of still unknown nuclear transient). Future observations of SDSS1335+0728 are crucial to further understand its behaviour. Key words. galaxies: active– accretion, accretion discs– galaxies: individual: SDSS J133519.91+072807.4
Anti-Universe And Emergent Gravity and the Dark UniverseSérgio Sacani
Recent theoretical progress indicates that spacetime and gravity emerge together from the entanglement structure of an underlying microscopic theory. These ideas are best understood in Anti-de Sitter space, where they rely on the area law for entanglement entropy. The extension to de Sitter space requires taking into account the entropy and temperature associated with the cosmological horizon. Using insights from string theory, black hole physics and quantum information theory we argue that the positive dark energy leads to a thermal volume law contribution to the entropy that overtakes the area law precisely at the cosmological horizon. Due to the competition between area and volume law entanglement the microscopic de Sitter states do not thermalise at sub-Hubble scales: they exhibit memory effects in the form of an entropy displacement caused by matter. The emergent laws of gravity contain an additional ‘dark’ gravitational force describing the ‘elastic’ response due to the entropy displacement. We derive an estimate of the strength of this extra force in terms of the baryonic mass, Newton’s constant and the Hubble acceleration scale a0 = cH0, and provide evidence for the fact that this additional ‘dark gravity force’ explains the observed phenomena in galaxies and clusters currently attributed to dark matter.
TOPIC OF DISCUSSION: CENTRIFUGATION SLIDESHARE.pptxshubhijain836
Centrifugation is a powerful technique used in laboratories to separate components of a heterogeneous mixture based on their density. This process utilizes centrifugal force to rapidly spin samples, causing denser particles to migrate outward more quickly than lighter ones. As a result, distinct layers form within the sample tube, allowing for easy isolation and purification of target substances.
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...PsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
Microbial interaction
Microorganisms interacts with each other and can be physically associated with another organisms in a variety of ways.
One organism can be located on the surface of another organism as an ectobiont or located within another organism as endobiont.
Microbial interaction may be positive such as mutualism, proto-cooperation, commensalism or may be negative such as parasitism, predation or competition
Types of microbial interaction
Positive interaction: mutualism, proto-cooperation, commensalism
Negative interaction: Ammensalism (antagonism), parasitism, predation, competition
I. Mutualism:
It is defined as the relationship in which each organism in interaction gets benefits from association. It is an obligatory relationship in which mutualist and host are metabolically dependent on each other.
Mutualistic relationship is very specific where one member of association cannot be replaced by another species.
Mutualism require close physical contact between interacting organisms.
Relationship of mutualism allows organisms to exist in habitat that could not occupied by either species alone.
Mutualistic relationship between organisms allows them to act as a single organism.
Examples of mutualism:
i. Lichens:
Lichens are excellent example of mutualism.
They are the association of specific fungi and certain genus of algae. In lichen, fungal partner is called mycobiont and algal partner is called
II. Syntrophism:
It is an association in which the growth of one organism either depends on or improved by the substrate provided by another organism.
In syntrophism both organism in association gets benefits.
Compound A
Utilized by population 1
Compound B
Utilized by population 2
Compound C
utilized by both Population 1+2
Products
In this theoretical example of syntrophism, population 1 is able to utilize and metabolize compound A, forming compound B but cannot metabolize beyond compound B without co-operation of population 2. Population 2is unable to utilize compound A but it can metabolize compound B forming compound C. Then both population 1 and 2 are able to carry out metabolic reaction which leads to formation of end product that neither population could produce alone.
Examples of syntrophism:
i. Methanogenic ecosystem in sludge digester
Methane produced by methanogenic bacteria depends upon interspecies hydrogen transfer by other fermentative bacteria.
Anaerobic fermentative bacteria generate CO2 and H2 utilizing carbohydrates which is then utilized by methanogenic bacteria (Methanobacter) to produce methane.
ii. Lactobacillus arobinosus and Enterococcus faecalis:
In the minimal media, Lactobacillus arobinosus and Enterococcus faecalis are able to grow together but not alone.
The synergistic relationship between E. faecalis and L. arobinosus occurs in which E. faecalis require folic acid
Evidence of Jet Activity from the Secondary Black Hole in the OJ 287 Binary S...Sérgio Sacani
Wereport the study of a huge optical intraday flare on 2021 November 12 at 2 a.m. UT in the blazar OJ287. In the binary black hole model, it is associated with an impact of the secondary black hole on the accretion disk of the primary. Our multifrequency observing campaign was set up to search for such a signature of the impact based on a prediction made 8 yr earlier. The first I-band results of the flare have already been reported by Kishore et al. (2024). Here we combine these data with our monitoring in the R-band. There is a big change in the R–I spectral index by 1.0 ±0.1 between the normal background and the flare, suggesting a new component of radiation. The polarization variation during the rise of the flare suggests the same. The limits on the source size place it most reasonably in the jet of the secondary BH. We then ask why we have not seen this phenomenon before. We show that OJ287 was never before observed with sufficient sensitivity on the night when the flare should have happened according to the binary model. We also study the probability that this flare is just an oversized example of intraday variability using the Krakow data set of intense monitoring between 2015 and 2023. We find that the occurrence of a flare of this size and rapidity is unlikely. In machine-readable Tables 1 and 2, we give the full orbit-linked historical light curve of OJ287 as well as the dense monitoring sample of Krakow.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...
GNU Linux - Introduction and Administration
1. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
Data Science
(ciencia de los datos):
Aplicaciones a la biología y a la
medicina con Python y R
(Edición 2024)
Curso de Experto Universitario
Universidad de Barcelona (UB)
Con el soporte de:
https://www.ub.edu
2. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
2
GNU/Linux OS
Introduction
Administration
Xavier de Pedro, PhD.
April 3, 2024
Course «Data Science» UB
Image source: http://tekopsglobal.com
3. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
3
Xavier de Pedro Puente, Ph.D.
xdepedro@bcn.cat
Academics:
Degree in Biology
(University of Barcelona - UB)
Ph.D. in Ecology
(University of Barcelona - UB)
Postgraduate in Bioinformatics
(Open University of Catalonia – UOC)
Current Work:
Senior technician at Climate Change and
Sustainability Office (Barcelona City Council)
Past (related) Work:
Bioinformatics technician & System administrator
(UEB, VHIR)
Senior technician at Municipal Data Office
(Barcelona City Council)
Senior technician at Municipal Institute of
Informatics (Barcelona City Council)
4. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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(1) GNU/Linux Introduction
– Concepts, History, "Distributions”,
Ubuntu
– Basic Differences compared with:
●
MS Windows
●
Mac OSX
– Command line runs
– Aliases
Session Outline
(2) GNU/Linux Administration
– Installation
– Package Management
– User Management
– Permission Management
– Device Management
– Backup Management
– Security
– Computer Client Management
5. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
5
Tool: Virtual Environment with Ubuntu GNU/Linux
3 alternate options:
(1) Connect to a Posit.cloud Linux terminal
(2) Import VirtualBox VM (.ova file) locally
(3) Connect to remote VM with program X2Go.
Option 1
Option 3
Option 2
6. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Option 1: Connect to a Posit.cloud Linux Terminal
●
Register to: https://posit.cloud/plans/free
●
Login & create
a New Space
– Datascience2024
Linux
7. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Option 2: Import VirtualBox VM (.ova file)
●
Download from:
– 64 bit computers: (6.2 Gb)
http://cloud.seeds4c.org/lubuntu_1804_64bit_v03.ova
See: https://www.virtualbox.org
2
8. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Option 2: VirtualBox VM with Lubuntu GNU/Linux
See: https://www.virtualbox.org
●
Import VM locally
– Follow instructions
around slide 47, in
linux admin section:
“Importing VirtualBox
(.OVA)”
9. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Option 3: Connect to remote VM with X2Go
See: https://wiki.x2go.org/doku.php/doc:installation:x2goclient
●
Install X2Go Client:
https://wiki.x2go.org
●
Add new session prefs:
– Host: datascience.seeds4c.org
– Login & pass:
●
Generic: datascience / datascience
●
Private: (sent to your email
accounts)
– Session type: LXQt
10. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Option 3: Connect to remote VM with X2Go
3
11. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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What is GNU/Linux?
It is ...
An Open Source (Free/Libre) operating system
Sum of GNU surroundings and the Linux kernel/core
Compatible with UNIX systems
GNU/Linux
(a.k.a «Linux»)
12. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Operating System (in context)
Desktop Environments
Operating System
Hardware
End User Applications
Aqua Luna (XP)
Aero (Vista +)
13. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux
Some basic concepts
GNU Project
Hardware vs software
Open Source & Free software (as in «free» seats)
●
FLOSS: Free/Libre Open Source Software
Free Software Foundation (FSF)
Free Operating Systems
●
GNU/Linux, GNU/Hurd, [Open,Free,Net]-BSD,
OpenSolaris, ReactOS...
Open Source Hardware
14. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Historical Evolution
Source: A. G. Stankevicius. Departarmento de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. http://cs.uns.edu.ar/~ags/linux/
In the origins of software....
Software was born free.
In the decade of the '60, when buying HW, access
was granted to the manufacturer’s SW catalogue
All software distributed together with source code
At the end of the '70, IBM announced their intention
to sell parts of their SW separately.
From then on, proprietary SW (no free) became
common
15. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Historical Evolution
Source: A. G. Stankevicius. Departarmento de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. http://cs.uns.edu.ar/~ags/linux/
GNU/Linux History
1983. Richard M.
Stallman (RMS):
GNU project
1984. Free Software Foundation
(FSF).
First components of the GNU
system, all written by RMS:
●
a C compiler (gcc)
●
an text editor (emacs)
●
and a debugger (gdb)
16. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Historical Evolution
Derived from: A. G. Stankevicius. Departarmento de Ciencias e Ingeniería de la Computación. Universidad Nacional del Sur. http://cs.uns.edu.ar/~ags/linux/
GNU/Linux History
To guarantee the four freedoms,
RMS invented the concept of
copy-left (reverse of copy-right).
1990: GNU system was almost
complete, only missing to finish
an ambitious kernel (core).
1991: Linus Torvalds wrote a
monolithic kernel
GNU + Linux kernel (by Linus T.):
GNU/Linux
1996: A penguin bit to Linus.
Logo: penguin Tux
17. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux History
Source: https://www.elprocus.com/linux-operating-system/
18. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Desktop Environments (in context)
Desktop Environments
Operating System
Hardware
Applications
Aqua Luna (XP)
Aero (Vista +)
19. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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History of Desktop Environments
Source: https://en.wikipedia.org/wiki/Desktop_environment
20. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Desktop Environments (DE)
Desktop Environments
...
KDE
Source: https://en.wikipedia.org/wiki/Desktop_environment
21. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux DE:
Desktop Environments
...
22. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux DE:
Desktop Environments
...
KDE
23. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux DE:
24. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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GNU/Linux DE:
25. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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What is a GNU/Linux «distribution»?
A collection of free software
Core + drivers (modules)
Desktop Environment
Extra + programs + utilities
Support? + Documentation?
KDE
Desktop
Environment
26. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Distributions of GNU/Linux
Ubuntu
Debian Slackware Gentoo
Redhat
Fedora Mandriva Suse
27. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Ubuntu (GNU/Linux)
Main characteristic
Distribution based in Debian
Developed by Canonical Ltd.
(South Africa)
Ubuntu:
Philosophy zulú: “Mankind to
others”, “I am because we are”
Slogan Ubuntu: “Linux for
human beings” (or “beans”?)
Definitely, it is the easiest to
install/use
28. Data Science 2024, April 3. | GNU/Linux: Introduction and Administration | Xavier de Pedro Puente
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Variants
1st Release
Ubuntu 4.10
Kubuntu 5.04
Edubuntu 5.10
Xubuntu 6.06 LTS
Mythbuntu 7.10
UbuntuStudio 7.10
Lubuntu 11.10
Ubuntu GNOME 13.04
Ubuntu Kylin 13.04
Source: https://itsfoss.com/which-ubuntu-install/
Ubuntu (GNU/Linux)
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●
Technical differences
– User: root vs. administrator
– Case sensitive vs. Case insensitive
●
"MyFile != myfile" vs. "MyFile = myfile"
– "Symbolic or Hard Links" vs. "Shortcuts"
– Paths: Slash ("/") vs. Backslash ("")
– Main harddrive/partition: "/" vs. "C:"
– Partition formats (file systems): ext2, ext3, ext4, ... vs. fat16/fat32/ntfs
– User default folder: /home/username vs. "C:Documents and Settings" or
"C:UsersusernameMyDocuments"
– USBdisk default folder: /media/username/usbdiskname vs. "X:usbdiskname"
– Secure (Viruses???) vs. Insecure (viruses, bots, worms, trojans, backdoors, ...)
– It can extend computer useful life vs. Planned & perceived obsolescence
– Performance, with same hardware: Faster vs. Slower (Antivirus, antispyware,...)
– Run as admin: "sudo program" in console vs. "Run program as administrator"
GNU/Linux vs. Windows
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Phylosophical differences
– Freedom: "Free/Libre Open Source Software
(FLOSS)" vs. "Closed Source/Propietary software"
●
Software Sustainability: High vs. Low
– Usually: product given for free (at no Cost) vs.
product for (excessive?) profit
– Money comes through: customizations and
training vs. Selling Software
– FLOSS Fosters local economies as well as big
companies vs. Big & remote Corporations growth.
GNU/Linux vs. Windows
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●
Technical differences
– Users:
– Case:
– Links:
– Paths:
– Main harddrive/partition
– Partition formats: ext2, ext3, ext4, ... vs. HFS+
– User default folder: /home/username vs. "/Users/Username"
– USBdisk default folder:
– Secure (Viruses???) vs. Secure (Viruses?)
– It can extend computer useful life vs. Planned & perceived obsolescence
– Performance, with same hardware: Faster??? vs. Extremely Fast
– Run as admin:
GNU/Linux vs. Mac OS X
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●
Phylosophical differences
– Freedom: "Free/Libre Open Source Software
(FLOSS)" vs. "Closed Source/Propietary software"
●
Software Sustainability: High vs. Low
– Usually: product given for free (at no Cost) vs.
product for (excessive?) profit
– Money comes through: customizations and
training vs. Selling Software & Hardware
– FLOSS Fosters local economies as well as big
companies vs. Big & remote Corporations growth.
GNU/Linux vs. Mac OS X
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Ubuntu (GNU/Linux)
See it in action ...
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Command line runs (i)
●
Shell = Terminal = Console ("Black" text screen to run
commands)s
– Secure Shell = ssh = a safe way to connect to remote
computers or servers (encrypted)
– ftp: File Transfer Protocol
●
to transfer files between computers or servers
●
you can NOT run commands (other than listings)
– sftp: like FTP but "secure" (best: using ssh libraries)
●
Local terminal window
– > whoami
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Command line runs (ii)
●
Example of simple local commands:
> ps -e
> ls -l
> df -h
> top
> tree . | head
> du . -h | grep G
●
Example of simple editors:
> nano (simple editor: press "Ctrl + X" to eXit)
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Command line runs (iii)
●
Example of network-related commands:
> ping google.com
> ifconfig
●
Example of system administration (sysadmin) commands:
> sudo apt update & sudo apt install tree
> sudo adduser foo
> sudo passwd foo
> sudo service apache restart
> sudo kill -9 java
●
Example of simple editors:
> nano (simple editor: press "Ctrl + X" to eXit)
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Command line runs (iv)
●
Example of other shell-based programs:
> htop (type "q" to quit/exit)
> mc (Midnight Commander).
Click on F10 (with mouse or trackpad) to quit
> R ( Type "q()" to quit)
●
Serial vs. Parallel tasks
– https://www.datascienceatthecommandline.com/chapter-8-parallel-
pipelines.html
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Midnight Commander (mc)
●
Powerful dual-pane file manager in terminals. A Life-
saver for human beans when no X windows in servers
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More information...
●
Linux intro (short version):
– http://applied-r.com/linux-intro/
●
Linux OS Basics:
– http://applied-r.com/linux-os-basics/
●
Linux File Management:
– http://applied-r.com/linux-file-management/
●
Linux help:
http://applied-r.com/linux-help/
●
Linux aliases:
– http://applied-r.com/linux-aliases/
●
Linux Utilities:
– http://applied-r.com/linux-utilities/
●
Package management (console based):
– http://applied-r.com/linux-apt/
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Pause...
●
Coffee / soda
time?
Source: http://wallpaperpicture--photo.blogspot.com.es/2015/01/funny-ads-pictures-0.html
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(2) GNU/Linux Administration
Installation
Package Management
User Management
Permission Management
Device Management
Backup Management
Security
Computer Client Management
Computer Clusters
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Image Source: https://www.linux.com/blog/sysadmin-ebook/2017/9/future-proof-your-sysadmin-career-advancing-open-source
Evolution in Technology
Image source: http://ars.userfriendly.org/cartoons/?id=19990718
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Installation
How to use or install GNU/Linux?
LiveCD/LiveUSB: Without installing it in the hard disk
Install in the hard disk
More efficient using your hardware, and you can install next
to your other installed OS. You choose OS at booting time.
Install in a disk USB or pendrive
Install in a local virtual machine (or in the cloud)
From scratch (from .iso file), or from a previously
exported virtual machine (.ova file or equivalent)
Windows + andLinux/CoLinux
Win10 + «WSL» (Windows Subsystem for Linux)
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Exporting VirtualBox (.OVA)
With current parameters
See: https://www.virtualbox.org
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Willing to export to USB? Set it up
...
See: https://www.virtualbox.org
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Willing to copy&paste to and/or from Host/Client?
...
See: https://www.virtualbox.org
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Importing VirtualBox (.OVA)
VT-x option disabled in BIOS allows only 1 cpu
See: https://www.virtualbox.org
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Importing VirtualBox (.OVA)
VT-x option enabled in BIOS
allows 2+ cpu
See: https://www.virtualbox.org
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Where to enable/disable it?
VirtualBox VM config for VT-x setting in BIOS
Lubuntu: Lightweidht Desktop on a Ubuntu GNU/Linux Distribution. http://lubuntu.net
See: https://www.virtualbox.org
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Other Options to use VirtualBox VM
Connection to remote VBox using X2Go (ssh)
X2Go: Program to connect to a remote computer through GUI (Graphical User Interface)
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Other Options to use VirtualBox VM
Connection to remote VBox using X2Go (ssh)
X2Go: http://wiki.x2go.org
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Other Options
LiveUSB (example: LXLE Lubuntu-based; BIOS to boot from USB)
LXLE: A Lubuntu-based GNU/Distribution with improved desktop http://www.lxle.net
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Other Options
andLinux (side to side to Windows - http://andlinux.sf.net )
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Other Options
WSL (Windows Subsystem for Linux)
●
Info:
– https://en.wikipedia.org/wiki/Windows
_Subsystem_for_Linux
●
Installation Guide for Windows 10
– https://docs.microsoft.com/en-us/wind
ows/wsl/install-win10
–
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●
GNU/Linux Installation
– Dual/Multi-boot
●
Ubuntu (GNU/Linux) + Windows (or Mac OSX, ...)
●
From USB or CD/DVD
– Requirements
●
Desfrag Hard Drive (in Windows) – if needed
●
Backup Data in external device (usb, network drive, ...)
●
Identify Partitions in your hard drive
– You may have 4 primary partitions (maximum)
– You need 1 free partition (minimum)
●
To make (preferably) 3 logic partitions inside
Installation on Hard Disk
(non WSL but native)
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Using Live USB/CD/DVD
Start from a Live USB or CD/DVD for inspecting
& safer partition management
Required: setup computer BIOS to allow booting
from USB or CD/DVD
Press a key to enter configuration
Usually: DEL, F2, ESC, ....
Once there, look for the start sequence (Boot, Boot
device, ...)
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Hard Drive Partition Management before Installing GNU/Linux.
Challenging example:
●
HP Laptop from 2015 with M$ Win7
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Package Management
(installing «programs»)
Standard Package Management
●
Console based:
●
APT (Debian/Ubuntu/Mint/LXLE)
●
YUM (Redhat/CentOS/Fedora Core)
●
YAST2 (SUSE)
●
Portage (Gentoo)
●
GUI based
●
Synaptic (Debian-based)
●
Many others (distro-specific)
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sudo apt install foo
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Package Management
From extra repositories
add-apt-repository & apt update & apt install
●
Oracle Java
●
sudo add-apt-repository -y ppa:webupd8team/java
●
R (updated version)
●
sudo add-apt-repository -y ppa:marutter/rrutter
●
Dependencies for R GIS packages (such as tmap)
●
sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
●
sudo add-apt-repository -y ppa:opencpu/jq
Source: https://seeds4c.org/16.04
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Oracle Java
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Add missing gpg repo keys
datascience@dspc ~> sudo add-apt-repository -y ppa:nilarimogard/webupd8
datascience@dspc ~> sudo apt install launchpad-getkeys
datascience@dspc ~> sudo launchpad-getkeys
datascience@dspc ~> sudo apt update
With a helper: launchpad-getkeys
Source: https://seeds4c.org/16.04
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Add all required ubuntu packages (dependencies)
& dev helpers for some R packages
datascience@dspc ~> sudo add-apt-repository -y ppa:marutter/rrutter
datascience@dspc ~> sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
datascience@dspc ~> sudo add-apt-repository -y ppa:opencpu/jq
datascience@dspc ~> sudo apt update
datascience@dspc ~> sudo apt install -y r-recommended r-cran-xml libgraphviz-dev
libcairo2-dev r-cran-cairodevice freeglut3 freeglut3-dev r-cran-rglpk r-cran-rgl r-cran-misc3d
libx11-dev libxt-dev libcurl4-gnutls-dev libxml2-dev r-cran-xml libgraphviz-dev libcairo2-dev
bwidget tk-table libv8-dev r-cran-rjava libmpfr-dev libc6 libssl-dev texlive-latex-extra texlive-
lang-spanish libx11-dev libxml2-dev libxml2:i386 libxt-dev r-cran-misc3d subversion git tk-
dev unaccent xvfb libgdal1-dev libproj-dev r-cran-rmysql libmagick++-dev r-cran-
rcolorbrewer r-cran-doparallel libssh2-1-dev libudunits2-dev libgdal-dev libgeos-dev libproj-
dev libv8-3.14-dev libjq-dev libprotobuf-dev protobuf-compiler libssl-dev libcairo2-dev
For Ubuntu 16.06 LTS with some extra repos:
Fix permissions
sudo chmod 777 /usr/lib/R/site-library /usr/lib/R/site-library/* -R
sudo chmod 777 /usr/lib/R/library /usr/lib/R/library/* -R
sudo chmod 777 /usr/share/R/doc/html/* -R
Source: http://seeds4c.org/R
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Package Management
From External sources
●
Example: Adobe Acrobar Reader 9.x
●
Example: Portable Signer:
To digitally sign PDF with certificates like FNMT (.p12)
http://portablesigner.sf.net
●
download, uncompress, make executable and run (java app)
Source: https://seeds4c.org/16.04
wget http://ardownload.adobe.com/pub/adobe/reader/unix/9.x/9.5.5/enu/AdbeRdr9.5.5-1_i386linux_enu.deb
sudo dpkg -i AdbeRdr9.5.5-1_i386linux_enu.deb; sudo apt-get -f install #For 32 bits
sudo dpkg -i --force-architecture AdbeRdr9.5.5-1_i386linux_enu.deb; sudo apt-get -f
install #For 64 bits
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Package Management (GUI)
Synaptic
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User (& Group) Management
GUI based
Console based: adduser, passwd, ...
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datascience@dspc ~> sudo su #become root user («Switch User»)
[sudo] password for datascience:
root@dspc:/home/datascience# adduser foo
Adding user `foo' ...
Adding new group `foo' (1001) ...
Adding new user `foo' (1001) with group `foo' ...
Creating home directory `/home/foo' ...
Copying files from `/etc/skel' ...
Enter new UNIX password: (new-user password typed here)
Retype new UNIX password: (new-user password typed again)
passwd: password updated successfully
Changing the user information for foo
Enter the new value, or press ENTER for the default
Full Name []: Foo Bar
Room Number []:
Work Phone []:
Home Phone []:
Other []:
Is the information correct? [Y/n] Y
root@dspc:/home/datascience# exit
exit
datascience@dspc ~>
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User (& Group) Management
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Permission Management
Console based
●
chmod – change permissions. chown – change ownership
u – user g – group o – other
r – read w – write x – execute
sudo chmod -R ug+rw /DATA/SHARE
sudo chmod -R 660+rw /DATA/SHARE
●
-R → it modifies permission of parent folder & child objects within
●
ug+rw (= 660) → it gives User & Group (but not Others) read and
write access (but not execute access).
●
See:
https://www.linux.com/learn/understanding-linux-file-permissions &
https://www.linux.com/learn/how-manage-file-and-folder-permissions-linux
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Permission Management
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Permission Management (GUI)
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Device Management
Gnome Disks: https://wiki.gnome.org/Apps/Disks
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Device Management
Gparted: https://gparted.org
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Backup Management: tips
Keep copies elsewhere than same computer
«Elsewhere»: different hardware, different device, different room,
different building, ...
Automatic (regular) backups
«Smart remove» even more important
Efficiency vs. resilience
Simple enough so that some team mates can restore them?
Complex RAID disk setups vs redundant external hard drives
elsewhere?
Encrypted vs unencrypted?
Advice: Use your team crowd wisdom; stay away from single-man
freaks with too-techie solutions
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Backup Management: tools
Déjà Dup (Duplicity GUI)
https://wiki.gnome.org/Apps/DejaDup/
https://wiki.gnome.org/Apps/DejaDup/
Backintime (GUI & console; rsync & hard link based)
https://github.com/bit-team/backintime
Luckybackup (rsync-based GU)
http://luckybackup.sourceforge.net/
Backup Ninja (console-based)
https://0xacab.org/riseuplabs/backupninja
Custom Bash Scripts
Some examples at: https://github.com/xavidp/bashscripts
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Backintime & Smart remove
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Computer Client Management
Epoptes - http://www.epoptes.org
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Computer Clusters, ...
Grid, program modules, job queue management ...
●
For newbies: Rocks Clusters distro (CentOS based)
Source: http://ueb.vhir.org/ClusterSeminar
http://www.rocksclusters.org
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Computer Clusters
Source: http://ueb.vhir.org/ClusterSeminar
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Did you Export your VM (.OVA) to your USB?
Otherwise, you’ll loose your changes when you reboot a computer in
a UB computer classroom or equivalent (frozen images at work)
See: https://www.virtualbox.org
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If (1): Shutdown local Lubuntu VM within
VirtualBox
See: https://www.virtualbox.org
1
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If (2): Logout X2Go Session to remote host
datascience.seeds4c.org
See: https://www.virtualbox.org
2
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More information
●
Ubuntu GNU/Linux:
– http://www.ubuntu.com
●
Data Science Virtual Machine for Linux (Ubuntu)
– https://azuremarketplace.microsoft.com/en-us/marketplace/apps/microsoft-
ads.linux-data-science-vm-ubuntu
●
Linkat (Ubuntu):
– Manual Installation with custom partitions (advanced, or for servers):
http://linkat.xtec.cat/portal_linkat/wikilinkat/index.php/Wiki_Linkat_edu_14.04
●
Forums for help and support:
– Ubuntu-es Forums: https://www.ubuntu-es.org/forum
– Ubuntu (Catalan LoCo Team): http://ubuntuforums.org/forumdisplay.php?f=206
●
Data Science Toolbox (to run locally or in the cloud with AWS):
– http://datasciencetoolbox.org/
– https://www.datascienceatthecommandline.com