Monthly Archives: October 2019

You’re getting on my biscuits

Jaffa cakes are God’s own snacks and I will brook no opposition. I don’t mind if they’re McVitie’s brand Jaffa cakes, or Pim’s, the suspicious European variety. Even Sainsbury’s Basics Jaffa cakes float my balloon. Take a soft sponge base, slap some jam and chocolate on that puppy, and you’re golden.

But if you describe your love of these glorious creations, the conversation takes a familiar turn. Are they cakes or are they biscuits? it goes. HMRC tried to classify them as cakes – or was it biscuits? Something like that. It had to do with VAT…

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Common denominators between a PhD and an Oxford ball

One of the things I love about Oxford is the way it pushes you to become a well-rounded person. It does so by means of a wealth of talks and lectures, and also through the college system that encourages meeting people from different disciplines, but above all through the strong culture of student projects. This place will encourage you, perhaps even push you, to take part in fantastic projects that will make the already very demanding workload even worse… but also teach you incredible skills and get you to work with wonderful, inspiring people.

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What are Hotspots in Structural Biology?

“Hotspot” is one of those extremely versatile words, similar to “model” and “buffer”, which can mean a variety of things depending on context. According to Merriam-Webster, a hotspot is “a place of more than usual interest, activity, or popularity”. This is the most general definition of the concept I could find in a quick search, and the one I find closest in spirit to the way hotspots are perceived in a structural biology context. What this blog post is definitely not about are hotspots as “areas of political, military, or civil unrest” (my experience with them has so far been mostly peaceful), or anything to do with geology, WiFi connections, or forest fires.
However, even within the context of structural biology and structure-based drug design, the word “hotspot” has multiple meanings. In this blog post, I will try to summarise the main ones I have come across, the (sometimes subtle) differences between them, and provide a few useful papers to serve as an entry point for interested readers. Continue reading →

GitHub Link to Text Mining Tool

I have created a GitHub page to share some of the codes that I used to conduct text mining to extract HBV-related genetic information from PubMed Central. This code is easily adaptable to search through sentences that satisfy your keyword search, so please take a look if you are interested: https://github.com/angoto/HBV_Code.

Note: GitHub page is currently unavailable online, but will be accessible in due course.

SAbBox – the easy way to obtain our antibody tools

A significant part of the work we do here in OPIG revolves around antibodies, the proteins of the immune system that bind to and help remove any foreign entities that find their way into the body. Since antibodies can be developed that target basically anything, they have become extremely useful as therapeutics. In our research, we develop computational tools that can be incorporated into various points along the antibody discovery pipeline. These tools include our database of antibody structures, SAbDab, and a series of predictive tools (e.g. structural modelling algorithms like ABodyBuilder) which are known collectively as SAbPred.

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Things I’ve Learned from Hosting Speaker Events

For the past couple of years I’ve been involved in running the Oxford University Scientific Society. We host weekly talks in Oxford during the Undergraduate Term, inviting speakers from all scientific disciplines to come and discuss their field with our members. Here are four important lessons I’ve learned from being involved!

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Tsar Nicolas II and the curious case of the mismatched bases in his maternal mitochondrial DNA – was Tsar Nicolas II really killed in a cellar in 1917?

The Death of the entire ruling Romanov Family in 1917

In 1917, Tsar Nicolas II, together with his wife, the Tsarina Alexandra, their five children (Maria, Anastasia, Olga, Tatiana and crown prince Alexei), and four servants, was executed and hastily buried in non-marked graves. His death ended the monarchic rule of House Romanov in Russia; no Tsar would ever sit on the Imperial throne again. A house which included famous Tsars Peter the Great and Catherine the Great was literally eradicated overnight.

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A Gentle Introduction to the GPyOpt Module

Manually tuning hyperparameters in a neural network is slow and boring. Using Bayesian Optimisation to do it for you is slightly less slower and you can go do other things whilst it’s running. Susan recently highlighted some of the resources available to get to grips with GPyOpt. Below is a copy of a Jupyter Notebook where we walk through a couple of simple examples and hopefully shed a little bit of light on how the algorithm works.

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A few more reasons why UNIX is awesome

One could easily find dozens of reasons for which UNIX — mainly Ubuntu — is simply, the best operating system. Although I remember people in my proximity mentioning this for ages, it’s been only a few months that I’ve realized what are the true advantages. Helpful for this were all the people teaching/demonstrating in various modules during my first year in SABS/DTC: quite often we would be asked to do something in the console rather than by clicking the mouse. In the meanwhile, I’d wonder why using the console can be better from a nice, user-friendly GUI (i.e. Windows…). Tools like sed, grep, tar and of course alias-ing form a quick answer. I will not argue more about these but demonstrate two more tools/tricks.

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