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.
Continue readingComparative analysis of the CDR loops of antigen receptors
Allow me to present our recently accepted paper: Comparative analysis of the CDR loops of antigen receptors, to appear in Frontiers in Immunology [1]. In the blog post I will give a quick five-minute summary of the key messages in this work.
Continue readingNeurIPS 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”).
Continue readingOPIG 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.
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>.
Continue readingA collection of prion factoids
It’s been several years since I last presented a talk on prions to OPIG, so I thought a neat way of getting up to date would be to read “The prion 2018 round tables“. What’s the current understanding and are we any closer to determining a structure of PrPSc?
Continue readingLe 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.
Continue readingProf. 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:
Handling electron density in python for fun and profit
No-one ever observed a pdb file in nature. The experimental data we build our protein models from is not quite so nicely paramterised. The vast makority of models are fit into electron density maps, mostly produced from macromolecular crystalography or cryo-em.
Continue readingWhy you should care about startups as a researcher
I was recently awarded the EIT Health Translational Fellowship, which aims to fund DPhil projects with the goal of commercializing the research and addressing the funding gap between research and seed funding. In order to win, I had to deliver a short 5 minute startup pitch in front of a panel of investors and scientific experts to convince them that my DPhil project has impact as well as commercial viability. Besides the £5000 price, the fellowship included a week-long training course on how to improve your pitch, address pain points in your business strategy etc. I found the whole experience to be incredibly rewarding and the skills I picked up very important, even as a researcher. As a summary, this is why I think you should care about the startup world as a researcher.
Continue readingChat bots and the Turing test
When I recently tested out the voice activation features on my phone, I was extremely impressed with how well it understood not only the actual words I was saying, but also the context. The last time I used voice control features was years ago when the technology was still in its infancy. There was only a specific set of commands the voice recognition software understood and most of them were hard-coded. Given the impressive advances we have made utilizing machine learning for voice recognition and natural language processing to the point where I can tell my phone: “Hey Google, can you give me a list of the best BBQ restaurants near me?” and it will actually understand and do it, it is interesting that we still struggle with a language based technology that has been around for ages: chatbots.
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