Mastodawn

⚠️Important bugfix release, 0.5.1 of SciCommander (tool to track shell commands in a reproducible way), fixing the scanning of output files and audit files in subdirectories!
https://github.com/samuell/scicommander/releases/tag/0.5.1

Release 0.5.1: Fix handling of outputs in sub-folders · samuell/scicommander

This is a bugfix release that fixes #21 and makes sure that output paths in subfolders of the main directory are correctly handled. Thanks to @GuilloteauQ for reporting it! Changes Fixes #21 Adds ...

GitHub

Samuel Lampa Nov 7

Samuel Lampa Nov 6

📢 Just released 0.5.0 of SciCommander, a tool to automatically track provenance information about shell commands, into HTML reports with the full provenance graph for every output. This version brings much improved usability and better looks. https://github.com/samuell/scicommander #provenance #bioinformatics

Samuel Lampa Nov 6

Samuel Lampa Sep 19

Registered too late for a poster for @ESCMID #IMMEM #IMMEMXIV but happy to discuss SciCommander with anyone interested 😊 See: https://livesys.se/posts/rewrite-of-scicommander-in-go/

Captures provenance of ad-hoc commands while skipping already computed steps - "The benefits of a pipeline tool without the pipeline tool".

End goal is to integrate provenance tracking across pipeline tools and the inevitable ad-hoc analyses done on the results of the pipeline runs.

Samuel Lampa Sep 19

ESCMID Sep 19

We are on to day 3 of the #IMMEM conference in Porto after some great talks and the first poster session featuring the research that's being done by our community! Today we'll be covering environmental surveillance for #ID and #AMR and how best to share pathogen data. #IDsky #clinmicro

Samuel Lampa Sep 19

Nabil-Fareed Alikhan Sep 19

Come see my poster at #IMMEM XIV Poster 151.

🔬 QualiBact – provides robust, data-driven QC thresholds for 304 bacterial species, built from >2.4M assemblies (AllTheBacteria + RefSeq).
⚙️ SpecCheck – an open-source command-line tool that applies these standards using existing outputs (QUAST, CheckM, ARIBA, Sylph) to generate clean, reproducible QC reports.

https://happykhan.github.io/qualibact/species/

https://github.com/happykhan/speccheck

Samuel Lampa Dec 20, 2024

#YIL (Yesterday I learned) this #bioinformatics newbie gotcha: In original CIGAR strings, still widely used, 'M' denotes both matches and mismatches, while in a newer version, mismatches are separated into 'X'es 😳

Samuel Lampa Dec 18, 2024

I wrote a thing:
To do your best work you need to work like a sculptor
(How total focus, immersion and immediate feedback lets you create optimally)
https://open.substack.com/pub/livingsystems/p/to-do-your-best-work-you-need-to

To do your best work you need to work like a sculptor

How total focus, immersion and immediate feedback lets you create optimally

Living Systems

Samuel Lampa Dec 17, 2024

Ask HN: How do you use AI/LLMs to accelerate your own learning?
https://news.ycombinator.com/item?id=42439552

Ask HN: How do you use AI/LLMs to accelerate your own learning? | Hacker News

Samuel Lampa Dec 10, 2024

🧬 Are you a #bioinformatician with some Swedish skills & interest in #microbiology looking for a job in #genomics ? 🦠

Come work with Sofia, Lili, me & co at Clinical #Microbiology at Karolinska Uni Hospital in Stockholm!

Flexible role and great people!
https://regionstockholm.varbi.com/what:job/jobID:779571/

Bioinformatiker till Klinisk Mikrobiologi

Vill du vara med och utveckla framtidens bioinformatiska verktyg för genomisk mikrobiologisk diagnostik? Har du erfarenhet av bioinformatik, programmering och ett intresse för forskning och samarbet

GitHub	https://github.com/samuell
Biostars	https://www.biostars.org/u/1296
ORCID	https://orcid.org/0000-0001-6740-9212
Twitter	https://twitter.com/smllmp