Speaker
Description
PhysiCell (physicell.org) is an open source physics-based multicellular modeling framework. A cell is defined by a (off-lattice) centroid and volume and several phenotypic parameters that define its behavior (cell cycle, death, mechanics, motility, secretion, etc). It is bundled together with the BioFVM diffusion solver for cell secretion/uptake. PhysiCell has many predefined (but modifiable) model parameter values and several sample models bundled with the (C++/OpenMP and XML) software. A notable, recent addition is a simple English grammar that lets a modeler write rules that define cells’ behaviors based on one or more signals. PhysiCell also allows for intracellular models as addons, e.g., libRoadrunner for ODEs in SBML, and PhysiBoSS for boolean networks. PhysiCell Studio is a desktop GUI (written in Python) that makes it easier to build models and visualize simulation results. The Studio is also available as an interactive tool on the Web-based Galaxy platform. In this talk, I plan to show a live demo of immunology dynamics.
