ELIXIR organized last week (October 30th - November 03th, 2023) the BioHackathon Europe in Barcelona. Paul and Björn went there in person and represented the Galaxy Freiburg team. The event was a total blast: 5 days in a remote area to work, code, have fun, eat and discuss with the 150 other participants from all Europe (even Australia)!
Project 20: Genome annotation and other post-assembly workflows for the tree of life
In this project, we have assessed the performance of multiple Genome Annotation tools and workflows for various test organisms: Human chromosome 19 (HG38), Drosophila melanogaster, Sponge (Phakellia ventilabrum) Butterfly (Helleie helle), Shamrock (Trifolium dubium), Snail (Melampus), Coral (Pocillopora meandrina). We used tools like Braker3, Maker, Busco, Funannotate, Helixer, RepeatModeller, Eggnog, InterproScan and also included our annotations in a shareable JBrowse instance. During the workshop the need for RepeatExplorer emerged so we integrated it into Galaxy as well - thanks to Petr Novak and ELIXIR CZ and Thomas Harrop from the Australian Biocommaons. Check out the RepeatExplorer on Galaxy.
For more information, please check out our new blog post about general updates about the Galaxy Genome Annotation community https://galaxyproject.org/news/2023-10-30-gga-update and join us on Matrix.
Project 25: Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities
Paul was the co-lead for Project 25: Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities together with Nicola Soranzo and Johan Gustafsson. Bérénice participated online and was a great support. Matúš Kalaš helped with the connection to bio.tools and EDAM.
The project successfully implemented a pipeline that collects Galaxy tool wrappers, adds metadata from various sources, and filters the tools for a specific Galaxy community.
The generated tool list is then transformed into an interactive table, that can be embedded in e.g. hub pages and subdomains or here:
Crowd-sourced tool annotation
Furthermore, a crowd-sourced effort was made to improve the bio.tools annotation of the microGalaxy tool selection. Thanks to a dedicated and motivated group and the help of many people, especially the Australian outpost guided by Johan Gustafsson, the annotation effort was a great success with more then 50 tools annotated. We're currently writing a paper to summarize the results of this project. More information can be found in the GitHub Project Repository. A demo of the interactive table is hosted via the Github Pages for all the tools and for the microGalaxy community.
We discussed and contributed to many other projects:
- While we're at it, we also added an interactive table for the Image analysis community as described above.
- Project 6: BioModelsML: Building a FAIR and reproducible collection of machine learning models in life science and medicine for easy reuse
- Improvements to CWL support in Galaxy and other pull requests
- Table tennis double team champions (Björn and Nicola).
And we had an overall great time joining the sport events, escape game and amazing food !