PerMedCoE Summer School on Cell-level Simulations
25-30th of June 2023

Open application with selection – 30 places

Registration period – Forthcoming

You’ll receive an email when registration period opens

About the PerMedCoE Summer School

The PerMedCoE Summer School will take place from the 25th to the 30th of June 2023 at the Hotel Montanyà, Spain. The course will combine lectures and hands-on exercises to:

  • Introduce attendees to key practicalities of working with high-performance computing (HPC) clusters
  • Build first-hand experience in using PerMedCoE modelling tools (CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell and PhysiBoSS)
  • Develop a practical appreciation of using workflow managers and containerised PerMedCoE modelling tools to execute biomedical workflows

It will also include poster sessions where participants can present their work and plenty of time for interaction between participants and between participants and trainers.

Who is this course for?

This course is aimed primarily at PhD students and early postdoctoral researchers from Computational Biology, Systems Biology or Life Sciences with an interest in the area of cell-level simulations, gaining first-hand experience in using diverse biomedical modelling tools, and how such tools could be used as part of workflows on HPC environments.

Previous experience of using Python and command-line interfaces are considered a benefit. Experience of using workflow managers is also beneficial, but not mandatory for attending the course.

What will I learn?

At the end of these sessions, you will be able to:

  • Use a range of biological modeling and cell-level simulation software (CellNOpt, CARNIVAL, COBREXA, MaBoSS, PhysiCell and PhysiBoSS)
  • Describe and execute basic workflows using PerMedCoE modelling tools on a high-performance computing (HPC) cluster
  • Discuss current trends and challenges in cell-level simulations


Arnau Montagud

Barcelona Supercomputing Center

Henrik Nortamo

CSC – IT Center for Science Ltd

Javier Conejero

Barcelona Supercomputing Center

Miroslav Kratochvil

University of Luxembourg

Pablo Rodríguez Mier

University of Heidelberg

Vincent Noël

Institut Curie

More information & registration coming soon

You’ll receive an email when registration period opens