Travis Wheeler @wheelerlab.org · 03/09/2026Anthropic let the academics in, and everything fell apart within a week 000
Travis Wheeler @wheelerlab.org · 01/09/2026(Without saying your age, what was your favourite film that came out when you were 20 years old.) At the time, I'd have said #1 (still great, see photo on my lab website); now I'm partial to #2 000
Travis Wheeler @wheelerlab.org · 24/05/2026This is freakishly reminiscent of an image I got when trying to get various image generators to create a picture of a man using a hammer to pound a nail into a string. Are we sure that's a real photo of the Prince? 000
Travis Wheeler @wheelerlab.org · 20/04/2026Same. (my ride home is probably a little bit rockier than yours) 010
Travis Wheeler @wheelerlab.org · 19/04/2026Agree. But maybe more: it should be the standard to highlight (with neon lights) when software is produced entirely by an automated process. Meanwhile, these repos present the work with text like this, which disingenuously obscures the fact that no human has actually thought about the code 010
Travis Wheeler @wheelerlab.org · 10/04/2026Product of a terrific collaboration with @sdeorowicz.bsky.social, Marek Kokot, and Amit Roy: doi.org/10.1093/bioi... MDCompress produces compressed trajectory files that are up to 37% smaller than in the widely-used XTC format. Nice software library interfaces for fast (de-)compression. 061
Travis Wheeler @wheelerlab.org · 26/11/2025Reminiscent of the copy of Procrastinator's Handbook sitting on our bookshelf. 040
Travis Wheeler @wheelerlab.org · 12/09/2025I share this picture of a printed out genome every once in while. It just occurred to me: it's got to be cheaper to acquire a finished copy of your genome (high accuracy, phased, SV-resolved) than to print it as a collection of bound books. (back-of-envelope checks out - anyone done the math?) 185
Travis Wheeler @wheelerlab.org · 20/06/2025A Representation Learning approach to virtual ligand-screening. Produces good enrichment for active ligands, and can scan billions of candidate small molecules in a few hours.. Simpatico: www.biorxiv.org/content/10.1... 031
Travis Wheeler @wheelerlab.org · 04/06/2025Interesting read -- I'd have agreed whole-heartedly when it was written. Starting to feel a little dated: 120
Travis Wheeler @wheelerlab.org · 01/06/2025I guess she just really wants to be a GOAT (Matthew 25:31-46): 000
Travis Wheeler @wheelerlab.org · 29/05/2025I'm old enough to remember when Reagan was considered a conservative. This detestable description of our nation (below) proves that he was actually a Marxist, hellbent on destroying our great nation. www.reaganlibrary.gov/archives/spe... 021
Travis Wheeler @wheelerlab.org · 28/05/2025OMG, @deltahelp.bsky.social ... I'm trying to change a flight for my kid's trip to Europe. It's a change from a flight that was ~$600 to one that currently lists at $670. So maybe it makes sense to charge me $70. Maybe it makes sense to charge me some extra? But, uh ... $4,000 ???!!! JFC 110
Travis Wheeler @wheelerlab.org · 18/05/2025I don't think it's that. I paste the full url (or even just: globalfishingwatch.org), and it (usually, but not always) presents me with that "request is being verified" thing, then a 404. I think that green text means Cloudflare is over-protecting your site (see image). Maybe I'm just unlucky. 100
Travis Wheeler @wheelerlab.org · 17/05/2025Strange. I click the link, and I get sent to a page with "please wait while your request is being verified" (see image) then a really gross URL (see 2nd image) 100
Travis Wheeler @wheelerlab.org · 02/04/2025On second thought, we should be "Cautious, concerned, but **not dismissive**." So now we know how we should feel ... 000
Travis Wheeler @wheelerlab.org · 02/04/2025ChatGPT thinks there are potential concerns ... so we're all on the same page! (but wait, there's more) 100
Travis Wheeler @wheelerlab.org · 01/03/2025I think I'll just keep on meeting with you. I think understand things that gpt doesn't. 011
Travis Wheeler @wheelerlab.org · 09/01/2025There once was a writer who said, “AI is dull as cold bread.” But the bots, full of sass, Said, “You’d better not pass, Till you’ve laughed at the rhymes in your head!” (This make me nervous) 010
Travis Wheeler @wheelerlab.org · 25/12/2024We're still hunting for a real logo, but for now I'm going with this: it's a picture of a nail, with a ribbon diagram of P93604 draped over it. You can probably guess what language we used to implement nail. github.com/TravisWheele... 000
Travis Wheeler @wheelerlab.org · 25/12/2024A Christmas present for those who like fast and sensitive protein annotation tools! This shows runtime vs recall on a test with ~1400 query MSAs, with ~20 true matches per query planted among 2M decoy sequences. Speed gains over H3 grow for bigger datasets, and scale linearly with MMSeqs2 runtime. 120
Travis Wheeler @wheelerlab.org · 25/12/2024I made that shift early in my first winter in Montana. 020
Travis Wheeler @wheelerlab.org · 25/12/2024Version 0.3.0 of nail is out. nail (github.com/TravisWheele...) is a tool for protein sequence annotation. It bridges most of the sensitivity gap between the two excellent tools MMSeqs2 (fast) and HMMER3 (very sensitive), and is >20x faster than HMMER3. Search with profile HMMs or single sequences. 23613
Travis Wheeler @wheelerlab.org · 25/12/2024You sure you don't want to keep using cmake? It's not the worst thing ever made... 120
Travis Wheeler @wheelerlab.org · 23/12/2024Why the hell is there a Jack Russell Terrier looking straight out of the map at me? It's just East of Safford, Arizona. I circled it in the map to make it obvious. To see it yourself, I put a pin in the "nose": maps.app.goo.gl/cQDLXsFXBPhW... 011
Travis Wheeler @wheelerlab.org · 27/11/2024Asked my son (freshman in college), and he immediately noted the (twin-primes + 2) trick. Phew. We tried telling ChatGPT to constrain itself: "Design a method that will compute the number of pairs in run time that is subquadratic in the number of primes" It did not go well ... 110
Travis Wheeler @wheelerlab.org · 26/11/2024"how many pairs of prime numbers between 1-100000 have a difference that is also a prime number?" This is the (cubic) code it generated. Took almost a minute to return. Definitely doesn't get the trick. "where is the variable large_primes from?" "... generated using the sympy.primerange function." 000
Travis Wheeler @wheelerlab.org · 26/11/2024I think this tells us that the Quora AI bot is out of date, probably just spewing words instead of performing calculations. ChatGPT-4o got it right, I believe. 16 total. 110
Travis Wheeler @wheelerlab.org · 20/11/2024U Arizona Computer Science is seeking to fill 6 (six ... six!) new faculty positions cs.arizona.edu/currently-op... If you like warm winters, hikes in the desert, bread that doesn't get moldy, and a great scientific environment ... come to Tucson 0119
Travis Wheeler @wheelerlab.org · 05/10/2024And there's a reason it's unexpected. It makes zero sense. (Trust me, the nhmmer paper doesn't delve into matters involving the educational system) doi.org/10.1093/bioi... Honest mistake? AI-generated manuscript? 120
Travis Wheeler @wheelerlab.org · 01/10/2024Love what you did there. I regularly ask AI models to make haiku poems for some random thing I'm trying to communicate. It's a bad habit. Here's my new one: 020
Travis Wheeler @wheelerlab.org · 10/09/2024On the other hand, it's getting harder to get ChatGPT to screw up. As an example: here's what it did with the same input just now. It's a good explanation. So in a couple of months, enough things have changed that this kind of error mode is fixed (at least for today, with me) 110
Travis Wheeler @wheelerlab.org · 10/09/2024On one hand, these systems can be remarkably brittle. Historically, it's been really easy to get them to backtrack with simple queries like "are you sure?" ... and there are so many examples of laughable interactions like this one (from me, about 2 months ago) 110
Travis Wheeler @wheelerlab.org · 26/06/2024Announcing: 24th Genomic Standards Consortium - August 5-9, 2024 - Tucson, AZ - bit.ly/4eFgAQ9 Reproducibility Challenges - J. Gregory Caporaso Challenges of ‘Omic data reuse - Jonathan Eisen Genomics and Standards challenges - Jack Gilbert Reproducibility Challenges to Solutions - Rachel Gallery 100