SC22 Proceedings

The International Conference for High Performance Computing, Networking, Storage, and Analysis

Birds of a Feather Archive

After Covid-19: Building a Public Health Genomics HPC Community for the Future

Authors: Thomas Connor (Cardiff University, Wales; Public Health Wales)

Abstract: The Covid-19 pandemic has shone a light on the increasing importance of HPC in public health, particularly with respect to the genomics of key pathogens. This BoF aims to help to provide a starting point to build a new network of those from academic institutions, healthcare organizations, public health agencies, and industry who are responsible for the emerging HPC infrastructures that will be increasingly important in the delivery of Public Health. The BoF will be a forum to share experience and best practice, with the aim of creating a new network of professionals to work together for global benefit.

Long Description: The COVID-19 pandemic has seen the application of computational approaches to aggregate data from across healthcare systems and analyse this information in real-time to inform the pandemic response. The identification and characterisation of SARS-CoV-2 variants is underpinned by the application of high performance computing to analyse the fundamental blueprint of SARS-CoV-2 – its genome - taken from patients.

The pandemic has demonstrated the enormous utility of clinical pathogen genomics, and has also demonstrated that large scale sequencing of pathogen samples can be viably operated as a service within public health agencies around the world. The pandemic has also proven how important it is that systems that analyse data also have mechanisms to enable sharing of data for global benefit.

To analyse and use clinical pathogen genomics data, one requires significant computational infrastructure. In response to the pandemic, new systems have been built around the world to enable pathogen genomic data to be used to inform the pandemic response in real time.

Now, as the world begins to emerge from the pandemic, there is a need to take stock of what the global health community has built, to learn lessons, and derive a legacy from the COVID-19 pandemic that will have the potential to change how global public health is delivered.

Processing pathogen genomic data in real-time is a high performance workload, integrating different data from across organisations, and working out how to share data rapidly and safely across healthcare systems and globally is a data science, data security and data governance challenge. It depends on a core of staff - bioinformaticians and computing professionals - who are often not viewed in the same way as healthcare professionals in public health organisations.

While there are already great links between public health professionals through global organisations such as WHO, the same cannot be said of the links between those who build and operate the software and infrastructure upon which the public health agencies rely.

This meeting is intended to begin to build a new network of those from academic institutions, healthcare organisations, public health agencies and industry, to share best practice and lessons learnt, and begin to work on ways to better work together for global benefit. Instead of building this network in forums that are focused on the healthcare domain, Supercomputing offers an opportunity to link up staff whose natural domain is in the computational space.

This will be the first of what will hopefully become a series of meetings designed to build the international network of computing professionals interested in public health. The meeting will include an opportunity for attendees to introduce the systems that have been built within their institutions, share best practice and identify opportunities for collaboration and data sharing.

We plan to develop the meeting in partnership with the Public Health Alliance for Genomic Epidemiology, to reach interested parties internationally and build momentum from the initial meeting, with the aim of establishing a series of meetings to support global co-operation and collaboration in this area.


Back to Birds of a Feather Archive Listing