Category Archives: Events

Bioinformatics 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.

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OPIGmas 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.

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Curious 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…

Image of a punched card, showing 80 columns and 12 rows, with particular rectangular holes representing the 1 bits of binary numbers. The upper right corner is cut at an angle, to facilitate feeding the card into a punched card reader. The column numbers are printed along the bottom. The words “IBM UNITED KINGDOM LIMITED” are printed along the very bottom. This card is line 12 from a Fortran program, “12 PIFRA=(A(JB,37)-A(JB,99))/A(JB,47) PUX 0430”. Image Credit: Pete Birkinshaw, Manchester, U.K. CC BY 2.0

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.

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BioDataScience101: 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.

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CCK-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!

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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.

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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Dimensions: The Mathematics of Symmetry and Space

Update: The exhibition was Highly Commended in Oxford’s The Vice-Chancellor’s Public Engagement with Research Awards 2019! [Link]

As part of outreach efforts, I have been involved with the exhibition “Dimensions: The Mathematics of Symmetry and Space” at the Ashmolean Museum. This exhibition is a great opportunity to explore a selection of the Ashmolean’s impressive collection from a mathematical (but very accessible) point of view.

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