Introduction to Linux
The operating system for bioinformatics
Linux is the operating system of high performance clusters and supercomputers all over the world. Learning to use Linux is a key part of making use of cutting edge bioinformatics tools. This course provides an extensive introduction to Linux, covering both basic and advanced use.
Instructors
- Govind Chandra
Audience
Any students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct their own analyses on a Linux platform. Those intending to register for the upcoming Introduction to HPC course are very strongly encouraged to attend this short (two morning) course and it should be seen as a prerequisite for later courses to be offered on ChIP-Seq analysis and command line/Galaxy implementations of NGS workflows.
Overview
The Linux operating system underlies the HPC cluster at the NBI, and other clusters throughout the world. Unlike Windows and OS X, we usually interact with these systems through the command line. The course will teach the basics of Linux use.
Schedule
Day 1
9:30 Start
11:00 Coffee break
13:00 End
Day 2
9:30 Start
11:00 Coffee break
13:00 End
Learning outcomes
By the end of the course you should be able to:
- Have some idea of the architecture of the Linux operating system.
- Have some understanding of the organisation of the file system on Linux.
- Understand the general structure of Linux commands.
- Understand what plain text files are.
- Be able to do simple things like view and edit the contents of files, copy and move files.
- Have an overview of how computers are used to analyse data.
- Know who to talk to if you are interested in further developing your skills in computing and data analysis.
Pre-requisites
You are strongly encouraged to apply for an account on the NBI HPC cluster so that you can continue to practice your skills in your spare time, although temporary student accounts will be available for those who do not.
Full course syllabus
- Operating System basics (briefly). What is an OS?
- The Linux file system: mount points and links, the home directory, moving around the file system.
- File permissions.
- Shells (Bash).
- Structure of commands: Options, arguments, return values.
- The environment and some important environment variables.
- Plain text files. How plain text files differ from word processing files. Line endings on different platforms. Character encoding.
- More about files; filehandles, redirection and piping.
- A (very simple) data analysis exercise to demonstrate the use of most of the above concepts.
Course materials
Course book
The operating system for bioinformatics
Instructors
- Govind Chandra
Audience
Any students, postdocs or RAs who have an interest in bioinformatics and who intend to conduct their own analyses on a Linux platform. Those intending to register for the upcoming Introduction to HPC course are very strongly encouraged to attend this short (two morning) course and it should be seen as a prerequisite for later courses to be offered on ChIP-Seq analysis and command line/Galaxy implementations of NGS workflows.Overview
The Linux operating system underlies the HPC cluster at the NBI, and other clusters throughout the world. Unlike Windows and OS X, we usually interact with these systems through the command line. The course will teach the basics of Linux use.Schedule
Day 1
| 9:30 | Start |
| 11:00 | Coffee break |
| 13:00 | End |
Day 2
| 9:30 | Start |
| 11:00 | Coffee break |
| 13:00 | End |
Learning outcomes
By the end of the course you should be able to:- Have some idea of the architecture of the Linux operating system.
- Have some understanding of the organisation of the file system on Linux.
- Understand the general structure of Linux commands.
- Understand what plain text files are.
- Be able to do simple things like view and edit the contents of files, copy and move files.
- Have an overview of how computers are used to analyse data.
- Know who to talk to if you are interested in further developing your skills in computing and data analysis.
Pre-requisites
You are strongly encouraged to apply for an account on the NBI HPC cluster so that you can continue to practice your skills in your spare time, although temporary student accounts will be available for those who do not.Full course syllabus
- Operating System basics (briefly). What is an OS?
- The Linux file system: mount points and links, the home directory, moving around the file system.
- File permissions.
- Shells (Bash).
- Structure of commands: Options, arguments, return values.
- The environment and some important environment variables.
- Plain text files. How plain text files differ from word processing files. Line endings on different platforms. Character encoding.
- More about files; filehandles, redirection and piping.
- A (very simple) data analysis exercise to demonstrate the use of most of the above concepts.