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Thank you Jake & Ben for the feedback! Interesting & informative to read. I will also note: some interesting technical details on the of UML in PAML have been discussed in a few different places in the PAML Github issues (I found recently via searching), & those were interesting to read as well, although I didn't appreciate them fully.
On the manuscript, not sure if you are still taking comments, but I have some brief ideas for citations that could be added (citations that I found especially helpful as learning more about this workflow description field as a wet & dry lab biologist - unrelated to my current work). I can direct message those comments if interested.
All the best,
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