Robin Rohwer

This is a compelling argument @froggleston.carpentries.org That blindly trusting the random person who wrote a package is not the same as blindly trusting an llm

This sentiment is not so different than wanting to understand generally what a package or library does, without worrying about the internal implementation.

Just noticed the Q&A comment boxes on peerJ articles now- wow! neat idea, curious if they'll be used

I dunno, yes you can dig for it, but does anyone actually? Like actually click through *all* old versions of a preprint to check for comments???

Biorxiv reviews just feel like reviewing into the void- public doesn't notice them, authors can ignore/bury them, now we learn even authors don't see it?

Missing from this discussion is that if authors want to bury a comment they don't like on their biorxiv preprint, all they have to do is just upload a new version. It happens even if they wanted it left in the public discussion, but want to address the comments with a new version!

I was discouraged from giving biorxiv reviews when I realized they are buried as soon as a new version is posted.

I think you should apply ;p After all it will fit "seamlessly into your existing commitments", and you've probably got an inside vote on the hiring committee

Pocket casts?

It is really cool that V4-V5 captures organelles so well... but I LOLed a little when I realized JEDI was just new branding for good old v4-v5 16S primers

What's up with isme having uncorrected manuscripts up for months? How are papers "published in April" still not actually published? Since when was this a thing??

Parallelle 😉

Another option in addition to sandpiper is IMNGS. Sandpiper searches NCBI metagenomes for markers, IMNGS searches NCBI amplicon datasets (and since you know the 16S... there are a lot more of those datasets out there)

Ha cool. My first thought was a breast pump flange...ouch 😂

A screenshot of the NYT article linked in the original post. In the "Consider early vaccination for children" section, the following is highlighted: "In the normal vaccination schedule, children who get the first M.M.R. at 1 get their second M.M.R. at 4 to 6 years, but in fact, children who have already had that first dose can get the second as early as 28 days after the first"

I had to change pediatricians to do this.

I was met with derision when I asked about early vaccination. After seeing how parents are treated when requesting a "nonstandard vaccination schedule" I feel like I understand why parents become antivax.

This is cool. Have long thought journal reviews/publishing should follow the WI DNR earn-a-buck model

Congrats!! Well-deserved!

Yes but just not the type of coding the original post was using ggplot downloads as a proxy for.

Also lots of people code in python and then use ggplot to make their figures. And that's not what you mean when you say "coding in R" right?

A photo of my laptop, with a new TACC sticker that says "my other computer is super". There's also an NTL-LTER logo sticker.

New swag from the @taccutexas.bsky.social machine learning training 😂

So nice to be back in Texas for a week, see my labbies IRL and learn some new things

Why did I study bacterial evolution when I could have studied pasta evolution? 🍝🤤

Imagine the fieldwork...

For the large fraction being lower, do you think that is because proportionally more euk reads in those metaGs?

Ahh thanks! Ok so yeah, def higher than 5% but I guess even with very carefully made mags I should not expect to get close to what I'm used to with water!

(And I do like your combined marker+mag approach for dealing with this too)

Yes I did not see the mag coverage listed explicitly since they used marker genes for the diversity part. Suspect that number was less impressive?

I realized I had no baseline for a sanity check! Does make you think about interpreting mag data differently by system though.

Ok wow, thanks. I was thinking only ~5% was really bad! 😅
Used to wanting to see ~50% in lake water!!

Ha yes, and can you ever assemble until saturation anyway?!

What percent reads mapped to MAGs is "good" for soil or sediment samples?

is lower than water samples OK/expected due to more complex communities?

🙏
🖥️🧬 microbiome, metagenomics

A screen shot of The Atlantic's daily word game called Bracket City. Clues are nested inside multiple layers of brackets, similar to the Newick format that uses nested parentheses to display phylogenetic tree structure.

@theatlantic.com has made reading a Newick tree as a text file into a fun game 😂

You need to find a way to quickly make 950 contributions today :p

SingleM is run on raw reads, looks for a variety of marker genes