Prenomics

Learn the basics of command-line programming.
Registration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.

Dates for the next Prenomics workshop will be finalised shortly.

Prenomics teaches the basics of command-line programming, including:

Target audience

  • Learners who are intending to do bioinformatics but do not have any prior experience.
  • PhD Students & Researchers
  • Learners who wish to complete the Genomics Course

Check out testimonials from previous attendees!

“The prenomics module run by Cloud-SPAN is the best course for people interested in bioinformatics and recognises people with no experience. It was my first time using a command line to navigate the computer file system. It was worth the time. You guys are amazing with what you do. The patience, time, and demonstration of knowledge were all important in delivering the lectures. Thank you so much for this opportunity. As a first-year PhD student, this experience will be instrumental during my bioinformatics analysis and subsequently in the future. I am hoping to join the next course on genomics.” Doctoral student | University of Nottingham

“I really enjoyed the Prenomics course. I was initially worried going into it as I was a complete beginner but the leaders were amazing at explaining everything which made for a comfortable environment to ask any questions. I will definitely be recommending this course to others!” Early Career Researcher | Deep Branch

“I was scared of bash or using the Terminal previously. But, after attending Prenomics, I manage to conquer the fear:) Thanks to the team! Early Career Researcher | University of Leeds

Registration

Registration has now closed please contact cloud-span-project@york.ac.uk for further information on future courses.

There are 30 places available for this online workshop. This course is free of charge.

Pre-requisites

Knowledge: To ensure that you would benefit from participating in this course please complete the short self-assessment quiz self-assessment quiz. This course assumes no prior experience with the tools covered in the workshop however learners are expected to have some familiarity with biological concepts, including the concept of genomic variation within a population.

Software: view the required software set-up.

Programme

Day 1 10:00 - 12:30 Session 1 - Project management for cloud genomics
• Intro to local and remote files, hierarchical structure of files and folders
• Intro to the files which will be used in the Genomics course
• Logging onto the Cloud
• Introducing the Shell.
Day 2 10:00 - 12:30 Session 2 - Using the command line
• Navigating Files and Directories
• Working with Files and Directories
• Redirection

Learning outcomes

Following completion of this course, learners will be able to

  • explain the hierarchical structure of a file system
  • understand the structure of the file system on their own machine
  • find, create, move and delete folders and files on their machine
  • explain what is meant by a working directory, a path and a relative path
  • write down paths that they will need for the Prenomics and Genomics courses
  • describe the files and file structure used in Prenomics and Genomics courses
  • start a Terminal (Mac) or Git Bash Terminal (Windows)
  • navigate a file system using the command line
  • log in to and exit their AWS instance (the cloud)
  • use common commands such as ls, pwd and cd, on the command line

Scholarships

We offer scholarships to enable members of underrepresented groups and those with financial difficulties to participate in our training courses.

The scholarship scheme can cover approximately £150 per application, for costs such as:

  • childcare
  • accessibility needs
  • other costs that might otherwise prevent participation
  • second monitors and headsets.

To request a scholarship please indicate this in the registration form, before the given deadline. Submissions after this date will not be considered. We will contact you within a week after the deadline to confirm whether you have been awarded a scholarship.