Since late 2017 the US CDC, the Bedford lab at Fred Hutch and the Bill & Melinda Gates Foundation conducted a landscape analysis of the use of pathogen genomics in public health. One central theme that has emerged from these discussions has been the growing need for open, accessible, interoperable and reproducible bioinformatics tools and infrastructure. Despite a range of open-source bioinformatics tools to support public health, the utility of these tools is limited by the technical challenges facing many health departments.
An expert working group meeting was convened at the Bill and Melinda Gates Foundation Offices in Seattle, USA to:
- Define and prioritize gaps, architectural and implementation challenges that will limit the feasibility of pathogen genomics in public health, using low- and middle-income countries (LMICs) as a test case.
- Propose consensus, high-level architecture for reproducible, deployable bioinformatics infrastructure
- Propose consensus on interoperability standards; common APIs and Data formats.
- Establish this effort as a community-driven project.
- Determine what model of governance and financial support would be necessary to sustain core development
