BIO00087H

Genomics

Published

January 30, 2024

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

The deadline for prject submission is now Wednesday 22nd January at 12:00 noon

Student services requested that we change this to avoid students having a deadline during an exam.

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1 Staff

  • Daniel Jeffares
  • Andrew Mason

3 Preparation

There will be sufficient time during the semester for you to learn everything you need to know to pass this module with a high grade.

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 BIO00087H.

3.0.0.1 1. Start to learn the Linux operating system.

During the semester, students will use the Introduction to Shell course on DataCamp to learn about Linux. You could begin this course for free before the semester starts here. This is the most important preparation you can do. See below for completing this course during semester time.

DataCamp Classroom

During Semester 1 (16 September 2024 – 31 January 2025) you can join the BIO00087H Genomics 2024 ‘DataCamp Classroom’ using this link. Sign in with your University of York Google account. This will provide free access to the entire Introduction to Shell course.

3.0.0.2 2. Revise your RStudio skills

We suggest revising your work from Becoming a Bioscientist: Research in Action (BIO00066I). The cell biology Workshops are here. Other streams will also be useful. There is also a lot of teaching material for RStudio from a previous module here.

3.0.0.3 3. Review lecture material

Lectures will be made available here when updated versions are available. Please note that we improve and update our lectures before we present, so these are subject to change.

3.0.0.4 4. Review workshop material

The workshop material is available on this web site (see above). Apart from workshop 1 and 2, these are subject to be updated.

About the workshops

Workshops are not a test.

It’s OK to make mistakes. It’s OK to need help. You should be familiar with independent study content before the workshop, but you don’t need to understand every detail. The workshop will help you to build and consolidate your understanding. Tips:

  • there are no stupid questions (ask us anything!)
  • don’t worry about making mistakes (we all make mistakes)
  • discuss code with your neighbors and with the staff
  • outside of workshop times, Google is a good resource

3.0.0.5 5. 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.

4 Working from home

Working from home is only for exceptional circumstances

We can not 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 Daniel Jeffares to discuss this before hand.

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. 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.

  1. Open a Terminal app. The Terminal on PC is Windows Powershell. On a Mac, the app is called Terminal.

  2. Sign into the teaching0 server with: ssh [username]@teaching0.york.ac.uk. Use your usual University of York password to sign in.

  3. You are now within a Linux environment.

  • Your work is available in the usual place: /shared/biology/bioldata1/bl-00087h/students/[username]
  • 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].

5 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)

5.1 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/students/[username]/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/students/[username]/workshop3.


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5.2 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.

5.2.1 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 [username]@teaching0.york.ac.uk:[path]/[file wildcard] .

For example

scp [username]@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students/[username]/workshop3/*jpg .

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

5.2.2 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/students/[username]/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 [username]@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 [username]@teaching0.york.ac.uk:/shared/biology/bioldata1/bl-00087h/students/[username]/workshop3/*jpg

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