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.
Continue readingAuthor Archives: Alex Greenshields Watson
Antibody Engineering & Therapeutics 2023
San Diego
And I wish I been out in California
Jagger & Richards
When the lights on all the Christmas trees went out
Festive conference blog here, dreaming of my December days in sunny California where I attended Antibody Engineering and Therapeutics 2023. Replete with Stones lyrics, Science and Sunset imagery. Hope y’all enjoy!
Continue readingWhere do we go from here?
This is an experiment.
We will prompt a model with a piece of text and assess how well it understands the contents.
The model sits behind your eyes.
The data used to train this model is your entire life, up to and including this very moment.
Continue readingOPIG 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.
Continue readingThe 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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