Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Get familiar with Linux and its command line in order to access the full range of bioinformatics tools available to researchers.
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Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Explore the full range of bioinformatics software through Linux command line
Bioinformatics is a rapidly growing academic field, and one that promises to change how we analyse and compare biological data.
On this course, you’ll get familiar with Linux – the operating system often used to access and analyse biological data. You’ll come away able to navigate it using the command line, understanding how to write scripts and prepare data files for further analysis and visualization.
Explore basic commands and file system in Linux
Much bioinformatics software is available for use through Linux, via the command line, which many biologists are unfamiliar with.
Alongside international team of bioinformatics, you’ll learn what the main features of Linux are, and how it’s used in biology. You’ll be able to describe how a Linux file system is structured and learn how to use Linux commands to navigate the file system.
Discover how to work with biological data files
You’ll use Linux commands to manipulate biological data files, preparing them for export into other environments for further analysis. The course will introduce you to the basics of R language and RStudio software environment.
You’ll also learn the basics of writing and executing simple Bash scripts in order to automate data processing.
Learn from an international team of bioinformatics experts
The Wellcome Genome Campus (WGC) is one of the globe’s leading bioinformatics centers, pioneering vital research into genome analysis.
On this course, the educators from WGC Advanced Courses and Scientific Conferences are joined by experts from the Institute Pasteur de Tunis, to give you practical training using real biological data in different biological scenarios. This will help you see how you can work with data in your own field of biology.
What topics will you cover?
- What is Linux? Why Linux for biologists?
- The Linux file system and navigating around it via the command line
- Manipulation and searching of data files using the command line to access useful biological data
- The basics of writing Bash scripts and its use for process automation
- Guidelines and recommendations for best practice preparation of data files under Linux for exporting to other environments (use of R for further analysis and visualization)
- Exercising on biological data using different case scenarios
When would you like to start?
Start straight away and join a global classroom of learners. If the course hasn’t started yet you’ll see the future date listed below.
Available now
Learning on this course
On every step of the course you can meet other learners, share your ideas and join in with active discussions in the comments.
What will you achieve?
By the end of the course, you‘ll be able to...
- Identify main characteristics of Linux and its use in biology
- Describe the structure of a Linux file system
- Use Linux commands to navigate the file system
- Perform Linux commands to manipulate and interrogate biological data files
- Prepare biological data files under Linux for exporting into other environments such as R
- Write and execute simple shell scripts in order to automate processing of data
Who is the course for?
This course will appeal to students, biologists, and research scientists with an interest in bioinformatics.
Learners are expected to have some knowledge of or experience with life sciences, but no prior knowledge of computing or bioinformatics is expected. There are no formal prerequisites.
What software or tools do you need?
Windows users might need to download and install a Unix emulation program. Linux and Mac users can run Unix commands natively in a terminal session. The course examples can also be run using a browser-based online emulator.
For the best learning experience, learners should have a computer available to them, not just a handheld device.
Who will you learn with?
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