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Thu 6 Feb 2020
09:30 - 17:30

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Introduction to working with UNIX and bash

Thu 6 Feb 2020


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 this foundation, the course will use a bioinformatics example to demonstrate how the skills learnt can be applied to connecting to external resources/servers, installing specialist tools and ultimately combining commands into scripts for automation and reproducibility.

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

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here

No previous experience required


Number of sessions: 1

# Date Time Venue Trainers
1 Thu 6 Feb 2020   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Argyris Zardilis,  Paul Judge
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
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here


Core skills

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