The PerMedCoE summer school: from pathway modelling tools to cell-level simulations, ran in June 2023. Here, we have made the course materials available for you to access any time.

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Using these materials

These course materials provide a mixture of presentations and practicals to help advance your knowledge and skills in pathway modelling and cell-level simulations. You may select your topic of interest from the Course content page to view the relevant materials or work your way through all the course materials. 

To find out more about the trainers who created these materials, go to the Trainer biographies page. You can also find the software requirements for the practicals in the Software page.

In the Further learning section you may explore the details about PerMedCoE training material and the EMBL-EBI’s free access online tutorials and webinars on a variety of life sciences topics.

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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

Material collection editors

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

DOI: 10.6019/TOL.PermedSummerSchool-t.2023.00001.1