Ian Sealy
@iansealy.com
Bioinformatician in buschlab.org at qmul.ac.uk. Previously citiid.cam.ac.uk, sanger.ac.uk and bbk.ac.uk. Product of ILRT, Bristol.
Reposted by Ian Sealy
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/
(See if you can make it show where the Danelaw is.)
conradgodfrey.com/grep_britain/
Grep Britain
conradgodfrey.com
December 15, 2025 at 10:57 AM
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/
(See if you can make it show where the Danelaw is.)
conradgodfrey.com/grep_britain/
Reposted by Ian Sealy
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...
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 An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 8, 2025 at 7:21 AM
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...
Reposted by Ian Sealy
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.
🧪🧬🧫
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.
🧪🧬🧫
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.
www.statnews.com
November 8, 2025 at 1:39 PM
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.
🧪🧬🧫
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.
🧪🧬🧫
Reposted by Ian Sealy
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
November 3, 2025 at 2:35 PM
Anyway, we need some joy, so here's the Egyptian foreign minister being given a Lego Pyramid by the Danish foreign minister.
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!
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!
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.
www.bbc.co.uk
August 17, 2025 at 1:07 PM
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!
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.
Ensembl have confirmed that the human gene name issue will be fixed in Ensembl 115. Yay!
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.
June 30, 2025 at 11:00 AM
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.
Reposted by Ian Sealy
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
studio--glasto-planner-g2nbd.us-central1.hosted.app
Glasto Planner
Plan your Glastonbury 2025 schedule
studio--glasto-planner-g2nbd.us-central1.hosted.app
June 27, 2025 at 3:52 PM
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
studio--glasto-planner-g2nbd.us-central1.hosted.app
Ensembl have confirmed that the human gene name issue will be fixed in Ensembl 115. Yay!
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.
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.
I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.
May 19, 2025 at 3:46 PM
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".
May 17, 2025 at 9:04 PM
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".
May 17, 2025 at 9:04 PM
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.
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.
I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.
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.
github.com
May 17, 2025 at 9:02 PM
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.
Reposted by Ian Sealy
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...
www.ncbi.nlm.nih.gov/datasets/gen...
Danio rerio genome assembly GRCz12tu
- Danio rerio
www.ncbi.nlm.nih.gov
April 8, 2025 at 9:44 PM
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...
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.
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.
April 10, 2025 at 7:26 AM
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.
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.
Reposted by Ian Sealy
RealityF1 returns for the 2025 season. The new season is now live and you can sign in and create your team at: realityf1.com
March 12, 2025 at 6:40 PM
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.)
TIL about the existence of OpenHistoricalMap, an open collaborative project where people can contribute features to a world map over history (currently from 1825 onwards).
March 4, 2025 at 10:41 PM
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.)
Reposted by Ian Sealy
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 🧬
Would highly recommend it to anyone looking at working with RNAseq data in the future 🧬
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
Want to join us in 2026? Take a look at our courses: www.ebi.ac.uk/training/liv...
🧪🧬🖥️ #GeneSky
March 4, 2025 at 9:45 AM
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 🧬
Would highly recommend it to anyone looking at working with RNAseq data in the future 🧬
Reposted by Ian Sealy
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
Want to join us in 2026? Take a look at our courses: www.ebi.ac.uk/training/liv...
🧪🧬🖥️ #GeneSky
March 4, 2025 at 9:36 AM
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
Want to join us in 2026? Take a look at our courses: www.ebi.ac.uk/training/liv...
🧪🧬🖥️ #GeneSky
Reposted by Ian Sealy
@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...
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...
Air, an extremely fast R formatter
We are thrilled to announce Air, a new R formatter.
www.tidyverse.org
February 21, 2025 at 3:10 PM
@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...
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...
It's worse than that:
www.mancity.com/news/club/ma...
www.mancity.com/news/club/ma...
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.
www.mancity.com
February 8, 2025 at 4:40 PM
It's worse than that:
www.mancity.com/news/club/ma...
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...
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.
I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.
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.
github.com
February 4, 2025 at 6:03 PM
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...
github.com/iansealy/ens...
January 21, 2025 at 10:48 PM
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...
github.com/iansealy/ens...
#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.
January 21, 2025 at 10:48 PM
#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.
But it's not just names. Many #zebrafish genes are no longer annotated to #ZFIN genes or to GO terms or to Reactome pathways.
January 21, 2025 at 10:46 PM
But it's not just names. Many #zebrafish genes are no longer annotated to #ZFIN genes or to GO terms or to Reactome pathways.
Many #zebrafish genes have changed name in recent releases, with more now having HGNC (human) names rather than #ZFIN ones.
January 21, 2025 at 10:44 PM
Many #zebrafish genes have changed name in recent releases, with more now having HGNC (human) names rather than #ZFIN ones.
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.
I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.
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.
github.com
January 21, 2025 at 10:41 PM
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.
I'll summarise here, but the TL;DR version is that we are just using Ensembl 109's annotation, including for enrichment analyses.