iiinova — where your digital self keeps evolving

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Jared Yates Sexton @jysexton.bsky.social · 26/09/2026

Just helping with editing here. These bots aren’t sentient. They’re doing what they’re programmed to do. OpenAI, a private company supposedly bound by laws, committed federal crimes.

Screenshot of BBC article: OpenAI bots (struck through) meddled with multiple US government agency sites

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Puff the Magic Hater @mskellymhayes.bsky.social · 08/09/2026

Something has really bothered me about the Gloria Steinem discourse—something that's not really about Gloria Steinem. So, I wrote about it.

organizingmythoughts.org

Grief Is Not a Verdict: This Is Not Really an Essay About Gloria Steinem

We grieve the worlds we’ve known and what it felt like to live in them.

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Chris Miller @chrismiller.science · 22/07/2026

I pushed a package to bioconda 2 weeks ago and it's still waiting for review. Anyone here a maintainer that could help get it unstuck? github.com/bioconda/bio... (We have a paper in review that mentions an option for bioconda install - would like to make that aspirational sentence reality!)

github.com

Add vatools by chrisamiller · Pull Request #67110 · bioconda/bioconda-recipes

Adds a new recipe for vatools (https://github.com/griffithlab/vatools), a package designed to ease manipulation of genomic data stored in VCF format

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If you know you know @privatechand.bsky.social · 14/06/2026

I don’t even follow basketball and I am not from and have never lived in NYC but this thread is genuinely lovely.

Mamdani skeets: HISTORY. First reply: MY MAYOR MUSLIM. Next: MY BAGELS JEWISH. Next: THE POPE’S ON OUR SIDE. Last: KNICKS IN FIVE.

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Dr Kathleen Millen @neurodevkathy.bsky.social · 07/05/2026

I'll be happily wearing my @flomask.bsky.social on each and every flight for the rest of my life. It is crazy how few people wear masks on flights these days.

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public health guy @publichealthguy1.bsky.social · 24/04/2026

i'm not a hardcore anti-AI guy, but i cannot think of a single benefit of genAI that could possibly outweigh the harm it is doing to our social fabric, shared reality, and most basic abilities to parse information and learn.

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Heng Li @lh3lh3.bsky.social · 17/04/2026

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

lh3.github.io

The AI Rewrite Dilemma

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Oliver Hofmann @fiamh.bsky.social · 10/04/2026

I have mixed feelings about re-writing existing tools (fragmentation, maintenance burden, etc) but a ton of thought has gone into the `rewrites` manifest. Worth discussing.

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Tim Fennell @tfenne.bsky.social · 20/03/2026

Such a cool project from @nilshomer.com.

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Katie Mack @astrokatie.com · 24/02/2026

I'm constantly trying (/failing) to get this point across. If you're a trained expert in a field, then it may be worthwhile to question the scientific consensus of your peers. If you're not, the scientific consensus is absolutely the best you can do and it's arbitrary foolishness to disregard it.

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Steph Stammel @stephstammel.bsky.social · 29/01/2026

Are there any R users working for the Australian federal dept of health? I’d love to hear from you! New gig, new people to meet :)

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Chris Hayes @chrislhayes.bsky.social · 04/02/2026

I think it's best for everyone to understand that the unified class project of billionaires right now is to do to white collar workers what globalization and neoliberalism did to blue collar workers.

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Cat Hicks @grimalkina.bsky.social · 05/02/2026

I've been in SF for four days and on each day I've had multiple conversations where people (self included) express deep feelings, fear, wonder and worry about their skills being replaced or (this is less named explicitly but an assumed driver I think) no longer valued by others. Big threats to feel

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Philipp Bayer @philippbayer.bsky.social · 03/02/2026

was banging my head against a bug (VEP classifying my in-exon variants as 'downstream') that Claude Sonnet 4.5 fixed in about 5 minutes. I can understand the scepticism on LLMs being jammed into every corner of life, but there's merit in these tools

he VEP command looks correct, but the issue is that VEP is annotating based on ALL transcripts/features in the region, and "downstream_gene_variant" is being picked as the consequence. Since you didn't specify --pick or --pick_allele, VEP returns consequences for multiple transcripts, and your code is just taking the first one.

Let me check how you're extracting the consequence from the VEP output:

Found it! You're extracting only the second field from the CSQ column with map_chr(2). This is getting the consequence from the first transcript annotation, which might be a pseudogene or non-canonical transcript.

Let me check what a VEP CSQ field actually contains:

Perfect! I can see the issue now. The VEP CSQ field contains multiple transcript annotations separated by commas. The first annotation is for TSC2 (a different gene!) and shows "downstream_gene_variant". But if you look at the second annotation (after the first comma), you'll see it's for PKD1 ENST00000262304 and shows "3_prime_UTR_variant" for exon 46 (which is correct - exon 46 contains the 3' UTR).

Your code is only extracting the consequence from the first transcript annotation (TSC2), not the PKD1 transcript!

The fix is to parse all transcript annotations and filter for the PKD1 canonical transcript (ENST00000262304). Let me create the fix:

PKD1_mutation_rate.qmd+24-1
Now let's test the fix by re-running the code to see if we get proper consequences for exons 40-46:

Perfect! The fix worked! Now you're seeing proper consequences for exons 40-46:

Missense variants (the most common)

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HTTP 1.1/418 Eldritch Teapot of R'lyeh @rmd1023.bsky.social · 03/01/2026

Reminder for everyone operating at situationally-diminished capacity.

Screencap of post from tumblr user nitewrighter
Me: I don't get it. I thought I was doing a lot better than I was a few years ago. I'm like 10 times more on top of things than I used to be. How does everything feel terrible now?
The Tiny Me in OSHA-approved Hi-Vis Gear Who lives in my brain and pulls all the levers: Boss, it's the fascism. You're completely gunked up with cortisol due to the fact that your entire daily life is now underscored with a haunting awareness of the rapid erosion of your rights, dignity, and any and all social safety nets, and you're also bearing witness to the most vulnerable people immediately being persecuted. This creates a natural stress response that basically means you're going to continue having memory and organizational problems, as well as emotional imbalances.
Me: BUT I HAVE A BULLET JOURNAL AND I MEDITATE NOW.
Tiny OSHA Me: BOSS, THE FASCISM.

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RM @dorsalstream.bsky.social · 29/12/2025

Getting older is like being out on the ocean in the Ship of Theseus but then at some point the guys just decided against replacing the decayed parts.

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Bec Shaw @brocklesnitch.bsky.social · 26/12/2025

The comments on this are all about how sweet it is and I feel insane. Using AI to make fake memories of your grandma with dementia and telling her they happened and then filming her reaction

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Andrew Heiss @andrew.heiss.phd · 17/11/2025

I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!

We strongly suggest using the following labels:

praise: Praises highlight something positive. Try to leave at least one of these comments per review. Do not leave false praise (which can actually be damaging). Do look for something to sincerely praise.
nitpick: Nitpicks are trivial preference-based requests. These should be non-blocking by nature.
suggestion: Suggestions propose improvements to the current subject. It’s important to be explicit and clear on what is being suggested and why it is an improvement. Consider using patches and the blocking or non-blocking decorations to further communicate your intent.
issue: Issues highlight specific problems with the subject under review. These problems can be user-facing or behind the scenes. It is strongly recommended to pair this comment with a suggestion. If you are not sure if a problem exists or not, consider leaving a question.
todo: TODO’s are small, trivial, but necessary changes. Distinguishing todo comments from issues: or suggestions: helps direct the reader’s attention to comments requiring more involvement.
question: Questions are appropriate if you have a potential concern but are not quite sure if it’s relevant or not. Asking the author for clarification or investigation can lead to a quick resolution.
thought: Thoughts represent an idea that popped up from reviewing. These comments are non-blocking by nature, but they are extremely valuable and can lead to more focused initiatives and mentoring opportunities.
chore: Chores are simple tasks that must be done before the subject can be “officially” accepted. Usually, these comments reference some common process. Try to leave a link to the process description so that the reader knows how to resolve the chore.
note: Notes are always non-blocking and simply highlight something the reader should take note of.

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Global Alliance for Genomics and Health @ga4gh.org · 17/11/2025

Join the Clinical Genomics Laboratory Community (CGLC) meeting on 24 November. This session will explore how artificial intelligence and large language models (LLMs) are transforming variant interpretation. Register for the meeting: us02web.zoom.us/meeting/regi...

us02web.zoom.us

Welcome! You are invited to join a meeting: Clinical Genomics Laboratory Meeting. After registering, you will receive a confirmation email about joining the meeting.

The topic for this meeting will be AI and LLMs in Variant Classification

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Reposted by Oliver Hofmann

Alejandra Caraballo @esqueer.net · 15/10/2025

You have to wonder if White House staffers are simply showing him AI videos at this point and he thinks it's reality.

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Joshua Weitz @joshuasweitz.bsky.social · 22/09/2025

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished. jamanetwork.com/journals/jam...

jamanetwork.com

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

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James Bonfield @jbonfield.bsky.social · 15/09/2025

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

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Brian Merchant @bcmerchant.bsky.social · 04/09/2025

Breaking Google up was one of the last best hopes for preventing the free press from getting squeezed into oblivion and harvested into AI slop, and for saving the open web. The ruling that effectively lets Google continue operating as a monopoly isn't just disappointing, it's a disaster.

bloodinthemachine.com

One of the last, best hopes for saving the open web and a free press is dead

The Google ruling is a disaster. Let the AI slop flow and the writers, journalists and creators get squeezed.

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Rob Patro @robp.bsky.social · 26/08/2025

At scale, the way that we store (and process) data matters! Many may think that the way we keep data, the file formats we adopt, and the way that we compress data are unimportant details, but they are, in fact, critical considerations to allow science to move forward at scale!

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Molly Jong-Fast @mollyjongfast.bsky.social · 21/08/2025

In case you missed it, this is fucked www.nytimes.com/2025/08/21/u...

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Imani Gandy @angryblacklady.blacksky.app · 11/07/2025

He's gonna buy up the only remaining left leaning outlets, give them the WaPo treatment which means more people are gonna end up launching substacks and I'm gonna walk into the sea

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Buy Mass Effect The Board Game! @ithayla.bsky.social · 05/07/2025

happy birthday to bill watterson who gave me the gift of encapsulating my entire ethical approach in one comic panel.

A panel from a Calvin and Hobbes comic. Calvin's mom, eating dinner, says "Life could be worse, Calvin." Calvin, clearly upset, his mouth huge says "Life could be a lot BETTER too!"

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Stone Cold Jane Austen @abbyhiggs.bsky.social · 22/06/2025

It’s a good thing Congress isn’t alive to see this

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Katie Mack @astrokatie.com · 17/06/2025

I still can't get past the idea that people in America are now supposed to accept that this is a valid form of law enforcement and just assume it's fine when random dudes in groups with face-coverings, no ID, no warrant, & no uniform grab people off the street and force them into unmarked vehicles

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Hayes Brown @hayesbrown.bsky.social · 05/06/2025

this is a day for those of us who have spent the last six months terminally online. this is for us and honestly, we deserve it.

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Colette Delawalla, PhD @cdelawalla.bsky.social · 25/05/2025

Do not give them an INCH! It's not: Well, maybe there are some areas where DEI has become too much a focus. It's: FREE COUNTRIES DON'T SEND OUT BANNED WORDS LISTS TO THEIR SCIENTISTS It's not: Well, science isn't perfect... It's: FREE COUNTRIES DO NOT HAVE SCIENCE COMMISSARS

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Brendan Keogh @brkeogh.bsky.social · 06/05/2025

We dodged right-wing populism this time because of Trump. We won't dodge it a second time if everyone's day-to-day living is still shit and the progressive side of politics hasn't offered real, courageous solutions.

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sarah jeong @sarahjeong.bsky.social · 25/04/2025

one of the radicalizing incidents of my youth was when the NYPD brutalized a judge who was volunteering as a legal observer at a protest. I'm afraid that "Feds arrest judge" is the incident that has fully broken my brain

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Ella Ampongan @meampongan.bsky.social · 25/04/2025

All the games I played on game day ranked. Top spot is Signal by @dvcgames.bsky.social In the game you’re experts trying to communicate with aliens. A great deduction game similar to First Contact but instead of words you work with objects. Really great fun especially if you’re drinking wine 😆

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Harvey Smith @harvey1966.bsky.social · 14/04/2025

From George Monbiot at the Guardian.

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Ketan Joshi @ketanjoshi.co · 10/04/2025

De-extinction is the carbon removal of biodiversity world Promises to magically undo the harm that in reality can only be prevented before it occurs.

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Kim Cooper @ucsdcooperlab.bsky.social · 07/04/2025

If Colossal makes a horse with a midline horn and says they've made a mythical unicorn while cancer trials are being defunded, may self-immolate.

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Jess Calarco @jessicacalarco.com · 03/04/2025

The problem is: they've mistaken correlation for causation. They think their parents and grandparents had a good life *because* of manufacturing jobs. When, in reality, their parents and grandparents had a good life *despite* manufacturing jobs, because of unions, high taxes, and social policies.

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Global Alliance for Genomics and Health @ga4gh.org · 24/03/2025

Hello BlueSky community! We are excited to be here. Stay tuned for news, announcements, and updates from GA4GH and the broader genomics and health community.

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Yvette Cendes @whereisyvette.bsky.social · 16/03/2025

Pet peeve: I hate how often ppl claim “all the researchers will just move to Europe/Canada!” You vastly under-estimate how little money there is there vs the USA- and unless that changes ASAP this loss is just going to decimate global science, full stop. 🧪🔭

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Sarah Ford 🐍🎨🖥️ SleepyTime Holiday @angeloslh.bsky.social · 06/04/2024

Welp they have a section on 1999 in the historical lives section of the museum I'm going to the grave bye

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Philipp Bayer @philippbayer.bsky.social · 06/03/2025

The most niche but also the truest meme in history

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Katie Hinde @mammalssuck.bsky.social · 08/02/2025

And Academic T&P committees, maybe take a beat & consider how the continuous & unsustainable push for CV conspicuous production has been a competitive inhibitor of scientists & scholars being engaged in their communities in meaningful ways as a bulwark to the shitstorm happening now.

media.tenor.com

a woman in a black and white jacket is sitting at a table in a diner .

Alt: a woman in a black and white jacket is sitting at a table in a diner saying "There, I said it."

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Liz Neeley @lizneeley.bsky.social · 08/02/2025

This is the kind of simple and direct message we need right now: long-term damage aside, this attack is going to very quickly make it even harder for people to have the jobs and medical care they need.

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