galaxyprojectOct 2

On Day 2 of European Galaxy Days, Anthony Bretaudeau presented 'Modern genome browsing in Galaxy with Jbrowse2'.
Read more: https://usegalaxy.eu/root?tool_id=jbrowse2

@abretaud @galaxyfreiburg
#genomics #jbrowse2 #EGD2025 #genome #galaxyproject #eosc #fair #genome_browsing #open_science

Show threadScott CainJan 17, 2024
2/3 along side any other data in #JBrowse2, either provided by the hosting site or loaded by the user. I have an example of what it would look like here: https://test.d2jjb0xowet5mr.amplifyapp.com/?session=share-wsg_ds7a0b&password=hZsD4 where you can see the manhattan plot for the whole genome, and if you zoom in on a peak, you’d see the Curated Genes track too. This example JBrowse isn’t ready for release yet
JBrowse

A fast and flexible genome browser

Scott CainJan 17, 2024
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
Scott CainJan 14, 2024
#JBrowse2 workshop about to start at #pag31 in town and country D. Get some updates and a hands on tutorial for setting up your own JBrowse 2!
Scott CainJan 11, 2024
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
Plant and Animal Genome 31

The Toot of GMODNov 6, 2023
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
Office hours and community meetings | JBrowse

This is a special announcement that we starting a new outreach effort for our

Scott CainJun 25, 2023
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
Introduction to JBrowse 2 at WormBase

YouTube
Scott CainJun 24, 2023
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
Scott CainJun 23, 2023

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.

WormBase : Nematode Information Resource

Show threadScott CainJun 7, 2023
@EpicBear @ianholmes Ooh, that is pretty! Nice use of color. Yes, I think #JBrowse2 has a lot to offer.