Situation: I've come back from the Galaxy Community Conference with a lot of ideas!

Task: Discuss the following list of topics/ideas as a team and decide which may be worth pursuing. Then, create tickets for each topic/idea we decide to pursue.

1. Genome Resources: Confirm that we've looked into these resources for pulling genomes already - 1) EBI's Biodiversity Portal, 2) Genome Ark, and 3) the Vertebrate Genomes Project BioProject on NCBI.
2. Copy Number: I talked to a researcher who was working with calculating copy numbers. My understanding of this is limited but she said that she's been calculating copy number in an excel spreadsheet with a formula that uses variables that we already have in the browser (number of reads in a position, gene name, etc). Is there a way to view this in IGB already (i.e., Is this the same as the number in the Selection Info box in the top right when all of the reads at a locus are highlighted by clicking and dragging over them?) If not, sounds like we could look into this and add some functionality.
3. Speaking opportunity: I talked to a member of the ERGA (European Reference Genome Atlas) and he said I could give a talk later this year if we'd like. I would join their annotation committee and present about what IGB is and our quest to add more genomes/make it more accessible to more individuals.
4. Embedding IGB into Galaxy: Many people came up to me and said they would like to see IGB embedded into Galaxy such that they don't have to install anything first. That's why they tend to use UCSC and IGV in Galaxy more often! Here's documentation on how IGV went about doing this: https://github.com/igvteam/igv.js/
5. Viewing Hi-C Genomes: Someone suggested we should add a way to view Hi-C data in IGB! Click on the following link to see an example of how that might look in the browser: https://pygenometracks.readthedocs.io/en/latest/
6. Exporting IGB to Galaxy (and vice versa): Is there a way to drag and drop data from Galaxy into IGB? I also got some interest in implementing a way to easily export IGB to Galaxy (so clicking a button in IGB that would send the genome .fasta and any data tracks/files over to Galaxy for further data analyses).
7. Galaxy Training Network (GTN): I've been talking with the admin for Galaxy Australia and he'd think we would really benefit in terms of user engagement if we create a short training material for the GTN. Basically, since IGB isn't a tool in Galaxy, there's no way to search for it, and only certain file types can be used with IGB, Galaxy users are likely not finding IGB very easily. So, by creating training materials, at least when people search for IGB in Galaxy that material will come up with information about what kind of file types they can visualize in IGB and how to go about doing so.
8. New App Store idea: The same woman I connected with about adding Hi-C capability to IGB also creates a tool called BREW3R (https://github.com/lldelisle/BREW3R.r). Essentially, it uses publicly available data to identify where gene annotations are too short (e.g., those genes we can see in IGB where the coverage graphs extend just past the gene model) and then create a new version of those reference annotations with longer UTR's or new exons. I think this could be a great app to include in IGB so that researchers can visualize their data, see this phenomenon happening, update their reference genome in IGB with this tool, then view re-analyse their data and visualize it again!
9. Training opportunity: There's a global online training event for the Galaxy Training Network/Galaxy Training Academy. They're looking for trainers that want to teach a tutorial (such as the IGB one we might create) or contribute a new track if we don't have it done quite in time. This is 7-11 October 2024.
10. Conference opportunity: There's an online conference happening in November focused on all things genome sequencing for all types of biodiversity: https://www.biodiversitygenomicsconference.org/
11. Documentation check: Check that our documentation currently explains that a link from NCBI to a fasta file doesn't work in IGB – instead, users should try to use EBI or another resource where a direct link to the genome is provided. Someone approached me today saying they were having issues figuring this out and I've also run into this hitch myself.