I got up pretty early to watch the WormBase workshop at #worm23 (the international c. elegans meeting) but they aren't streaming any of the workshops 😢
I can at least post a link to a video of my section of the workshop, an intro to #jbrowse2 at #WormBase: https://youtu.be/8IBOotP48Dw

Are there #celegans #worm researchers on mastodon? I'm curious about whether I should spend development time creating a plugin for #jbrowse2 to search for DNA motifs that is similar to the search in JBrowse 1. It would be a non-trivial undertaking. #worm23

I've had a busy week writing. For people who are interested in C. elegans and use http://wormbase.org/, or are more general #JBrowse2 users, I've written several user-focused help documents at the WormBase blog: https://blog.wormbase.org/tags/jbrowse2/

Topics covered include:
*adding your own data
*working with synteny data
*working with lists, bookmarks and sessions
*searching for seqs and features
*getting sequence

Let me know if there are other topics that might be of interest.

@EpicBear @ianholmes Ooh, that is pretty! Nice use of color. Yes, I think #JBrowse2 has a lot to offer.

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

I am very happy to announce that the #JBrowse2 paper has be published in Genome Biology. There is lots of cool stuff in here: synenty, structural variation, plugins, multi chromosome and multi genome views, a graphical configuration editor, a desktop app, and easy-to-embed app.
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02914-z

The combination of #JBrowse2 and #AWS is pretty great: during a worm call today, somebody mentioned a genome related to elegans, so (during the call), I spun up an EC2 instance, did a minimap2 comparison between the two genomes, loaded the result in a local JB2 instance to check, then committed a config change to the stage branch, which got picked up by AWS Amplify, and 30 min into the call, I posted a link to the new comparison: https://staging.wormbase.org/tools/genome/jbrowse2/?session=share-mollwNOrzu&password=VSvit

To go along with the #JBrowse2 tutorial at #PAG30 a few weeks ago, we also have three talks by JBrowse folks:

@rbuels gave an intro to JBrowse: https://youtu.be/oxdhe_ZLGYs

Colin Diesh gave an overview of JBrowse 2 features: https://youtu.be/jl0BzcBhGqk

Caroline Bridge talked about the JBrowse 2 plugin architecture: https://youtu.be/hJmV97odZ1w

At #PAG30 earlier this month, we presented a hands on #JBrowse2 tutorial, where the attendees could log into a server, run through setting up a JBrowse 2 instance and added quite a lot of data, including #synteny and #structuralVariation. A video of that tutorial and accompanying updated tutorial to make it easier to do "on your own" are now available at YouTube: https://youtu.be/0MtYsAFEMXI and the tutorial page is at http://gmod.org/wiki/JBrowse2_Tutorial_PAG_2023

@jogoodma Yeah, #WormBase 's GBrowse is going away at the end of January as well. It's been a heck of a workhorse and can go out to pasture now. Time to move on to #JBrowse2 https://jbrowse.org/ !