D1.1 Life Sciences Use Case: Initial Requirements and Scenario Definitions

This deliverable describes the requirements and scenario definitions of the biological use case in accordance with expert users’ questionnaires. By using a Boolean model of carcinoma cell lines (AGS) and a lattice-free physics-based cell simulator for 3D multicellular modelling, PhysiBoSS, we aim to replicate experimental data of growth profiles of cancer cells treated with different drug regimes. The ultimate goal of this use case is to provide a "virtual laboratory" for studying cancer growth and evolution by using multi-scale models of tumour systems. The development of such a framework will facilitate the design, test, and optimization of cancer treatments based on combinations of different drugs and dose scheduling strategies. 

In our simulations, we will explore two alternative geometries for cell arrangement: i) one-cell-thick 2D monolayers, representing cells growing in a plate such as those observed in in-vitro cell cultures; and ii) 3D spheroids, representing cells growing in three-dimensional space, an arrangement that resembles cancer cells growing in-vivo. These simulations will be scaled up by several orders of magnitude using the Barcelona Supercomputing Center (BSC) MareNostrum4 allowing the incorporation of forecasting techniques for various events of interest. Moreover, interactive learning techniques will be used to assist the calibration of such in-silico models. 

In particular, we aim to scale up simulations of cancer cell 3D spheroids from 5,000 up to 500,000 cells using high-performance computing. This scenario will allow the design of different set-ups that tally cancer tumour growth conditions with increased number of cells, altered microenvironmental physical properties, different cell types, as well as to study the interaction between cancer cells and the immune system. In addition, this will allow the consideration of different simulations’ set-ups beyond cancer tumour growth such as in-vitro streak experiments, microfluidic designs, among others.