iiinova — where your digital self keeps evolving

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Trevor A. Branch @trevorabranch.bsky.social · 08/09/2026

Millennium math problem solved by OpenAI may have "regurgitated" competitors unpublished work... also they spent more than $22 million in computing power in one week to scoop them. techcrunch.com/2026/09/08/o...

techcrunch.com

OpenAI fought dirty on career-making math problem, says NYU mathematician | TechCrunch

There is a $1 million bounty for the first person providing a solution to the Navier-Stokes existence and smoothness problem.

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James Bonfield @jbonfield.bsky.social · 09/07/2026

Note with the new release (1.24) of samtools / bcftools / htslib, we took the decision to drop CRAM 4.0 support. This is because htslib was the only thing that implemented it AFAIK, it was an experimental prerelease and not an adopted standard, and sadly it wasn't as well engineered as it should be

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Andrew Whitwham @whitwham.bsky.social · 09/07/2026

Release 1.24 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪🧬🖥️

htslib.org

Samtools

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Nils Homer @nilshomer.com · 28/06/2026

🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/

bwa-mem3.readthedocs.io

Home - bwa-mem3

Accelerated short-read alignment, derived from bwa-mem2

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Heng Li @lh3lh3.bsky.social · 16/06/2026

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

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Tim Fennell @tfenne.bsky.social · 01/05/2026

Finally pushed out a 5.0.0 release of HTSJDK. Headlines: - CRAM 3.1 write support (finally!) - Much faster CRAM reading (46%) and writing (20-43%) - Much faster BAM reading (6-31%) and writing (51-58%)

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Olivia Guest · Ολίβια Γκεστ @olivia.science · 02/04/2026

jonny over on masto doing god's work: > anthropic [is running] an ENTIRE AD CAMPAIGN around "Claude code is written with claude code" and after the source was leaked that has got to be the funniest self-own in the history of advertising because OH BOY IT SHOWS. neuromatch.social/@jonny/11632...

neuromatch.social

jonny (good kind) (@jonny@neuromatch.social)

Attached: 1 image reminder that anthropic ran (and is still running) an ENTIRE AD CAMPAIGN around "Claude code is written with claude code" and after the source was leaked that has got to be the funn...

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Dan Neidle @danneidle.bsky.social · 15/03/2026

On Friday we revealed the Companies House vulnerability letting anyone access the private dashboard of any UK company. This is the moment I first saw it demonstrated. My reaction says it all. What do we know? What don't we know? What should companies do now?

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Martin Widlake @martinwidlake.bsky.social · 10/03/2026

At last! All remaining hereditary peers in the UK House of Lords will go in May 92 men, mostly old, will no longer have a significant voice in our governance simply due to *who their parents were*, usually based on a forgotten deed by a long, long dead ancestor www.bbc.co.uk/news/article...

bbc.co.uk

Hereditary peers to be removed from Lords as bill passes

The bill abolishes the 92 seats reserved for peers who inherit their titles through their families.

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LynnZ 🦋 @zizij.bsky.social · 09/03/2026

woke up

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Guillotine Hunger Force @handle.invalid · 03/12/2023

nobel prize. right fucking now. im serious.

Certain types of sea urchins will pick up a shell with their tube feet and ‘wear’ it, with a behavior known as “covering reaction”, mainly because they shy away from light.

So aquarium enthusiasts 3D-printed tiny hats and they actually wear them.

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Mark Moxon @markmoxon.bsky.social · 02/01/2026

I am delighted to announce the release of my latest project: Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece. Here’s the repository; deep dives coming soon. See thread for details. 1/9 github.com/markmoxon/th... #retrocomputing #retrogaming #bbcmicro #c64 #8bit

github.com

GitHub - markmoxon/the-sentinel-source-code-bbc-micro: Fully documented and annotated source code for The Sentinel on the BBC Micro

Fully documented and annotated source code for The Sentinel on the BBC Micro - markmoxon/the-sentinel-source-code-bbc-micro

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ᒪᑰᓯ Mark Springer @markspringer.bsky.social · 24/12/2025

@funranium.bsky.social Always be stealing Dune memes!

Dressed in a Santa suit with snowflakes falling a jolly old elf wrangles a Dune sandworm.
(ed. note: meme swiped from @SoDakTruth on Twitter)

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James Bonfield @jbonfield.bsky.social · 16/12/2025

SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.

htslib.org

Samtools

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James Bonfield @jbonfield.bsky.social · 25/11/2025

The usual process ofbuilding modern C++ packages from GitHub... Step 1: download and build yet another new version of cmake. Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.

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James Bonfield @jbonfield.bsky.social · 23/11/2025

A lovely collection of fungi from WildlifeTrustBCN's Gamlingay Woods. #fungi

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Prof. Stefan Rahmstorf @rahmstorf.bsky.social · 13/11/2025

Never forget: At breakneck speed we are leaving the stable Holocene climate in which human society developed and thrived. Weather extremes are outside historical experience. Sea-level rise is accelerating. Dangerous tipping points are ahead. Graph: ed-hawkins.github.io/climate-visu...

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James Bonfield @jbonfield.bsky.social · 29/10/2025

It's curious to see grokipedia is up and has samtools, SAM and BAM pages all with a flurry of edits. Oddly, most of those edits are correcting minor edits in the Wikipedia pages it based its content on (presumably via some AI rewriting tool). A shame the originals weren't edited too.

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Reposted by James Bonfield

Rob Patro @robp.bsky.social · 09/10/2025

The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...

nature.com

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

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Adam Phillippy @aphillippy.bsky.social · 22/09/2025

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

biorxiv.org

A complete diploid human genome benchmark for personalized genomics

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

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James Bonfield @jbonfield.bsky.social · 18/09/2025

Note: OLD POST! (2023), but I just noticed it. While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools? Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)

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Dr. Nick Posegay @nposegay.northsky.social · 17/09/2025

I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose??? This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.

By creating an Account with Academia.edu, you grant us a worldwide, irrevocable, non-exclusive, transferable license, permission, and consent for Academia.edu to use your Member Content and your personal information (including, but not limited to, your name, voice, signature, photograph, likeness, city, institutional affiliations, citations, mentions, publications, and areas of interest) in any manner, including for the purpose of advertising, selling, or soliciting the use or purchase of Academia.edu's Services.

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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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Aaron Rupar @atrupar.com · 03/09/2025

Nigel Farage looks uncomfortable as Jamie Raskin uses his opening statement to absolutely demolish him

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Antoine Limasset @npmalfoy.bsky.social · 02/07/2025

Preprint alert! We present K2Rmini, an ultra-fast, grep-like tool that extracts sequences of interest from FASTA/FASTQ files based on their k-mer content. www.biorxiv.org/content/10.1... A thread

biorxiv.org

Accelerating k-mer-based sequence filtering

The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k - mer-based indexing has improved scalability over traditional alignment fo...

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James Bonfield @jbonfield.bsky.social · 27/06/2025

Are juvenile common lizards normally black, or is this a melanistic one? It was tiny. Seen at #RSPB #Fowlmere.

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Andrew Whitwham @whitwham.bsky.social · 30/05/2025

Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪 #samtools #bcftools #htslib #bioinformatics

htslib.org

Samtools

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Human Pangenome Reference Consortium @humanpangenome.bsky.social · 12/05/2025

📢 HPRC Release 2 is here! Now with phased genomes from 200+ individuals, a 5x increase from Release 1. Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️: humanpangenome.org/hprc-data-re...

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James Bonfield @jbonfield.bsky.social · 05/05/2025

The magnificent seven: Oh deer! Fallow deer, Potton Wood, Beds. Small herds like this are fine and magical to behold, but like everything in nature things need to be kept in balance. We killed the wolves, hence deer stalking has its place as the man-made alternative to the wild balance.

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James Bonfield @jbonfield.bsky.social · 03/05/2025

Some of the lovely blue #wildflowers in the garden currently. #nature

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James Bonfield @jbonfield.bsky.social · 20/04/2025

Marvelling at a wonderful patch of Herb Paris (Paris quadrifolia) in a #wildlifebcn West Cambs ancient woodland. Plus my first (Midland) Hawthorn of the year in flower, and some lovely Bugle. #wildflowerhour, even though none of them are tiny plants.

Midland Hawthorn in blossom ("Mayflower")

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James Bonfield @jbonfield.bsky.social · 14/04/2025

Delightful Pasque Flowers on this evenings walk. A brief stop-over to Therfield Heath on the way home from work. #wildflowers #easter #nature

Many pasqueflowers against an evening sky

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James Bonfield @jbonfield.bsky.social · 11/04/2025

A beautiful morning for walking around #gamlingaywood today. Nice to see the ash stool has regained the Wood Anemone crown again. The Herb Paris patch is lookling spendid too

Bluebells. Plentiful, but not yet in full swing

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James Bonfield @jbonfield.bsky.social · 10/04/2025

My first fresh looking Large White butterfly of the year, fluttering around the greenhouse until I caught it.

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Matt Rich @mattrich.bsky.social · 08/04/2025

Going to recode the C. elegans genome to make a direworm

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Adam Rutherford @adamrutherford.bsky.social · 07/04/2025

Public service announcement. They are not Dire Wolves. They have 20 single letter changes in their entire genomes. I’ve done shits with more mutations. Every time journalists write up a Colossus press release, They are making people stupider. Client journalism by a ridiculous company.

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James Bonfield @jbonfield.bsky.social · 28/03/2025

An early trendsetter - the English Bluebell, in Gamlingay Wood. I only saw 2 of them out of hundreds of thousands (or more). Signs of things to come. Lots of wood anemones, lesser celandines, primroses, oxlips and wild strawberries too. #wildflower #sssi #uknature

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James Bonfield @jbonfield.bsky.social · 26/03/2025

A reminder to SAMtools / HTSlib users, from the next release (probably April 2025) CRAM 3.1 will be the default version used. Use "samtools view -O cram,version=3.0" to switch back to the current 3.0. (But note 3.1 should be smaller and faster, especially on Illumina.)

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Alice Roberts @profaliceroberts.bsky.social · 22/03/2025

Blimey. Looks like pretty much ALL of my books have been pirated by LibGen - the place that’s been scraped by generative AI developers. (thanks @gregjenner.bsky.social): www.theatlantic.com/technology/a...

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Rachael Sirianni, PhD @docsirianni.bsky.social · 15/03/2025

This is horrible to post, but I may as well post it. We are essentially shutting down research operations in my group, which is focused on treatments for pediatric brain cancer. I’m a well funded investigator, and there’s no choice. Science can’t function without the stability of NIH

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James Bonfield @jbonfield.bsky.social · 13/03/2025

I don't know how I avoided it so long, but I'm currently weathering the storm of my first bout of Covid. Ugh! It feels every bit as uncomfortable as flu. :(

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James Bonfield @jbonfield.bsky.social · 07/03/2025

Yesterday I saw my first Brimstone butterfly of the year. It's looking good all weekend. What will I see today I wonder? Making the most of early spring before the next inevitable cold snap.

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Guy Shrubsole @guyshrubsole.bsky.social · 06/03/2025

Huge win! Government announces plans to open up the Land Registry. If delivered, will finally reveal more about who owns land in England and Wales. Read my blog post for more details & how you can write to the Minister to make sure this now happens: whoownsengland.org/2025/03/06/h... 🧵1/

whoownsengland.org

Huge win! Government announces plan to open up Land Registry

This post is by Guy Shrubsole. Today the UK Government has announced plans to open up the Land Registry – which, if delivered, will finally reveal more about who owns land in England and Wale…

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AdyBee 🐝 @adybee.bsky.social · 07/03/2025

Stay the hell away 🤨 …

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James Bonfield @jbonfield.bsky.social · 04/03/2025

Good morning from bright blue Bedfordshire

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