Talk at Lawrence Livermore National Laboratory on February 13, 2015


Scalable 3-D Agent-Based Simulations of Cells and Tissues in Biology and Cancer


Diverse fields such as developmental biology, tissue homeostasis, autoimmune disorders, tissue engineering, and cancer share a striking commonality: dynamical interactions between large multicellular populations and the surrounding microenvironment shape the emergent behaviors and evolution of the larger systems, often in surprising ways. These interactions can occur over small or large distances (e.g., cell-cell adhesion or phenotypic responses to circulating factors), and over short and long times (e.g., cell motility and tissue remodeling). Advances in experimental techniques have yielded incredible data on cell processes from molecular to whole-body scales. Yet making sense of these data and connecting them into a bigger picture to steer disease treatment remains difficult.

One approach to this issue is to create simulation models of cells and tissues, which can form a platform for hypothesis testing, engineering, and therapeutic planning. In this talk, we will introduce common approaches to simulating cells in 3-D tissues, and present work by our lab to create a suite of open source tools and data standards for simulated biology and medicine. We will introduce PhysiCell: a parallelized agent-based model that can simulate cell cycling, apoptosis, necrosis, volume regulation, and biomechanics-based movement in 3-D systems of 500,000 to 1,000,000 cells on desktop computers. We will introduce BioFVM: a parallelized solver that simulates the movement of oxygen, glucose, growth factors, and drugs in large 3-D tissues. We will discuss MultiCellDS and digital cell lines: a data language to standardize and aggregate cell and tissue measurements for use in simulations. And we will discuss work by our lab to connect these tools to combine clinical and experimental data into patient-tailored cancer simulations.

This talk is intended for a mixed audience of biologists and modelers. 

Further information:

Macklin Lab: 

MultiCellDS (MultiCellular Data Standard): 

BioFVM (Finite Volume Method for biology) and PhysiCell (physics-based cell simulator) are undergoing final code testing and documentation, and are being prepared for early 2015 publication and open source release. See for updates.