Galaxy and its community
The Freiburg Galaxy team is highly involved in many projects of the Galaxy community:
- Galaxy core development and maintenance.
- Tool integration into Galaxy and their maintenance through:
- Galaxy Training Material, a collection of Galaxy-related tutorials and its infrastructure, developed and maintained by the community.
- Galaxy Docker, to provide an easy distributable full-fledged Galaxy installation.
- Development and maintenance of different Galaxy flavours:
- Jupyter integration into Galaxy.
- GalaxyP, a Galaxy community dedicated to develop tools, workflows and training material for proteomic research.
- Galaxy Genome Annotation (GGA), a group of projects focused on supporting genome annotation inside Galaxy.
Bioconda and BioContainers
Spending valuable time in compilation/installation hell should not be a problem nowadays. Therefore, the Freiburg Galaxy team is leading the Bioconda and BioContainers projects, which together form the best stack for reproducible science ever.
Bioconda is a channel for the conda package manager specializing in bioinformatics with around 8000 bioinformatics packages ready to use with
BioContainers is an open source and community-driven framework which provides system-agnostic executable environments for bioinformatics software, with more than 40000 containers ready to use.
HiCExplorer is a set of programs to process, normalize, analyze and visualize Hi-C data. It addresses the common tasks of Hi-C analysis from processing to visualization.
The Freiburg Galaxy team is involved in the maintenance and new development of HiCExplorer, and particularly, its integration into Galaxy: https://hicexplorer.usegalaxy.eu
de.NBI and ELIXIR
The Freiburg Galaxy team is part of de.NBI, the German Network for Bioinformatics Infrastructure, through the RNA Bioinformatics Center. Via de.NBI, the Freiburg Galaxy team is also involved in ELIXIR, as technical coordinator for the the German node.
As part of the Collaborative Research Centre 992 - Medical Epigenetics, we are helping researchers to analyse their epigenetic data. In this framework, we are developing and maintaining deepTools and HiCExplorer together with the group of Thomas Make from MPI-IE.
MIRACUM (Medical Informatics for Research and Care in University Medicine) – this is eight universities with eight university hospitals, two universities of applied sciences and one industrial partner spread over five German states – and we are one of them! :)
As part of the MTB (Molecular Tumor Board) use-case we are developing and maintaining together with Melanie Börries the EXOM-seq pipeline in Galaxy.
COST Action CA16212
Plants are vital to human life and health and are essential to mitigate the effects of climate change. In this COST Action for Impact of Nuclear Domains On Gene Expression and Plant Traits we are helping to connect the European plant community and foster FAIR data principles.