Jonathan Z Simon · @jzsimon
238 followers · 377 posts · Server fediscience.org


Are any other NIH funded scientists out there having trouble with their NIH NCBI My Bibliography? Mine went crazy this past week, generating dozens of duplicates over and over again, forgetting about Public Access Compliance status, not retaining changes, etc.
(I might not have otherwise noticed it, except that NSF recently required biosketches only be submitted using NCBI SciENcv, which gets publications from NCBI My Bibliography, so it’s a bit of a nightmare.)

#NCBI #mybibliography

Last updated 1 year ago

Fabian van Beveren · @fabian
38 followers · 7 posts · Server ecoevo.social

Idea: make a script to search papers for accessions/links to , and check if the data is actually public.

#NCBI #opendata

Last updated 1 year ago

Rob Edwards · @linsalrob
312 followers · 90 posts · Server genomic.social

Super excited to see that serratus.io has consumed the , part of project STRIDES to put all data on AWS and GCP

#sra #NCBI

Last updated 1 year ago

Michael Rosenberg · @msrosenberg
58 followers · 91 posts · Server ecoevo.social

A few days ago I discovered that the My Bibliography section of My had suddenly duplicated almost all of my publications. Because the system is so poorly designed and buggy, it took me a few hours to delete the duplicates.

Today I discovered that all (?) of the duplicates have returned. Given that wants us to be using it to do things like declare access compliance, they need to get the system working properly.

Anyone have a clue what's going on here?

#NCBI #nih

Last updated 2 years ago

Dong-Ha Oh · @inspirace
194 followers · 114 posts · Server genomic.social

A bit more detailed on how to navigate genome alignments on CGV (and you can request to add alignments for any pairs of chromosome-level assemblies if they are on NCBI) (and they are not too far apart) (and with similar ploidy levels, for now) :)
youtu.be/_TA86Tu1N0c

#comparativegenomics #NCBI

Last updated 2 years ago

Pierre Lindenbaum · @yokofakun
905 followers · 1048 posts · Server genomic.social

is there a way to suggest a new link dbsnp ↔️ pubmed to the ?

#NCBI #variant #pubmed

Last updated 2 years ago

Marc Robinson-Rechavi · @marcrr
799 followers · 865 posts · Server ecoevo.social

I learned recently that while the and literature overwhelmingly use the term , it is an obsolete junior synonym to .
taxonomy uses Metazoa, consistent with the use in molecular fields ncbi.nlm.nih.gov/Taxonomy/Brow
but @gbif uses Animalia gbif.org/species/1, as does @Wikipedia en.wikipedia.org/wiki/Animal
As for , they don't seem to care for modern concerns about phylogeny and such animalbase.uni-goettingen.de/z

#evodevo #Phylogenomics #metazoa #animalia #zoology #NCBI #iczn

Last updated 2 years ago

I need to download genome sequences occasionally (often enough to be annoying, not often enough to be "good" at it) and it used be a real hassle. The fine folks at did a nice job at creating a new datasets portal (ncbi.nlm.nih.gov/datasets/) enabling commands like this to get whole genome datasets:

`datasets download genome accession GCF_000146045.2 --include genome --filename GCF_000146045.2.zip`

commands that they also helpfully provide on each page.

#NCBI

Last updated 2 years ago

António Domingues · @keyboardpipette
153 followers · 740 posts · Server genomic.social

Does anyone know if there is a up-to-date count of (human) RNAseq and / or microarray samples in / ?

My best estimate comes from which processed 750,000 but I wonder if there is more to process, or if that number is the most up-to.date.
genomebiology.biomedcentral.co

Alternatively, is there a way to query this?

cc' @benlangmead

#geo #sra #NCBI #recount3

Last updated 2 years ago

Dr Thomas Shanahan · @clifford0584
113 followers · 2102 posts · Server med-mastodon.com

RT @laing_simon@twitter.com

First-Attempt Intubation Success Among Emergency Medicine Trainees by Laryngoscopic Device and Training Year: A National Emergency Airway Registry Study - PubMed pubmed.ncbi.nlm.nih.gov/366699

🐦🔗: twitter.com/laing_simon/status

#NCBI

Last updated 2 years ago

Nicholas Bauer, PhD · @BioTurboNick
820 followers · 1273 posts · Server mstdn.science

PubMed keeps throwing 500 errors this morning.

#Science #biology #NCBI #pubmed

Last updated 2 years ago

Elliot Lefkowitz · @Elliot_Lefkowitz
32 followers · 8 posts · Server mstdn.science

@florian_krammer GISIAD is not a public repository. It requires individuals to agree to restrictive conditions to access data that limit use and prevent access by anyone who disagrees with their conditions. It is not open science. has none of those conditions for accessing sequence data. If someone wants to submit sequence data to GISAID, fine (we do). But please also submit your data to NCBI to ensure true open access by all.

#NCBI

Last updated 2 years ago

Hunter · @hunter
4 followers · 2 posts · Server genomic.social

I saw 's post about the scaling problem. What if we replaced the backend with an in memory database like ? This could reduce latency by avoiding Disk I/O and improve scalability through sharding/threading. Not sure how big the current dataset is/will be but offers EC2 instances with up to 24 TiB of RAM engineered specifically for low latency.

Is LMDB the bottleneck, or is the corpus of nt's just too large to search quickly? Would love to hear thoughts on this

#NCBI #BLAST #lmdb #Redis #aws

Last updated 2 years ago

Pierre Lindenbaum · @yokofakun
621 followers · 453 posts · Server genomic.social

" Update: Proximity Search Now Available in PubMed" nlm.nih.gov/pubs/techbull/nd22

To create a proximity search in PubMed, enter terms using the following format:

"search terms"[field:~N]

Search terms = Two or more words enclosed in double quotes.
Field = The search field tag for the [Title] or [Title/Abstract] fields.
N = The maximum number of words that may appear between your search terms.

#pubmed #NCBI #eutils

Last updated 2 years ago

Danstan Bagenda · @xolaniboy
1 followers · 1 posts · Server mastodon.world

🧵Combining & aligning the only available 2022 shared sequence with all sequences from I've this that indicates with the #2011 () "outbreak". Some thoughts:

#mubende #ebola #uvri #sudv #NCBI #computed #phylogenetic_tree #intriguing #similarity #still_perplexing #nakisamata #luwero

Last updated 2 years ago

Danstan Bagenda · @xolaniboy
5 followers · 9 posts · Server mastodon.world

🧵Combining & aligning the only available 2022 shared sequence with all sequences from I've this that indicates with the #2011 () "outbreak". Some thoughts:

#mubende #ebola #uvri #sudv #NCBI #computed #phylogenetic_tree #intriguing #similarity #still_perplexing #nakisamata #luwero

Last updated 2 years ago

Danstan Bagenda · @xolaniboy
1 followers · 1 posts · Server mastodon.world

🧵Combining & aligning the only available 2022 shared sequence with all sequences from I've this that indicates with the #2011 () "outbreak". Some thoughts:

#mubende #ebola #uvri #sudv #NCBI #computed #phylogenetic_tree #intriguing #similarity #still_perplexing #nakisamata #luwero

Last updated 2 years ago

Anthony Barente · @AnthonyBarente
33 followers · 8 posts · Server genomic.social

Does anybody know of any well characterized serine or threonine phosphomimetic (change to Asp or Glu) missense variants in ? I took a first pass to match against known phosphosites in humans but didn't come up with much.

#signaling #NCBI #genetics #ClinVar

Last updated 2 years ago

Peter Cock · @pjacock
200 followers · 148 posts · Server fediscience.org

Interesting, due to scaling problems are considering splitting up the massive NT nucleotide database into chunks like Eukaryotic, Prokaryotic, Virus, and synthetic/other ncbiinsights.ncbi.nlm.nih.gov/ - they invite feedback

#blast #NCBI #bigdata

Last updated 2 years ago