Ian Holmes
@ianholmes.org
Berkeley professor (Bioeng, Compbio). Visiting Scientist at Calico. JBrowse genome browser / Apollo annotation editor, ML for gene regulation / molecular evolution / synbio. Occasional music, games, jokes
Pinned
Ian Holmes
@ianholmes.org
· Jan 25
Sophie Wilson - Wikipedia
en.m.wikipedia.org
I feel moved to write about one of my technological heroes, possibly the most influential on my youth as an 8-bit hacker: a trans woman named Sophie Wilson. en.m.wikipedia.org/wiki/Sophie_...
Everyone picks a different order for the nucleotides, and of course Vince Gilligan picked GUAC. Cute enough to forgive the scene where they plate RNA viruses on growth media
November 9, 2025 at 6:20 PM
Everyone picks a different order for the nucleotides, and of course Vince Gilligan picked GUAC. Cute enough to forgive the scene where they plate RNA viruses on growth media
In my academic career I came to view scientific conferences much the same as I did nightclubs in my 20s: Small is better. Cool subcultures inevitably get mobbed, become meat markets. It takes effort to stay underground. Don’t get lippy with the bouncers (I never tested that one in academia)
100%. Genome Informatics and ProbGen are friendly. BDS positively down to earth. BofG is the one where the prestige obsession becomes cloying
Honestly, it's a meeting specific thing. Genome Informatics and Biological Data science are pretty great without much "celebrity".
November 9, 2025 at 2:37 AM
In my academic career I came to view scientific conferences much the same as I did nightclubs in my 20s: Small is better. Cool subcultures inevitably get mobbed, become meat markets. It takes effort to stay underground. Don’t get lippy with the bouncers (I never tested that one in academia)
100%. Genome Informatics and ProbGen are friendly. BDS positively down to earth. BofG is the one where the prestige obsession becomes cloying
Honestly, it's a meeting specific thing. Genome Informatics and Biological Data science are pretty great without much "celebrity".
November 9, 2025 at 1:24 AM
100%. Genome Informatics and ProbGen are friendly. BDS positively down to earth. BofG is the one where the prestige obsession becomes cloying
I do remember the CSHL Biology of Genomes meeting right after Watson’s racist comments were published. Several luminaries of the field organized a reception to show him their support. Such receptions are not uncommon at CSHL. A few of us pointedly turned our backs at the edge of the crowd. Not many
November 8, 2025 at 11:26 PM
I do remember the CSHL Biology of Genomes meeting right after Watson’s racist comments were published. Several luminaries of the field organized a reception to show him their support. Such receptions are not uncommon at CSHL. A few of us pointedly turned our backs at the edge of the crowd. Not many
Reposted by Ian Holmes
I havent read such a banger of an essay in a very long time. This is so well-written!
Maybe Don’t Talk to the New York Times About Zohran Mamdani
It’s remarkable, the people you’ll hear from. Teach for even a little while at an expensive institution—the term they tend to prefer is “elite”—and odds are that eventually someone who was a studen…
lithub.com
November 8, 2025 at 5:37 PM
I havent read such a banger of an essay in a very long time. This is so well-written!
LinkedIn: Thrilled to announce my new role as First Confessor at Galadriel Inc, where I’ll be an internal evangelist for Torment Nexus 2.0
BlueSky: Humbled to share our 5-year study of a novel torment-sensing circuit bridging the parietal operculum… in mice
X: TormentPedia will revolutionize truth
BlueSky: Humbled to share our 5-year study of a novel torment-sensing circuit bridging the parietal operculum… in mice
X: TormentPedia will revolutionize truth
November 8, 2025 at 1:42 AM
LinkedIn: Thrilled to announce my new role as First Confessor at Galadriel Inc, where I’ll be an internal evangelist for Torment Nexus 2.0
BlueSky: Humbled to share our 5-year study of a novel torment-sensing circuit bridging the parietal operculum… in mice
X: TormentPedia will revolutionize truth
BlueSky: Humbled to share our 5-year study of a novel torment-sensing circuit bridging the parietal operculum… in mice
X: TormentPedia will revolutionize truth
It's true, James Watson rode to glory on Rosalind Franklin's data; but to be fair, he also rode on Francis Crick's knowledge of Bessel functions
November 7, 2025 at 9:08 PM
It's true, James Watson rode to glory on Rosalind Franklin's data; but to be fair, he also rode on Francis Crick's knowledge of Bessel functions
Reposted by Ian Holmes
I don't see anything in the Cornell agreement that keeps the US government from coming back with new adverse actions in the future. The agreement is only about current actions, and it explicitly says: "The United States is not releasing Cornell ... from any other liability."
November 7, 2025 at 7:57 PM
I don't see anything in the Cornell agreement that keeps the US government from coming back with new adverse actions in the future. The agreement is only about current actions, and it explicitly says: "The United States is not releasing Cornell ... from any other liability."
Life hack: place your carnivorous plants near your kitchen counter compost bin. (Why did I take this long to figure it out?)
November 7, 2025 at 5:23 PM
Life hack: place your carnivorous plants near your kitchen counter compost bin. (Why did I take this long to figure it out?)
Reposted by Ian Holmes
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
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 7, 2025 at 2:41 PM
I want to spell this out in case the implications aren't clear:
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
This means all public tools/webapps of GISAID data (all the ones you've been used to seeing thru the pandemic, as far as we can tell) are prohibited.
The file allowed this. Cut that - cut off all tools the public & others were using.
I’m more than a little confused by this story. It is (surely) transparently obvious that any set of equations involving complex variables can be expanded into twice as many equations involving reals. The article notes this in several places. The only counterargument is that someone once tried… 1/
For the first time, physicists have formulated quantum theory without imaginary numbers, overturning a 2021 claim that these unreal numbers are essential for describing the quantum world.
www.quantamagazine.org/physicists-t...
www.quantamagazine.org/physicists-t...
Physicists Take the Imaginary Numbers Out of Quantum Mechanics | Quanta Magazine
Quantum mechanics has at last been formulated exclusively with real numbers, bringing a mathematical puzzle at the heart of the theory into a new era of inquiry.
www.quantamagazine.org
November 7, 2025 at 4:51 PM
I’m more than a little confused by this story. It is (surely) transparently obvious that any set of equations involving complex variables can be expanded into twice as many equations involving reals. The article notes this in several places. The only counterargument is that someone once tried… 1/
Not something I’ve been attending to up close, but GISAID’s access policies always seemed a bit dubious, and their responses to Nextstrain’s questions in the PDF attached to this post are not impressive
GISAID on providing data to @Nextstrain.org: "After consulting with our staff and advisors on the feasibility of keeping your global tree up-to-date, there was a clear consensus that continuing to generate, zip and move big files back and forth is not sustainable and a waste of resources."
🙃
🙃
Nextstrain: Interruption to GISAID-based SARS-CoV-2 sequence analyses
Nextstrain blog post from 2025-11-06; author(s): Trevor Bedford, Richard Neher and the Nextstrain team
next.nextstrain.org
November 7, 2025 at 12:47 PM
Not something I’ve been attending to up close, but GISAID’s access policies always seemed a bit dubious, and their responses to Nextstrain’s questions in the PDF attached to this post are not impressive
Still waiting for a version of the internet that looks halfway as good as the 1981 TV version of Hitchhiker’s Guide
November 6, 2025 at 1:50 AM
Still waiting for a version of the internet that looks halfway as good as the 1981 TV version of Hitchhiker’s Guide
Reposted by Ian Holmes
Design stable, folded proteins using only the 10 "ancient" amino acids.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 31, 2025 at 7:40 PM
Design stable, folded proteins using only the 10 "ancient" amino acids.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ian Holmes
Explore a haunted movie studio. Learn the fates of the tormented souls bound to it. End a 50-year curse inscribed in blood and celluloid.
KINOPHOBIA, my first piece of noncommercial interactive fiction in eight years, is now available to play.
brunodias.itch.io/kinophobia
KINOPHOBIA, my first piece of noncommercial interactive fiction in eight years, is now available to play.
brunodias.itch.io/kinophobia
Kinophobia by Bruno Dias
Explore a haunted movie studio. Learn the fates its tormented souls. End a curse inscribed in blood and celluloid.
brunodias.itch.io
October 31, 2025 at 3:14 AM
Explore a haunted movie studio. Learn the fates of the tormented souls bound to it. End a 50-year curse inscribed in blood and celluloid.
KINOPHOBIA, my first piece of noncommercial interactive fiction in eight years, is now available to play.
brunodias.itch.io/kinophobia
KINOPHOBIA, my first piece of noncommercial interactive fiction in eight years, is now available to play.
brunodias.itch.io/kinophobia
Reposted by Ian Holmes
We're reading Charlie & the Chocolate Factory. Our son noted it was v. unlikely Charlie found a golden ticket with only 5 in world. I explained that there were many kids who didnt find a ticket & didnt have books written about them, so really it was about conditional prob.
He groaned & went to sleep
He groaned & went to sleep
October 31, 2025 at 4:59 AM
We're reading Charlie & the Chocolate Factory. Our son noted it was v. unlikely Charlie found a golden ticket with only 5 in world. I explained that there were many kids who didnt find a ticket & didnt have books written about them, so really it was about conditional prob.
He groaned & went to sleep
He groaned & went to sleep
Reposted by Ian Holmes
“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at multiple places in a draft manuscript.
#science #academia
#science #academia
November 11, 2024 at 2:52 PM
“Bonferonni correction”, an invaluable method in #statistics, refers to the act of repeatedly correcting misspellings of the word Bonferroni at multiple places in a draft manuscript.
#science #academia
#science #academia
Reposted by Ian Holmes
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Thank you for giving a name to this strategy. “Stake-driving” has fallen out of use since Van Helsing sold out and “criminal” was getting cliché
By proceeding with the demolition of the White House East Wing before seeking approval from federal agencies for a new ballroom, President Donald Trump forced the issue. It's a strategy known as "stake-driving."
How Trump Demolished the White House East Wing
By putting the demolition of the East Wing before the necessary approvals for his ballroom, President Donald Trump borrowed a tactic known as “stake-driving” to force an outcome.
bloom.bg
October 26, 2025 at 5:11 PM
Thank you for giving a name to this strategy. “Stake-driving” has fallen out of use since Van Helsing sold out and “criminal” was getting cliché
Reposted by Ian Holmes
Yes. 25 years on, I teach differently: I read to them, we read silently together, we have weekly experiments week of setting different situations to read (with/out food, company, music; in/outdoors; varying light; &c) & discuss them. It's made ALL the difference to foreground reading as a process.
I've been teaching at Princeton over the same period and the drop-off in reading stamina has been staggering.
I'm not sure of the cause -- some blame K-12 shifts to "chunk reading" while others pin it on COVID -- but it's undeniable.
I'm not sure of the cause -- some blame K-12 shifts to "chunk reading" while others pin it on COVID -- but it's undeniable.
July 15, 2025 at 4:31 PM
Yes. 25 years on, I teach differently: I read to them, we read silently together, we have weekly experiments week of setting different situations to read (with/out food, company, music; in/outdoors; varying light; &c) & discuss them. It's made ALL the difference to foreground reading as a process.
Bricked Smartbeds are the Golgafrincham B Ark
October 23, 2025 at 3:43 PM
Bricked Smartbeds are the Golgafrincham B Ark
Gave an on-paper midterm today, my first in… decades? Ever? It will be ironic if the true water cost of chatbots is all the paper that gets printed because internet use is now verboten in exams
October 23, 2025 at 3:24 AM
Gave an on-paper midterm today, my first in… decades? Ever? It will be ironic if the true water cost of chatbots is all the paper that gets printed because internet use is now verboten in exams
Reposted by Ian Holmes
In the event of an encounter with immigration agents in the East Bay, make sure you and your family know your rights. (1/2)
October 23, 2025 at 1:12 AM
In the event of an encounter with immigration agents in the East Bay, make sure you and your family know your rights. (1/2)
Reposted by Ian Holmes
Reposted by Ian Holmes
