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# Practical Linux Course

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Designed for researchers, including PhD students and postdocs, this course
provides attendees with an introduction to the Linux operating system. Linux
powers more than 90% of the world’s supercomputers, most internet servers,
and more than a billion Android devices. Additionally, bioinformatics depends
heavily on Linux since a lot of scientific software is written specifically for
it.

This short and concise hands-on course will teach you how to effectively use
Linux using the command line interface. You will be able to swiftly start using
Linux both on a server, e.g., the
[LUMC Shark cluster](https://git.lumc.nl/shark/SHARK/wikis/home), as well as on
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your personal computer. Learning outcomes:
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- Understand and navigate through the filesystem structure.
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- Obtain information about files and directories.
- Manipulate, i.e., create, delete, move, and rename files and directories.
- Inspect and edit files content.
- Gather disk storage information.
- Search for and within files.
- Manage file and directory access permissions.
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- Connect to other computers.
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## Coordinates

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- Date: TBA
- Time: TBA
- Location: TBA
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- Teachers:
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  - Mihai Lefter
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- Register via www.medgencentre.com. Direct access to the
[registration form](https://forms.lumc.nl/lumc2/LINUX).
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## Program and Materials
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| **Time**  | **Activity**        | **Contents**                                      |
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|-------|-----------------|-----------------------------------------------|
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| 10:00 | [Lecture 1](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/introduction.pdf)   | **Introduction**: operating systems, linux, course outline. |
| 10:15 | [Lecture 2](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/core1.pdf)   | **Core 1**: the filesystem, the shell, the command line interface. |
| 10:40 | [Practical 1](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/handouts_core1.pdf) |                           |
| 11:10 | Break           |                           |
| 11:20 | [Lecture 3](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/core2.pdf)   | **Core 2**: basic commands, output redirection. |
| 12:00 | [Practical 2](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/handouts_core2.pdf) |                           |
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| 12:30 | Break           |                           |
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| 13:00 | [Lecture 4](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/user_environment_2.pdf)   | **User Environment**: users, groups, file permissions, and ownership. |
| 13:20 | [Practical 3](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/handouts_user_environment.pdf) |                           |
| 13:50 | Final Questions |                           |
| 14:00 | Closing         |                           |
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## Other material
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You can find the practical start point files
[here](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/practical_files.tar.gz)
and the commands cheat sheet
[here](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/commands_cheatsheet.pdf).
More information on how to connect to other machines
[here](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/connecting_extras.pdf).
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If you would to practice more you can find additional exercises
[here](https://git.lumc.nl/courses/practical-linux-course/wikis/files-most-recent/extra_practice.pdf).
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## Past sessions

You can access the materials for the previous sessions below:
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- [December 6th, 2017](https://git.lumc.nl/courses/practical-linux-course/wikis/session-december-6th-2017) (same
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for the February, May, September, and November 2018 sessions).
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- [November 1st, 2017](https://git.lumc.nl/courses/practical-linux-course/wikis/session-november-1st-2017).
- [June 12th, 2017](https://git.lumc.nl/courses/practical-linux-course/wikis/session-june-12th-2017) (same for the July and September sessions).
- [May 3rd, 2017](https://git.lumc.nl/courses/practical-linux-course/wikis/session-may-3rd-2017).
- [April 6th, 2017](https://git.lumc.nl/courses/practical-linux-course/wikis/session-april-6th-2017).
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## Prerequisites

None.

## Follow Up

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The Practical Linux course is mandatory for the following courses:
- [Introduction to the Shark Cluster](https://git.lumc.nl/shark/SHARK/wikis/home)
- [Code and Data Management with Git](https://git.lumc.nl/courses/gitcourse)
- [Scripting for Life Science Researchers](https://git.lumc.nl/courses/scriptingcourse)