Category Archives: Group Meetings

What we discuss during cake at our Tuesday afternoon group meetings

Prerecording Conference Talks and Posters using OBS Studio

Seemingly every conference due to take place this year has either been cancelled or will be run virtually due to the COVID-19 pandemic. Many organisers have decided that running entirely live virtual programmes causes more trouble than it’s worth (e.g. due to unforseeable IT and internet issues disrupting the schedule), and so are asking their presenters to prerecord their talks, which are then broadcast “live” on the day.

I recently “presented” two virtual prerecorded talks at the ISMB conference using Open Broadcast Software Studio (OBS Studio), a free open-source software package most commonly used by live-streamers on Twitch and Youtube. It is super simple to use and achieves a professional output, with video overlaying a presentation slide deck/poster PDF. This blog is a “how-to” on getting started with OBS for conference talks/poster presentations.

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The Coronavirus Antibody Database (CoV-AbDab)

We are happy to announce the release of CoV-AbDab, our database tracking all coronavirus binding antibodies and nanobodies with molecular-level metadata. The database can be searched and downloaded here: http://opig.stats.ox.ac.uk/webapps/coronavirus

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HERO proteins are here to save you (assuming you’re another protein or a fruit fly)

For one of OPIG’s short talks, I recently introduced the work done by Kotaro Tsuboyama et al. found in the paper A widespread family of heat-resistant obscure (Hero) proteins protect against protein instability and aggregation. As the name implies, HERO proteins have been found to retain function even after being boiled at 95C and have been found both in Drosophila and human HEK293T cell lines. Whilst it’s not impossible to find proteins which can “survive” 90+ Celsius, these are expected to be the reserve of extremophiles, not found in humans or fruit flies.

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Non-specialist intro: Convalescent sera and some thoughts on its relevance to structural biology

A couple of weeks ago, I gave a group meeting talk on my current research. Interestingly most of the questions I received were not directly related to my research methods, but rather, on the broader application of antibody-related therapies, as I used the example of convalescent sera as a potential ‘quick fix’ in the current COVID-19 pandemic, to motivate why antibody research is important! So I thought in this blog post, I would give a quick introduction to convalescent sera. (Disclaimer: This does not contain any clinical information.)

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Molecular dynamics analysis in MDAnalysis

Any opportunity to use rigorously tested and supported analysis tools rather than in-house code is, in my opinion, an opportunity you owe it to yourself to explore.

My preferred tool for analyzing the output of molecular dynamics (MD) simulations is MDAnalysis, a Python library that provides robust and easy-to-use tools for analyzing most common files output by MD packages (including PDB, DCD, COR, and XTC file formats). But, of course, MDAnalysis can analyze any PDB file, not just one output from an MD simulations. There may be an opportunity in your workflow to incorporate MDAnalysis to save time or to provide more robust error handling than whatever in-house code you currently use.

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Journal Club: Is our data biased, and should it be?

Jia, X., Lynch, A., Huang, Y. et al. Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis. Nature 573, 251–255 (2019) doi:10.1038/s41586-019-1540-5 https://www.nature.com/articles/s41586-019-1540-5

Last week I presented the above paper at group meeting. While a little different from a typical OPIG journal club paper, the data we have access to almost certainly suffers from the same range of (possible) biases explored in this paper.

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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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