W. Maier, B. Batut, R. Backofen, Albert Ludwigs University of Freiburg
Service center: RNA Bioinformatics Center – RBC
Driving scientific knowledge forward to the community, high-quality training material, workshops, webinars, and hackathons are an important pillar for us to educate researchers demanding bioinformatics training. The Galaxy training network is functioning as a community effort and provides over 150 tutorials for data analysis of different scientific disciplines. Tutorials provided here cover e.g. the introduction to Galaxy, assembly of genomes, climate research, computational chemistry, ecology, epigenetics, genome annotation, imaging, metabolomics, metagenomics, proteomics, sequence analysis, statistics and machine learning, transcriptomics, variant analysis, and visualisation.
The RBC Freiburg and de.NBI-epi Freiburg have used all these training formats to support SARS-CoV-2 research. Dedicated training material and webinars for the analysis of the SARS-CoV-2 genome and the investigation of potential drug candidates have been developed already since February 2020 to make it more convenient for researchers to dive into data analysis by provisioning easy access of the corresponding data, tools, workflows, and related tutorials through Galaxy. The recently developed webinar series (start 30th April 2020) includes an introduction to Galaxy and the Galaxy workflows for SARS-CoV-2 data analysis, genomics/variant calling, cheminformatics for screening of the main protease, evolution of the virus, and to teach the global open infrastructures at work. During the #WeVsVirus Hackathon organised by the German government, the RBC offered compute resources, interactive environments (like Jupyter Notebooks and RStudio instances) and taught people about drug design and virtual screening techniques using the Galaxy training material. The Virtual BioHackathon has been used to integrate tools specifically for variation graphs into Galaxy and create Conda packages as well as BioContainers for the COVID-19 research community. The de.NBI cloud was used for the assembly of SARS-CoV-2 and to run Jupyter Notebooks. Moreover, an international team of researchers published all Galaxy related COVID-19 workflows into the preview version of the WorkflowHub.eu.
For further information visit: https://elixir-europe.org/events/webinar-galaxy-elixir-covid19, https://training.galaxyproject.org
To access the de.NBI cloud visit de.NBI Cloud https://www.denbi.de/cloud
Tutorial:
- https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/tutorial.html
- https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/tutorial.html
