bio.tools COVID-19 tools list

[hansioan]

This issue is a placeholder for a discussion related to the bio.tools COVID-19 related tools list.

There is a COVID-19 related subdomain in bio.tools at: https://covid-19.bio.tools

Everyone is encouraged to populate the tools list at the bio.tools subdomain above. In order to populate the subdomain you can:

• post a link to a bio.tools entry in this thread as a comment
• Tag tools in bio.tools with the COVID-19 collection
• Email registry-support@elixirmail.cbs.dtu.dk with tool recommendations (less recommended, only if you don't have a bio.tools or GitHub account)
• Post a link to a tool not in bio.tools (less recommended, might take a long time until the tool actually gets into bio.tools)

If you post a tool here or tag tools with the COVID-19 collection, I (and other willing folks) will update the https://covid-19.bio.tools subdomain as soon as possible. In the meantime the tagged tools will show up at: https://bio.tools/t?collectionID="COVID-19"&sort=score or more generally at: https://bio.tools/t?q="covid-19"&sort=score https://bio.tools/t?q="covid"&sort=score

Please only post or add tools that are of real relevance to COVID-19! What is of real relevance is open to discussion and we should have that discussion, but let's not spam this thread with arguments on what is relevant. Let's use #506 for this discussion.

Please feel free to tag anyone who would like to join the discussion.

@bio-tools/core-dev @albangaignard @bgruening @joncison @frederikcoppens @mr-c @veitveit @magnuspalmblad @MigleSur @hhbj @hmenager @khillion @OlegZharkov @ValentinMarcon @matuskalas @inkuzmin @egonw @piotrgithub1 @annalenalamprecht @jvanheld @krab1k @smoe @ahtosalumets @thomasrosnet

[DrYak]

Hello, we have now released a SARS-CoV-2 version of V-pipe. I has tagget the bio.tools entry.

(But for some reason, it doesn't show up on the COVID-19 list. Did I do something wrong ?)

[hansioan]

@DrYak You didn't do anything wrong, it just takes some time until the list gets updated.

[dfornika]

I've registered the ARTIC tool (https://bio.tools/artic) that is used for the ARTICnetwork nCoV-2019 bioinformatics SOP

[hansioan]

Hi @dfornika

I added the COVID-19 collection to https://bio.tools/artic and added the tool to the COVID-19 domain https://covid-19.bio.tools/

[kvechera]

A lab software for optimizing mass testing with samples pooling method. It helps to plan, execute, and analyze the data from assays. The method is applicable for PCR for SARS-CoV-2 RNA or other qualitative methods allowing mixing of samples in a single assay.

https://lomt.jetware.org

[hansioan]

@bio-tools/core-dev I simplified the way tools can be tagged as COVID-19 in bio.tools, it's basically just one click to tag a tool now. The one click just adds the collection of COVID-19 to a tool annotation. To help find these COVID-19 tools perhaps we can tag tools with more than just the COVID-19 collection, there could be others (sort of synonyms) like:

• SARS-CoV-2
• Coronavirus
• Other? What others can we use? @matuskalas you had some ideas at the Tools workshop, could you elaborate here? Thanks

[matuskalas]

To help find these COVID-19 tools perhaps we can tag tools with more than just the COVID-19 collection, there could be others (sort of synonyms) like:

SARS-CoV-2
Coronavirus
Other? What others can we use?
@matuskalas you had some ideas at the Tools workshop, could you elaborate here?
Thanks

It would be super-awesome to allow alternative names (like synonyms) for collections and tools. At least for collections, it would be extremely useful!

[hansioan]

What I had in mind was, when a user tags a tool as COVID-19 is to add a bunch of collection names like COVID-19, Coronavirus, SARS-CoV-2. I guess these can act as synonyms for each other. This is mostly to help with searching. I think collections is the way to go, don't know about alternative tool names, unless there is a case to be made that these can actually help with any tool.

My question was also about the values of these synonyms, are there others we can use?

[ahmedaq]

Hi @hansioan

I have registered the COVIDep tool (https://bio.tools/covidep). Please add it to the COVID-19 domain.

Thanks, Ahmed

[hansioan]

@ahmedaq Done, thanks, Hans