Spring Training Day, 27th March 2024, University of York

The Spring Training Day will bring together the whole DTP cohort on 27th March at the University of York.

Click on each of the sections below for more information about the training for each year group.

There will also be time for social activities and cohort building.

We look forward to welcoming you all to the 2024 Spring Training Day!

1st Years: Analytics 1 Introduction to Reproducibility in R

Training programme for first year PhD students on the White Rose Universities (York, Sheffield, Leeds) DTP. It is designed and delivered by Emma Rand of The University of York.


An increase in the complexity and scale of biological data means biologists are increasingly required to develop the data skills needed to design reproducible workflows for the simulation, collection, organisation, processing, analysis and presentation of data. Developing such data skills requires at least some coding, also known as scripting. This makes your work (everything you do with your raw data) explicitly described, totally transparent and completely reproducible. However, learning to code can be a daunting prospect for many biologists! That’s where an Introduction to reproducible analyses in R comes in!

R is a free and open source language especially well-suited to data analysis and visualisation and has a relatively inclusive and newbie-friendly community. R caters to users who do not see themselves as programmers, but then allows them to slide gradually into programming.


I recognise that people will enter this training with a diverse range of previous experience in R. This is a challenge to manage but the aim is for everyone to get something out of the training no matter where they start. There will be sessions for those with and without previous experience. I recommend you:

  • sit close to the front of the class if you are completely new to R and towards the back if you have some experience
  • bring headphones to allow you to ignore tutor-led material when needed

Pre-course instructions for participants are given below.

Philosophy and approach

It is impossible to cover everything to you might ever need! Different people will use different methods and tools. Topics have been chosen because they are: foundational, widely applicable and transferable conceptually.

Learning outcomes

After this workshop the successful learner will be able to:

  • Find their way around the RStudio windows
  • Create and plot data using the base package and ggplot
  • Explain the rationale for scripting analysis
  • Use the help pages
  • Know how to make additional packages available in an R session
  • Understand what is meant by the working directory, absolute and relative paths and be able to apply these concepts to data import
  • Summarise data in a single group or in multiple groups
  • Recognise tidy data format and carry out some typical data tidying tasks
  • Develop highly organised analyses including well-commented scripts that can be understood by future you and others
  • Use R Markdown to produce reproducible analyses, figures and reports

Pre-course instructions for participants

Precourse survey

To help me direct you to useful training and manage diversity in previous experience during the sessions, please complete this form to indicate your current level: https://forms.gle/cpSjdcjVa7niz6iq5

Results 2023


There are Windows PCs at the venue and you are not required to bring your own machine. Participants from outside of York will be provided with a temporary IT account. However, if you prefer to work on your own machine please follow the instructions in Computing requirements

Schedule for workshop

1015 – 1030 Tutor-led for Everyone: Introduction and Principles of reproducibility

1030 – 1200 Tutor-led for Beginners: Introduction to R and working with data or Supported learning for those with some R experience Tidying data and the tidyverse including the pipe

1200 – 1300 Lunch

1300 – 1330 Tutor-led for Everyone: Project-oriented workflow

1330 – 1445 Tutor-led for Everyone: Quarto for reproducible reporting

1445 – 1515 Tea and coffee break

1515 – 1645 Continuation of Tutor-led for Everyone: Quarto for reproducible reporting

Computing requirements

Laptops should have the following installed prior to attending attempting the materials.

Installing packages


Once you have installed R and RStudio, start RStudio up and go to the Packages tab in the bottom right pane; click Install and type the name of the package you want to install in the box that appears. Then wait until you get the cursor (>) back in the console window.

RStudio Cloud

If installing R and RStudio is tricky or impossible with your set up (e.g., if you only have a chrome book) then you can use https://rstudio.cloud/. This is a version of RStudio that runs in your browser. It is free for 15 hours but you will need to make an account. You will still need to install packages.


White Rose BBSRC Doctoral Training Partnership (DTP) in Mechanistic Biology Analytics 1: Introduction to reproducible analyses in R by Emma Rand is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Please cite as: Rand E. (2023). White Rose BBSRC DTP Training: An Introduction to Reproducible Analyses in R (version v1.2). DOI: https://doi.org/10.5281/zenodo.3859818 URL: https://github.com/3mmaRand/pgr_reproducibility

You can obtain all the workshop materials here

2nd Years: Analytics 2: Introduction to the command-line for Bioinformatics

Course Content

This course offers an introduction to working with Linux. We will describe the Linux environment so that participants can start to utilize command-line tools and feel comfortable using a text-based way of interacting with a computer. We will also introduce the “Git” version control system, which is a very powerful tool to help us secure our code from data loss. We’ll cover the terminology, how you can use it for your own projects and then how you can use it to make collaboration on a project easy.


No prior programming experience is required. Computers will be provided. You can bring your own laptop to the workshop if you wish but it will need a working wi-fi connection and you will have to let the tutor know in advance so a temporary York password can be created for you.

Learning Outcomes

After this course you should be able to:

  • Connect to a Unix / Linux system
  • Navigate around a file system by issuing commands; rather than using a Desktop environment
  • Move and copy files and directories within the Linux system
  • Work with text files
  • Run programs from the command-line
  • Write short scripts to document an analysis
  • Use version control (git) to track and document changes to a file

Schedule (Provisional)

Unix “cheatsheet”

Course Feedback

Please use this short form to give us feedback on the workshop. This will be used to inform the planning of future White Rose DTP training

3rd Years: Biorenewables Development Centre

Chris Hiscocks and Tom Frere from the Biorenewables Development Centre will be running training sessions focussing on:

  • Essentials of building fruitful relationships with industry partners
  • Translating your research into commercial success
  • Developing the confidence and skills to pitch your ideas effectively

More information about BDC can be found here: https://www.biorenewables.org/

4th Years: Job Search & Interviews for PGRs

Janice Simpson, Careers Consultant with the University of York Careers service, will be running a session covering:

  • Job interviews
  • Job hunting: where to start
  • How to find and build networks
  • How to prepare for job interviews
  • Asking for and acting on feedback after a job interviews

4th Years: Thesis Writing, Vivas and Surviving Your Career

Tom Bennett and Megan Wright will be running sessions on Thesis Writing and Vivas, and Surviving your career:

Thesis writing & vivas

In this session, we will cover the process of thesis writing, and provide specific advice on how to structure the thesis overall, how to structure each chapter, and how to go about the process of actually writing a chapter. We’ll then look at the timelines for thesis submission, what you need to do before you submit (apart from writing), and what happens after you submit. We’ll discuss the viva process, the criteria by which PhDs are examined, and the possible outcomes of the viva. We’ll provide specific advice on how to make sure you have a smooth and enjoyable viva!

Surviving your career

In this session we will draw on our extensive experience to provide advice on making the transition to a new career – whether academic or non-academic. We’ll cover areas like how to build survive the transition to a new job, how to build a CV, how to cope with colleagues, how to get the best out of people you manage…and anything else you want us to cover! We’ll also provide some specific advice on becoming a post-doc for those of you remaining in academia, including the essential dos and don’ts, and the next steps you can take to build an academic career.