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”!
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OPIGlets go Kayaking
The 1st of July was the day that the OPIGlets went kayaking!
Brennan very kindly offered to guide a kayaking session from the Oxford University Canoeing and Kayaking Club (OUCKC). There was great uptake from the group, with 10 members joining for a paddle.
The first task was to find a kayak long enough for Jack’s legs. Once he managed to wedge himself in to the largest kayak available, we moved onto being pushed down the ramp one by one, hoping that this would not lead to an immediate capsize.
Continue readingBioinformatics Hackathon Reflection
A week ago I participated in Copenhagen Bioinformatics Hackathon 2021, a hackathon focusing on machine learning and proteins, as a mentor for a challenge proposed by our group. The whole experience was fun, but I am also sitting here contemplating over a lot of things I wish I had done differently. For this blog text, I therefore want to highlight two changes which I believe would have greatly improved my challenge and which can hopefully also work as an inspiration for others presenting a hackathon challenge.
Going into this event I had some experience from a few hackathons I had previously attended. Based on this, I wanted to create a challenge containing two parts. First, a simple task which everyone would be able to create a solution for, and second, a more challenging addition to the first task for more experienced participants. I decided to go with the challenge of predicting which heavy and light chains can form a pair, where the additional challenge was to try to visualize which residues were relevant for this interaction. Together with OAS containing a really nice positive dataset of paired chains, I thought this was going to be an amazing challenge, but as soon as the event began I started seeing the flaws of the challenge.
Continue readingOPIGmas 2020, Pandemic Edition
Not even a global pandemic can halt our annual celebrations. Festivus, move over. OPIGmas is here.
We were all lucky enough to have electricity; computers with webcams and microphones (Dan’s dalek incantations notwithstanding); and network connections; and somehow (for some of us) the time, to gather together around our twenty-first century electronic hearths and celebrate: Zoom, Gather Town, Among Us, Skribbl.io, and Codenames.
The much-awaited Secret Santa often reveals how naughty or nice the sender is, and sometimes surprising details about the relationship of the sender and recipient (I’m looking in the general direction of Dominik and Brennan). The rules are simple: spend up to £10 GBP, and don’t buy anything the boss wouldn’t buy for someone… But despite the hypothesis that the longer someone had been in OPIG, the more ‘pointed’ the gift would be, exceptions could still be found.
Armed with her new Easy Learning “Times Tables Bumper Book”, the boss was anointed “CEO of ******* Everything”, with her new desk name plate. Without coordinating, the boss’ PA independently received a desk name plate as “Fixer of Everything”. Perfect, on both counts.
Continue readingCurious About the Origins of Computerized Molecules? Free Webinar Dec 22…
After the stunning announcement at CASP14 that DeepMind’s AlphaFold 2 had successfully predicted the structures of proteins from their sequence alone, it’s hard to believe we began this journey by representing molecules with punched cards…
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Tales of carrying stacks of punched cards to the computer centre with a line drawn diagonally on the side of the stack, to help put them back in order should you trip and fall—seem like another universe—but this is what passed for the human-computer interface in much of the mid-20th century.
Continue readingBioDataScience101: a fantastic initiative to learn bioinformatics and data science
Last 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 readingCCK-18 is Going Virtual
We are going virtual! Our next Comp Chem Kitchen, CCK-18, will be via a Zoom Webinar, on Friday, March 27, 2020, at 5-6 pm. We are delighted to announce that Prof. Andreas Bender from the University of Cambridgewill be speaking, as well as Dr Vicky Hellon from F1000 Research. To attend the CCK-18 webinar, you must sign up for a free Eventbrite ticket (limit 100).
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!
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.
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 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.
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