Fresh off the pages of Therapeutic Advances in Endocrinology and Metabolism comes a warning no self-respecting sweet tooth should ignore.
“Liquorice is not just a candy,” write a team of ten from Chicago. “Life-threatening complications can occur with excess use.” Hold on to your teabags. Liquorice – the Marmite of sweets – is about to become a lot more sinister.
Continue readingI had an opportunity to visit Basel, Switzerland for a month between mid-July to mid-August. The first week began with the ISMB/ECCB Conference 2019, which was a 5 days event. The average temperature was 35 °C with a hottest day reaching up to 39 °C, which was rather too hot compared to a British weather. This weather was perfect to try out ‘floating’ in the Rhine river, which I missed the opportunity to, but would highly recommend it if anyone is visiting Basel in the future.
Read moreBack in July a litter of OPIGlets went rooting for interesting science at ISMB/ECCB 2019 in Basel, Switzerland. When not presenting, working on my sunburn, or paying nine Francs for a beer, I made a point to attend talks outside my usual bubble of machine learning and drug discovery. In particular, I spent the latter half of the conference in the Education track, and am very glad I did. I love teaching, and am always excited to learn from more experienced educators and trainers. Today I’m going to talk about a fantastic presentation by Stevie Bain from the University of Edinburgh about introducing practical bioinformatics to high school biology classrooms through the 4273pi project.
Continue readingHi everyone,
My blogpost this time around is a list of conferences popular with OPIGlets. You are highly likely to see at least one of us attending or presenting at these meetings! I’ve tried to make it as exhaustive as possible (with thanks to Fergus Imrie!), listing conferences in upcoming chronological order.
(Most descriptions are slightly modified snippets taken from the official websites.)
In this blog post I will share with you the materials that I found most useful when I started doing some Bayesian Optimisation in my research. Bear in mind, I am a Chemist by training, so I approached this topic from a non-mathematical background (my eyes have to be persuaded to look at mathematical equations). Out of all the materials I have come across, I found these to be the most accessible.
Continue readingWhen I came to OPIG this past March I realized I had a novel opportunity – there was no one to tell me which molecular dynamics (MD) program I had to use! Usually, researchers do not have much choice in the matter due to a number of practical concerns. Conflicts between input and output file formats, forces, velocities, and basically everything else between MD suites make having multiple programs flying around tenuous at best if you want group members to be able to help one another. After weighing my options, I settled on OpenMM – and so far I am very happy with the decision.
I would like to advertise the research from Pearce et al. (https://doi.org/10.1101/401067) whose talk I attended at ISMB 2019. The talk was titled ‘Learning dynamical information from static protein and sequencing data’. I got interested in it as my field of research is structural biology which deals with dynamics systems, e.g. proteins, but data is often static, e.g. structures from X-ray crystallography. They presented a general protocol to infer transition rates between states in a dynamical system that can be represented with an energy landscape.
Continue readingI recently spent some time working out how to include mini inset plots within ggplot2 facets, and I thought I would share my code in case anyone else wants to achieve a similar thing. The resulting plot looks something like this:
As of last week, many members of OPIG have custom mugs. Each comes with an illustration of its owner’s favourite protein, as well as, the OPIG logo. There is an additional `unofficial’ OPIG logo on the backstamp (the outside bottom).
Continue readingFor scientists, units are like money: a few people obsess about them, but the less you have to think about units, the better. And, like switching a bank account, changing your units is usually tiresome and complicated for little real advantage. But spare a thought for the many units that have been lost to the inexorable march of scientific advance, and for the few that are still in regular use.
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