First paper from my student Daria Frolova's PhD now on biorxiv:
www.biorxiv.org/content/10.1...
The key question: plasmids change structurally ~as fast as they mutate, so how can we decide whether 2 plasmids are "the same plasmid" for epi purposes?
1/n

A 2024 Plea for Lean Software (with running code) - Bert Hubert's writings This post is dedicated to the memory of Niklaus Wirth, a computing pioneer who passed away January 1st. In 1995 he wrote an influential article called “A Plea for Lean Software”, and in what follo...

In 1995 computer pioneer Niklaus Wirth wrote "A Plea for Lean Software". Today it is normal to ship simple software as a 350MB package, or with 1600 dependencies. In appreciation of Wirth's legacy, I wrote a Plea for Lean Software, updated for today's computing horrors: berthub.eu/articles/pos...

Awesome!

Gute Besserung

Carp is everywhere, as the platypus.

I'm recruiting PhD students for Oct 24 start at University of Bath. Fully funded for UK students only. If interested in developing data structures/algorithms for bacterial genomics, or exploring plasmid epidemiology, or ML/AI on bacterial/phage geno/pheno data, give me a call!

👩‍🔬New **PostDoc** Opportunity!👨‍🔬

My new Epidemiology & Virus Evolution (EVE) group at SwissTPH is looking for a PostDoc in evolution & phylogenetics of respiratory viruses 🦠🌳

Interested? See here for more details & to apply!
jobs.swisstph.ch/Vacancies/92...

Please share!😁

Excited to share our preprint introducing MGX 2.0, which
adds metagenome (co-)assembly (including binning and bin assessment) as well as de novo metatranscriptome assembly.

Wow. Ok. Normally I feel like it's a bit overplayed to individually comment on #MDPI in the whole #AcademicChatter conversation, but this is really a must-see:

A Special Issue where the guest editors are lead or senior author on 27 of the 28 papers it published 🤯
www.mdpi.com/journal/proc...

Bar chart showing increase in throughput for nanopore flow cells if shielded from light during run. Most dramatic increase is on 10.4.1 minion flow cells with 488% increase in yield. Prom flow cells and flongles show much more modest increase at 11-34%.

Image showing new light shields that will be shipped with new flow cells.

Breaking news! Time to get the tinfoil out for existing flow cells...

So, 'responsible release' seems to be equal to 'no release' now...

As an unpaid anonymous peer reviewer who handles probably 30 manuscripts a year, I am absolutely not in the position of running and evaluating code any more than I am in the position of running gels to evaluate lab results. If this is important to you, I suspect you can find a consultant who will do it at a reasonable rate.

AITA, academic publishing edition.

Flashy for-profit journal sends a review back to me for further consideration because as reviewer I did not run the code and replicate the results.

My reply is below.

Am I the asshole?