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Michael Baym
@baym.lol
Asst Prof @HarvardDBMI. Microbial evolution, antibiotic resistance, algorithms, phages, etc. Find me on Google Images under "floating dumpster fire"
2.6k followers648 following300 posts
MBbaym.lol

First rule of Red Queen Running Club: all our runs start and end in the same place

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MBbaym.lol

No, looks fine to me, why?

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MBbaym.lol

If this is where the evo people went, I hope you’ll all appreciate my new running shirt I’m unreasonably delighted by

An athletic shirt layer flat reading “Evolve” in stylized script
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Reposted by Michael Baym
MHmichaelhoffman.bsky.social

11/You'd think there wouldn't be a need for code sharing for a commentary, but you'd be wrong. Tony picked an "interesting" way of assigning author order. github.com/agitter/ai-c...

This repository is used to order authors (except the first author) in the commentary manuscript A renewed call for open artificial intelligence in biomedicine. The algorithm was designed in advance so that the final author order would be unknown to any of the authors, who were only told the "author list will be sorted by some unexpected, non-alphabetical key". It can accommodate adding new authors during revisions.

Ordering algorithm:

    Remove all characters besides the 20 canonical amino acids
    Concatenate 10 copies of the amino acid sequence
    Use the ESMFold API to predict a protein structure from the sequence
    Extract the pLDDT from the structure
    Sort the names by the corresponding pLDDT in descending order

Running the script

The script order_authors.py orders authors from an input text file with no header and one author per line.

Example using data available in the repository:

python order_authors.py --input test/example_authors.txt --output ordered_authors --p
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Reposted by Michael Baym
KLlindorfflarsen.bsky.social

How amino acids taste 🧪

Chart showing the chemical structures of the common amino acids as well as brief notes of their tastes. The latter are taken from:
https://doi.org/10.3758/BF03203878
https://doi.org/10.1016/0031-9384(81)90298-5

The original chart is modified from one made by @etymology_nerd on "How amino acids got their names" available e.g. here:
https://x.com/etymology_nerd/status/1310560462329831425
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MBbaym.lol

(To clarify: you’re likely infectious, but unlikely infect-every-last-mf-in-the-room infectious)

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MBbaym.lol

Unambiguously positive, sorry. Probably not super infectious (yet) but you’ve definitely got Covid

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MBbaym.lol

Apparently everything named Norumbega at Wellesley is because he gave a bunch of money and wanted things named after not him, but the mythical viking settlement he was convinced was on the Charles river

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MBbaym.lol

Walked down Thingvalla road today, which sent me down a rabbit hole of Even Norton Horsford, the Harvard chemistry professor who started a baking powder company and also was obsessed with the idea that Cambridge was the site of Leif Erickson’s lost Vineland colony en.m.wikipedia.org/wiki/Eben_No...

Eben Norton Horsford - Wikipedia
Eben Norton Horsford - Wikipedia

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MBbaym.lol

I cannot save you from deliciousness

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MB
Michael Baym
@baym.lol
Asst Prof @HarvardDBMI. Microbial evolution, antibiotic resistance, algorithms, phages, etc. Find me on Google Images under "floating dumpster fire"
2.6k followers648 following300 posts