Two weeks ago, members of Melbourne Bioinformatics (Andrew Lonie (Director Australian BioCommons) and Simon Gladman) contributed to an extraordinary open science effort to pull together all the current public genomic data on SARS-CoV-2, in demonstration of a collaborative, globally accessible, rapid, reproducible research response to this current public health crisis. It’s a wonderful example of the benefit of shared bioinformatics infrastructure for medical research.
The current state of much of the Wuhan pneumonia virus (COVID-19) research shows a regrettable lack of data sharing and considerable analytical obfuscation. This impedes global research cooperation, which is essential for tackling public health emergencies, and requires unimpeded access to data, analysis tools, and computational infrastructure. Here we show that community efforts in developing open analytical software tools over the past ten years, combined with national investments into scientific computational infrastructure, can overcome these deficiencies and provide an accessible platform for tackling global health emergencies in an open and transparent manner. Specifically, we use all COVID-19 genomic data available in the public domain so far to (1) underscore the importance of access to raw data and to (2) demonstrate that existing community efforts in curation and deployment of biomedical software can reliably support rapid, reproducible research during global health crises.
Their draft paper concludes:
“… anyone can use the open workflows described here to analyze the new data. In an age of digital connectedness, open, highly accessible, globally shared data and analysis platforms have the potential to transform the way biomedical research is done, opening the way to ‘global research markets’, where competition arises from deriving understanding rather than access to samples and data. Other disciplines have embraced the benefits of global data generation and sharing, astronomy and high energy physics being two highly successful examples. We have the opportunity to mirror their successes in infrastructure funding by demonstrating that biological research can embrace the same global perspective on common infrastructure investment and data sharing…”
This resource is also empowering our global Galaxy community (we’ve run workshops in Africa, SE Asia, EU, USA, AU) and our students who have trained with us on the Galaxy platform who can now get in and do their own research.
Galaxy Australia is hosted by the University of Melbourne and the Queensland Cyber Infrastructure Foundation and funded through NCRIS. It is one of the 4 global Galaxy platforms that participated in the project.