Also, relating to the severe slowdown of my work on GMOD, I'm very happy to announce that I've (mostly) completed the migration of https://gmod.org/ from a (very aged) MediaWiki site running on an AWS EC2 machine to a GitHub.io hosted instance (repo at https://github.com/GMOD/gmod.github.io). It's not perfect, and in need up updating, but at least now it will be easy for other people to pick it up and make changes. (And, I won't be charged for keeping that machine running on my personal AWS account!)

That feels "final": my GitHub avatar has been the logo of the project I've run for the last 22 years. Today is the last day working on the project full time (I imagine there will still be things I can be talked into doing). Anyway, I changed the avatar to a nice, close up picture of a California poppy I took last year.

JBrowse v2.11.2 released, with a new feature to allow users to interactively add filters to features on genome browser tracks https://jbrowse.org/jb2/blog/2024/06/03/v2.11.2-release/

I have to migrate the contents of http://gmod.org/ away from an EC2 machine running Mediawiki to something else that is free, since soon I will no longer be able to get reimbursed for it. I was hoping to use https://github.com/outofcontrol/mediawiki-to-gfm to convert it to Github flavored markdown, but that is a long road since it doesn't seem to deal with templates, which we used *A LOT* on gmod.org. Does anybody have other suggestions for capturing all the information on the wiki and putting somewhere "useful"?

@abretaud @scottcain

figured out how to easily re-order it by @gmod component documented, so we can have sections specific to the individual tools which is more user-friendly I think for folks familiar with GMOD.

will likely merge this soon :) https://github.com/galaxyproject/training-material/pull/4750

-@hexylena

New GTN post: GTN ❤️ GMOD

https://training.galaxyproject.org/training-material/news/2024/02/29/new-gmod-topic.html

JBrowse v2.10.2 released, with a new feature to launch the breakpoint split view directly from raw reads https://jbrowse.org/jb2/blog/

I posted this question in the C. elegans slack, but I thought I'd ask here to a different (wider but probably sparser) audience: I went to a non-worm genomics conference this week and was struck by how much #GWAS data was being presented. I’m wondering if the same trend is occurring in your research, and if so, if researchers would be interested in our adding functionality to our #JBrowse2 instance that would allow users to view (while not uploading to anywhere) GWAS data ... 1/3

How flipping happy does it make me to hear about two students looking to learn about bioinformatics picked up @gmod tools (#tripal, #jbrowse) and put together a full blown genome database Bharat https://www.bharatgenomedatabase.org/

Exciting news from the Tripal folks (https://tripal.info):

I'm so excited to announce that Tripal v4.0.0-alpha2 is now released! This release represents a major update to Tripal v4. Most importantly, site developers can now begin exploration for how to upgrade their Tripal v3 sites to Tripal v4 because we now have support for publishing all content types and we have most fields for all Chado content. 1/2

Gearing up for the #JBrowse2 workshop at #PAG31. We'll be in Town and Country D (used to be called the California room) on Sunday, Jan 14, 1:30 PM to talk about JBrowse 2 and Apollo 3, and run a hands-on workshop on installing and configuring your own JBrowse 2 instance. I hope to see you there! https://plan.core-apps.com/pag_2024/event/0121205505a9f11e6727dfd2f4a4a067

New jbrowse 2 release, w/ new "directional feet" added to arcs when viewing "breakend" type structural variants in VCF https://jbrowse.org/jb2/blog/2024/01/09/v2.10.1-release/

New video on the JBrowse YouTube channel demonstrating an Apollo genome annotation workflow that uses RNAseq and synteny data https://www.youtube.com/watch?v=jYYLKd0I8NU

if you haven't seen it yet, we now have community meetings and office hours (where you can schedule 1-on-1 appointments with us!) more info here https://jbrowse.org/jb2/contact/

New JBrowse 2 community chats and office hours. Here's a blog post describing what we're doing:
https://jbrowse.org/jb2/blog/2023/11/03/office-hours/
#gmod #JBrowse2

I'm wondering if anybody has tried (considered even) #tabix indexing #PAF files. These files are used for #ComparativeGenomics, so you'd need two indexes, one on the reference and one on the query. Conceptually it makes sense to me but I've not seen it done anywhere.

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.

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 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