Next-next experiment might involve using adaptive sampling on the ONT platform. I'm curious, did anyone try adaptive sampling with older mid-GPU models, like 3060? Wondering if slower real-time basecalling on those cards will impact the output in someway.

I'm thinking @Psy_Fer_ might have the answer to this!

very exciting Google Summer of Code project idea around @wikipathways for a great student with a lot of enthusiasm and drive to learn a lot of new things and get things done! https://github.com/nrnb/GoogleSummerOfCode/issues/264

HealthDataScience Day 2025 is coming!

Mark your calendar for 6 November & join a free #conference on all things #HealthDataScience! Hosted by #UCPH #HeaDS, this event is packed with exciting #speakers & #activities!
We will share details bit by bit - there is too much exciting information about speakers and activities to share all at once!

6 Nov 2025
Reg opens 1 Apr
https://heads.ku.dk/calendar/2025/events/hdsd2025/

#lablife #science #bioinformatics The kids are ok

Creating #Python tools for biological sequence analysis? #EuroSciPy2025 is seeking proposals on genomic data parsing, phylogenetics, and structural #bioinformatics.

Show us how you're decoding life's data! #ComputationalBiology

CfP: https://pretalx.com/euroscipy-2025/cfp

We are happy to invite interested parties to the second talk in our new cycle of hybrid #Bioinformatics Seminar hosted jointly by #CEITEC and Faculty of Informatics at the Masaryk University Brno, Czech Republic.

Our online guest today will be Andrea Guarracino from University of Tennessee to talk about his work on #pangenomes

The webinar starts today (Mar 19) at 4PM via an MS Teams link (click the title) available at:

https://bioinf.pages.fi.muni.cz/posts/iv106/

See you there! #genomics #genome

Pipeline release! nf-core/genomeassembler v1.0.1 - 1.0.1 - Aluminium Pigeon!

Please see the changelog: https://github.com/nf-core/genomeassembler/releases/tag/1.0.1

Pipeline release! nf-core/scnanoseq v1.1.0 - nf-core/scnanoseq v1.1.0 - Iron Alligator!

Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.1.0

TALKING HeaDS - March 2025

Join us for an afternoon of #healthdatascience, #drinks, and #networking!

Talk by Cedric Notredame on pumping structural data into protein phylogeny using the Nextflow pipeline language.

25 Mar, 15:00–17:00
Panum, University of Copenhagen
RSVP: https://heads.ku.dk/calendar/2025/talking-heads/talking-heads-mar2025/

A question while writing up a study proposal:

What are characters of a good prokaryotic gene alignment?

The way I learned it from no-one is a good alignment gives well-scoring inferred tree later, but that feels a bit iffy and takes too long to confirm. Any great articles/insights on this would be appreciated!

Is there a linux command-line tool to copy files while specifying the source and *target path of each file*?

'rsync' can read an input list of files, but has no way of specifying individual target paths.

I am thinking of using the '--transform' option of `tar` and do a tar - untar pipe, but it would only work for short substitution scripts and when you can figure out the target given the source path only.

Using #Python to unlock the secrets of life? Whether it’s #bioinformatics, genomic technologies, or protein folding prediction, we want to hear from you! Submit your proposal to EuroSciPy 2025.
https://pretalx.com/euroscipy-2025/cfp
#EuroSciPy

I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.

Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.

We're also covering both #ONT and #PacBio for each species - so 2x the count.

I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.

What's better: VS code or JupyterLab?

#rstats Bioconductor conference is with Galaxy #bioinformatics. There is still some time for early registration (and abstract submission). https://gbcc2025.bioconductor.org/

Submit your abstract about #OpenSource #Bioinformatics to #BOSC2025! Deadline is April 17 (sorry, no extensions). More info: https://www.open-bio.org/events/bosc-2025/

As I face the prospect of analyzing a dataset with 3 variables: time (3 time points), temperature (2), exposure to chemical (2); but only 2 biological replicates, please, people, consult a biostatistician before doing your experiments.

Please, please, please, talk to someone in data analysis *before* running these kinds of experiments. If there isn't enough money for *more samples*, drop one of the factors so there are more "N" for the remaining ones.