skip to navigation skip to content
Mon 26 Apr 2021
13:00 - 17:00

Venue: Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

Provided by: Bioinformatics


Bookings cannot be made on this event (Event is completed).

Other dates:

No more events

[ Show past events ]

Register interest
Register your interest - if you would be interested in additional dates being scheduled.

Booking / availability

Introduction to Command Line Linux (Online)

Mon 26 Apr 2021


PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online, with tutors available to help you work through the course material on a personal copy of the course environment. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

This short (0.5 day) intensive course serves to introduce you to the command-line interface in Linux.

It is based upon elements of the Software Carpentries Shell(novice) and Shell(extras) courses. It is recommended for those CI personnel planning on attending the CI High Performance Computing facilities (Cluster) course.

This course is run by the CRUK CI Bioinformatics and IT core.

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
  • The course is recommended for all staff and students who use Linux in their research or plan on attending the CI High Performance Computing facilities (Cluster) course.
  • 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 Mon 26 Apr   13:00 - 17:00 13:00 - 17:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter) Mark Fernandes,  Dr A. Edwards
Topics covered



After this course you should be able to:

  • Run programs from the Linux Command-line environment
  • Create and organise files in the enviornment
  • Write simple automated scripts of commands.

During this course you will learn about:

  • Files, directories & paths (organising your data)
  • The anatomy of a command in the Command-line Interface
  • Creating & navigating directories, creating, deleting and renaming files
  • Using the output of one command as an input to another (Pipes & Filters)
  • Finding files and searching through files
  • Doing commands more than once (loops)
  • Making a commands pipeline (scripts)
  • Logging into other Linux machines using Secure Shell (SSH) and copying files to them using Secure Copy (SCP)

Presentations and practicals

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

This is subject to change in line with the online training schedule.

Session 1 Introducing the Shell
Session 2 Navigating Files and Directories
Session 3 Working with Files and Directories
Coffee break
Session 4 Redirection
Session 5 Writing Scripts and Working with Data
Session 6 Project Organization



Several time per year

Related courses
Core skills

Booking / availability