Introducing PerMedCoE Building Blocks and workflows to streamline biological analysis pipelines

15th Dec 2022 – 14h CEST

This webinar will present some of the main practical ways PerMedCoE seeks to make data analysis pipelines more manageable and accessible to researchers. In particular, the webinar will provide an overview of how the project addresses many biological use cases using a single, shared approach in which semi-automated workflows are constructed using purpose-designed building blocks.

Data-driven modeling of intercellular interactions in the tumor microenvironment

25th Jan 2023 – 15h CEST

Monocyte-derived macrophages help maintain tissue homeostasis and defend the organism against pathogens. In tumours, recent studies have uncovered complex macrophage populations, including tumour-associated macrophages, which support tumorigenesis through cancer hallmarks such as immunosuppression, angiogenesis or matrix remodelling. In the case of chronic lymphocytic leukaemia, these macrophages are known as nurse-like cells and they protect leukemic cells from spontaneous apoptosis contributing to their chemoresistance.

This webinar will describe the challenges of data-driven modelling &
cite simple models of immuno-oncology dynamics in simplified experimental systems.

PerMedCoE/BioExcel PATC course on Introduction to HPC for Life scientists

7-8 March 2023, Barcelona

This course will include lectures and hands-on exercises to introduce HPC to life science researchers, focusing on the aspects that are most important for those new to this technology to understand. It will help you judge how HPC can best benefit your research, and equip you to go on to successfully and efficiently make use of HPC facilities in the future. The course will cover basic concepts in HPC hardware, software, user environments, file systems, and programming models. It will also provide an opportunity to gain hands-on practical experience and assistance using an HPC system (MareNostrum) through examples drawn from the life sciences, such as biomolecular simulations and multicellular simulations.

PerMedCoE Summer School: From pathway modelling tools to cell-level simulations

25-30 June 2023

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