26/03/2020
The recent public health emergency arising from the COVID-19 outbreak has demonstrated the necessity for a rapid, collaborative and international response.
The development of fast and effective countermeasures relies on the global research community’s ability to share data and perform fast and reproducible analyses.
A joint paper by Galaxy teams from Australia, Europe and the United States demonstrated how the COVID-19 genome data can be shared, analysed and reproduced in an efficient and transparent way.
The study “No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics” re-analysed all COVID-19 genomic data available in the public domain using Galaxy platforms and open software tools.
The publication highlighted the inadequate accessibility of raw data associated with COVID-19 research and described how the work completed on Galaxy opened up the possibility for any researcher worldwide to perform their own analyses with the data, analysis pipelines and public computational infrastructure freely available.
The international Galaxy network provides highly accessible, globally shared data and analysis platforms, and offers the potential to transform the way biomedical research is done. By offering access to data and an open and reproducible analytics environment, it can ensure that progress is no longer hampered by access to samples and data.
The various Galaxy facilities provide community-based infrastructure for research in recognition of exactly what the paper’s authors found: “there is a global need to ensure access to free, open, and robust analytical approaches that can be used by anyone in the world to analyze, interpret, and share data.”
This recent work involved Galaxy Europe (operated by ELIXIR Germany), usegalaxy.be (operated by ELIXIR Belgium and the Flemish Supercomputer Center), Galaxy US and Galaxy Australia.
The Galaxy Australia team rapidly implemented the COVID-19 analysis workflows across Galaxy Australia’s distributed national compute infrastructure, operated by Melbourne Bioinformatics and QCIF.
Galaxy Australia is widely accessible through its deployment on the Australian Research Data Commons’ (ARDC) Nectar Research Cloud and receives funding from the Australian BioCommons.
All analyses performed by the Galaxy teams are fully documented and accessible at:
Accessible on Galaxy Australia at: https://usegalaxy.org.au/workflows/list_published; Tag: covid-19.
Full paper available here: No more business as usual: agile and effective responses to emerging pathogen threats require open data and open analytics Galaxy and HyPhy developments teams, Anton Nekrutenko, Sergei L Kosakovsky Pond, bioRxiv 2020.02.21.959973 doi: https://doi.org/10.1101/2020.02.21.959973
See also:
- UseGalaxy, SARS-CoV-2 / COVID-19, and how effective responses to emerging pathogen threats require open data and open analytics: Galaxy Project
- Coronavirus data analysis: Galaxy Europe
- Open collaborative infrastructure to tackle public health emergencies: ELIXIR Europe.
Galaxy Australia is hosted by the University of Melbourne and QCIF and is enabled by NCRIS via Australian BioCommons funding through Bioplatforms Australia and the Australian Research Data Commons (ARDC).
This article was first published on the Australian BioCommons website on 27 February 2020.