Workshops > Frontiers in Mathematical Oncology

Frontiers in Mathematical Oncology


Using Compucell3D as a platform for the Rapid Development of Flexible and Sharable Simulations to Address Problems in Cancer Biology

James Glazier

Indiana University
[SLIDES]

Abstract:  

CompuCell3D is an open-source, cross-platform virtual-tissue simulation development and execution environment which allows rapid development of complex multiscale simulations of development, homeostasis and developmental diseases like cancer. CompuCell3D supports subcellular molecular network dynamics specification though SBML, cell objects with varying levels of spatial detail and behavioral complexity, continuum PDE modeling of chemical fields and basic finite-element mechanics. Users specify CompuCell3D simulations with Python scripts, allowing very compact definitions of complex models. These scripts are modular, allowing their components to be reused and shared. Learning the basics of CompuCell3D model specification is not demanding, even for non-experts. I will illustrate the capabilities of CompuCell3D with two classic cancer simulations, a model of vascularization of a growing tumor spheroid and a simple model of microenvironmental selection pressures on somatic evolution in a solid tumor.