Rob Patro
@robp.bsky.social
Associate Professor of CS @ University of Maryland. Proud Rust advocate! I ♥ science & compiled, statically-typed programming languages! Views are my own. Tech stack: https://github.com/rob-p/tech-stack.
Trust public transport, they say. You won't get caught in the infinitely recursive self referential bus loop, they promise us.
So this happened in Oslo yesterday. Four articulated buses got stuck in a roundabout.
November 26, 2025 at 1:37 PM
Trust public transport, they say. You won't get caught in the infinitely recursive self referential bus loop, they promise us.
Reposted by Rob Patro
You know, we’ve got a saying
November 26, 2025 at 8:25 AM
You know, we’ve got a saying
Glad to see the spirit of the simpleAF (academic.oup.com/bioinformati...) naming scheme is catching on with "CLEAR-AF" www.biorxiv.org/content/10.1...!
CLEAR-AF: Improved Autofluorescence Subtraction for Multiplexed Tissue Imaging via Polar Transformation and Gaussian Mixture Models
Cyclic Multiplexed ImmunoFluorescence (cMIF) can profile dozens to hundreds of proteins at subcellular resolution, offering unprecedented insights into tissue architecture in health and disease. Howev...
www.biorxiv.org
November 25, 2025 at 5:00 PM
Glad to see the spirit of the simpleAF (academic.oup.com/bioinformati...) naming scheme is catching on with "CLEAR-AF" www.biorxiv.org/content/10.1...!
Reposted by Rob Patro
OH. MY. GOD. TYPST IS SO SMOOOOOTHHH.
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
November 25, 2025 at 2:43 PM
OH. MY. GOD. TYPST IS SO SMOOOOOTHHH.
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
100ms recompiles on save, by the time my eyes move from Emacs to pdf viewer it's already updated. I'm literally too slow to even see it update.
Also, this is why escape now maps to save. Saving allll the time. And Lshift-># (alongside much older Rshift->$).
And when you're trying to write an elite Rust implementation of something, who do you want on board? That's right! I was lucky enough to convince @curiouscoding.nl to join the mim team!
This can remove a key bottleneck in high throughput sequencing analysis tasks that are decompression & parsing limited. We implemented a mim index enabled parser in C++ & are working on one in Rust (and then Python bindings for that). We hope this makes using .fastq.gz a little less horrible! 2/2
November 25, 2025 at 2:41 PM
And when you're trying to write an elite Rust implementation of something, who do you want on board? That's right! I was lucky enough to convince @curiouscoding.nl to join the mim team!
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:38 PM
Unrelated to mim itself, but this is also the first preprint I've prepared in @typst.app rather than LaTeX. It was soooo much nicer. Folks; what are we doing? Why don't our journals accept manuscript sources in Typst!
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 25, 2025 at 2:13 PM
Ok; mim (github.com/COMBINE-lab/...) preprint submitted! Excited for folks to see it and share thoughts. The key takeaway; mim allows the quick, one-time, building of a small auxiliary index that then allows scaling gzipped FASTQ parsing linearly in # of threads. 1/2
Reposted by Rob Patro
@imartayan.bsky.social talks about Scalable comparison of long sequences at #Seqbim
Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !
Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !
November 25, 2025 at 1:42 PM
@imartayan.bsky.social talks about Scalable comparison of long sequences at #Seqbim
Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !
Can't wait to see what comes out of it @robp.bsky.social @camillemrcht.bsky.social !
So what standardized measures should one use instead? We've seen that test-free admissions seem to have caused even more problems (which is unfortunate, because I was certainly in favor of dropping the SATs when the idea was initially being pursued).
Opinion | Why the SAT Is a Poor Fit for Public Universities
The SAT may suit the Ivies, but it undermines the mission of America’s public institutions. https://bit.ly/4oe4Qrq
#EDUSky #HigherEd #AcademicSky
The SAT may suit the Ivies, but it undermines the mission of America’s public institutions. https://bit.ly/4oe4Qrq
#EDUSky #HigherEd #AcademicSky
November 25, 2025 at 12:43 AM
So what standardized measures should one use instead? We've seen that test-free admissions seem to have caused even more problems (which is unfortunate, because I was certainly in favor of dropping the SATs when the idea was initially being pursued).
Reposted by Rob Patro
Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀
#SEQBIM2025 is about to start, Bonsai presents 4 works this year in Nantes seqbim.cnrs.fr/seqbim-2025/...
seqbim.cnrs.fr
November 24, 2025 at 9:14 AM
Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀
Reposted by Rob Patro
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
November 24, 2025 at 2:42 AM
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
Reposted by Rob Patro
Microbiologist Dr. Rita Colwell was born #OTD in 1934. She is recognized for her study of global infectious disease spread through water sources. Her research on cholera helped save 𝘤𝘰𝘶𝘯𝘵𝘭𝘦𝘴𝘴 lives.
She was the first female director of the National Science Foundation (NSF), 1998-2004. #WomenInSTEM
She was the first female director of the National Science Foundation (NSF), 1998-2004. #WomenInSTEM
November 24, 2025 at 12:17 AM
Microbiologist Dr. Rita Colwell was born #OTD in 1934. She is recognized for her study of global infectious disease spread through water sources. Her research on cholera helped save 𝘤𝘰𝘶𝘯𝘵𝘭𝘦𝘴𝘴 lives.
She was the first female director of the National Science Foundation (NSF), 1998-2004. #WomenInSTEM
She was the first female director of the National Science Foundation (NSF), 1998-2004. #WomenInSTEM
2/3; Ravens win and Steelers loss. I'll take it.
November 24, 2025 at 12:02 AM
2/3; Ravens win and Steelers loss. I'll take it.
Did CS in college w/the goal of doing 3D engine programming at ID software w/John Carmack. Decided I liked graphics research senior year & applied to PhD. Did graphics while hanging out w/ppl who are now bioinfo legends. Decided to switch in my 4th year (I know) & am now a CS prof w/a bioinfo lab 😜!
November 23, 2025 at 5:53 AM
Did CS in college w/the goal of doing 3D engine programming at ID software w/John Carmack. Decided I liked graphics research senior year & applied to PhD. Did graphics while hanging out w/ppl who are now bioinfo legends. Decided to switch in my 4th year (I know) & am now a CS prof w/a bioinfo lab 😜!
Reposted by Rob Patro
How to preprocess GEO bulk RNAseq fastq file with salmon youtu.be/_Q8fYokTCTs
How to preprocess GEO bulk RNAseq fastq file with salmon
script link: https://divingintogeneticsandgenomics.com/post/how-to-preprocess-geo-bulk-rnaseq-data-with-salmon/Learn how to efficiently preprocess GEO bulk R...
www.youtube.com
November 22, 2025 at 2:45 PM
How to preprocess GEO bulk RNAseq fastq file with salmon youtu.be/_Q8fYokTCTs
Typst makes nice tables!
November 21, 2025 at 8:13 PM
Typst makes nice tables!
Lolz --- the mim parser (fastq parser that takes advantage of the auxiliary mim index if it is built) is actually way faster than I had been measuring. The example application was counting nucleotides, and there was false sharing in the vectors of counters used by different threads ;P.
November 21, 2025 at 5:05 PM
Lolz --- the mim parser (fastq parser that takes advantage of the auxiliary mim index if it is built) is actually way faster than I had been measuring. The example application was counting nucleotides, and there was false sharing in the vectors of counters used by different threads ;P.
Reposted by Rob Patro
Somewhat spicier take: It's still too short or convenient of a name. Let's rename it "fuck_it_well_do_it_live_well_do_it_live_fuckin_thing_sucks()"
#rustlang hot take: We should rename .unwrap() to .or_panic(). (And .expect() to .or_panic_with().) "Unwrap" is a terrible name for the panicking function, especially since we also have things like .unwrap_or() and .unwrap_or_default() which never panic.
November 19, 2025 at 1:02 PM
Somewhat spicier take: It's still too short or convenient of a name. Let's rename it "fuck_it_well_do_it_live_well_do_it_live_fuckin_thing_sucks()"
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
GitHub - COMBINE-lab/mim: A small, auxiliary index to massively improve parallel fastq parsing
A small, auxiliary index to massively improve parallel fastq parsing - COMBINE-lab/mim
github.com
November 19, 2025 at 3:01 AM
@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2
Does anyone know of a canonical reference for the BGZF format? What should I cite for it? cc: @lh3lh3.bsky.social
November 17, 2025 at 9:44 PM
Does anyone know of a canonical reference for the BGZF format? What should I cite for it? cc: @lh3lh3.bsky.social
Reposted by Rob Patro
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Specialization!
SIMD!
Arbitrary self types and pointers!
Coroutines!
Box patterns!
Gen blocks!
Negative bounds and negative impls!
Allocator API!
SIMD!
Arbitrary self types and pointers!
Coroutines!
Box patterns!
Gen blocks!
Negative bounds and negative impls!
Allocator API!
The 2025 State of Rust Survey: Which unimplemented (or nightly only) features are you looking for to be stabilized?
Me: YES
www.surveyhero.com/c/state-of-r...
Me: YES
www.surveyhero.com/c/state-of-r...
2025 State of Rust Survey
www.surveyhero.com
November 17, 2025 at 4:46 PM
Specialization!
SIMD!
Arbitrary self types and pointers!
Coroutines!
Box patterns!
Gen blocks!
Negative bounds and negative impls!
Allocator API!
SIMD!
Arbitrary self types and pointers!
Coroutines!
Box patterns!
Gen blocks!
Negative bounds and negative impls!
Allocator API!
Really excited for the south park episode that airs after the Epstein files are released!
November 16, 2025 at 10:17 PM
Really excited for the south park episode that airs after the Epstein files are released!
Paired-end parsing now works with our lightweight, auxiliary FASTQ.gz indexing scheme! Now I hope to get some benchmarks and a preprint out soon.
November 16, 2025 at 3:33 PM
Paired-end parsing now works with our lightweight, auxiliary FASTQ.gz indexing scheme! Now I hope to get some benchmarks and a preprint out soon.