A full software stack for epidemic disease management: Unlocking the joint potential of software technology and supercomputing

Abstract

Infectious diseases remain a major threat to human societies. During the recent COVID-19 pandemic, mathematical modeling and extensive computer simulations proved highly effective in supporting public health experts and decision makers. Despite these advances, the full potential of modern modeling approaches and digital technologies has not yet been realized. Many critical tasks -- including expert consultations, model execution, scenario analyses, report preparation, and result communication -- still relied heavily on manual, human-driven processes with each manual interaction introducing avoidable delays and limiting responsiveness during rapidly evolving outbreaks. Pandemic preparedness should opt for automated workflows and seamlessly integrated software modules that can improve pandemic mitigation capabilities by substantially reducing response times. For this step, we require robust and flexible computational infrastructure capable of supporting heterogeneous hardware and continuously evolving infectious-disease models. In addition, data sources need to be dynamically integrated. Managing such demands needs infrastructure that supports automated high-performance computing (HPC) workflows. Beyond computational performance, software infrastructure must ensure secure user and data management to comply with data-protection regulations and provide clear, transparent presentation of results to both decision makers and the public. Meeting the aforementioned challenges requires tight integration of state-of-the-art scientific software with modern, scalable infrastructure that can leverage supercomputing resources when necessary. For rapid deployment in future epidemic or pandemic scenarios, adherence to the FAIR principles for research software is critical to ensure reusability and sustainability.