This month we said Goodbye to a few OG members of OPIG 🙁 among them was one of my favourites, Lucy! (should I apologise to the others?)
Lucy did some amazing work on improving output of generative models during her time in OPIG. One of her recent works involved increasing the plausibility of 3D molecular diffusion models using distorted training data. Check it out here.
Early in her PhD she worked on PointVS with Jack Scantlebury. PointVS is a machine learning scoring function that predicts protein-small molecule binding affinity by learning actual binding physics rather than dataset biases.
Word on the street is she also has some secret works in the making…
Bikes and pints across 5 pubs – what could be better (and what could go wrong). The year is 2025 and the date 06.06.25. Starting from the Stats department the customary picture was taken before the horn blown and a flood of ~30 structural biologists was unleashed onto the streets of Oxford to raid and plunder. Despite being the new kid I think Fergus will be proud to see my accurate version controlling unlike past more experienced members of the group, and that this reference doesn’t seem like copying his homework too much.
Of course even though it was June the weather was tumultuous. Having to make an educated guess on the probability of experiencing rain I took a Bayesian approach to calculate the posterior of rain occurring given the data of the entirety of British history which suggested that despite seeing sun on the BBC weather report that did not in anyway improve the likelihood of there being later rain. In light of this everyone came aptly dressed in waterproofs which turned out to be a smart choice after a later event of spontaneous beer spillage where a certain individual knocked his entire pint over Sophie and proceeded to say “at least you were wearing a raincoat”. This was a fantastic play by the newest member of the group who destroyed what little dignity (if any) he had so far amassed and simultaneously embroiled himself in the responsibility of this blog post. So to Charlotte who I know will be reading this (as I was warned!) perhaps this blog post will be an adequate first step to redemption.
And so the convoy departed towards our first stop, the Up in Arms (thanks Charlotte for the round). The inaugural table tennis tournament was held and it was great to see a real world application of the groups protein folding experience with Odysseus’s portable bike.
Next stop, the Victoria (thanks Matt for the round), before the 3.5 mile cycle to The Plough (I recommend going to the toilet before this after drinking units in the metric of pints).
Being far removed from our hunter gatherer past we settled down on the crisp summer grass with Oxford’s famous White Rabbit pizza delivered directly to the local meadow. I hadn’t grounded myself and connected to the earth like that in months (preferring to spend my days with my quadruple monitor workstation setup in the department) which combined with the beautiful settings of port meadow was making the trees look huggable. After scavenging 4 more pieces of pizza for a profit of 50% on my original contribution despite my intolerance to onions – whilst arguing that tolerance is a mental game aided by alcoholic bravery – we walked down the field to the river to reach our final destination – the idyllic medley looking over the Thames.
Reaching our last stop it dawned on me that despite proclaiming an ambitious target of 2 pints per pub I was sitting well below that at 3 pints total. It was clear desperate actions were needed to raise my average to stand up to any later scrutiny. Perhaps it was this subconscious desire to complete my self-assigned quest that at this last point of interest I executed the “swill Sophie” manoeuvre. Yet, despite my insistence that by getting through 2 pint glasses this was “technically” equivalent two my 2 pints per pub target, this did not stand up to the scrutiny of Charlotte.
After a month of wrangling with HPC molecular dynamics I’ve been getting more contact with the Slurm e-mail notification service than real human beings so it was refreshing to escape the GROMACS simulation that my brain has become and get to know the group better. Yet by the end of the night some of us (myself) couldn’t resist entering a tirade about how fractals and symmetry is the underlying representation of consciousness with the source being a strong “trust me bro”, and so it seemed liked a fitting time to put myself to bed.
This week (2024-08-07) instead of our usual group meeting, OPIG took to the high seas. The OPIGlets pooled our resources and procured punts from many different berths. Organised by Admiral Nele, we departed from the Cherwell boathouse and shipped out the 0.5 nautical miles (3.28801867e-6 light seconds for those playing along in metric) upriver to the Vicky Arms.
Despite visiting the odd bush on the way, scurvy scallywags one and all were herded in a generally upstream direction with Matt and Eoin leading the way. With the first two punts having safely reached dry land and refuelled their ethanol fuel cells, the question remained where on earth everyone had got to. Sagely concluding they’d probably all sunk another pint was had in their honour.
With much experience of all things farcical, it was my delight to have returned just in time for the 2024 edition of OPIG’s Tour de Farce, which took place on 11th July. This year’s route was 8 miles long and encompassed four of the finest establishments Oxford has to offer (nothing “unusually conservative” to see here Eoin).
With the new academic year approaching, OPIG flew off to the rural paradise of Wilderhope Manor in sunny Shropshire for their annual group getaway. The goal of this retreat was assumed to be a mixture of team building, ‘conference-esque’ academic immersion, a reconnection with nature in the British countryside, and of course, a bit of fun. It is fair to say OPIG Retreat ‘23 delivered on all accounts, leaving the OPIGlets refreshed and ready for what the next year may bring.
I don’t believe punting comes up much in Biggie Smalls’ raps (we live a pretty shielded life here in Oxford). Nevertheless, here are some photos from our recent OPunting trip, paired, very questionably and entirely for the pun’s sake, with some of the titles of songs he wrote/featured in.
Ever wondered whether opiglet keep their ketchup in the fridge or cupboard. Perhaps you’ve wanted to know how to create nice figure to display lots of information simultaniously. Publication quality figures are easy within R with the ggplot package. We may also learn some good visualisation.
16:30 BST 27/06/2023 Oxford, UK. A large number of scientists were spotting riding bicycles across town, to the consternation of onlookers. The event was the Oxford Protein Informatics Group (OPIG) “tour de farce” 2023. A circular bike ride from the Department of Statistics, to The Up in Arms (Marston), The Trout Inn (Godstow), The Perch (Port Meadow) and The Holly Bush (Osney Island). This spurred great bystander-anxiety due to one of a multitude of factors: the impressive size of the jovial horde, the erraticism of the cycling, the deplorable maintenance of certain bikes, and the unchained bizarrerie of the overheard dialogue.
Jamboree (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
Oxford Dictionary
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.
From the first student (Sanne Abeln, rightmost in the second row) to the most recent (Kate, whose hair can barely be seen on the leftmost third row), we are all here!Continue reading →
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