Virtual course: Drug studies in signalling pathways models and their integration into multiscale models

22 and 23 June 2022, 9-13 h CEST, online

Overview

Current cancer treatments are faced with the ever growing problem of drug resistances. Unfortunately, researching and testing new drug treatments is a costly endeavour for industry and academics. Simulation of cell systems can provide interesting tools and methods to repurpose drugs, and screen new drug treatments and their combination before going to the bench.

In these sessions, we will present the use of two tools that allow the study of drugs and their synergies at two levels: intracellular signalling pathways using Boolean modelling and cell populations using agent-based modelling.

Firstly, we will use MaBoSS to simulate drug treatments in signalling pathways at the scale of individual cells. MaBoSS stochastic Boolean modelling allows probabilistic results of the effect of a drug in a given pathway and how this probability can change with different patient-tailored models.

Secondly, we will use PhysiBoSS, a multiscale tool that embeds MaBoSS inside PhysiCell, to simulate similar treatments on a scale of a population of cells. PhysiBoSS can simulate the precise transport of a given drug for which pharmacodynamic data is available or can use more coarse-grained drug effects on the viability of the cells.

All in all, this virtual course provides an example of two complementary methodologies that give different insights into the study of drug synergies and the optimisation of drug treatments.

Learning outcomes

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

  • Explain different ways to model the drugs’ effect in cancer biology.
  • Simulate signalling pathways models and predict drug treatments using MaBoSS.
  • Simulate agent-based models and predict drug treatments using PhysiBoSS.
  • Personalise Boolean models with patients’ omics data.
  • Modify and run existing sample projects

Audience

This course is aimed at researchers from Computational Biology, Life Sciences or Computer Sciences who would like to learn to use Boolean modelling and agent-based modelling to simulate intracellular signalling and multicellular behaviour in the context of drug treatments in cancer biology. It is a beginners course for using PhysiCell and MaBoSS.

Pre-requisites:

  • Basic use of command line and access to Unix shell terminal
  • Previous knowledge of C++/Python is an advantage, although the scripts needed for the course will be provided
  • Technical requirements:
    • We recommend using the Zoom desktop app for the sessions, and (ideally) having a microphone and webcam
    • A web browser will be needed to perform part of the hands-on exercises. Chrome and Firefox are strongly recommended
    • Participants will receive instructions with the technical tasks needed to be completed prior to the course

Registration

Click here to register for the course.
Applications are first-come first-served based. We will review applications on a rolling basis to select suitable candidates until the 25 places available are filled. A waiting list will be established if needed.

How the course will run

The course will combine lectures and hands-on exercises using WebMaBoSS (MaBoSS’s web interface), Jupyter notebooks, PhysiBoSS and MareNostrum4 supercomputer. 

The training will take place virtually in Zoom. It will consist of two sessions on the 22nd and 23rd of June 2022, 9-13 h CEST, including breaks. Participants are expected to attend all sessions.

Please note that the course might be recorded.

Trainers

If you have any questions or comments, you can contact Daniel Thomas López (dthlopez@ebi.ac.uk).