Samuel Lampa
@smllmp
Fascinated by Living Systems | Clin Micro Bioinfo @ Karolinska | PhD | Reproducibility, #SciWorkflows | Curious: Genomic Algos, TEs etc R&D: livesys.se Thinking: Married. Dad. Sinner saved by grace.
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
I've fought with lynx, w3m & other cryptic cli web readers to try'n keep a website in one of my tmux panes (for ref etc) & had not realized u can get any URL as text into less with its familiar vim bindings with just a bit of curl & pandoc! 🤯
First time I see some minor use of color coding the CIGAR string: Catching a pattern that is almost trivial though ... where one can see that reads that align diagonally (due to multiple shifted hits), don't get soft-clipped on the left end (no pink) - ofc cuz they're subseqs of longer seq in ref 🤔
Excited & mildly stressed that already 460 people signed up for next week's course on 16S @nanoporetech.com #metagenomics analysis via @ecdc.europa.eu. 😌 Anna, Elin, Sofia, @lilianderssonli.bsky.social & me hoping it will be a great experience for y'all! 🙏 learning.ecdc.europa.eu/course/view....
Look fwd to teach short course (June 1&5) on @nanoporetech.com-based 16S metagenomic sequencing for diagnostics via @ecdc.europa.eu:s #GenEpiBioTrain with @AnnaNoren, Elin Loo, Sofia Stamouli & @lilianderssonli.bsky.social Open to the public! #bioinformatics learning.ecdc.europa.eu/enrol/index....
Cool to see brother Jonathan's new terminal-based issue tracking tool, making the rounds on @hackernews (The world's probably most read developer forum, for those who don't know). Was at least #8 👍 Show HN: Epiq – Distributed Git based issue tracker TUI news.ycombinator.com/item?id=4815...
I guess every bioinformatician has done this at some point ... being mesmerized by repetitive sequences in the human genome 😅
A bit intrigued how useful the combination of a bit of coloring, formatting + a really fast terminal app (alacritty), can be for visually inspecting reads. This one had me realize these are all pretty much the same (contaminating) sequence 👇
Having fun learning #rustlang and making CIGAR strings a little easier to visually explore in my little experimental sequence exploration tool🧐
Well I see someone much more famous than me stated quite much the same very succinctly 😌
Just released 🚀 Epiq: Distributed Git-backed CLI native issue tracker TUI 💻 news.ycombinator.com/item?id=4794... (Very cool project by (much) younger brother Jonathan 😎)
Better workflow graph (more compact for long commands and paths by auto-folding), coming up in the next release of #scicommander ... #sciworkflows
📢 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. github.com/samuell/scic... #provenance #bioinformatics
The @scikit-learn.org docs are such a nice overview of the common types of learning in classical machine learning! A great visual overview and guide for newcomers. scikit-learn.org
Always nice when someone has not only cited you, but also actually read your paper 😊 Hat tip to the authors! 👍 doi.org/10.1016/j.co... #sciworkflows
"Pro tip": If you are in a restricted environment & need quick access to a linux terminal running locally in the browser for some #bioinformatics messing around - check the sandbox.bio terminal playground. Made a bitly link for for convenience: bit.ly/bioterminal
Having a blast at the #IMMEMXIV @escmid.bsky.social conference on microbial typing in Porto, Portugal. So much to learn as a newcomer in the field and so many knowledgeable people in the same place! #microsky
Yes, I am relieved to have finally finished the Coursera specialization in Genomic Data Science from Johns Hopkins Uni. Started this some 2.5 years ago and should have been finished *way* earlier. The problem? Got a job in the field before finishing it 😅 www.coursera.org/specializati...
I found I had a rage-written draft about why #Rstats is so confusing ... that actually had some good content in it, so I finished it up into a full blog post. Enjoy! 😊 livesys.se/posts/why-is...
📜New (and apparently first) post📜 1,5 years ago I pivoted into genomics from pharmaceutical bioinformatics. Pulling off such a pivot besides a full-time job is not easy though so I'm here sharing my experiences and recommendations for anyone else wanting to do the switch! livesys.se/posts/learni...