Sebastian Schmidt
@tsbschm.bsky.social
Lecturer in Microbiome & Health at @apcmicrobiomeirel.bsky.social & @ucc.bsky.social
Alumnus @borklab.bsky.social
Microbiome, microbial ecology & metagenomics.
Alumnus @borklab.bsky.social
Microbiome, microbial ecology & metagenomics.
The manuscript is in press, so… soon :-)
October 31, 2025 at 9:44 PM
The manuscript is in press, so… soon :-)
Together, these dbs allow one to address 'big' questions in microbial ecology & evolution with 'big' data, at unprecedented scales.
Give it a try, and feedback is always welcome!
Give it a try, and feedback is always welcome!
October 31, 2025 at 3:24 PM
Together, these dbs allow one to address 'big' questions in microbial ecology & evolution with 'big' data, at unprecedented scales.
Give it a try, and feedback is always welcome!
Give it a try, and feedback is always welcome!
Metalog contains manually curated contextual data (and much more) for >100k (!!) metagenomes. It is also integrated with several other resources, such as spire.embl.de which holds assemblies & MAGs (and much more) for the same data or vire.emble.de for viral genomes.
SPIRE
SPIRE holds data derived from ~100k metagenomic samples in 739 studies encompassing ~500Tbp of publicly available raw metagenomes. It holds five main data types: manually curated contextual data, including annotations against a custom microntology
spire.embl.de
October 31, 2025 at 3:24 PM
Metalog contains manually curated contextual data (and much more) for >100k (!!) metagenomes. It is also integrated with several other resources, such as spire.embl.de which holds assemblies & MAGs (and much more) for the same data or vire.emble.de for viral genomes.
Congratulations to @biocs.bsky.social and everyone involved @borklab.bsky.social ! See Michael's thread on the preprint for more details:
bsky.app/profile/bioc...
bsky.app/profile/bioc...
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
October 31, 2025 at 3:16 PM
Congratulations to @biocs.bsky.social and everyone involved @borklab.bsky.social ! See Michael's thread on the preprint for more details:
bsky.app/profile/bioc...
bsky.app/profile/bioc...
[while the inner monologue goes...]
October 28, 2025 at 3:28 PM
[while the inner monologue goes...]
That can be a very frustrating experience as well. I think one can read a paper at 'lightning speed' and still be critical, at least if it's roughly within-field. But I want to rely on editors and reviewers to have requested much of the critical revising and clarifying already.
October 28, 2025 at 2:43 PM
That can be a very frustrating experience as well. I think one can read a paper at 'lightning speed' and still be critical, at least if it's roughly within-field. But I want to rely on editors and reviewers to have requested much of the critical revising and clarifying already.
I agree.
But the problem lies (as always) also with peer review. I try to be a constructive and 'nice' reviewing peer in general, but often you get these hype papers where you feel the editor wants them no matter what and you have to 'prove' they're problematic, rather than the other way round.
But the problem lies (as always) also with peer review. I try to be a constructive and 'nice' reviewing peer in general, but often you get these hype papers where you feel the editor wants them no matter what and you have to 'prove' they're problematic, rather than the other way round.
October 28, 2025 at 2:40 PM
I agree.
But the problem lies (as always) also with peer review. I try to be a constructive and 'nice' reviewing peer in general, but often you get these hype papers where you feel the editor wants them no matter what and you have to 'prove' they're problematic, rather than the other way round.
But the problem lies (as always) also with peer review. I try to be a constructive and 'nice' reviewing peer in general, but often you get these hype papers where you feel the editor wants them no matter what and you have to 'prove' they're problematic, rather than the other way round.
We're on it though. Turns out uploading a lot of MAGs to INSDC databases isn't as easy as you'd think...
October 23, 2025 at 9:07 AM
We're on it though. Turns out uploading a lot of MAGs to INSDC databases isn't as easy as you'd think...
Reposted by Sebastian Schmidt
Psychologists everywhere frantically scribbling.
September 23, 2025 at 2:56 PM
Psychologists everywhere frantically scribbling.
Reposted by Sebastian Schmidt
I don’t think I’ve ever seen America so embarrassed in front of the entire world.
September 23, 2025 at 2:31 PM
I don’t think I’ve ever seen America so embarrassed in front of the entire world.
