Course outside EMBL-EBI

PerMedCoE summer school: from pathway modelling tools to cell-level simulations

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.

This course will take place at the Hotel Montanyà in Seva, less than an hour away from Barcelona.

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.

Participants will need to bring their own laptop to the course. Further information about the computing requirements will be provided for the application process.


What will I learn?

Learning outcomes

At the end of these sessions, the participants 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
Course content

Visit the PerMedCoE summer school website for more information.


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


Browse the programme on the PerMedCoE summer school website.

Applications close
06 March 2023

25 - 30 June 2023
400 €
Juanita Riveros
Open application with selection
30 places

  • Daniel Vincent Thomas Lopez
  • Marta Lloret Llinares
  • Jesse Harrison
    CSC - IT Center for Science Ltd
  • Jose Carbonell Caballero
    Barcelona Supercomputing Center
  • Laurence Calzone
    Institut Curie

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