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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NeurIPS 2019: Chemistry/Biology papers

NeurIPS is the largest machine learning conference (by number of participants), with over 8,000 in 2017. This year, the conference will be held in Vancouver, Canada from 8th-14th December.

Recently, the list of accepted papers was announced, with 1430 papers accepted. Here, I will highlight several of potential interest to the chem-/bio-informatics communities. Given the large number of papers, these were selected either by “accident” (i.e. I stumbled across them in one way or another) or through a basic search (e.g. Ctrl+f “molecule”).

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OPIG Retreat, 2019

For the third year running, the Oxford Protein Informatics Group of Professors Deane and Morris traveled to a bucolic, remote location for a series of talks (long and lightning), journal clubs, and hands-on practicals—not to mention evenings of quizzes, board games, and an afternoon of exploration of local attractions.

Kington, Herefordshire

Thanks to the organization of OPIG Members Mark Chonofsky and Javier Prado Diaz, five hire cars and one motorbike, some two dozen of us traveled from Oxford to the rolling hills and orchard country of Herefordshire, and Kington, near the border with Wales. We had the whole YHA Kington to ourselves from Wednesday until Friday, September 18-20, 2019. Our schedule was packed with great talks, and a few opportunities to press, watch people press, or tell people to press, <shift><enter>.

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Le Tour de Farce v7.0 (or: How I learned to Stop Worrying and Love the Wheels)

Come rain or shine, every summer we leave our desks and journey across Oxford’s finer drinking establishments. This year’s Le Tour de Farce was held on 11 June [1]. The trip is traditionally done by bike; however, as long as you have a helmet and lights, anything goes. To emphasise this point, Charlotte jokingly suggested rollerblades were also welcome.

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Prof. Charlotte Deane on the World Service

Prof. Charlotte Deane, the new Deputy Executive Chair of the EPSRC, Deputy Head of Division of MPLS, and Head of the Oxford Protein Informatics Group, was interviewed by BBC World Service’s programme “Tech Tent”, about the role of AI in drug discovery; jump to about 13:30 to hear Charlotte, and the segment on AI in healthcare starts at 9:45:

https://www.bbc.co.uk/sounds/play/w3csymsv