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_...
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
November 17, 2025 at 6:05 PM
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
Reposted by Ian Holmes
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.
@gbretman.bsky.social Excellent: A period of abstinence from Microsoft Office
November 16, 2025 at 10:48 PM
@gbretman.bsky.social Excellent: A period of abstinence from Microsoft Office
Reposted by Ian Holmes
Job description
2024: Software Developer
2026: Debug log emoji remover
2024: Software Developer
2026: Debug log emoji remover
November 16, 2025 at 6:47 PM
Job description
2024: Software Developer
2026: Debug log emoji remover
2024: Software Developer
2026: Debug log emoji remover
Blending husbandry and governance, Caligula appoints his horse Incitatus to the Senate
November 16, 2025 at 4:28 PM
Blending husbandry and governance, Caligula appoints his horse Incitatus to the Senate
What’s your favorite river separating the realm of the living from the underworld? Are you an oath-swearing Styxie, a forgetful Lethite, or are you into one of the more esoteric rivers like Acheron or Phlegethon? Sad-sack Cocytus fans with your endless lamentations need not bother to respond
November 15, 2025 at 5:53 PM
What’s your favorite river separating the realm of the living from the underworld? Are you an oath-swearing Styxie, a forgetful Lethite, or are you into one of the more esoteric rivers like Acheron or Phlegethon? Sad-sack Cocytus fans with your endless lamentations need not bother to respond
Reposted by Ian Holmes
BREAKING: We won a court order blocking Pres. Trump’s attempt to stifle First Amendment rights and gain political control over the University of California system.
The President can't force people to think or believe only the way he does. This is a key victory for our clients and the rule of law.
The President can't force people to think or believe only the way he does. This is a key victory for our clients and the rule of law.
November 15, 2025 at 1:07 AM
BREAKING: We won a court order blocking Pres. Trump’s attempt to stifle First Amendment rights and gain political control over the University of California system.
The President can't force people to think or believe only the way he does. This is a key victory for our clients and the rule of law.
The President can't force people to think or believe only the way he does. This is a key victory for our clients and the rule of law.
Reposted by Ian Holmes
Congratulations @hilarycmartin.bsky.social from @sangerinstitute.bsky.social on being awarded the 2026 Balfour Lecture!
November 14, 2025 at 12:35 PM
Congratulations @hilarycmartin.bsky.social from @sangerinstitute.bsky.social on being awarded the 2026 Balfour Lecture!
Reposted by Ian Holmes
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
November 14, 2025 at 12:36 PM
Congratulations to @zaminiqbal.bsky.social from @milnerevolution.bsky.social on being awarded the 2026 Mary Lyon Medal!
Reposted by Ian Holmes
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
November 14, 2025 at 12:40 PM
Congratulations to Richard Durbin on being awarded our Genetics Society Medal!
Reposted by Ian Holmes
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
November 14, 2025 at 12:41 PM
Congratulations to Joe Felsenstein on being awarded the 2026 Mendel Medal!
Reposted by Ian Holmes
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 13, 2025 at 5:08 PM
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Reposted by Ian Holmes
Every office has an executive tier whose emails are like:
saw on news , , can we replce complianc dept with web 3
and a worker tier whose emails are like:
Dear Jim,
First of all, I *love* this idea! Unfortunately, I spoke with Legal and identified a few issues with this approach. For starters…
saw on news , , can we replce complianc dept with web 3
and a worker tier whose emails are like:
Dear Jim,
First of all, I *love* this idea! Unfortunately, I spoke with Legal and identified a few issues with this approach. For starters…
Well, it's a little clearer now why billionaires are so invested in technology that produces better written emails.
November 13, 2025 at 12:10 AM
Every office has an executive tier whose emails are like:
saw on news , , can we replce complianc dept with web 3
and a worker tier whose emails are like:
Dear Jim,
First of all, I *love* this idea! Unfortunately, I spoke with Legal and identified a few issues with this approach. For starters…
saw on news , , can we replce complianc dept with web 3
and a worker tier whose emails are like:
Dear Jim,
First of all, I *love* this idea! Unfortunately, I spoke with Legal and identified a few issues with this approach. For starters…
Reposted by Ian Holmes
The room is
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
November 13, 2025 at 12:13 AM
The room is
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
almost all
elephant.
Almost none
of it isn’t.
Pretty much
solid elephant.
So there’s no
room to talk
about it.
-Kay Ryan, “The Elephant in the Room”
#everynightapoem
Horrifying detail of a tragic story
“In the 1940s and 50s, boys at the Fernald were unknowingly exposed to radiation in an experiment led by Harvard and MIT professors and sponsored by Quaker Oats… to study how cereal affected the way the body absorbed minerals”
www.nytimes.com/2025/11/12/u...
“In the 1940s and 50s, boys at the Fernald were unknowingly exposed to radiation in an experiment led by Harvard and MIT professors and sponsored by Quaker Oats… to study how cereal affected the way the body absorbed minerals”
www.nytimes.com/2025/11/12/u...
He Died at a School for Disabled People. Decades Later, His Brother Sought Answers.
www.nytimes.com
November 13, 2025 at 12:48 AM
Horrifying detail of a tragic story
“In the 1940s and 50s, boys at the Fernald were unknowingly exposed to radiation in an experiment led by Harvard and MIT professors and sponsored by Quaker Oats… to study how cereal affected the way the body absorbed minerals”
www.nytimes.com/2025/11/12/u...
“In the 1940s and 50s, boys at the Fernald were unknowingly exposed to radiation in an experiment led by Harvard and MIT professors and sponsored by Quaker Oats… to study how cereal affected the way the body absorbed minerals”
www.nytimes.com/2025/11/12/u...
Reposted by Ian Holmes
Reposted by Ian Holmes
If you pick up an old shell, can you hear the C?
November 12, 2025 at 5:33 PM
If you pick up an old shell, can you hear the C?
Moved the pitcher plants closer to the compost bin. Hopefully they and the Venus fly traps will get along. I imagine it a bit like “My Dinner With André”
Life hack: place your carnivorous plants near your kitchen counter compost bin. (Why did I take this long to figure it out?)
November 11, 2025 at 9:42 PM
Moved the pitcher plants closer to the compost bin. Hopefully they and the Venus fly traps will get along. I imagine it a bit like “My Dinner With André”
Reposted by Ian Holmes
NEWS: The UK is no longer sharing intelligence with the US about suspected drug trafficking vessels in the Caribbean because it does not want to be complicit in US military strikes and believes the attacks are illegal, sources familiar with the matter told CNN. edition.cnn.com/2025/11/11/p...
Exclusive: UK suspends some intelligence sharing with US over boat strike concerns in major break | CNN Politics
The United Kingdom is no longer sharing intelligence with the US about suspected drug trafficking vessels in the Caribbean because it does not want to be complicit in US military strikes and believes ...
edition.cnn.com
November 11, 2025 at 3:06 PM
NEWS: The UK is no longer sharing intelligence with the US about suspected drug trafficking vessels in the Caribbean because it does not want to be complicit in US military strikes and believes the attacks are illegal, sources familiar with the matter told CNN. edition.cnn.com/2025/11/11/p...
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