Virtual course by EMBL-EBI Training. Introduction to RNA-seq and functional interpretation. 9 - 13 February 2026. EMBL's European Bioinformatics Institute.

Thanks for joining us this week at 'Introduction to RNA-seq and functional interpretation' by EMBL-EBI Training! We had such a great time.

Wish you were here? Sign up for alerts on the 2027 edition of the course and be the first to hear as the course develops: www.ebi.ac.uk/training/eve...

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Wish we'd known about this tool from @conradgodfrey.com when we made our last episode of Map Men. Instantly visualise where place names are across Britain. Excellent stuff!

(See if you can make it show where the Danelaw is.)

conradgodfrey.com/grep_britain/

What Rosalind Franklin truly contributed to the discovery of DNA’s structure Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.

If I see one more stupid Rosalind Franklin take I'm going to lose my mind. Thank god for @matthewcobb.bsky.social and @nccomfort.bsky.social. www.nature.com/articles/d41...

James Watson, dead at 97, was a scientific legend and a pariah among his peers James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.

A Sharon Begley byline, almost 5 years after her death.

Upon hearing the news James Watson had died, a STAT reporter said in our Slack, "I wish I could read what Sharon would have written."

Incredible news: Sharon in fact did pre-write a Watson obit. And it is masterful and excoriating.
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Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.

Guernsey FC expelled from FA Cup after playing ineligible player Guernsey FC are expelled from the FA Cup after fielding an ineligible player in their 1-1 draw with Bedfont Sports.

Glad you added the vice versa, otherwise I'd have assumed you thought both teams were Bedfont!

We saw their previous FA Cup game, away to Guernsey. Was quite a fun 1-1 at the new fortress of Sarnian football, but ultimately pointless as Guernsey were expelled for fielding an ineligible player!

g:Profiler released a new version a couple of weeks ago that uses data from Ensembl 113, so I've updated a few of the plots. It doesn't actually change anything though and we still await Ensembl 115 eagerly! See github.com/iansealy/ens... for all the details.

For anyone who doesn't want to miss their favourite Glastonbury act on iPlayer, I made a quick-and-dirty Firebase app that allows you to select the acts you want to watch from the schedule then download them as an iCal file.

studio--glasto-planner-g2nbd.us-central1.hosted.app

Ensembl have confirmed that the human gene name issue will be fixed in Ensembl 115. Yay!

Similarly, zfin.org/ZDB-GENE-030... and www.ensembl.org/Danio_rerio/... are both about "titin, tandem duplicate 2", but ZFIN call the gene "ttn.2", whereas Ensembl again repeat the human name "TTN".

Despite having ZFIN IDs and ZFIN descriptions, thousands of genes have human names. For example, compare zfin.org/ZDB-GENE-030... and www.ensembl.org/Danio_rerio/.... Both have a description of "titin, tandem duplicate 1", but ZFIN correctly call the gene "ttn.1" and Ensembl call it "TTN".

I've updated this for the recently released Ensembl 114. Things are looking better - there are more genes than ever before annotated to ZFIN IDs, which is great. But there seems to be a major problem still.

GRCz12tu is available on Genbank. This will be one of two genomes that will be considered "reference" genomes, there will also be a GRCz12ab assembly coming. It has entered the NCBI annotation pipeline and will also go into the Ensembl annotation pipeline.
www.ncbi.nlm.nih.gov/datasets/gen...

Post a movie from the year you turned 18

I think I might have been the only person in the cinema who hadn't seen the trailer and didn't know there was a twist coming.

RealityF1 returns for the 2025 season. The new season is now live and you can sign in and create your team at: realityf1.com

Wish I'd known about www.openhistoricalmap.org when I was reading Jonn Elledge's "A History of the World in 47 Borders" recently. (Recommended.)

I had a great time on @ebi.embl.org ‘s RNAseq course last week.

Would highly recommend it to anyone looking at working with RNAseq data in the future 🧬

A group of around 35 people are on a zoom screen and smiling at the camera The text reads: EMBL-EBI course Introduction to RNA-seq and functional interpretation 24 - 28 February 2025, EMBL's European Bioinformatics Institute Virtual

A group of around 35 people are on a zoom screen and smiling at the camera The text reads: EMBL-EBI course Single-cell RNA-seq analysis with Python 17 - 21 February 2025, EMBL's European Bioinformatics Institute Virtual

It's been great to get our 2025 courses underway over the last few weeks! We've already run two virtual courses, with attendees learning more about #RNAseq and use of #Python for data analysis.

Want to join us in 2026? Take a look at our courses: www.ebi.ac.uk/training/liv...

🧪🧬🖥️ #GeneSky

Air, an extremely fast R formatter We are thrilled to announce Air, a new R formatter.

@lionelhenry.bsky.social and I are so excited to finally announce Air - an extremely fast R code formatter! 🎉

With Air, you'll never need to worry about styling your #rstats code ever again. All you need to do is save, and Air takes care of the rest.

www.tidyverse.org/blog/2025/02...

City launch club font for 2024/25 season, designed by Noel Gallagher Manchester music legend and lifelong City fan Noel Gallagher will be with Pep Guardiola’s team every step of the way next season.

It's worse than that:
www.mancity.com/news/club/ma...

Slight update to this, as g:Profiler have updated to use Ensembl 112 data. The advice stays the same though - we're using Ensembl 109 for #zebrafish analysis. See: github.com/iansealy/ens...

I contacted #Ensembl and they are talking to #ZFIN in order to improve things. We're hoping to see a big improvement in Ensembl 114. But for now, in our lab, we are using the Ensembl 109 annotation for #zebrafish. For more info see:

github.com/iansealy/ens...

g:Profiler results for Ensembl 109.

g:Profiler results for Ensembl 110. The terms are less specific than for 109.

g:Profiler results for Ensembl 111. There are only two terms.

#Ensembl 110 had the same issue when it was first released, which affected anyone who downloaded the data immediately. For example, g:Profiler results can vary by Ensembl release.

Graph showing the number of genes annotated with ZFIN IDs, GO terms and Reactome pathways for various Ensembl versions. All numbers decrease for Ensembl 112 and 113.

But it's not just names. Many #zebrafish genes are no longer annotated to #ZFIN genes or to GO terms or to Reactome pathways.

Graph showing number of genes with the same name as in Ensembl 108. The number drops dramatically for Ensembl 112 and 113.

Graph showing the source of gene names by Ensembl version. The number of ZFIN names goes down in Ensembl 112 and 113, but the number of HGNC names goes up.

Many #zebrafish genes have changed name in recent releases, with more now having HGNC (human) names rather than #ZFIN ones.

GitHub - iansealy/ens-zf-annotation-issue: Ensembl zebrafish annotation issues Ensembl zebrafish annotation issues. Contribute to iansealy/ens-zf-annotation-issue development by creating an account on GitHub.

Someone on Mastodon recently posted about issues they've seen with #zebrafish annotation in recent #Ensembl versions, so I wrote down some of what I've noticed.

I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.

The Disappearance of an Internet Domain How geopolitics can alter digital infrastructure

@ruthmichaelson.com Lovely to see you both today. By the way, this is the .io thing I mentioned as we were leaving: every.to/p/the-disapp...

I had no idea this even existed. There's more info at www.theguardian.com/culture/2018.... Plus en.m.wikipedia.org/wiki/English... lists other versions.

I'm doing the same thing! I started in March 2022 and am currently reading The Complete Case Files 17, which is somewhere around 1992 (roughly when, as a student, I stopped reading 2000 AD). I'm looking forward to Wagner's return!

Three ballots in a row now. Making a grand total of three for the season so far.