Eli Roberson (he/him)Jul 15

#Genomics
#Genetics
#Academia

Huh. #Ensembl is acting really weird.

I go to Biomart. I choose Mouse for current build. I enter a list of a few (4? 5?) genes to limit the list to. I go to results to see four defaults (gene ids and transcript ids I think).

Instead of results, the next only contains the URL of the requested pasted as text into the body of the page. Odd.

Edit: Ah something about the page rendering made the Results button temporarily disappear. All fine now.

Show threadSIB Swiss BioinformaticsApr 16

💡 Join our tutorial to explore the new Ensembl platform and Ensembl VEP (Variant Effect Predictor). Gain hands-on experience with the updated interface and learn to analyse and annotate various genomic data.

👉 Register here: https://tinyurl.com/3y8ay2d6

🔹 Workshop organized by Jorge Batista da Rocha, Louisse Mirabueno and Aleena Mushtaq (EMBL-EBI)

@P_Palagi @valentynbez
#Genomics #Ensembl #bc2basel #BioinformaticsTraining

Registration

The [BC]2 Basel Computational Biology Conference is Switzerland's main event in the domain of Computational Biology and one of the major events of its kind in Europe. The conference unites scientists from academia, industry and healthcare.

Beth FlintJan 29

If you're interested in finding out more about the new Ensembl Genome Browser, there's a webinar today (29/01/25) @ 15:30 GMT

Click the link to register - https://www.ebi.ac.uk/training/events/introducing-new-ensembl-genome-browser/

#ensembl #genoneBrowser #genomics

Introducing the new Ensembl Genome Browser -

Introducing the new Ensembl Genome Browser -

Beth FlintJan 27

Happy birthday Ensembl!! 🎂

25 years of serving data! 🥳

#services #data #Ensembl #genomics

Luca VisentinJan 16
Can I bypass #biomart when asking for #ensembl genomic data? I use many Biomart calls to get a bunch of data but it's slow, and Biomart has been offline for a while now, so it might be time to update my approach.
Pierre LindenbaumJan 7

There is my email in my ${HOME}: /home/me@univ-nantes.fr/ . When using #ensembl VEP, the '@' is not escaped in VEP/Perl/BioPerl

https://github.com/Ensembl/ensembl-vep/issues/1824

VEP (+conda ?) fails when there is a '@' in the path. · Issue #1824 · Ensembl/ensembl-vep

Describe the issue Hi all, I'm not sure the current issue is a problem with the conda recipe, with VEP itself or something else. So feel free to close this issue if this is more a bioconda problem....

GitHub
Beth FlintDec 5, 2024

Ensembl 2025

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1071/7916352

#ensembl #genomics

Ensembl 2025

Abstract. Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic spe

OUP Academic
kupac^ESC:wqDec 4, 2024
Does any of you people of Mastodon have a clue why the rat genes are missing from Ensemble Biomart? Rat genome is part of the latest release. Asked the help desk but no response yet.
#ensembl #bioinformatics
Beth FlintNov 20, 2024

We have frozen the Ensembl Rapid site. Genomes which would have previously been released on Rapid will now only be released on our new site - https://beta.ensembl.org/

Rapid will remain accessible for the foreseeable future, but the data and species will no longer be updated.

This is a really exciting milestone for the beta project!

More info on the blog - https://www.ensembl.info/2024/11/14/we-will-be-freezing-ensembl-rapid-release/

#ensembl #genomics

Ensembl

The new website of the Ensembl project

Egon WillighagenAug 14, 2024
I found this morning that the @wikidata page of #Ensembl did not link many of their articles so added a bunch of 'main subject' links. Now its @wdscholia pages is a nice starting point to read up on the history, evolution, and content of this gene database: https://scholia.toolforge.org/topic/Q1344256
Scholia

Scholia