---
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  "@id": "https://cloud-span.github.io/prenomics00-intro/"
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  about:
  - "@id": "http://edamontology.org/topic_3372"
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  abstract: "Prenomics prepares learners for the Cloud-SPAN Genomics course. It teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file navigation and basic script writing."
  author: ["Emma Rand", "Sarah Forrester", "Annabel Cansdale", "Jorge Buenabad-Chavez", "Evelyn Greeves"]
  contributor: ["James Chong", "Emma Barnes", "University of York", "Software Sustainability Institute"]
  educationalLevel: "Beginner"
  identifier: "https://doi.org/10.5281/zenodo.6354056"
  name: "Cloud-SPAN Prenomics Course"
  url: "https://cloud-span.github.io/prenomics00-intro/"
  inLanguage: "en"
  keywords: "shell, command line tools, cloud computing, AWS, genomics, HPC, data analysis"
  license: CC-BY 4.0
  timeRequired: "PT6H"
  mentions: ["Git for Windows", "Cloud-SPAN Genomics course", "Data Carpentries Genomics workshop"]
---

[Cloud-SPAN](https://cloud-span.york.ac.uk) is a collaboration between the [Department of Biology](https://www.york.ac.uk/biology/) at the University of York and [The Software Sustainability Institute](https://www.software.ac.uk/) funded by the UKRI innovation scholars award. It aims to train researchers to effectively generate and analyse a range of 'omics data using Cloud computing resources.

This Prenomics module is designed to prepare people for the [Cloud-SPAN Genomics module](https://cloud-span.github.io/00genomics/). We have found that people taking the Genomics module can vary the amount of experience they have had in navigating file systems and using the command line. We have designed the Prenomics module to allow more time for those with less experience to cover some foundation concepts. We have a [Self-assessment Quiz](https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why) to help you decide if you would benefit from attending Prenomics before the Genomics module.

The Prenomics and Genomics modules are based on the Data Carpentry's [Genomics Workshop](https://datacarpentry.org/genomics-workshop/).

Prenomics teaches the basics of command-line programming, including: (1) file directory structure, (2) use of command-line utilities to connect to and use cloud computing and storage resources and (3) basic shell commands for file navigation and basic script writing.

The module is designed for a two half-day, tutor-led workshop, or for self study.

> ## Getting Started
>
> Carry out our short [Self-assessment Quiz](https://shiny.york.ac.uk/er13/prenomics-quiz/#section-why) to help you decide if you would benefit from attending Prenomics before the Genomics module.
> 
> This lesson uses an Amazon Machine Instance (AMI). If you are attending a tutor-led workshop your AMI will be created for you and will be sent the log in information you will need to use it. If you are self-studying Prenomics, you will need to set up your own instance using our [Create Your Own AWS Instance](https://cloud-span.github.io/create-aws-instance-0-overview/) module before starting.
> 
> This module assumes that learners have no prior experience with the tools covered.
>
> To get started, follow the directions in the [Setup](setup) tab to get access to the required software and data for this workshop.
> 
{: .prereq}

# Overview

| Lesson                     | Overview |
| -------------------------- | ---------|
| [Files and directories](https://cloud-span.github.io/prenomics01-file-directories/) |Learn about files and directories, log onto a cloud instance and get a basic introduction to the shell.|
| [Using the command line](https://cloud-span.github.io/prenomics02-command-line/)  |Learn more about using the shell to navigate directories, manipulate and search files and use basic loops to iterate commands.|

# Before a tutor-led course

You will need a shell. Please follow the directions in the [Setup](setup).