Olin Silander

Our paper on the evolution of gene regulation was published today bitly.ws/td4G. Years of hard work and hard thinking by @m_vlkova. I really like this paper. (1/8)

@baym wtaf. [deleting this reply in one hour in case my phone is ever inspected while returning to the US]

Yesterday, the NIH R35 “Outstanding Investigator” grant to fund scientists in my lab studying antibiotic resistance was terminated for reasons not related to the content of the science, or any actions taken by me or members of my lab

A High-quality Oxford Nanopore Assembly of the Hourglass Dolphin (Sagmatias cruciger) Genome dlvr.it/T7lfBf

@ppgardne Nice section header "Stop using highly curated datasets for training and testing"

the tools that underperformed in this benchmark are designed to solve a nonexistent problem in genomics: distinguishing error-free, curated coding sequences from shorter non-coding RNA sequences.

@cabbagesofdoom @rrwick @nanopore note that parsing the cigar string can't get you identity as 'M' means match or mismatch, I think the md tag would work. The .paf col division is way easier :)

@rrwick @nanopore Thanks! I am going to do some QV analysis in January (on holidays now!) and was thinking of parsing the cigar string but this sounds easier. Are you worried about lower quality sequences that don’t align so well getting missed and thus inflating the QV?

It hasn't been long since I last quantified @nanopore accuracy, but the release of Dorado v0.5.0 demanded another test: rrwick.github.io/2023/12/18/ont… Biggest improvement I've seen in a while! Most of these ONT-only bacterial genomes are now >Q60 😲

@skryazhi The Uni on the other side of the city

@osilander Where are you going to be @osilander after this?

yup done.

I'm in the very lucky position of having another option, but I have excellent colleagues who do not yet.

The disestablishment will disrupt or even destroy the trajectory of many people's careers. Not sure what else to say.

New blog post: rrwick.github.io/2023/11/06/acc… I took the ONT data from my last post, subsampled to various depths and assembled with Flye. Reveals what ONT-only accuracy looks like with a 'normal' read depth and Flye assembly (as opposed to extra-deep reads and Trycycler assembly).

@bellbirdsong_NZ @Jamienzherald

@MrsRieB Leigh Bardugo Grishaverse! Also I f he reads a lot he should be able to finish the eight or so Percy Jackson before the tv show starts in Dec. My 11yo has has read every PJ at least twice and has been waiting for two years for the tv series. Rick Riordan is great.

@CatharineAquino @FGCZ_EN Just overall impressive or were there specific bits/methods they were most impressed by? Interested in what people see as best practices at genomics facilities (or, cutting edge practices)

A team from a core in Belgium visited and toured @FGCZ_EN Genomics today. They said how we do things and our set up is impressive and inspiring . Thanks! I think I will be smiling about this for a week 😁. Super positive feedback from people in the same biz is the best!

Dorado v0.4.0 is live! - barcode demux & trimming - simplex read splitting - improved 6mA, 5mC/5hmC GpG models - new 5mC/5hmC all context model - increasing duplex pairing rates Plus a whole bunch more.. github.com/nanoporetech/d…

@matthewmatix @Jamienzherald 2022 sign in the elevator: ISC Innovation Science Complex

I asked Massey a) whether the Innovation Complex was partly designed/purposed for science programmes now facing cuts/disestablishment b) whether these formed part of its business case c) what happens to the complex once those programmes are cut/disestablished. It’s responded:

@TroyBaisden @REasther @gringene_bio @Jamienzherald It is the staff who occupy this building @masseyUni whom are being made redundant (Ecology, Molecular Bio, Chemistry, Food tech, etc). The space was purpose-built for them, opened in Feb this year. So many talented staff are being fired; terminating many postgrad projects.

CATASTROPHIC LOSSES TO NATURAL SCIENCES, FOOD TECH AND ENGINEERING AT @MasseyUni PROPOSED TODAY. 60% of staff to go across these areas. Shut down of these capabilities at Albany. Engineering cut altogether. Plant science also cut. Massey: taking the 'Universal' out of University.

@Psy_Fer_ The most confusing thing is why it helps MinION the most? Is t that the least exposed to light? As opposed to P2, gridion, and promethion, which have glass?

There are no error bars, no experiment details, and no workup of the chemistry/wavelength analysis, I'll treat this how I treat someone who pats the pokie machine before having a slap for now. While it's probably true, scientists expect a little more rigour...