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Kai Blin

@kblin.bsky.social

1K followers 340 following 540 posts

Microbiology PhD, co-author of antiSMASH, Open Source geek, views are my own. @[email protected]

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Kai Blin @kblin.bsky.social · 13h

It's because biology is a gigantic piece of improv theatre. Every time you go "this is how things work", biology goes "yes, and..." and runs off on a completely new tangent.

Kai Blin @kblin.bsky.social · 3d

AI rights? April’s fools is coming early (or late), apparently

Kai Blin @kblin.bsky.social · 4d

Which funnily enough is also the origin of the "ninja" look. They basically started as kind of a neat fourth wall break by having stage hands come in and suddenly interact with their victims on stage.

Kai Blin @kblin.bsky.social · 5d

I’m not even sure if that generates a notification either way. I just unfollowed and re-followed you to test. It sure does happen to me a lot as well.

Kai Blin @kblin.bsky.social · 7d

A cup with the text "CSS is awesome" in a box. And because CSS is so awesome, there is a text overflow issue, and the word "awesome" is flowing out of said box.

Kai Blin @kblin.bsky.social · 7d

Ew, that does sound unpleasant. The one I ended up in mainly was too narrow, squishing my shoulders together for an hour or two. But of course 19 year old me could shrug that off afterwards like today me wouldn't in a week.

Kai Blin @kblin.bsky.social · 7d

They seem to have that effect. I participated in an MRI study during military service and can only imagine being stuck in that tube for a medical reason.

Kai Blin @kblin.bsky.social · 11d

I beg to differ. Southern Germany makes a proper potato salad as well. It's only north of the Weißwurstequator that mayonnaise is added.

Kai Blin @kblin.bsky.social · 13d

On top of that, "Lageweilewut" doesn't work as a word. I mean, sure, you can just paste some words together to create a compound word. But this one feels off, like using multiple adjectives in the wrong order in English. Knapp daneben ist auch vorbei, as usual for these AI things.

Kai Blin @kblin.bsky.social · 17d

Doesn't have the right ring to it

Kai Blin @kblin.bsky.social · 17d

Take two aspirin and call again tomorrow.

Kai Blin @kblin.bsky.social · 17d

That happens if you try to summarise the changes, but all commit messages are "change some stuff" or "some fixes".

Kai Blin @kblin.bsky.social · 17d

Also, I wouldn't necessarily try and replicate the Bio* APIs, personally. I think back in the day they were well-designed, but best practices have shifted.

Kai Blin @kblin.bsky.social · 17d

I'm just saying that because the GenBank format is a mess, with every tool having its own ideas how to handle things. I spent the past 15 years fixing weird edge cases in BioPython's parser, and some years before that, I did the same for BioPerl. This is not trivial.

Kai Blin @kblin.bsky.social · 17d

NAR is always a bit touchy around preprints, but I can look into it. The database is already running at antismash-dbv5.secondarymetabolites.org , but might still have a few rough edges.

antiSMASH bacterial version

antismash.secondarymetabolites.org

Kai Blin @kblin.bsky.social · 17d

Is there a good Rust parser for GenBank these days? Or generally, a replacement for BioPython?

Kai Blin @kblin.bsky.social · 17d

See our upcoming paper for what we think is the best strategy.

Kai Blin @kblin.bsky.social · 17d

Not sure "everything on GenBank" adds a lot of value to the set in the antiSMASH database. We filter for high quality and dereplicate for a reason.

Kai Blin @kblin.bsky.social · 19d

Oooh, that's on my to-do list as well. I hope it has (decent) swordfighting.

Kai Blin @kblin.bsky.social · 23d

As a person working with a lot of data, I have lots of garbage files. I’m happy to share some if you want.

Kai Blin @kblin.bsky.social · 23d

"What if the US was the periodic table"

Kai Blin @kblin.bsky.social · 24d

More like a greengrocer, because that was a textbook greengrocer’s s

Reposted by Kai Blin

Ewan Birney @ewanbirney.bsky.social · 25d

Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.

James Bonfield @jbonfield.bsky.social · 25d

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.

Ie: it's not us (Samtools team)! Be warned

Kai Blin @kblin.bsky.social · 24d

Manuscript submitted. Now we only need to get that grant proposal done, and then I’ll just stay in bed for a week to catch up on all the sleep I lost in the past weeks.

Kai Blin @kblin.bsky.social · 25d

Dear Microsoft, I open your tools when I absolutely have to. When I do, I need to get work done. I never, ever want to leave a review on how much I’m enjoying that experience. Just sod off with that irritating pop up.