Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R

Duration: 2 weeks, 5 hours per week
Free Certificate of Achievement available on satisfactory completion

Start Date: The course is run ‘live’ for 3 weeks from the start date above. Once this period is over there will be no live monitoring of the forums, but you can still join and complete the course during the remaining period.

Why join this course? 

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.

Who is this 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.

Course start dates

This course will be repeated twice a year.

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)
• Exercises on biological data using different case scenarios

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

Lead Educators

Martin Aslett
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.

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

Victoria Offord
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.

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

Wellcome Genome Campus Advanced Courses and Scientific Conferences 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