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.
This is one of my favorite new interactions with coding agents:
"hrm, the test failed. Let me look why"
"Oh, it's because of X. I was doing it like Y, but I should be doing Z; I see that clearly now."
Meanwhile, I told it explicitly to avoid the Y footgun by doing Z in at least 4 places.
"hrm, the test failed. Let me look why"
"Oh, it's because of X. I was doing it like Y, but I should be doing Z; I see that clearly now."
Meanwhile, I told it explicitly to avoid the Y footgun by doing Z in at least 4 places.
February 10, 2026 at 4:02 AM
This is one of my favorite new interactions with coding agents:
"hrm, the test failed. Let me look why"
"Oh, it's because of X. I was doing it like Y, but I should be doing Z; I see that clearly now."
Meanwhile, I told it explicitly to avoid the Y footgun by doing Z in at least 4 places.
"hrm, the test failed. Let me look why"
"Oh, it's because of X. I was doing it like Y, but I should be doing Z; I see that clearly now."
Meanwhile, I told it explicitly to avoid the Y footgun by doing Z in at least 4 places.
Reposted by Rob Patro
What's your biggest practical issue with large gzip files?
I've been polishing the mim API and CLI the last few days and could integrate it in some tools.
I've been polishing the mim API and CLI the last few days and could integrate it in some tools.
February 10, 2026 at 2:02 AM
What's your biggest practical issue with large gzip files?
I've been polishing the mim API and CLI the last few days and could integrate it in some tools.
I've been polishing the mim API and CLI the last few days and could integrate it in some tools.
There's meta-cognition, which is most often thinking about your own thinking. What do people call it when they watch AI models talk to themselves (Opus/Codex), and then think about the model's own "internal" monologue?
February 10, 2026 at 12:50 AM
There's meta-cognition, which is most often thinking about your own thinking. What do people call it when they watch AI models talk to themselves (Opus/Codex), and then think about the model's own "internal" monologue?
Reposted by Rob Patro
US science is in trouble, and it doesn't have to be
stevensalzberg.substack.com/p/making-ame...
stevensalzberg.substack.com/p/making-ame...
Making America Weak
The biggest own goal in modern history
stevensalzberg.substack.com
February 8, 2026 at 9:38 PM
US science is in trouble, and it doesn't have to be
stevensalzberg.substack.com/p/making-ame...
stevensalzberg.substack.com/p/making-ame...
Reposted by Rob Patro
So i've been doing this, and spamming another thread with updates. I will move that over here now.
I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.
I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.
Any bioinformatics friends out there have a huge load of AI code credits & want to try smth crazy (but amazing if it works)? What if we ask Claude to port STAR to Rust?
Current development and maintenance on this central tool has largely stalled, but I think a lang change would reinvigorate it!
Current development and maintenance on this central tool has largely stalled, but I think a lang change would reinvigorate it!
February 7, 2026 at 7:33 AM
So i've been doing this, and spamming another thread with updates. I will move that over here now.
I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.
I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.
I think this oversimplifies several possibilities. First, not all people have the same notion of wonderful place to live. Second, the market is not always a true reflection of value. Third, extreme distortions in the local economy along with employers disallowing remote work has big implications.
I feel like this should be more obvious to people? Any city where people are willing to pay this much to live in totally normal-ass houses has to be a wonderful place to live?
February 7, 2026 at 10:29 PM
I think this oversimplifies several possibilities. First, not all people have the same notion of wonderful place to live. Second, the market is not always a true reflection of value. Third, extreme distortions in the local economy along with employers disallowing remote work has big implications.
Counterpoint: I don't want a slimmer macbook pro. I think I'll go with the M5 Max before the redesign.
www.creativebloq.com/design/produ...
www.creativebloq.com/design/produ...
Apple's redesigned MacBook Pro can't come soon enough
It's what creatives have been waiting for.
www.creativebloq.com
February 7, 2026 at 3:58 PM
Counterpoint: I don't want a slimmer macbook pro. I think I'll go with the M5 Max before the redesign.
www.creativebloq.com/design/produ...
www.creativebloq.com/design/produ...
This is a very interesting and relevant PPoPP paper from this year for genomics folks! dl.acm.org/doi/10.1145/...
BWA-compatible (identical) output w/o the massive index size increases of BWA2 or BWA-MEME... & faster than both. To boot, no requirement for special hardware; it uses SIMD on CPUs.
BWA-compatible (identical) output w/o the massive index size increases of BWA2 or BWA-MEME... & faster than both. To boot, no requirement for special hardware; it uses SIMD on CPUs.
Faster and Cheaper: Pushing the Sequence Alignment Throughput with Commercial CPUs | Proceedings of the 31st ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming
dl.acm.org
February 6, 2026 at 5:37 PM
This is a very interesting and relevant PPoPP paper from this year for genomics folks! dl.acm.org/doi/10.1145/...
BWA-compatible (identical) output w/o the massive index size increases of BWA2 or BWA-MEME... & faster than both. To boot, no requirement for special hardware; it uses SIMD on CPUs.
BWA-compatible (identical) output w/o the massive index size increases of BWA2 or BWA-MEME... & faster than both. To boot, no requirement for special hardware; it uses SIMD on CPUs.
Put in a request to order some equipment on Jan 20. The university still hasn't placed the order. Since then, the main hardware price has increased about $1,500. How do I convey that time is literally $, and that it's critical to order ASAP?!!
February 6, 2026 at 5:24 PM
Put in a request to order some equipment on Jan 20. The university still hasn't placed the order. Since then, the main hardware price has increased about $1,500. How do I convey that time is literally $, and that it's critical to order ASAP?!!
And a pedophile.
Donald Trump is a racist.
February 6, 2026 at 4:45 PM
And a pedophile.
Or malicious incompetence!
What about ✨incompetent malice✨????
Never attribute malice to what can be easily explained by incompetence.
February 5, 2026 at 12:44 AM
Or malicious incompetence!
Reposted by Rob Patro
$ jj describe -m "Hello, world!"
February 4, 2026 at 9:09 PM
$ jj describe -m "Hello, world!"
I wonder if this is the kind of project that @anthropic.com might be willing to sponsor? If so, please let me know how to get in touch!
Any bioinformatics friends out there have a huge load of AI code credits & want to try smth crazy (but amazing if it works)? What if we ask Claude to port STAR to Rust?
Current development and maintenance on this central tool has largely stalled, but I think a lang change would reinvigorate it!
Current development and maintenance on this central tool has largely stalled, but I think a lang change would reinvigorate it!
February 4, 2026 at 4:40 PM
I wonder if this is the kind of project that @anthropic.com might be willing to sponsor? If so, please let me know how to get in touch!
Reposted by Rob Patro
Community service:
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
GitHub - RagnarGrootKoerkamp/oxford-bioinformatics-template: Improved version of the Oxford Bioinformatics paper template
Improved version of the Oxford Bioinformatics paper template - RagnarGrootKoerkamp/oxford-bioinformatics-template
github.com
February 4, 2026 at 4:23 PM
Community service:
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
Updated the oxford-bioinformatics template repo because apparently the template changed again, and it's still the top google hit, and figuring out the right parameters remains messy, and they are still inconsistent.
github.com/RagnarGrootK...
@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...
crates.io: Rust Package Registry
crates.io
February 3, 2026 at 7:36 PM
@mikelove.bsky.social : There was PyDESeq2, and now there is rust_deseq2! crates.io/crates/rust_...
I have to believe in the many worlds hypothesis because, somehow, we ended up in the worst of all possible worlds. I have to believe worlds that evaded this horrific fate must exist.
February 2, 2026 at 4:26 PM
I have to believe in the many worlds hypothesis because, somehow, we ended up in the worst of all possible worlds. I have to believe worlds that evaded this horrific fate must exist.
I think that all of the decision makers for @montgomerycountymd.bsky.social should be sent (at tax payer expense) to spend the rest of the winter in and around Boston, with a duty to report back what the shape of competence looks like, and a concrete (snowcrete?) plan to improve their operations!
February 2, 2026 at 3:36 PM
I think that all of the decision makers for @montgomerycountymd.bsky.social should be sent (at tax payer expense) to spend the rest of the winter in and around Boston, with a duty to report back what the shape of competence looks like, and a concrete (snowcrete?) plan to improve their operations!
Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240
arxiv.org
February 2, 2026 at 2:26 PM
Cool paper on representing a collection of sets via a spanning tree of their differences. This builds upon work by Bookstein ('91 )! as well as work we did in using this representation to compress color sets in Mantis MST. I think this repr. has many important applications! arxiv.org/pdf/2601.23240
No @mcdotnow.bsky.social schools; it is not reasonable to cancel school again tomorrow. You've and an *entire* week to perform snow and ice removal. Businesses are open, Universities are open, recreational activities & museums are open. Children need to return to school tomorrow! This is wrong.
February 1, 2026 at 8:54 PM
No @mcdotnow.bsky.social schools; it is not reasonable to cancel school again tomorrow. You've and an *entire* week to perform snow and ice removal. Businesses are open, Universities are open, recreational activities & museums are open. Children need to return to school tomorrow! This is wrong.
I'm looking to update the SRA growth curve for the intro lecture of my computational genomics course, and I noticed that the data traces provided by SRA end in 2024 ... Does anyone have an idea what's up here or how to get more up-to-date data? www.ncbi.nlm.nih.gov/sra/docs/sra...
Getting Started
www.ncbi.nlm.nih.gov
February 1, 2026 at 6:37 PM
I'm looking to update the SRA growth curve for the intro lecture of my computational genomics course, and I noticed that the data traces provided by SRA end in 2024 ... Does anyone have an idea what's up here or how to get more up-to-date data? www.ncbi.nlm.nih.gov/sra/docs/sra...
I cannot begin to convey how frustrating it is that different systems choose subtly different default installation paths (e.g. `lib` vs `lib64`, even though they are both 64-bit systems) when building the *same* project (in this case zlib-ng) from source. WHY?!?!
January 31, 2026 at 11:05 PM
I cannot begin to convey how frustrating it is that different systems choose subtly different default installation paths (e.g. `lib` vs `lib64`, even though they are both 64-bit systems) when building the *same* project (in this case zlib-ng) from source. WHY?!?!
E.g. here anaconda.org/channels/con...
January 31, 2026 at 3:49 PM
E.g. here anaconda.org/channels/con...
Ok a new bioconda recipe question. Any idea why the build
system seems unable to find the package ‘zlib-ng-compat’, despite the fact that this package clearly exists on conda forge?
system seems unable to find the package ‘zlib-ng-compat’, despite the fact that this package clearly exists on conda forge?
January 31, 2026 at 3:48 PM
Ok a new bioconda recipe question. Any idea why the build
system seems unable to find the package ‘zlib-ng-compat’, despite the fact that this package clearly exists on conda forge?
system seems unable to find the package ‘zlib-ng-compat’, despite the fact that this package clearly exists on conda forge?
I have a better idea, why don't @montgomerycountymd.bsky.social schools explain why they've cancelled school for an entire week for ~7" of snow, and why it's not a deriliction of their duties? I think it's time for some new leadership, some legal action, or both... mocoshow.com/2026/01/29/m...
MCPS Explains Why Snow Days Are Not Virtual Learning Days - The MoCo Show
Montgomery County Public Schools has clarified why it is not shifting to virtual learning during weather related school closures, despite ongoing questions from families. According to MCPS, virtual i...
mocoshow.com
January 30, 2026 at 5:14 PM
I have a better idea, why don't @montgomerycountymd.bsky.social schools explain why they've cancelled school for an entire week for ~7" of snow, and why it's not a deriliction of their duties? I think it's time for some new leadership, some legal action, or both... mocoshow.com/2026/01/29/m...
What nonsense. You do what you want, Carl, but I think silencing yourself for being called out for such imagined "transgressions" is counterproductive. Personally, I feel people going around policing such speech calling out fascism, and insufficient responses to it, are "problematic".
January 30, 2026 at 1:40 PM
What nonsense. You do what you want, Carl, but I think silencing yourself for being called out for such imagined "transgressions" is counterproductive. Personally, I feel people going around policing such speech calling out fascism, and insufficient responses to it, are "problematic".