Author Archives: Alex Greenshields Watson

Why the vegans will say “I told you so…”

I am writing this on Wednesday 2nd October 2024. The news has all eyes on the middle eastern skies. Yesterday a story was circulating on BBC news warning of a drop in uptake of the seasonal flu jab.

https://www.bbc.co.uk/news/articles/c62d8r0nnl6o

Four days ago, on Friday 27th September, several news outlets reported that several healthcare workers had shown flu-like symptoms following exposure to the first patient known to have contracted avian flu (H5N1) without any animal contact. PCR testing has been inconclusive, with none of these workers testing positive for signs of the virus.

https://www.bbc.co.uk/news/articles/czd1v3vn6ero

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Useful metrics and their meanings

Short and selfish blog here. Probably been done before, but I shall carry on regardless. I am going to review some metrics relevant to our area of Immunoinformatics. In other words, I will try dissect things such as perplexity, logits, pTM, pLDDT and the ABodyBuilder2 confidence score. These numbers can help inform us on the likelihood of predictions, and whether we should have confidence in them.

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OPIG Retreat 2023

With the new academic year approaching, OPIG flew off to the rural paradise of Wilderhope Manor in sunny Shropshire for their annual group getaway. The goal of this retreat was assumed to be a mixture of team building, ‘conference-esque’ academic immersion, a reconnection with nature in the British countryside, and of course, a bit of fun. It is fair to say OPIG Retreat ‘23 delivered on all accounts, leaving the OPIGlets refreshed and ready for what the next year may bring.

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The dangers of Conda-Pack and OpenMM

If you are running lots of little jobs in SLURM and want to make use of free nodes that suddenly become available, it is helpful to have a way of rapidly shipping your environments that does not rely on installing conda or rebuilding the environment from scratch every time. This is useful with complex rebuilds where exported .yml files do not always work as expected, even when specifying exact versions and source locations.

In these situations a tool such a conda-pack becomes incredibly useful. Once you have perfected the house of cards that is your conda environment, you can use conda-pack to save that exact state as a tar.gz file.

conda-pack -n my_precious_env -o my_precious_env.tar.gz

This can provide you with a backup to be used when you accidentally delete conda from your system, or if you irreparable corrupt the environment and cannot roll back to the point in time when everything worked. These tar.gz files can also be copied to distant locations by the use of rsync or scp, unpacked, sourced and used without installing conda…

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