Investigate JBrowse v2

[kimrutherford]

V2 has a bunch of new features compared to v1 but I don't think there's a huge hurry to upgrade.

When we add v2 to PomBase, I think we should run v1 and v2 in parallel for a while to give the community time to get used to it. (And time for us to fix any problems)

There's a bunch of demo instances here: https://jbrowse.org/jb2/demos/

It's now published which is what reminded me to make an issue: https://link.springer.com/article/10.1186/s13059-023-02914-z

[kimrutherford]

I'm taking the JBrowse v2 paper on the flight with me. :-)

[ValWood]

What are the new features? Anything snazzy?

[ValWood]

Can include in upcoming paper, if time

[ValWood]

from
#1842
The inline JBrowse isn't always at the top when it's displayed on gene pages. We should check for the bug after the next update and report it if it's still there.

[kimrutherford]

"Setting Up the JBrowse 2 Genome Browser":
https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.1120

[kimrutherford]

I've been looking at getting JBrowse V2 set up as pombase.org/jbrowse2/. It's not there yet. :-)

My aim is to get the gene tracks up and running first and then work on the other tracks and features.

I initially wasn't sure that V2 supported embedding in gene pages, but there's a nice tutorial for it:
https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/01_introduction/

The tutorial also covers how to set up a default session. That will be helpful to us for users who are used to using JBrowse V1. Without a default session we'll see a page like this: https://jbrowse.org/code/jb2/v2.18.0/

It looks like FlyBase, SGD, XenBase and RGD are still using JBrowse V1 so we're not the only ones.
The Alliance is using V2: https://www.alliancegenome.org/jbrowse2/

[ValWood]

Fantastic!

[kimrutherford]

My aim is to get the gene tracks up and running first and then work on the other tracks and features.

First attempt:
https://desktop.kmr.nz/jbrowse2/?session=share-puR-5oWX0L&password=mfhN9
(I'm not sure that link will work)

[kimrutherford]

JBrowse 2 is now updated each night with the rest of the site: https://www.pombase.org/jbrowse2/

It only has a gene track for now. The next thing I'll do is split the track into forward and reverse strands.

[ValWood]

OK, looks great though!

[kimrutherford]

There are still a few bugs to fix.

I've fixed one of the problems: you can now type a gene name into the JBrowse 2 search box to go to that gene. It doesn't work for systematic IDs yet.

[kimrutherford]

Jobs to do:

• add links from feature in JBrowse to gene pages
• colour features by type - use different colours for at least:
  • protein coding genes
  • pseudo-genes
  • RNA genes
  • other (LTR, centromeres, low_complexity_region, ...)

[kimrutherford]

add links from feature in JBrowse to gene pages

That's done now. You need to click on the gene and then look in the details panel:

[kimrutherford]

colour features by type

That's done too:

[kimrutherford]

you can now type a gene name into the JBrowse 2 search box to go to that gene.

That's broken again. I'll fix it tomorrow.

[kimrutherford]

That's broken again. I'll fix it tomorrow.

I can't work out the problem so I'll report it as a bug.

[kimrutherford]

I can't work out the problem so I'll report it as a bug.

• 416 "Range Not Satisfiable" from text index for some search terms GMOD/trix-js#19

[kimrutherford]

I can't work out the problem so I'll report it as a bug.

I've implemented a work-around so the search box works now, even for "wtf22".

There are two more things I'd like to sort out:

• link directly to a chromosome position from gene pages
• default to showing chromosome 1 and the gene tracks

[kimrutherford]

The genes are now coloured by characterisation status (I hope!). I've made the RNA genes grey. Let me know if you see anything that's the wrong colour.

[ValWood]

That looks correct!

[kimrutherford]

There are two more things I'd like to sort out:

Any objections to me closing this issue and creating a new issue for the remaining JBrowse tasks/bugs?

[ValWood]

Not from me. It's just you talking to yourself and me occasionally saying "fantastic" ;)

[kimrutherford]

OK, moved to:

• Remaining JBrowse V2 issues #2327