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Mon 5 Sep 2022
09:30 - 17:30

Venue: Bioinformatics Training Facility - Online LIVE Training

Provided by: Bioinformatics


Bookings cannot be made on this event (Event is not taking bookings).

Other dates:

Mon 17 Jun 2024

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Introduction to working with UNIX and bash (ONLINE LIVE TRAINING)

Mon 5 Sep 2022


CRUK Bioinformatics Summer School: Unix and R Foundations

Using the Linux operating system and the bash command line interface, we will demonstrate the basic structure of the UNIX operating system and how we can interact with it using a basic set of commands. Applying this, we will learn how to navigate the filesystem, manipulate text-based data and structure simple pipelines out of these commands.

Building on the techniques learnt so far, we will then construct bash scripts combining the commands and structures already learnt into more complex, reusable tools. We will look at how we can apply these scripts to common problems faced in UNIX environments such as: communicating with remote servers; managing custom software installations and integrating these tools into our simple pipelines.

This course is targeted at participants with no prior experience working with UNIX-like systems (OSX, Linux) or command line interfaces.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Target audience
  • Part of CRUK Bioinformatics Summer School: Unix and R Foundations 2022
  • Participants organised through CRUK Cambridge Centre

No previous experience required


Number of sessions: 1

# Date Time Venue Trainers
1 Mon 5 Sep 2022   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Hugo Tavares,  Paul Judge,  Shahriar Zamani,  Raquel Manzano-Garcia,  CRUK Training Programme
Topics covered

UNIX, Linux, Bash, Data handling


During this course you will learn about:

  • The basic features of a UNIX operating system
  • Navigating the filesystem using a terminal(text based interface)
  • Using bash as a tool for data manipulation and automation
  • Incorporating external tools and resources into your UNIX environment
  • Best practices for managing and maintaining scripts written in bash

After this course you should be able to:

  • Know how to look for help when writing bash commands
  • Navigate the file-system using the bash command line
  • Perform basic file and data manipulation in bash
  • Structure bash commands into simple pipelines
  • Run commands on external servers
  • Access data on external servers
  • Manage the installation of third-party tools into a UNIX environment
  • Write bash scripts to automate multiple commands


Related courses
Basic Skills and Programming

Booking / availability