BIO00087H

Genomics

Published

30 October 2026

This site is to contain the workshop material for the module BIO00087H Genomics.

1 Staff

Daniel Jeffares
Andrew Mason

2 The assessment

The assessment for this module is a 2000 word report. The deadline for submission is Monday 19th January 2027, 12 noon. See the report guide for more details.

3 Useful links for this module

How to use DataCamp Classroom

This will give you access to the entire Introduction to Shell course.

Join the BIO00087H Genomics 2026-27 Classroom using this link
Sign in with your University of York Google account
Work through the Introduction to Shell course

These sections will be required for workshops in this module:

Manipulating files and directories
Manipulating data
Combining tools

There is no need to work though these sections:

Batch processing
Creating new tools

4 Optional preparation

There will be sufficient time during the semester to learn the necessary skills for this module.

However, if you would like to prepare yourself, here are some activities that will help. This preparation is entirely optional.

Note: As teaching staff also have research responsibilities, we will not support this preparation outside of the scheduled teaching times for this module.

4.1 Revise your RStudio skills

We suggest revising your work from Becoming a BioScientist: Research in Action (BIO00066I). The cell biology Workshops are here.

4.2 Review workshop material

The workshop material is available on this web site (see above).

4.3 Peruse text books

The textbooks we used as a guide for this module are below. We do not keep strictly to these books (as genomics changes too fast) and it is not necessary to buy or read these text books to pass the module. Genomes 5 (TA Brown) is particularly good, if you like to have text books.

Genomes 5. TA Brown, 2023.
A Primer of Genome Science. 3rd edition, Gibson and Muse 2009.

DataCamp

Thanks to DataCamp for providing access to the Introduction to Shell course for free! DataCamp also has courses in R, and other programming languages.

5 Working from home

Working from home is only for exceptional circumstances

We are unable to support students who wish to take workshops from home for convenience. This is because it is not feasible to run dual (live and remote) classes with such large class sizes. In exceptional circumstances (that are verified with the Department of Biology), it is possible to conduct workshops from home. Special support may be required for this, so please contact Andrew Mason or Daniel Jeffares to discuss this beforehand.

It is possible to work from home, even without a Linux computer. This may be useful for completing your report. We describe below how to do this.

Install and set up the GlobalProtect Virtual private network (VPN) tool. You will need two-factor authentication.

You will not need GlobalProtect if you are working from within the campus network.
NB: Software installations on your computers should be directed to IT Support.

Open a Terminal app. The Terminal on PC is Windows Powershell. On a Mac, the app is called Terminal.
Sign into the teaching0 server with: ssh $USER@teaching0.york.ac.uk. Use your usual University of York password to sign in.

Note that $USER is your username

You are now within a Linux environment.

Your work is available in the usual place: /shared/biology/bioldata1/bl-00087h/students2627/$USER
The data is at: /shared/biology/bioldata1/bl-00087h/data
NB: Modules will have slightly different names within the teaching0 server. To find the relevant module use module spider [keyword].

6 Moving files off the network drive

When we work in Linux all your files are located on the network drive space /shared/biology/bioldata1/bl-00087h/.

You may wish to move files, such as plots or data files off this space, onto your personal computers/laptops. There are several ways to do this.

Transfer files to your Google Drive (or email them to yourself)
Move files from the server to your laptop/PC/Mac using secure copy (scp)

6.1 Transfer files to your Google Drive (or email them to yourself)

To do this:

open the File Browser App (as below).
do to the terminal window and use pwd to obtain the path where you are working. It will be something like /shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3
paste the path of your directory into the top panel of the file browser
open Firefox and sign into your Google account
upload or attach files as usual

Fig. 1 and Fig. 2 below show how to do this.

Figure 1. Ubuntu Linux desktop. Showing where the File Browser, and Show Apps buttons are.

Figure 2. Using the Ubuntu file browser. How to find a network directory using a path, such as /shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3.

____

6.2 Download files from the server to your laptop/PC/Mac using secure copy (scp)

This will work only if you are within the University of York network, or have signed into the GlobalProtect VPN (see above). This is a simpler option once you get used to Linux, particularly if you want to transfer many files.

6.2.1 About secure copy (`scp`)

Like the cp command, secure copy (scp) copies files from one place to another. Except scp copie files from one machine to another. This can be from your PC, to the teaching0.york.ac.uk server, or vice versa.

We to use scp to transfer from the teaching0.york.ac.uk server to a local machine (eg: your PC), do this:

scp $USER@teaching0.york.ac.uk:[path]/[file wildcard] .

For example

scp $USER@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/*jpg .

Note the dot (.) at the end of this command.

6.2.2 Using secure copy to copy a file from the server to your laptop

Be sue you know the location of the files on the server. eg. this might be /shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/something*
Then Open a Terminal app on your laptop. The Terminal on PC is Windows Powershell. On a Mac, the app is called Terminal.
Then use cd to navigate to the location on your laptop you want to download the files to.
Finally within the Terninal app on your laptop, use secure copy (scp) to copy files, like so:

scp $USER@teaching0.york.ac.uk:[path]/[file] .

Don’t for get the dot at the end. One example for [path] and [file wildcard] would be:

scp $USER@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/*jpg

Of course replace $USER with your username. The server will ask you to sign in, before this completes.

7 Running Long Analyses

Some analyses many minutes, or even hours, to complete. It is possible to set an analysis running on the teaching0.york.ac.uk server, log out, come back to it later. If you use the methods below to set up a screen, your analysis will continue after you have logged out.

screen

screen is a tool that lets you run background terminal sessions that keep working even if you close your terminal (or disconnect from Wi-Fi). By naming a session with screen -S <screen_name>, you can easily reconnect later using screen -r <screen_name> to pick up your running code or long process exactly where you left it.

Log in to the teaching0.york.ac.uk server as described here. You can do this from any York Linux machine or PC, or your own PC or Mac. This server has all the same files and software as the Linux computers you have been using already.
Navigate to the relevant directory where you want to work.
Open a screen with screen -S <screen_name> Its best to name the screen something that will help you remember what is running in there.
Set your analysis tool or software running.

Check that is is running properly before you leave!

To detach from your screen and leave it running in the background: Press Ctrl + a, release both keys, and then press d. This detaches the session so your tasks keep running. You can then log out from the server.
You can log in again later, and reattach to the screen using screen -r <screen_name>.

--- title: "BIO00087H" subtitle: "Genomics" date: today date-format: "D MMMM YYYY" format: html: code-copy: true code-tools: true code-link: true toc: true number-sections: true toc-location: right toc-depth: 2 highlight-style: github editor: source --- This site is to contain the workshop material for the module BIO00087H Genomics. # Staff - Daniel Jeffares - Andrew Mason # The assessment The assessment for this module is a 2000 word report. The deadline for submission is **Monday 19th January 2027, 12 noon**. See the [report guide](https://docs.google.com/document/d/19fI94usu-mPuBSbQf5j22jP1yhvExZE8EXied95IaQ0/edit?usp=sharing) for more details. # Useful links for this module - [Report guide](https://docs.google.com/document/d/19fI94usu-mPuBSbQf5j22jP1yhvExZE8EXied95IaQ0/edit?usp=sharing) - [Poster guide](https://docs.google.com/document/d/1AFWJ4uj8zTXn968W7cVdPoQpEJqNoyebiVHNGpTxF28/edit?usp=sharing) - [Poster groups](https://docs.google.com/spreadsheets/d/1xwef3Ca-x-Dbp2uigc4wzy3qtGn7pj88EPUYsypZEc8/edit?usp=sharing) - [VLE site](https://vle.york.ac.uk/ultra/courses/_112124_1/outline) - [Module description](https://www.york.ac.uk/students/studying/manage/programmes/module-catalogue/module/BIO00087H/latest) - [Previous years posters](https://drive.google.com/drive/folders/1aWEfZUtdisWic53DsqyWJ7sUCUxWnY9S?usp=drive_link) ::: {.callout-note title="How to use DataCamp Classroom"} This will give you access to the entire Introduction to Shell course. 1. Join the **BIO00087H Genomics 2026-27** Classroom using [this link](https://www.datacamp.com/groups/shared_links/79f0b64733cd1837fdffe60c96b67de25b3dd0a0f022997427ecfb258582d55f) 2. Sign in with your University of York Google account 3. Work through the [Introduction to Shell course](https://www.datacamp.com/courses/introduction-to-shell) These sections will be required for workshops in this module: 1. Manipulating files and directories 2. Manipulating data 3. Combining tools There is no need to work though these sections: 4. Batch processing 5. Creating new tools ::: # Optional preparation **There will be sufficient time during the semester to learn the necessary skills for this module.** However, if you would *like* to prepare yourself, here are some activities that will help. This preparation is entirely optional. **Note**: As teaching staff also have research responsibilities, we will not support this preparation outside of the scheduled teaching times for this module. ## Revise your RStudio skills We suggest revising your work from Becoming a BioScientist: Research in Action (BIO00066I). The [cell biology Workshops are here](https://djeffares.github.io/BIO66I/). ## Review workshop material The workshop material is available on this web site (see above). ## Peruse text books The textbooks we used as a guide for this module are below. We do not keep strictly to these books (as genomics changes too fast) and it is *not necessary* to buy or read these text books to pass the module. Genomes 5 (TA Brown) is particularly good, if you like to have text books. - Genomes 5. TA Brown, 2023. - A Primer of Genome Science. 3rd edition, Gibson and Muse 2009. ::: {.callout-tip title="DataCamp"} Thanks to [DataCamp](https://app.datacamp.com/) for providing access to the Introduction to Shell course for free! DataCamp also has courses in R, and other programming languages. ::: # Working from home ::: callout-important # Working from home is only for exceptional circumstances **We are unable to support students who wish to take workshops from home for convenience.** This is because it is not feasible to run dual (live and remote) classes with such large class sizes. In exceptional circumstances (that are verified with the Department of Biology), it is possible to conduct workshops from home. Special support may be required for this, so please contact Andrew Mason or Daniel Jeffares to discuss this beforehand. ::: It is possible to work from home, even without a Linux computer. This may be useful for completing your report. We describe below how to do this. 1. **Install and set up the GlobalProtect** [Virtual private network (VPN) tool](https://www.york.ac.uk/it-services/tools/vpn/). You will need two-factor authentication. - You will not need GlobalProtect if you are working from within the campus network. - NB: Software installations on your computers should be directed to [IT Support](https://www.york.ac.uk/it-services/contact/). 2. **Open a Terminal app.** The Terminal on PC is *Windows Powershell*. On a Mac, the app is called *Terminal*. 3. **Sign into the `teaching0` server** with: `ssh $USER@teaching0.york.ac.uk`. Use your usual University of York password to sign in. Note that `$USER` is your username 4. **You are now within a Linux environment.** - Your work is available in the usual place: `/shared/biology/bioldata1/bl-00087h/students2627/$USER`\ - The data is at: `/shared/biology/bioldata1/bl-00087h/data`\ - NB: Modules will have slightly different names within the teaching0 server. To find the relevant module use `module spider [keyword]`. # Moving files off the network drive When we work in Linux all your files are located on the network drive space `/shared/biology/bioldata1/bl-00087h/`. You may wish to move files, such as plots or data files off this space, onto your personal computers/laptops. There are several ways to do this. - Transfer files to your Google Drive (or email them to yourself) - Move files from the server to your laptop/PC/Mac using secure copy (scp) ## Transfer files to your Google Drive (or email them to yourself) To do this: - open the File Browser App (as below). - do to the terminal window and use `pwd` to obtain the *path* where you are working. It will be something like `/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3` - paste the *path* of your directory into the top panel of the file browser - open Firefox and sign into your Google account - upload or attach files as usual Fig. 1 and Fig. 2 below show how to do this. ![](ubuntu-desktop.jpg){width="50%"} **Figure 1. Ubuntu Linux desktop.** Showing where the *File Browser*, and *Show Apps* buttons are.\ ![](ubuntu-desktop2.jpg){width="50%"} **Figure 2. Using the Ubuntu file browser**. How to find a network directory using a path, such as `/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3`. \ \_\_\_\_\ ## Download files from the server to your laptop/PC/Mac using secure copy (scp) This will work only if you are within the University of York network, or have signed into the GlobalProtect VPN (see above). This is a simpler option once you get used to Linux, particularly if you want to transfer many files. ### About secure copy (`scp`) Like the `cp` command, secure copy (`scp`) copies files from one place to another. Except `scp` copie files from one **machine** to another. This can be from your PC, to the `teaching0.york.ac.uk` server, or vice versa. We to use `scp` to transfer from the `teaching0.york.ac.uk` server to a local machine (eg: your PC), do this: `scp $USER@teaching0.york.ac.uk:[path]/[file wildcard] .` For example `scp $USER@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/*jpg .` Note the dot (`.`) at the end of this command. ### Using secure copy to copy a file from the server to your laptop - Be sue you know the location of the files on the server. eg. this might be `/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/something*` - Then **Open a Terminal app** on your laptop. The Terminal on PC is *Windows Powershell*. On a Mac, the app is called *Terminal*. - Then use `cd` to navigate to the location on your laptop you want to download the files to. - Finally within the Terninal app on your laptop, use secure copy (`scp`) to copy files, like so: `scp $USER@teaching0.york.ac.uk:[path]/[file] .` Don't for get the dot at the end. One example for \[path\] and \[file wildcard\] would be: `scp $USER@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students2627/$USER/workshop3/*jpg` Of course replace `$USER` with your username. The server will ask you to sign in, before this completes. # Running Long Analyses {#running-long-analyses} Some analyses many minutes, or even hours, to complete. It is possible to set an analysis running on the `teaching0.york.ac.uk` server, log out, come back to it later. If you use the methods below to set up a `screen`, your analysis will continue after you have logged out. ::: callout-note # screen `screen` is a tool that lets you run background terminal sessions that keep working even if you close your terminal (or disconnect from Wi-Fi). By naming a session with `screen -S <screen_name>`, you can easily reconnect later using `screen -r <screen_name>` to pick up your running code or long process exactly where you left it. ::: 1. Log in to the `teaching0.york.ac.uk` server [as described here](https://djeffares.github.io/BIO87H/#working-from-home). You can do this from any York Linux machine or PC, or your own PC or Mac. This server has all the same files and software as the Linux computers you have been using already. 2. Navigate to the relevant directory where you want to work. 3. Open a `screen` with `screen -S <screen_name>` Its best to name the screen something that will help you remember what is running in there. 4. Set your analysis tool or software running. - Check that is is running properly before you leave! 5. To *detach* from your screen and leave it running in the background: Press **Ctrl + a**, release both keys, and then press **d**. This detaches the session so your tasks keep running. You can then log out from the server. 6. You can log in again later, and reattach to the screen using `screen -r <screen_name>`.