Mathematical modelling as knowledge mapping in PhysiCell: a guided tour

Tissues are complex multiscale biological systems where cells communicate to modulate their behaviour in response to dynamical microenvironmental conditions. Small perturbations to cells—such as injuries or therapy—can have unanticipated "ripple effects" that percolate through the system. We can use computational models as "virtual laboratories" to explore these complex systems.

In this talk, we will introduce PhysiCell, an open source agent-based modelling platform that can simulate many individual cell agents as they interact in tissue with multiple diffusing chemical signals. We will give examples drawn from hypoxic cancer invasion, mechanics-driven "reawakening" of dormant micrometastases, and innate and adaptive immune responses to viral pathogens (like SARS-CoV-2) and tumour micrometastases.

We will close with new developments (and a live demonstration!) to integrate knowledge mapping directly into the modelling process, where expert-driven biological hypotheses (chemical signal X increases cell behaviour Y) are directly transformed into mathematics and code. In our vision, multidisciplinary teams will curate biological knowledge to jointly develop mathematical models in real time to better evaluate our knowledge gaps and exploit our knowledge to treat disease.

Outcomes

By the end of this webinar, you will be able to:

• Describe how PhysiCell can simulate the interaction of different cell agents
• Identify PhysiCell new developments

Speakers

• Paul Macklin
  Indiana University