iiinova — where your digital self keeps evolving

Reposted by Samuel Lampa

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 29/09/2026

Detecting Random Mutations in 16S rRNA Sequences www.biorxiv.org/content/10.64898/20…

Reposted by Samuel Lampa

Samuel Lampa @smllmp.bsky.social · 25/09/2026

New blog: Emu runs an order of magnitude faster for high quality (sup) R10 @nanoporetech.com 16S data, with the lr:hq preset for minimap2, in addition to improving downstream analysis as previously blogged by @mbhall88.bsky.social: livingsystems.cc/posts/lrhq-s... #bioinformatics #microbinfie

Bar graph showing how Emu with the lr:hq preset is running ca 10 times faster than with map-ont, for three different data sizes: 1k, 5k and 10k reads.

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Reposted by Samuel Lampa

Comfortably Numb @numb.comfortab.ly · 28/09/2026

Claude making a scientific discovery

Black-and-white three-part comic. In the first scene, one simple cartoon figure holds out a small round handmade-looking object and says, “I MADE THIS.” Another figure replies, “YOU MADE THIS?” In the second scene, the second figure is shown alone holding the object. In the final scene, that figure holds it proudly and says, “I MADE THIS”

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Samuel Lampa @smllmp.bsky.social · 28/09/2026

As someone earlier also noted, that even if they don't train on chats (I think they do) the practice of constantly scanning the internet for content wo credits is already enough to force science to become less open, as otherwise researchers will be constantly scooped wo credit for anything mentioned

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Reposted by Samuel Lampa

Wytamma @wytamma.bsky.social · 28/09/2026

One of the reasons I'm interested in local AI models is you're data can't be used for training - people say “I already put my data in onedrive so what's the difference to uploading it to an AI model?” Well one difference is that onedrive won't use your data to scoop you

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Samuel Lampa @smllmp.bsky.social · 28/09/2026

For the folks who are wise enough not to work late Friday nights ...

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Samuel Lampa @smllmp.bsky.social · 25/09/2026

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Reposted by Samuel Lampa

🦋Dr. Natalia🕊🌻🪬 @solnatamd.medsky.social · 24/09/2026

❗️Artificial intelligence agents for OpenAI infiltrated a government-run public health care website in Australia in June and accessed nonpublic information. The case prompted a government investigation into the breach and raised alarm about rogue activities by fast-advancing A.I. systems.❗️

nytimes.com

Australia Says OpenAI ‘Infiltrated’ Public Health Care Portal (Gift Article)

Australia is exploring potential legal action after an artificial intelligence agent accessed nonpublic information on the country’s universal health care system.

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 21/09/2026

It's here! new preprint: Gravlax, an annotation-independent molecular evidence archive for scRNA-seq. A count matrix freezes one annotation. Molecules never change. Instead, gravlax keeps the evidence. Requantify, query, and discover under any annotation. 🧵 www.biorxiv.org/content/10.6...

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Reposted by Samuel Lampa

Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 28/08/2026

I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...

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Samuel Lampa @smllmp.bsky.social · 11/09/2026

Super stoked that SciCommander (track provenance for any file produced by your ad-hoc shell usage into HTML reports & more) is now on @conda-forge.org! 🥳 Install with: conda install conda-forge::scicommander pixi add scicommander anaconda.org/channels/con... Poster for info 👇

Poster with title: SciCommander - Track provenance of interactive shell usage. Showing a longer text explaining it, some screenshots of using scicommander in shell mode and an example HTML report, together with some artistic line drawings.

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Reposted by Samuel Lampa

Quadram Institute @quadraminstitute.bsky.social · 07/09/2026

Would you like to join us as a Group Leader in Microbes and Food Safety? The priorities for the research programme are to reduce enduring and emerging threats to the safety of UK food supplies. 💷 Competitive 🗓️ Apply by 30 September 2026 ➡️ buff.ly/CG8vwJK

A photo of a ham and cheese salad with a teal quadrangle and the text "Group Leader (Microbes and Food Safety), with a research focus on ensuring food safety and security, salary: competitive, apply by 30 September"

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Reposted by Samuel Lampa

The New York Times @nytimes.com · 06/09/2026

A woman was rescued on Saturday from a mostly buried house in Betrawati, Nepal, 10 days after flooding devastated the area. Her recovery was the second improbable rescue of the day. trib.al/W4ihQgE

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 24/08/2026

New salmon release 2.6.0! Now, salmon is deterministic-by-default (dbd)! This was an oft-requested features, & one that we had as optional over the past few released via the `--deterministic` flag. Now, salmon is deterministic by default with `--online` giving the previous behavior. 1/3

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Reposted by Samuel Lampa

Merriam-Webster @merriam-webster.com · 19/08/2026

People who don’t know the difference between ‘entomology’ and ‘etymology’ bug us in ways we cannot put into words.

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Samuel Lampa @smllmp.bsky.social · 20/08/2026

Are telling me that typing the code was the bottleneck? And that we weren't able to build the abstractions to make this not be the case … … and so we had to take a shortcut using non-deterministic blobs of numbers trained on the whole of internet to work around this fact? 🤔

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Reposted by Samuel Lampa

Robert Aboukhalil @robert.bio · 13/08/2026

I made a Nextflow tutorial you can run from your browser!! Nothing to install, and cloud costs are sponsored by @carolinacloud.io You build a pipeline to find how much sequencing you need to detect Listeria in ice cream, with interactive challenges along the way. sandbox.bio/tutorials/ne...

sandbox.bio

Introduction to Nextflow

Interactive Nextflow tutorial: write your first pipeline and run it on real cloud infrastructure, for free and with no installation. Also learn to use existing nf-core pipelines.

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Reposted by Samuel Lampa

Adam Phillippy @aphillippy.bsky.social · 13/08/2026

"Filling the holes in whole genomes: A vision for personalized genomics from telomere to telomere" Brief commentary from me, @khmiga.bsky.social, @msikic.bsky.social, Yu Kang and Yafei Mao for the T2T special issue. Why do we need complete genomes? Check it out! www.cell.com/cell/fulltex...

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Samuel Lampa @smllmp.bsky.social · 13/08/2026

Prompting is real work. Even G*d, after six days of prompting, had to rest for a full seventh day 😎

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Reposted by Samuel Lampa

Toby Baril @tobybarilbio.bsky.social · 12/08/2026

Thrilled to share that I'll be starting my lab at the Swedish Museum of Natural History in Stockholm as a DDLS Fellow in November! 🧑‍🔬🧬🎉 Of course, we will be delving into all things mobile DNA & evolution, as well as developing AI approaches for biodiversity genomics #newPI #TEsky #TEworldwide

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Reposted by Samuel Lampa

Robert Aboukhalil @robert.bio · 12/08/2026

Today, Sandboxbio is releasing an interactive companion to @carpentries.carpentries.org's excellent Python workshop 🐍 From your browser, you write and run Python code to solve the exercises, with hints and instant feedback. carpentries.org/blog/2026/08...

carpentries.org

Interactive Carpentries exercises on sandbox.bio

Sandbox.bio is a free bioinformatics training platform, where all the tools you need run in the browser, so no setup is needed. This week, Sandbox.bio is releasing Programming with Python Exercises, a...

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Samuel Lampa @smllmp.bsky.social · 11/08/2026

Completely agree. Been my #1 reason not to use GenAI for open source coding in science too. The watermark debacle from Anthropic further underscores the problem of using content you haven't generated yourself: You don't own it & have no control over any hidden layers (tone, voice, watermark) added.

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Reposted by Samuel Lampa

Stephen Turner @stephenturner.us · 10/08/2026

Read to the end. This is the best, well-reasoned argument for a complete blanket ban on AI assisted writing.

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Samuel Lampa @smllmp.bsky.social · 11/08/2026

This has been my number one reason not to use GenAI for open source coding in science (as well as in writing, though I do less of that), though have only communicated about this personally with some colleagues and friends. I agree that this is a deal breaker indeed.

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Reposted by Samuel Lampa

Andrew Carroll @acarroll.bsky.social · 01/07/2026

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

andrewcarroll.github.io

The Best of Both Worlds - Assessing MiniBWA

Recently, Heng Li released MiniBWA (GitHub) alongside a paper by Heng Li and Nils Homer describing the method (paper). MiniBWA builds on the approaches in Minimap2 (also by Heng Li), but falls back on...

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 10/08/2026

salmon 2.5.0 is out: 28 PRs. Headline: -p is now one measured budget — gzip decode + mapping share it, and a live controller (thread-broker) solves the split from measurement instead of guessing. Quantification results unchanged; no index rebuild. github.com/COMBINE-lab/salmon 1/4

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Samuel Lampa @smllmp.bsky.social · 10/08/2026

Demonstrating in under 5 min how to use SciCommander, which captures provenance information for all outputs of shell commands ran through it, enabling to produce an HTML report specifically for any output file. www.youtube.com/watch?v=-gFG...

youtube.com

Demo of SciCommander - A small tool for capturing provenance from ad-hoc shell command usage

YouTube video by Samuel Lampa

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Reposted by Samuel Lampa

Robert Aboukhalil @robert.bio · 10/08/2026

You can now turn your GitHub repos into sandbox.bio tutorials! You get a shareable URL, where code blocks are runnable, and files are preloaded in the terminal. For example, @benlangmead.bsky.social used this in a recent kraken2 workshop. You can see it in action here: sandbox.bio/training/git...

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Reposted by Samuel Lampa

Stephen Turner @stephenturner.us · 10/08/2026

I'm Hiring! I have a grant starting in September to set up a new AIxBio / #biosecurity program, and I'm hiring a postdoc in AI biosecurity evaluation and study design blog.stephenturner.us/p/im-hiring-...

blog.stephenturner.us

I'm Hiring: Postdoc in AI + Biosecurity

I have a grant starting in September to set up a new AIxBio / biosecurity program, and I'm hiring a postdoc in AI biosecurity evaluation and study design

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Samuel Lampa @smllmp.bsky.social · 10/08/2026

Submitting SciCommander to conda-forge ... 👀

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Reposted by Samuel Lampa

European Centre for Disease Prevention and Control @ecdc.europa.eu · 22/07/2026

Update of the Ebola virus disease outbreak in DRC & Uganda - 22 July --- DRC: On 21 July, DRC reported a total of 2 473 confirmed cases & 999 deaths. 50 new cases & 32 deaths were reported since the last update. --- EU/EEA: 1 confirmed case reported in France on 24 June. #PublicHealth #Ebola #IDsky

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Samuel Lampa @smllmp.bsky.social · 23/07/2026

Just re-uploaded the tarballs with binaries, as I realized the tarballs contained an old version 😣 ... so grab the new one if you already did download a tarball!

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Reposted by Samuel Lampa

Robert Aboukhalil @robert.bio · 22/07/2026

grep is a fantastic tool, but it doesn't really work on sequencing data: it breaks when the pattern is in the read name, and doesn't support paired-end FASTQs. Thanks to @nilshomer.com, we have a new interactive guide on using fqgrep to find patterns in FASTQ files: ➡️ sandbox.bio/tutorials/fq...

sandbox.bio

Interactive bioinformatics tutorials

Learn bioinformatics from your browser, no setup required. Everything runs in a sandbox, so you can experiment all you want.

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Samuel Lampa @smllmp.bsky.social · 22/07/2026

SciCommander is a tool that automatically detects files produced from any shell commands ran inside the sci shell or via the sci run command, capturing audit information, and allows creating HTML reports or reproducing shell scripts for any outputs. It thus lets you keep track of ad-hoc shell usage

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Samuel Lampa @smllmp.bsky.social · 22/07/2026

Just released SciCommander v0.6.0 w much improved usability: - Don't swallow tool output - Create shell script to reproduce any output - More compact workflow graph - Make tohtml cmd work from any dir depth - And more See example report 👇 github.com/samuell/scic... #reproducibility

Example report from SciCommander, showing executed commands and a graph of commands and files produced.

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Reposted by Samuel Lampa

Rob Edwards @linsalrob.bsky.social · 22/07/2026

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.

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Reposted by Samuel Lampa

Physalia-courses@ONLINE @physaliacourses.bsky.social · 21/07/2026

📣 Help us shape our 2027 courses! What topics and formats would you like to see? More 1–2 day courses, short webinars, or longer hands-on training? We’d love your feedback! 💡 📝 forms.gle/4s8tFxyympyA...

forms.gle

Physalia Courses — Help Us Shape Our 2027 Programme

We’re planning our 2027 course programme and would love your input! 🎓 Whether you’ve attended one of our courses before or are simply interested in future training, your feedback can help us understan...

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Reposted by Samuel Lampa

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 13/07/2026

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing www.biorxiv.org/content/10.64898/20…

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Samuel Lampa @smllmp.bsky.social · 13/07/2026

It's not that LLMs are not cool and all, but the speed at which we threw out determinism and repeatability amazes me! 😱

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Samuel Lampa @smllmp.bsky.social · 13/07/2026

The whole history of computing has been about using machines for what humans are not good at: Do things in a deterministic, repeatable way. Now all that is mostly out of the window?! 😳🤔

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Reposted by Samuel Lampa

Rob Patro @robp.bsky.social · 12/07/2026

Excited to be at #ISMB2026 this year and to be presenting the work @jermp.bsky.social and I have done on improving the SSHash data structure academic.oup.com/bioinformati.... Presentation is tomorrow, July 13 at 2:20 in the International Ballroom Center. Stop by if you're attending!

academic.oup.com

Optimizing sparse and skew hashing: faster k-mer dictionaries

AbstractMotivation. Representing a set of k-mers—strings of length k—in small space under fast lookup queries is a fundamental requirement for several appl

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Reposted by Samuel Lampa

Ragnar {Groot Koerkamp} @curiouscoding.nl · 10/07/2026

What's faster? Searching a full 3GB human genome using Sassy, or windows opening a start menu? . . . . [they're the same 😭]

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Reposted by Samuel Lampa

Rebecca Berrens @rberrens.bsky.social · 10/07/2026

Hi #TEsky, please remember that we have an amazing community in the TransposonsWorldWide slack channel (join.slack.com/t/transposon...), which I encourage you to join. Another great resource is tehub.org. Please share !

join.slack.com

Join TransposonsWorldwide on Slack

Slack is a new way to communicate with your team. It’s faster, better organized, and more secure than email.

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Samuel Lampa @smllmp.bsky.social · 10/07/2026

I wrote a thing about something I've been pondering upon for a few years already: AI progress should upgrade our view of the human brain - not devalue it livingsystems.substack.com/p/ai-progres...

livingsystems.substack.com

AI progress should upgrade our view of the human brain - not devalue it

How AI can deepen our understanding of the wonders and quirks of the human mind

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Samuel Lampa @smllmp.bsky.social · 09/07/2026

If in the AI era the learnability of a programming language doesn't matter anymore as LLMs are the ones writing it anyway - meaning that safety and reliability are the only important factors, why aren't people having their LLMs write #ADAlang instead of #rustlang? 🤔

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Josie Bryant @josiebryant.bsky.social · 08/07/2026

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

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