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ianholmes.org
Berkeley professor (Bioengineering / Computational Biology). Visiting Scientist at Calico. JBrowse genome browser / Apollo annotation editor, ML for gene regulation, molecular evolution, phylogenetics, synthetic biology
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I spent some time cleaning up my repo demonstrating how to use the NCBI Datasets REST API to do automated and/or bulk retrieval of genomes, by accession or by taxonomy. It's not super well documented but it does all seem to work :). Enjoy!

submitted 23 hours ago • 1 comment

Everyone who ever got funding through NIAID should be aware of this bill and start sending messages to their US legislators. The bill intends to dissolve NIAID. This is Project 2025 www.congress.gov/bill/119th-c...

submitted 1 day ago • 3 comments

Join us! Science Homecoming helps scientists reconnect with communities by writing about the importance of science funding in their hometown newspapers. We’ve mapped every small newspaper in the U.S. and provide resources to get you started. Help science get back home 🧪🔬🧬 🏠 sciencehomecoming.com

submitted 5 days ago • 33 comments

submitted 4 days ago • 110 comments

Public comments are open for gender marker changes for trans people on passports. DS-11 Application for passport: www.federalregister.gov/documents/20... DS-82 Passport Renewal: www.federalregister.gov/documents/20... DS-5504 Name Change and Corrections. www.federalregister.gov/documents/20...

submitted 4 days ago • 22 comments

Everything is chaos, but I wanted to share some awesome recent science from the lab that hints at where the future of biomolecular simulation is headed: Foundation simulation models that can be fine-tuned to experimental free energy data to produce systematically more accurate predictions.

submitted 4 days ago • 2 comments

We are on the road for democracy and justice | Bernie Sanders

submitted 4 days ago • 17 comments

I just learned of the existence of “rwty” (R We There Yet), a package by @roblanfear.bsky.social et al for assessing convergence of Bayesian phylogenetic sampling runs, and I have no notes. Absolutely superb package name academic.oup.com/mbe/article/...

submitted 4 days ago • 1 comment

I think you have to be British and of a certain age to get this but I am those things and can’t stop laughing youtu.be/GyUNkmvAdwg

submitted 4 days ago • 0 comments

I escaped poverty because I am a scientist. And I am a scientist because of the National Science Foundation. A 🧵:

submitted 5 days ago • 73 comments

“Centuries ago, our peaceful kingdom was threatened by a giant comet. Our magi, by their scrying arts, foresaw the calamity and worked to shield the populace from the rain of fire and choking ash. Many lives were saved. And that is why magicians are now defunded and only supported by philanthropists

submitted 5 days ago • 1 comment

The BBC Master microcomputer, later used to develop and enable the ARM1

submitted 5 days ago • 3 comments

This is the preprint write up of my sabbatical work with Dave Kelley’s group at Calico. We tried out several transformer replacements for multi-task learning in functional genomics (i.e. what Borzoi does). Mamba, in particular, seems to outperform a mini version of Borzoi, especially when “striped”.

submitted 5 days ago • 1 comment

Exactly! An unjust peace agreement between Trump and Putin will not end the war and Europe will continue to support Ukraine.

submitted 10 days ago • 0 comments

Letters went out to federal workers this morning stating they were fired due to poor performance. However, all employees had been rated as “exceptional” performers by their supervisors. Please keep these records and pursue wrongful termination claims. Let the lawsuits begin.

submitted 7 days ago • 987 comments

Spoke to a former colleague who recently transitioned to a probationary role at USDA and was fired this week. They said everyone there felt like they were waiting for the guillotine.

submitted 7 days ago • 0 comments

I recently saw a thread by a scientist along the lines of “well what did you think was going to happen if we all endorsed left-wing positions? Science became too political”. This confuses cause & effect and fails to understand we are all caught in a political dynamic with a movement opposed to truth

submitted 7 days ago • 3 comments

Please. Do the science rallies. Go, build morale, network. Protest. But do not for a moment imagine that you can defend your professional interests without making common cause with the broader mass of people that this administration has targeted. If your dream is of an apolitical golden age, wake up

submitted 7 days ago • 1 comment

I’ve been thinking this too. Asplaining our important science is not a way out of this. Neither is wishing we could depoliticize science again. I suspect unless/until scientists find a way to make common cause with a much larger political movement, we’re sunk.

submitted 7 days ago • 1 comment

There is a well-worn saying in academia: No good deed goes unpunished. I never imagined it would apply to public health as a whole. Although, really, what has happened to climate scientists like @michaelemann.bsky.social should have clued me in.

submitted 7 days ago • 0 comments

Happy Valentine’s Day. Ah, love. Once you wear your heart on your sleeve, it’s so hard to put the genie back in the bottle and then you’ve opened Pandora’s box. Also, happy anniversary of Captain Cook’s death; sad really, he was a beloved Captain and a scientist, if admittedly a tool of colonialism

submitted 9 days ago • 1 comment

ESM2 in Jax!

submitted 11 days ago • 0 comments