Periodic Reporting for period 1 - PerMedCoE (HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE)
Reporting period: 2020-10-01 to 2022-03-31
The goal of the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance. It will accomplish so by 1) optimising four core applications for cell-level simulations to the new pre-exascale platforms; 2) integrating PerMed into the new European HPC/Exascale ecosystem, by offering access to HPC/Exascale-adapted and optimised software; 3) running a comprehensive set of PerMed use cases; & 4) building the basis for the sustainability of the PerMedCoE by coordinating PerMed and HPC communities, and reaching out to industrial and academic end-users, with use cases, training, expertise, and best practices. The combination of simulations and HPC computing are expected to have a great impact on society, health and business. The European healthcare systems are under great economic and social pressure, demanding better, faster and cheaper solutions. Cell-based simulations can contribute to speeding up the process of identifying diagnostic and finding patient-tailored treatments, fulfilling the promise of PerMed to save precious time and money for the healthcare systems and, more importantly, patient suffering.
The technical tasks completed in PerMedCoE to date have allowed us not only to implement distributed computing in all the core tools but also to add new functionalities that will be of great interest to both current and future user communities. In addition, the Building Block concept has been developed, which provides a software interface to encapsulate the core tools and other auxiliary tools for the development of workflows aimed at solving real biological problems. Precisely, this work has helped to define the preliminary workflows for implementing use cases UC2 (Drug synergies in cancer treatment) and UC5 (Modelling infection in COVID-19). These developments have been published through the official dissemination channels in PerMedCoE and used to carry out initial training activities
The improved scalability of the core tools has enabled the design of workflows capable of defining and solving very complex biological use cases. In this context, the resources needed to realistically simulate future use cases, including tissues and organs, are expected to grow exponentially, especially in the field of personalised medicine, where a specific number of simulations will be required for each patient available in a given study cohort. At the end of the project, we aim to provide the Personalised Medicine research community with a set of ready-to-use computational workflows leveraging core tools into pre-exascale HPC environments to design real use cases at an unprecedented scale.