Core Skills

Educational materials on Creating your own instance and Prenomics have been developed to support the learning path onto the Specialised skills courses. You also have the option of completing them on a stand alone basis if you wish to. A module on Core R is currently under development.

If you are new to the realm of navigating file systems and using the command line we recommend you complete the Prenomics course before completing the Genomics course. We have designed Prenomics to allow more time for those with less experience to cover some foundation concepts. If you aren’t sure how to gauge your skills take the self-assessment quiz to help you decide. You have the option of completing Prenomics by either attending the online workshop or undertaking materials in self-study mode. If you choose the self-study learning path you will also need to complete the course on Creating your own instance.

Create your own AWS instance

If you would to complete the Prenomics and Genomics materials using the self-study learning mode you will need to start by creating your own Amazon Web Services (AWS) instance on your own AWS account.

Registration

This course is free of charge, however we ask that you register for the Self-Study Genomics learning mode, so we have your details and we can provide you with additional information. Registration will open soon.

Study Mode

This course is a self-study course and you can work through the online materials at your own pace. If you require any additional support whilst completing this course, there will be an informal 1 hour weekly drop in session via zoom to ask instructors any questions, you will be provided with information on this when you register.

Pre-requisites

Knowledge 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.

Overview & programme

How to create and manage an AWS instance derived from the Cloud-SPAN AWS Machine Image (AMI).

Topics

  • Creating an AWS account

  • Estimated resources needed for our instance

  • Getting research credits

  • Cost without research credits

  • How to reuse our instances on AWS

  • Creating one new instance

  • Ending an instance

Target audience

  • PhD Students

  • Researchers

Learning outcomes

Following completion of this course, learners will be able to

  • create and manage an AWS instance derived from the Cloud-SPAN AWS Machine Image (AMI).

Understanding your file system and using the command line

This workshop on understanding your file system and using the command line is available as a self-study module or you can register for the online workshop which takes place over 2 half days on 22-23 November 2022.

Registration

Registration for the online workshop and self-study are now open. This course is free of charge.

Study Mode

You can either complete the course by self-study or attend the online course.

Pre-requisites

Knowledge 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. To ensure that you would benefit from participating in this course please complete the short self-assessment quiz. Please note, if you are completing the course on a self-study learning path you will need to complete the Creating your own instance course beforehand.

Software View the required software set-up.

Overview & programme

10:00-13:00, Tuesday 22 November
Topic: Understanding your file system
- Intro to local and remote files, hierarchical structure of files and folders, how to create a Cloud-SPAN folder
- Intro to the files which will be used in the Genomics course and
- Logging onto the Cloud
- Introducing the Shell

10:00-13:00, Wednesday 23 November
Topic: Using the command line
- Navigating Files and Directories
- Working with Files and Directories
- Redirection

Target audience

  • PhD Students

  • Researchers

  • Learners who are intending to do bioinformatics but do not have any prior experience.

  • Learners who wish to complete the Genomics Course

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 Diversity Scholarships to enable members of underrepresented groups to participate in online- or in person training. To apply, please complete the registration form and provide all details requested in the scholarship section before 12pm on 1 November 2022. All applicants will be notified of the results by 14 November 2022. Please note that, scholarships are not available to participants completing the course in the self-study mode.



Core R

This half-day course will introduce you to R, a free and open source language especially widely used for the analysis and visualisation of 'omics data. You have the option of completing Core R by either attending the online workshop or undertaking materials in self-study mode. This course, or the equivalent experience, is recommended for learners who wish to complete the Metagenomics course where we use an R package, phyloseq, to examine the diversity and taxonomy of metagenomes. This module is currently under development.