I just thought it was BLAST, but you’re telling me NCBI, as in all of it, like genbank and refseq, all the stuff Datasets points to, is offline?! New methods section: “Fasta were retrieved from [redacted].” Monday is gonna be a trip. (Anyone done a wellness check on MassIVE yet?) - ThreadSky

benneely.com • 1 day ago

I just thought it was BLAST, but you’re telling me NCBI, as in all of it, like genbank and refseq, all the stuff Datasets points to, is offline?!

New methods section: “Fasta were retrieved from [redacted].”

Monday is gonna be a trip.

(Anyone done a wellness check on MassIVE yet?)

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dalessandrolab.bsky.social•1 day ago

And eRA commons. In case anybody was trying to submit a renewal by March 5th…

omicsolivier.bsky.social•1 day ago

And MassIVE works too...

benneely.com•1 day ago

It does seem like they’re working it out. FTP is back so it’s coming back. Think it just startled everyone and the ncbi as well. I’m sure there’s a great explanation that isn’t nefarious or tin foil hatty.

omicsolivier.bsky.social•1 day ago

All NIH-related pages work for me, including new queries (NCBI, ERACommons, Pubmed, BLAST)...

mcenkidu.bsky.social•1 day ago

I think it's just a technical problem? NCBI GEO and SRA were down but I just got in again a moment ago. Pubmed is coming and going.

benneely.com•1 day ago

I am going with @odedrechavi.bsky.social take, not that the sky is falling.

benneely.com•1 day ago

Maintenance, right? Right?!

matteomics.bsky.social•1 day ago

So EMBL and https://www.ebi.ac.uk/uniprot/index are still there! Maybe time to sample the European tools and data sets! Personally I find the uniprot website richer and better designed than NCBI.

benneely.com•1 day ago

If only UniProt had all the same species as RefSeq. I’ve never quantified the discrepancy, but comparing eukaryotic species with annotate genome assemblies v proteomes on RefSeq and UniProt, respectively, would be illuminating, much less which aren’t updated on the latter.

But I get your point.

matteomics.bsky.social•1 day ago

That is a good point. Personally never occured to me that NCBI and refseq could ever actually be at risk. Possibly the EBI should look at complete replication for the sake of redundancy.
Sad US researchers wanting to replicate work in future need to consider risk of US databases disappearing.

benneely.com•1 day ago

I haven’t confirmed it’s more than maintenance but it is maybe a good warning.

supercoiled.bsky.social•1 day ago

Taxonomy browser is up:
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

Found the Taxonomy ID for Ramazzottius varieornatus
(947166) which I'd never searched for before (so it wasn't in my cache).

llparker100.bsky.social•1 day ago

The doge AI data vacuum/crawler must take up a lot of bandwidth

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