💡 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
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/
There is my email in my ${HOME}: /home/me@univ-nantes.fr/ . When using #ensembl VEP, the '@' is not escaped in VEP/Perl/BioPerl
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
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/
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
Downloading data from Ensembl: 140 kB/s using rsync/wget versus 20 MB/s using Globus.
Tricky decision.
More info here: https://asia.ensembl.org/info/data/ftp/index.html#:~:text=the%20command%20line.-,Globus,-For%20rapid%20bulk
@eric_normandeau #ensembl
(eg.: https://www.ensembl.org/Homo_sapiens/Location/Synteny?db=core;g=ENSG00000139618;r=13:32315086-32400268 )
If the genome is not in ensembl, then the assembly is probably not good enough to do any synteny analysis anyway, IMHO
Savez-vous si les données de plant.ensembl.org sont accessibles par une API #rest ? (quelle URL ?)
La doc ne mentionne que la version "animale".
#ensembl #bioinformatics #bioinfo
We hope that the comparative genomics analyses made available through this study will provide a route towards the application of genomics-informed conservation programmes across the great diversity of invertebrate species. A big thank to all the amazing people from the Darwin Tree of Life Project that made this reserch possible! #biodiversity #conservation #comparativegenomics #PacBio #DarwinTreeofLife #Ensembl #emblebi #sangerinstitute #wellcometrust
BioMart- of course we all know you can get #GeneOntology annotations with this great tool, but here's a fantastic #tweetorial about converting gene IDs!
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RT @ensembl
1/ Do you have a list of @ensembl IDs that you want to convert to IDs from other databases?
Here's how you can retrieve the @NCBI gene IDs from a list of #Ensembl IDs. A thread...🧵
#genomics #bioinformatics #tweetorial #Ensembltraining 🧬
https://twitter.com/ensembl/status/1646497467909767169
I did not realize that #Ensembl 's #mysql is built with MyISAM engines as the default.
Wondering if #Aria or #ColumnStore engines are a better choice when building with #MariaDB
The amount of #genomic data is just nuts. Just the #mysql dumps of the human and a few mouse genomes from #Ensembl are ~400GB compressed (have no idea what they uncompress to). Will definitely be experimenting with both ColumnStore #MariaDB (solid #Perl API) and #Spark (no nice api , but perhaps one can use pure #SQL to query stuff).
#BioinfoTools #bioinfotmatics #bigdata #genomics
