Ragnar {Groot Koerkamp}
@curiouscoding.nl
Postdoc on high troughput bioinformatics @ KIT Karlsruhe;
IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography
IMO, ICPC, Xoogler, Rust, road-cycling, hiking, wild camping, photography
If I see one more "Subsection title (for real)"...
January 15, 2026 at 8:00 AM
If I see one more "Subsection title (for real)"...
Guess how many citations the original FM-index paper has. Then look it up.
January 14, 2026 at 8:51 PM
Guess how many citations the original FM-index paper has. Then look it up.
Reposted by Ragnar {Groot Koerkamp}
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
HLi Lab - Vacancies
Openings
hlilab.github.io
January 14, 2026 at 3:44 PM
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
Reposted by Ragnar {Groot Koerkamp}
Why is it that, despite being behind a perpetual cloud flare fence, @biorxivpreprint.bsky.social feels like it’s down an awful lot?
January 14, 2026 at 3:01 PM
Why is it that, despite being behind a perpetual cloud flare fence, @biorxivpreprint.bsky.social feels like it’s down an awful lot?
Reposted by Ragnar {Groot Koerkamp}
HTML preview & export now available in the web app! With HTML export, you can create a website from the same Typst file as your PDFs. This makes it easy to create documents that feel just as at home on the web as they do in print.
January 13, 2026 at 6:21 PM
HTML preview & export now available in the web app! With HTML export, you can create a website from the same Typst file as your PDFs. This makes it easy to create documents that feel just as at home on the web as they do in print.
Guess my blog having a CC license is a good thing 🫤
January 12, 2026 at 10:06 PM
Guess my blog having a CC license is a good thing 🫤
Yes please!
All Git repository tool configuration files (CI, issue template, etc.) should go in to `.config` like Cargo Nextest: nexte.st/docs/configu...
Currently we have .gitlab, .config, .cargo, ..., and it creates clutter.
Currently we have .gitlab, .config, .cargo, ..., and it creates clutter.
Configuring nextest - cargo-nextest
Configuring nextest: information about profiles and hierarchical configuration.
nexte.st
January 12, 2026 at 9:58 PM
Yes please!
Reposted by Ragnar {Groot Koerkamp}
God help me I’ve actually started working on this
So the starting point is JSON but with Python aesthetics: indentations and newline-oriented syntax, but {} and [] still permissible. true/false the only booleans, of course.
I’d immediately get rid of the “documents” thing and anchors and many of the strings.
I’d immediately get rid of the “documents” thing and anchors and many of the strings.
January 12, 2026 at 8:46 PM
God help me I’ve actually started working on this
Reposted by Ragnar {Groot Koerkamp}
Minister Van Weel heeft bijna genoeg informatie verzameld om Holocaust te kunnen veroordelen
Minister Van Weel heeft bijna genoeg informatie verzameld om Holocaust te kunnen veroordelen
Hij werd er vandaag weer naar gevraagd: bent u ertoe bereid zich uit te spreken over de rol van Nazi-Duitsland in de Holocaust?
speld.nl
January 12, 2026 at 5:02 PM
Minister Van Weel heeft bijna genoeg informatie verzameld om Holocaust te kunnen veroordelen
Grew up 100m from the Waal, offspring of the Rhine. Biked a bridge across it to highschool for 6 years.
Then a year at 100m off the Thames, continued by 8 years on a tributary of the Rhine.
Now moving to mid-Rhine, but sadly 5km away from it.
So yeah, I'm a Rhine boy :)
Then a year at 100m off the Thames, continued by 8 years on a tributary of the Rhine.
Now moving to mid-Rhine, but sadly 5km away from it.
So yeah, I'm a Rhine boy :)
My favorite Twitter prompt was "RT this with your home river," so reskeet this with your home river.
Mine is the Patuxent.
Mine is the Patuxent.
January 12, 2026 at 9:43 PM
Grew up 100m from the Waal, offspring of the Rhine. Biked a bridge across it to highschool for 6 years.
Then a year at 100m off the Thames, continued by 8 years on a tributary of the Rhine.
Now moving to mid-Rhine, but sadly 5km away from it.
So yeah, I'm a Rhine boy :)
Then a year at 100m off the Thames, continued by 8 years on a tributary of the Rhine.
Now moving to mid-Rhine, but sadly 5km away from it.
So yeah, I'm a Rhine boy :)
Reposted by Ragnar {Groot Koerkamp}
Reposted by Ragnar {Groot Koerkamp}
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
January 8, 2026 at 1:57 PM
🚀 Our new paper on Alignoth just published in Bioinformatics!
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Alignoth generates self-contained interactive HTML read alignment plots from BAM files – Rust-based, portable, and ideal for headless workflows.
📄 doi.org/10.1093/bioi...
#bioinformatics #genomics #rust @johanneskoester.bsky.social
Reposted by Ragnar {Groot Koerkamp}
Reposted by Ragnar {Groot Koerkamp}
This. Also: Europe does not do visionary speeches the way the Americans do. Our public sphere works in fundamentally different ways. Just because we don't do change like you do doesn't mean we do not do change. Brexiteers got this wrong too.
The thing I think folks struggle to appreciate with this stuff tho is however hard it is to wean Europe off US tech is *at least as hard* as it will be for US tech to get back into Europe after that type of transition kicks into high gear
January 11, 2026 at 2:51 PM
This. Also: Europe does not do visionary speeches the way the Americans do. Our public sphere works in fundamentally different ways. Just because we don't do change like you do doesn't mean we do not do change. Brexiteers got this wrong too.
Reposted by Ragnar {Groot Koerkamp}
Yet, for e.g., n = 2^30 bits, the o(n) extra space is 6.67% +
60% + 0.18% = 66.85% of n, which is not so negligible.
- Gonzales, Grabowski, Makinen, Navarro
60% + 0.18% = 66.85% of n, which is not so negligible.
- Gonzales, Grabowski, Makinen, Navarro
January 10, 2026 at 5:04 PM
Yet, for e.g., n = 2^30 bits, the o(n) extra space is 6.67% +
60% + 0.18% = 66.85% of n, which is not so negligible.
- Gonzales, Grabowski, Makinen, Navarro
60% + 0.18% = 66.85% of n, which is not so negligible.
- Gonzales, Grabowski, Makinen, Navarro
When will the submission deadline for recomb-seq proceedings be?
@recombseq.bsky.social @pashadag.bsky.social @ksahlin.bsky.social
@recombseq.bsky.social @pashadag.bsky.social @ksahlin.bsky.social
January 10, 2026 at 3:00 PM
When will the submission deadline for recomb-seq proceedings be?
@recombseq.bsky.social @pashadag.bsky.social @ksahlin.bsky.social
@recombseq.bsky.social @pashadag.bsky.social @ksahlin.bsky.social
What's it called when you subtweet but it's the first sentence of a paper?
(The footnote goes to Rank9 and Dijkstra)
(The footnote goes to Rank9 and Dijkstra)
January 10, 2026 at 2:22 PM
What's it called when you subtweet but it's the first sentence of a paper?
(The footnote goes to Rank9 and Dijkstra)
(The footnote goes to Rank9 and Dijkstra)
What's your longest Oauth2 login chain?
January 10, 2026 at 1:45 AM
What's your longest Oauth2 login chain?
Reposted by Ragnar {Groot Koerkamp}
today in "cross-language RPC": Rust and Swift have a different bit pattern for pi
January 9, 2026 at 3:07 PM
today in "cross-language RPC": Rust and Swift have a different bit pattern for pi
Reposted by Ragnar {Groot Koerkamp}
This is the official GPS status website with an *animated* banner for an urgent advisory about GPS moving to a different control center. gwcc-ws.cce.af.mil/gpsoc/
January 9, 2026 at 11:16 AM
This is the official GPS status website with an *animated* banner for an urgent advisory about GPS moving to a different control center. gwcc-ws.cce.af.mil/gpsoc/
You find yourself in the middle of a fastq file. You see + and @ all over the place. How do you find the start of the current record?
January 9, 2026 at 1:29 AM
You find yourself in the middle of a fastq file. You see + and @ all over the place. How do you find the start of the current record?
When you fight the borrow checker for an hour, only to realize you shouldn't have been fighting it in the first place :sob:
January 9, 2026 at 1:15 AM
When you fight the borrow checker for an hour, only to realize you shouldn't have been fighting it in the first place :sob:
Reposted by Ragnar {Groot Koerkamp}
TIL that the final level pattern table commonly taught with Jacobson’s rank (incl by me!) does not, actually appear in Jacobson’s thesis (that has only 2 levels). The first actual description I can find is Munro et al. 2001 www.sciencedirect.com/science/arti.... Is anyone aware of an earlier ref?
Space Efficient Suffix Trees
We give first the representation of a suffix tree that uses nlgn+O(n) bits of space and supports searching for a pattern string in the given text (fro…
www.sciencedirect.com
January 6, 2026 at 3:03 PM
TIL that the final level pattern table commonly taught with Jacobson’s rank (incl by me!) does not, actually appear in Jacobson’s thesis (that has only 2 levels). The first actual description I can find is Munro et al. 2001 www.sciencedirect.com/science/arti.... Is anyone aware of an earlier ref?
Reposted by Ragnar {Groot Koerkamp}
Nothing to see here... just a young man screaming at a data structure
a cartoon of homer simpson is holding a newspaper that says old man yells at cloud
ALT: a cartoon of homer simpson is holding a newspaper that says old man yells at cloud
media.tenor.com
January 6, 2026 at 12:27 PM
Nothing to see here... just a young man screaming at a data structure