Is there a database of bioinformatics tools & databases?

Question

[LauferVA]

All - Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases.

I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class resources (tools and reference data), etc. etc. He wholeheartedly agreed. This made me worry, because if literally Sean Davis (figuratively speaking), agrees its difficult-to-unmanageable, what hope do I have?

Though five years has passed since this conversation, this feeling hasn't.

I thought I'd reach out to the BioStars community to ask, is there a curated database of bioinformatics tools? If not, we really ought to create one. What I am envisioning is all imputation algorithms, all GWAS association testing softwares, all aligners, etc. etc. for DNA, RNA, scRNA, ATAC, Chip, multi-omics, etc.

Take a look at this website: https://www.scrna-tools.org/. Currently, it lists 1139 tools for scRNA seq. What I'd like to see is this linked to each other seq type, along with databases of available info. as well...Right now good places to start include the NCBI, EBI, UCSC genome browser, etc., but there doesnt seem to me to be any comprehensive effort...

Does this exist in any form?

Running list so far:

scrna-tools.org
bio.tools
the annual NAR database issue
entrez
ebi
ensembl
???

[ariel]

IDK. But of you find some databases like that, we should make a database of them.

[Dunois]

It's a good idea, but I don't think it should become its own website or something. That'll just end up being one more website, and one more website that will probably get abandoned once the maintainer(s) lose(s) steam. Does Biostars have the ability to host a wiki?

Scope creep (or lack of scoping) will be a real issue here though.

Answer 1

[lieven.sterck]

check the elixir bio.tools website (and other elixir affiliated resources)

Answer 2

[Mensur Dlakic]

The first issue of the year in Nucleic Acids Research is always a database issue. Not all databases get a paper each year, so you would have to go back at least to 2015 to get a comprehensive list. I am listing the last three years below so you can see the naming pattern.

• https://academic.oup.com/nar/issue/49/D1
• https://academic.oup.com/nar/issue/48/D1
• https://academic.oup.com/nar/issue/47/D1

Mid-year they also publish a web server issue:

• https://academic.oup.com/nar/issue/49/W1
• https://academic.oup.com/nar/issue/48/W1
• https://academic.oup.com/nar/issue/47/W1

[LauferVA]

Thanks Mensur, I'll start a running list and add this. It's not complete of course by any means, but its still a very valuable resource.