Redeveloping the backend for critical COVID-19 response tools
We joined with researchers at the Nuffield Department of Health on building Global Pathogen Analysis System (GPAS) in order to provide critical tooling to response to the COVID-19 pandemic. Our role was to assist the team in turning Scalable Pathogen Pipeline Platform (SP3), an academic toolset, into industrial-grade software through migration of their database to Oracle and assisting in the development of a Flask web front end. This was then made available as a free resource to help combat COVID-19.
GPAS is already supporting the analysis of SARS-CoV-2 sequences in Canada, Chile, Vietnam, Australia, South Africa and Tanzania. It has the capacity to process 70,000-100,000 SARS-CoV-2 sequences/day, enabling us to monitor which variants (e.g. Alpha, Delta) are causing SARS-CoV-2 infection globally. We plan further rollout of GPAS to fight other major global disease-causing microbes, such as tuberculosis. These analyses can be used real-time to support national and international public health efforts.
More information about the project can be found in this published Oxford University news article.