New Sequence Read Archive standards, you have until next year to start uploading files with (checks notes) data in them ncbiinsights.ncbi.nlm.nih.gov/2026/06/29/s...
Rich Abdill
@richabdill.com
Bioinformatics, open data and meta-research at Sage Bionetworks
Just noticed Positron uses the Elastic License, and using MIT for some of the heavy components seems like a thoughtful approach. It would be interesting to get a legal perspective on how shops like Posit (and Elastic!) are balancing OSS with keeping the lights on positron.posit.co/licensing.html
Licensing – Positron
Positron is licensed under Elastic License 2.0, a source-available license. Free for personal, academic, and commercial use with minimal restrictions.
positron.posit.co
He kept coming back, repeatedly (in the way AI often loops) to this idea of AI (specifically Claude) representing "a position without an address", and it became increasingly clear to me that there was some odd mystification happening. Of course LLM products have an address. It's a corporate address.
🎉 JOSS turns 10 today! Ten years, 3,500+ papers, 11,000+ authors, 4000+ reviewers, and a community that built something remarkable together. Thank you to everyone who's reviewed, edited, authored, or cheered us on along the way 💚 joss.theoj.org #openscience #opensource
Journal of Open Source Software
Journal of Open Source Software (JOSS) is a developer friendly, open access journal for research software packages.
joss.theoj.org
Shared memory for R objects. This will make bioinformatics work so, so much faster. If you have a script that uses multiple threads but is limited by the amount of memory required for each thread, this might be just a drop-in replacement that opens up every core opensource.posit.co/blog/2026-04...
mori: Shared memory for R objects
mori is a new R package for sharing R objects across processes via OS-level shared memory. Parallel workers get zero-copy, lazy ALTREP access to the same physical pages — share once, read anywhere.
opensource.posit.co
This could be a game changer!! Diarrhea is global health's least sexy challenge, but it remains a top killer of children. E.coli is present in 98% of water sources in Guatemala, for example, and systematic water purification is incredibly challenging for low-resourced contexts.
Oral vaccine cuts up to 80.6% of E.coli-triggered diarrhoea cases
The oral ETEC vaccine will now enter a pivotal Phase III trial across different countries and populations.
clinicaltrialsarena.com
OMB has posted the full-year apportionments for NIH. openomb.org/file/11511545 I believe this means that NIH now has the spending authority to fund grants! There may be nuances and I will be tracking these as best I can.
National Library of Medicine and 24 other accounts | 11511545
Apportionment file 11511545 (National Library of Medicine and 24 other accounts) retrieved from OMB public records
openomb.org
As ProPublica journalists, we share a common purpose with inspectors general: to hold our government accountable by identifying waste, fraud and abuse. If you work in or have recently left the office of an inspector general, we want to hear from you.
An Open Letter to the Inspectors General Community
If you work in or have recently left the office of a federal inspector general, we need your insights to do important journalism.
propublica.org
(unless you work on climate change or racial disparities or LGBTQ health or…)
Max Kozlov@maxkozlov.bsky.social · 5mo agoThe US NIH is stepping back from 'top-down' science. My latest analysis for @nature.com shows that funding calls have plummeted by 90%, funneling billions into broad, 'investigator-initiated' ideas, rather than targeted, agency-driven ones. A massive shift for the American biomedical enterprise.
“The leftover money from those terminations went to the US Treasury, not back to NIH.”
Jeremy Berg@jeremymberg.bsky.social · 5mo agoGood story from Vox on falling numbers of new and competitive renewal R01 grants. [Gift Link] www.vox.com/future-perfe... 1/5
I don't have any insight into what the actual story is with the change to NIH data management plan requirements, but this clarification sounds like "We asked for lots of details, turns out we don't care" grants.nih.gov/grants/guide...
NOT-OD-26-046: Updated Elements of an NIH Data Management and Sharing Plan
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Updated Elements of an NIH Data Management and Sharing Plan NOT-OD-26-046. NIH
grants.nih.gov
I was just talking about this the other day, 404 Media has been doing an incredible job laying out the threats posed by data brokers www.404media.co/cbp-tapped-i...
CBP Tapped Into the Online Advertising Ecosystem To Track Peoples’ Movements
An internal DHS document obtained by 404 Media shows for the first time CBP used location data sourced from the online advertising industry to track phone locations. ICE has bought access to similar t...
404media.co
Quick paper highlights a fun twist on methods transparency and reporting—even thorough descriptions may be interpretable only to humans. Interesting to consider using standardized syntax ("n=") for LLMs rather than older "semantic web" techniques www.microbiologyresearch.org/content/jour...
Sample Size Reporting in Human Cancer Microbiome Research is Inconsistent and Unstandardized
Transparent and standardized sample size reporting is essential for reproducibility in microbiome research, and for enabling AI-driven data aggregation tools. This is of particular importance with reg...
microbiologyresearch.org
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
More than 400 people, including hundreds of citizens, were “sorted” at gun point into racial and ethnic groups by 200 ICE agents who fired flash-bang grenades into cars with people inside, pointed guns at children & demanded their zip tied parents not comfort them. apple.news/Ausdx6kWtT0e...
Idaho families sue over immigration raid that swept up hundreds, including U.S. citizens — NBC News
About 400 people, including children and U.S. citizens, were detained for four hours while they were denied food and water in the raid, according to the lawsuit.
apple.news
A Minnesota woman observing ICE agents in her car was cornered on one-way streets. An agent approached, called her by name—citing facial recognition. Days later, her Global Entry and TSA privileges were revoked, with no explanation.
How ICE Already Knows Who Minneapolis Protesters Are
nytimes.com
ICE's decision to just leave cars abandoned in the roads is one of those dystopian things that makes you recoil in shock when you encounter it.
Daniel Silliman@danielsilliman.bsky.social · 6mo agoA legal asylum-seeker who works at Chipotle and plays music at a church in Maine went missing. His pastor searched and searched, eventually finding his abandoned car with the keys on the floor. ICE grabbed him. No criminal record. No explanation.
What Americans Lose If Their National Center for Atmospheric Research Is Dismantled
What Americans Lose If Their National Center for Atmospheric Research Is Dismantled - Eos
Five ways dismantling NCAR will cost the American people, and two ways to save it.
eos.org
"We have a nice little database. Now you're considered a domestic terrorist." www.reddit.com/r/Maine/comm...
From the Maine community on Reddit: ICE tells legal observer she is a domestic terrorist for peacefully filming
Explore this post and more from the Maine community
reddit.com
Google's browser is now cutting off its own ads for eating up too many resources
We have the CDC-funded Hepatitis Vaccine trial in Guinea-Bissau protocol. It’s worse than you thought. Check it out, first in Inside Medicine… with @pauloffit.bsky.social David Boulware and others. insidemedicine.substack.com/p/scoop-the-...
Scoop: The leaked protocol of the CDC-funded Hepatitis B vaccine trial in Guinea-Bissau. “This is another Tuskegee.”
The protocol reveals that the trial will withhold the Hepatitis B birth dose from thousands—without placebos, without universal maternal screening, and with endpoints critics call indefensible.
insidemedicine.substack.com
New research from @uchicagobsd.bsky.social shows that microbes in breast milk actually populate the infant gut, laying the foundation for a healthy microbiome. biologicalsciences.uchicago.edu/news/microbe... #ScienceNews #Microbiome #GutHealth
Microbes in breast milk help populate infant gut microbiomes
New study provides one of the most detailed portraits yet of how different combinations of bacteria in human milk contribute to infants’ gut microbiomes.
biologicalsciences.uchicago.edu
You and your wife drop your 6-year-old off at school. You just moved here. You see ICE terrorizing your new neighbors. You film them, as is your legal right. Your wife complies with orders. She is then shot in the head. You still have to pick up your child later today. This could be you.
Minneapolis public schools canceled classes officials after Roosevelt High School said armed Border Patrol officers came on school property during dismissal Wednesday and began tackling people, handcuffed two staff members and released chemical weapons on bystanders www.mprnews.org/story/2026/0...
Minneapolis schools cancel classes after Border Patrol clash disrupts dismissal at Roosevelt
Minneapolis schools closed for the week citing safety concerns after an encounter involving armed Border Patrol agents near Roosevelt High School.
mprnews.org
According to my sources, the FBI was initially open to a concurrent investigation with the MN Bureau of Criminal Apprehension (the state agency that would do this investigation). Trumpy U.S. Attorney Daniel Rosen heard about this and intervened, barring the FBI from cooperating with local police.
Carl Quintanilla@carlquintanilla.bsky.social · 7mo agoMINNEAPOLIS (AP) - Minnesota investigators say they can't access evidence after fatal ICE shooting and FBI won't work jointly on probe. @reuters.com
Posts may be a bit more sporadic from me today as my kids are home from school because my city is being brutalized by the federal government to the extent that it's unsafe for schools to be open
via Minneapolis photographer Chris Juhn on Facebook
"I don’t know why my fellowship was terminated. I suspect that it has something to do with studying a species that doesn’t fit the binary of what we expect to see in nature, with completely different males and females." @carlzimmer.com profiles my wonderful coauthor @jjinsing.bsky.social Gift link.
He Studied Why Some Female Birds Look Like Males
nytimes.com
The point was never to save money. That was only ever a convenient justification for an effort to decimate the public sector and dismantle the US social safety net.
The Upshot@upshot.nytimes.com · 8mo agoOn DOGE’s watch, federal spending did not go down at all. It went up. But is still led to cuts that closed offices, canceled programs and deprived people of food, medicine and other aid. www.nytimes.com/2025/12/23/u...