PerMedCoE: Exascale-ready cell-level simulations

Coordinated by the Barcelona Supercomputing Center (BSC) and funded by the European Commission, this recently launched HPC centre of excellence will optimise codes for cell-level simulations in HPC/Exascale and bridge the gap between organ and molecular simulations, thus contributing to the European Personalised Medicine Roadmap.

Example of the framework that enables multiscale simulations

Example of the framework that enables multiscale simulations. PerMedCoE will allow the scaling-up of multiscale simulations that combine Boolean models that capture intracellular behaviours and agent-based models that study population dynamics. Image by Miguel Ponce de León (PerMedCoE)


The next generation of Exascale supercomputers will become a necessary tool to treat diseases on an individual level and make one step forward in personalised medicine. The recently launched European HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE) will provide an efficient and sustainable infrastructure to support the development of personalised medicine by showcasing HPC/Exascale-upgraded use cases such as translating the consequences of single cell omics information into actionable molecular disease models.

One of the most significant contributions of PerMedCoE will be to scale-up cell-level simulationsto HPC/Exascale level, which will fill the gap between the molecular-and organ-level simulations provided by other Centres of Excellence (CoEs) such as CompBioMed and BioExcel.

“PerMedCoE will boost the competitiveness of European personalised medicine and aims to become the community hub for Exascale-ready software in this domain”, says Alfonso Valencia, ICREA Research Professor, BSC Life Sciences Department Director and PerMedCoE Coordinator.

Personalised medicine opens unexplored frontiers to treating diseases at the individual level combining clinical and omics information. However, the performance of the current simulation software is still insufficient to tackle medical problems such as tumour evolution and response to treatment at the single-cell level or patient-specific treatments. For this reason, this European centre of excellence pursues the following main objectives:

  • To optimise key software for cell-level simulations to the new pre-exascale platforms to contribute to the European Personalised Medicine Roadmap.
  • To integrate personalised medicine into the new European HPC/Exascale ecosystem, by offering access to HPC/Exascale-adapted and optimised software.
  • To design and complete a comprehensive set of personalised medicine use cases to drive the development of cell-level simulations.
  • To build the basis for its sustainability by coordinating personalised medicine and HPC communities, and reaching out to industrial and academic end-users with use cases, training, expertise and best practices.

The centre will become the entry point to Exascale-readycell-level simulation software, able to transform personal omics data into actionable mechanistic models of medical relevance, supporting developers and end-users with know-how and best practices. It will also connect simulation software developers with HPC, HTC and HPDA experts atthe CoEsPOP and HiDALGO, and work with other biomedical consortia such as ELIXIR and LifeTime, also connecting pre-exascale infrastructures hosted by supercomputing centressuch as the BSC and CSC –IT Center for Science.

Find the press release in PDF here.