Typically after giving a presentation at least one person will approach me and ask if they could have access to my custom latex template to make slides with beamer that don’t look rubbish.
TL;DR Yes you can: https://github.com/npqst/latex-beamer-template
Continue readingJamboree
Oxford Dictionary
(1) a large gathering, as of a political party or the teams of a sporting league, often including a program of speeches and entertainment.;
(2) a large gathering of members of the Boy Scouts or Girl Scouts, usually nationwide or international in scope
This October marks twenty years since our supreme leader, Charlotte Deane, came to Oxford to start the first protein informatics group in this university.
Twenty years is a really long time, and at OPIG we like to celebrate things in style. From the beginning, it was clear that we would be doing what we know best: get together, consume lots of food and drinks, and perhaps talk about science. But, frankly, that’s what we do all the time. This simply wasn’t enough to celebrate two decades of scientific production. So Charlotte entrusted several of us with an ambitious goal: to reach out to our former members, and to ask them to join us, in Oxford, to celebrate two decades of protein informatics. And that’s what we did.
For two months, we painstakingly tracked down every person that has ever been part of our group, and attempted to gather their contact details to invite them to Oxford. Attempted to, for the most part. While LinkedIn gave us some early victories, some alumni had managed to cover their tracks very well, including one person we could only found after tracking down their three previous jobs. Nevertheless, after much digging, we managed to find updated contact details for every person that has ever passed by our lab, and nearly thirty of these former alumni (almost 50% of them!) made their way to Oxford on October 8th* to hold the first OPIG Jamboree.
Yep, it is very well known that the sugar coating (aka glycosylation) of viruses makes them invisible to the immune system, a strategy so effective that like in the case of HIV, whose spike is almost entirely covered by glycans, makes it so difficult to target by the human immune system.
Unsurprisingly, coronaviruses such as SARS, MERS, and SARS-CoV-1(2) not only benefit from this evolutionary strategy but there is evidence now that sugars provide stability to their spikes to be effective binders by glueing the spike chains, hence making them infectious.
This is the major finding of this paper that introduces very interesting results from all-atom MD simulations of a fully glycosylated model of the SARS-CoV-2 spike protein embedded in a realistic viral membrane. Researchers aimed to look into the stability of the protein spike (A, B, and C) chains in the “open” and “closed” conformation and how these changed upon key residue mutations to test how glycans sitting in the inter-chain space affect stability. It also aimed at quantifying glycans’ shielding effect from molecules ranging from 2 to 15 Angstroms, i.e., from small-sized to peptide- and antibody-sized molecules.
Continue readingToday’s group meeting was the GOAT (Greatest Of ALL Time) as we were honoured with the presence of Daisy (professional internet goat) from Cronkshaw Farm.
I recently spoke at the Festival of Biologics 2021 conference in Basel (in-person, just in time!), and was lucky enough to be offered the chance to chair a session of talks. As this was the first time I’d ever been asked to do this, I asked Charlotte for some hints to make things go more smoothly. I found her advice very useful, so I thought I’d share it here for other first-time “chairers”!
Continue readingLast week I attended the COXIC seminar (joint seminar Oxford – Imperial focused on networks and complex systems) organised by Florian Klimm from Imperial College London (and former OPIG member!). We had several interesting at the seminar. However, one of them caught my eye more than the rest. It was the talk of Dr Sanjukta Krishnagopal (UCL) titled Predicting Parkinson’s Sub-types through Trajectory Clustering in Bipartite Networks, of which I will give a quick insight. Hope you like it (at least) as much as I did!
This blogpost is based on these two articles:
Disclaimer: this post is an opinion piece based on the experience and opinions derived from attending the CASP14 conference as a doctoral student researching protein modelling. When provided, quotes have been extracted from my notes of the event, and while I hope to have captured them as accurately as possible, I cannot guarantee that they are a word-by-word facsimile of what the individuals said. Neither the Oxford Protein Informatics Group nor I accept any responsibility for the content of this post.
You might have heard it from the scientific or regular press, perhaps even from DeepMind’s own blog. Google ‘s AlphaFold 2 indisputably won the 14th Critical Assessment of Structural Prediction competition, a biannual blind test where computational biologists try to predict the structure of several proteins whose structure has been determined experimentally — yet not publicly released. Their results are so incredibly accurate that many have hailed this code as the solution to the long-standing protein structure prediction problem.
Continue readingLast Wednesday, I was fortunate enough to be invited as a guest lecturer to the 3rd BioDataScience101 workshop, an initiative spearheaded by Paolo Marcatili, Professor of Bioinformatics at the Technical University of Denmark (DTU). This session, on amino acid sequence analysis applied to both proteomics and antibody drug discovery, was designed and organised by OPIG’s very own Tobias Olsen.
Continue readingBoth the beauty and the downfall of learning-based methods is that the data used for training will largely determine the quality of any model or system.
While there have been numerous algorithmic advances in recent years, the most successful applications of machine learning have been in areas where either (i) you can generate your own data in a fully understood environment (e.g. AlphaGo/AlphaZero), or (ii) data is so abundant that you’re essentially training on “everything” (e.g. GPT2/3, CNNs trained on ImageNet).
This covers only a narrow range of applications, with most data not falling into one of these two categories. Unfortunately, when this is true (and even sometimes when you are in one of those rare cases) your data is almost certainly biased – you just may or may not know it.
Continue readingSeemingly every conference due to take place this year has either been cancelled or will be run virtually due to the COVID-19 pandemic. Many organisers have decided that running entirely live virtual programmes causes more trouble than it’s worth (e.g. due to unforseeable IT and internet issues disrupting the schedule), and so are asking their presenters to prerecord their talks, which are then broadcast “live” on the day.
I recently “presented” two virtual prerecorded talks at the ISMB conference using Open Broadcast Software Studio (OBS Studio), a free open-source software package most commonly used by live-streamers on Twitch and Youtube. It is super simple to use and achieves a professional output, with video overlaying a presentation slide deck/poster PDF. This blog is a “how-to” on getting started with OBS for conference talks/poster presentations.
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