Projects
Work in progress bot
Another Bluesky bot: @wkipbot.bsky.social
I enjoy reading Work in Progress, but each article is long (20 to 40 minutes reading) and I often forget about an issue once it’s published. Each issue has 6 or 7 articles.
So to help me keep up, I created a Bluesky bot to post a link and description of one of the 115 articles (at the time of writing) from the Work in Progress archive each week with a screenshot.
Our World in Data bot
A bot that posts a screen shot of the Our World in Data (OWID) Daily Data Insight to Bluesky: @owid-daily-data.bsky.social
It’s built upon Simon Willison’s GitHub shot-scraper template repository that takes an automated screenshot of a OWID Daily Data Insight web page using shot-scraper. I then wrote a short R script to get alt-text and links and create the post for Bluesky.
The bot runs using Github Actions yml as a cron job similar to my literature bot (Section 4).
My Github repo is here: https://github.com/ab604/owid-dd-bot
Moving from Hugo Academic to a Quarto website
Notes on how I built this site and customised it
These notes include how to update my publications page using a Google Sheet and notes on icons and styling.
Bluesky literature bot
Based on the bots of @roblanfear.bsky.social and @jbgruber.bsky.social I created a bot using R and Github actions to post journal articles published on PubMed and bioRxiv that are of interest to me to keep up with the literature. You can make your own.
Code on Github: prot-paper-bot
Bot on Bluesky: @protpapers.bsky.social
The Itchen Bridge: Construction in colour
A local history project created with our intern Pardeep Panesar and the Digital Scholarship team at the University of Southampton. The results are on our Itchen Bridge webpage.
Webpage Design Guide 2024
My 2024 guide to design for text and links webpages for University of Southampton librarians.
R for Librarians 2024
Premier League Predictions 2023/24
My super simple model attempting to predict the outcome of the second half of 2023/24 Premier League season. Wrong, but fun!
Coding togetheR 2019/20
Creating and using a colour palette in R 2018
A tutorial is to demonstrate one way to create a colour palette and corresponding gradients in R.
British Society for Proteomics 2018 Data Science Workshop
Machine Learning for MHC I peptide classification 2018
MHC dynamics dashboard 2017
A dashboard to display the results of the MHC I MS-HDX project.
Creating a heatmap using R d3heatmap 2015
A short tutorial for producing heatmaps in R using some sample data.
Selector function of MHC I molecules is determined by protein plasticity 2015
This project sought to explain the mechanism of peptide selection by two functionally distinct MHC I allotypes using a combination of molecular dynamics and mathematical modelling of biochemical experiments.
In collaboration with the Biological Computation Group at Microsoft Research Cambridge we used biochemical data to infer that a conformational intermediate of MHC I is significant for peptide selection, and molecular dynamics simulations to show that peptide selector function correlates with protein plasticity.
This led to the proposal that MHC I cofactor tapasin modulates MHC I plasticity by dynamically coupling the peptide binding region and membrane bound domain.
Publication:
A. Bailey, N. Dalchau, R. Carter, S. Emmott, A. Phillips, J. M. Werner, T. Elliott. Selector function of MHC I molecules is determined by protein plasticity. Sci Rep, (5), pp. 14928, 10.1038/srep14928, 2015.
Biochem calculator 2015
A small Shiny app for calculating the amount to weigh out or dilute for making solutions.