Biomedicine, supercomputers and simulations: in silico experiments and its applications in cancer research

At the lowest scale, PhysiCell uses BioFVM solver to simulate the chemical microenvironment using partial differential equations which model the diffusion, uptake and secretion of substrates and signalling molecules. At the cell scale, PhysiCell uses mechanical equations to model individual cell movement, cell-cell interactions, as well as interactions between cells and the microenvironment’s physical components, e.g. as extracellular matrix. Additionally, different cells types and heterogeneous populations can be defined by using different submodels for cell growth, death as well as user-defined custom behaviours.
Furthermore, PhysiCell can be extended to provide cell agents with more complex intracellular networks, such as signalling and metabolism. For instance, PhysiBoSS is an add-on based extension that provides cell agents with individual Boolean models of regulatory networks which are simulated using the MaBoSS algorithm. The Boolean model inputs can be connected to different cell variables and their outputs can be used to trigger changes in the cell behaviour. Altogether, PhysiBoSS bridges intracellular dynamics to the population level. Because of its flexibility, the PhysiCell Framework can be applied to a broad range of biological problems related to cancer, immunology, infectious diseases, and microbial ecology, among others. In this webinar, we will introduce the basic concepts of the PhysiCell/PhysiBoSS modelling framework and its HPC-based implementation using different biological examples focusing on applications to treatment optimisation in models of tumour growth.

Keywords: HPC, Biomodelling, cell simulations

Additional information

Target audience: Anyone interested in simulation of metabolic models, and in PerMedCoE tools and activities

Resource type: Webinar

Authors: Miguel Ponce de León

Scientific topics: Simulation experiment, Personalised medicine, Molecular interactions, pathways and networks

Operations: Modelling and simulation

External resources: