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Published 20 hours ago • verified publisher icon peterjc

BLAST visualizations

Open peterjc opened this issue 10 years ago • 10 comments
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It would be great to offer some way of displaying BLAST output (ideally at least BLAST XML and tabular) using the Galaxy Visualizations framework (Goecks et al. 2013).

peterjc avatar May 07 '15 15:05 peterjc

See also the work from Gildas Le Corguillé presented at GCC2014:

  • https://wiki.galaxyproject.org/Events/GCC2014/Lightning#Private_BLAST:_Using_Galaxy
  • https://wiki.galaxyproject.org/Events/GCC2014/Lightning?action=AttachFile&do=view&target=LeCorguill%C3%A9BLAST.pdf
  • http://jh.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7f7d2565-9090-45fe-9baf-0c1309fe5a74

peterjc avatar May 07 '15 16:05 peterjc

@peterjc the biojs project is working on a BlAST Vis. ping @greenify

bgruening avatar May 07 '15 21:05 bgruening

Hey :)

I did work on this a couple of months ago as part of the crossb.io project.

Here's the current demo of the BLAST dashboard - however it is in a very early stage. It takes the BLAST XML as input. Let me know if you have ideas or specific requirements - I would be glad to help you guys ;-)

wilzbach avatar May 07 '15 22:05 wilzbach

Hi Seb,

I had a first docker image if this running at some point. Have you updated the code since then? Would you be interested in putting this into a VIS/IE? We need approximately a few hours together?

Cheers, Bjoern

bgruening avatar May 07 '15 22:05 bgruening

Hi Björn,

I had a first docker image if this running at some point. Have you updated the code since then?

Nope - I did some minor modifications on the end of March, but only to get it work nicely with npm.

Would you be interested in putting this into a VIS/IE?

Sure - should we keep it as it is or do you want to modify some parts? As it is a npm package, I could use biojs2galaxy again :)

We need approximately a few hours together?

Yes - I do have time :)

wilzbach avatar May 08 '15 13:05 wilzbach

With the amazing help from @greenify we got this working:

blast

@peterjc where do you want to me put this VIS? Here? IUC? galaxytools next to the protein VIS? Or do you expect a different kind of visualization?

bgruening avatar May 08 '15 22:05 bgruening

That looks very slick. I'm happy for it to join the galaxy_blast repository, but https://github.com/galaxyproject/tools-iuc would work too.

[Long term, we could end up forking peterjc/galaxy_blast to galaxyproject/galaxy_blast, or even merged into https://github.com/galaxyproject/tools-iuc for IUC administration?]

peterjc avatar May 11 '15 09:05 peterjc

Commenting on this as I've done work in a related direction...

screenshot from 2015-05-20 18 33 23

Not technically a viz plugin (it's a tool) though.

hexylena avatar May 21 '15 14:05 hexylena

Just to collect a few more: http://brig.sourceforge.net/ (is not maintained anymore, as it seems)

bgruening avatar Aug 04 '15 09:08 bgruening

I tried to use that and nearly wrapped it for Galaxy, but ended up deciding it wasn't all that useful. Happy to wrap if need be.

hexylena avatar Aug 04 '15 13:08 hexylena