From @bmc.springernature.com Journal of #Biomedical #Semantics | FAIR in practice: minimum metadata schema for bioinformatics analytics by machines | #Bioinformatics #FAIR #Metadata #MachineActionability #OpenScience | 🧬🖥️🧪🔓🇳🇱 🇨🇭🇧🇪🇮🇹 ⬇️ link.springer.com/article/10.1...

FAIR in practice: minimum metadata schema for bioinformatics analytics by machines - Journal of Biomedical Semantics

Background One pillar of FAIR principles adoption is Reusability by machines to enable for example more efficient data analytics in fields such as Bioinformatics. However, it is not clear to what exte...

link.springer.com

Ok, I might have just fixed the last *really* annoying bug in SciCommander (or let's hope...) 🤔 github.com/samuell/scic...

Release 0.6.2 - Fix bug with unaligned prompt line in shell mode · samuell/scicommander

This is a bugfix release for #34 where the prompt line would get unaligned when re-using complex commands from history. Full Changelog: 0.6.1...0.6.2

github.com

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

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!

Samuel Lampa@smllmp.bsky.social · 2w ago

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

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...

Interactive bioinformatics tutorials

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

sandbox.bio

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

Samuel Lampa@smllmp.bsky.social · 2w ago

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

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

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

📣 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...

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...

forms.gle

At least 930 people have died in Congo's Ebola outbreak

At least 930 people have died in Congo's Ebola outbreak

Congo's health ministry said the deaths were recorded out of the 2,344 cases confirmed as of Saturday. Thirty-seven new deaths were recorded in the previous 24 hours in one of the highest totals.

npr.org

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing https://www.biorxiv.org/content/10.64898/2026.07.08.737305v1

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

Samuel Lampa@smllmp.bsky.social · 3w ago

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?! 😳🤔

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?! 😳🤔

Jake Gold@jacob.gold · 10mo ago

Hey AI, I want my determinism back!

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!

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

academic.oup.com

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

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 TransposonsWorldwide on Slack

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

join.slack.com

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...

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

livingsystems.substack.com

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? 🤔

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

I'm exploring the dev.to platform by cross-posting some technical posts there, starting with this small one: dev.to/sml/how-to-a...

How to align columnar output in the terminal

In bioinformatics we are handling a lot of tabular data. Be it VCF files, tabular Blast output, or...

dev.to

My deep thinking thought pieces are published at livingsystems.substack.com

Living Systems | Samuel Lampa | Substack

Observations and tidbits about systems and systems thinking, in technology, biology and beyond. Click to read Living Systems, by Samuel Lampa, a Substack publication. Launched 3 years ago.

livingsystems.substack.com

I am thrilled to share that UC Berkeley and UCSF have launched a joint initiative in Computational Biomedicine! cdss.berkeley.edu/news/uc-berk... We will soon be recruiting new faculty and postdoctoral fellows. Please repost to help spread the word.

UC Berkeley and UCSF Launch Computational Biomedicine Initiative

UC Berkeley and UCSF have launched a joint program called the Bakar Computational Biomedicine Initiative to develop the frontier of AI and biomedicine, tremendously accelerating advances in clinical c...

cdss.berkeley.edu

My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...

Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386

The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry

nature.com

Countries are passing laws that require you to prove you're an adult to use websites. This is technically onerous and a bad user experience for all, so why is it happening? imo Meta etc. want to construct a high barrier-to-entry for other would-be website/app makers, to damage smaller competitors.

Movi 2 has appeared (as an advance article) in Bioinformatics 🧬 Faster, leaner pangenome queries — half the memory of Movi 1, ~30% faster. Paper: academic.oup.com/bioinformati... Code: github.com/mohsenzakeri/Movi (1/6)

New week = New course Very happy to kick off the first edition of the course on Big Data Phylogeny and Comparative Methods with @martaalvarez.bsky.social & @meleonora-rossi.bsky.social www.physalia-courses.org/courses-work...

salmon 2.0 (the rust re-write) is now live! It's also the version you get if you install via bioconda. This is a from-scratch rewrite in rust, and the base for future development. I'll post a more detailed thread tomorrow, but you can read the docs here combine-lab.github.io/salmon/

A dense and very instructive resource on many recent k-mer algorithms and implementations, with algo/archi/data co-designs. I feel so lucky to work with Igor.

Igor Martayan@imartayan.bsky.social · 2mo ago

Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone

Just submitted my PhD thesis on algorithms for fast, large-scale k-mer-based sequence analysis. It's now available to read at phd.martayan.org Take a look and feel free to share! #Bioinformatics #PhDone

I'd gladly help!