• Wellcome Connecting Science

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.

29,183 enrolled on this course

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  • Duration

    3 weeks
  • Weekly study

    5 hours
  • Digital upgrade


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 visualisation.

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 bioinformaticians, 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 centres, pioneering vital research into genome analysis.

On this course, the educators from WGC Advanced Courses and Scientific Conferences are joined by experts from the Institut 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.

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Skip to 0 minutes and 8 seconds Bioinformatics is vital for the analysis, interpretation, and visualisation of biological data. And the Linux command line, bash scripting and R are among the most powerful tools available to bioinformaticians. This exciting, interactive course provides an introduction to all three. We will demonstrate how, with a few simple commands, Linux can be used to analyse and transform your own data. We’ll then walk through the basic steps of bash scripting together, moving from running commands one by one on the command line, to writing scripts which will run them for you. Along the way, you’ll discover bash scripting, almost endless capabilities for processing big data. You’ll start to find them as central to your day to day analyses as they are to me.

Skip to 0 minutes and 48 seconds We will also take you through the basics of analysing and visually representing your data by using R. Thanks to its ease of use and power, R extening now into many fields. And the number of R users worldwide is rapidly growing. By learning R with us, you’ll start on your path to performing and visually representing the analysis of your own data. So join us as we explore the ways in which the command line, bash scripting, and R can unleash the full power of bioinformatics.

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 visualisation)
  • Exercising on biological data using different case scenarios

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?

I am the IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests lie in bioinformatics and its application to microbial genomics.

Researcher at Institut Pasteur in Tunis and Trainer in Bioinformatics. Passionate about data analysis and visualization for pathogens related Genomics and Transcriptomics

As a Prinicipal Bioinformatician in Experimental Cancer Genetics at the Wellcome Sanger Institute, I develop and run pipelines for saturation mutagenesis, CRISPR screens, RNA-Seq and variant calling.

I am the Assistant IT Manager for the Wellcome Genome Campus Advanced Courses and Scientific Conferences team. My interests include machine learning and coding.

Who developed the course?

Wellcome Connecting Science

Wellcome Connecting Science develops and delivers open postgraduates courses and conferences focused on biomedicine.

What's included?

Wellcome Connecting Science are offering everyone who joins this course a free digital upgrade, so that you can experience the full benefits of studying online for free. This means that you get:

  • Unlimited access to this course
  • Includes any articles, videos, peer reviews and quizzes
  • Tests to validate your learning
  • A PDF Certificate of Achievement to prove your success when you’re eligible
  • Learning on FutureLearn

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    Join a global classroom

    • Experience the power of social learning, and get inspired by an international network of learners
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    Map your progress

    • As you work through the course, use notifications and the Progress page to guide your learning
    • Whenever you’re ready, mark each step as complete, you’re in control
    • Complete 90% of course steps and all of the assessments to earn your certificate

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