UseGalaxy.eu Use Case: Genetics research on dairy cattle


Tomas Klingström has sent us the context of his research in the Swedish University of Agricultural Sciences. Thank you Tomas for sharing it with us!

In a world where climate zones are changing it is absolutely critical for agricultural scientists to collaborate across borders. Using the Usegalaxy.eu platform we have been able to train veterinarians and animal scientists to use state-of-the-art bioinformatics tools in different collaborations. In Sweden, we are working on an infrastructure for automatic data collection on dairy cattle farms (the Gigacow infrastructure) where we will use Galaxy to analyse raw genotype data from SNP chips and impute whole genomes for genetics research on dairy cattle. Data will be analysed on a local server set up with the help of the ELIXIR Galaxy project but methods and workflows will be shared with international partners in Europe, Eastern Africa and South Africa. During 2020, we also used the Training Infrastructure as a Service - Galaxy Europe for the training of veterinarians in the DEFEND 2020 project which is is an international partnership of academic, industrial and governmental organisations working together to tackle the emergence of African swine fever and lumpy skin disease in European livestock. Lumpy skin disease is an epizootic disease that has spread throughout Africa in the 20th century and is currently spreading throughout Asia while European veterinarians, so far, has been successful in stopping the spread of Lumpy Skin Disease in South-Eastern Europe. African Swine Fever has so far proven more challenging to stop with the virus being carried by wild boar populations from Russia, through Ukraine and into the European Union. In both cases, the utilisation of the Training Infrastructure as a service has enabled us to continue training within the projects to help communicate between veterinarians and researchers in the front line and the facilities used for experimental research and sequencing of samples collected in affected areas. This training would under Covid-19 have been impossible to carry out without the Training Infrastructure as a Service and we will submit the tutorials to the service as well to make training accessible for future research and as a way to document the methods and approaches taken in the project.

The availability of the Usegalaxy.eu server is also a fantastic way to test and collaborate on new workflows. Here at the Swedish University of Agricultural Sciences, we did a survey a few years ago where PhD students reported that they spent approximately twice as much time on data management and analysis as they would if provided with the training and tools best suited for their work. Access to Usegalaxy.eu allows us to train students much more efficiently and also test many workflows quickly which allows us to perform data analysis which we otherwise would not have had the time to perform. Using the servers we can also use engage in international training which means that we can better coordinate research efforts to enhance the comparability between projects which provides a valuable alignment in methodology between universities which would otherwise invest significant time and effort in developing data analysis pipelines with little comparability between them.