CompuCell3D

I had the pleasure of working on the NIH-funded CompuCell3D project for about five years (part-time and full-time). My primary role was in software development for visualization and the graphical user interface. In addition, I ported CompuCell3D to a cluster to run simulation parameter sweeps. I also played an early role in convincing the team to adopt a source code version-control system (svn, later git), provided user support (via the community forum and workshops), and organized a workshop at NIMBioS.

Snapshot of the CompuCell3D desktop application showing a liver hepatocyte simulation.

Classic cell sorting simulation: lattice and glyphs visualization.

Snapshots from a wet foam simulation demonstrating coarsening. (movie1, movie2)

3D printed model showing necrotic core (purple) and vasculature (white spheres along vessels are simply artifacts to hold together disjoint pieces and offer support).

Visualizing Cells and their Connectivity Graphs for CompuCell3D
    R. Heiland, M. Swat, J. Sluka, B. Zaitlen, A. Shirinifard, G. Thomas, A. Lumsdaine, and J. Glazier
    IEEE BioVis Symposium, Oct 2012

Workflows for Parameter Studies of Multi-Cell Modeling
    Randy Heiland, Maciek Swat, Benjamin Zaitlen, James Glazier, Andrew Lumsdaine
    HPC 2010

Multi-Cell Simulations of Development and Disease Using the CompuCell3D Simulation Environment
    Maciej Swat, Susan D. Hester, Ariel I. Balter, Randy W. Heiland, Benjamin L. Zaitlen, James A. Glazier
    book chapter in Systems Biology Series: Methods in Molecular Biology Vol. 500 Maly, Ivan V. (Ed.) 2009, ISBN: 978-1-934115-64-0

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. 
    Sluka, J. P., Shirinifard, A., Swat, M., Cosmanescu, A., Heiland, R. W., & Glazier, J. A. (2014). 
    Bioinformatics 30 (16): 2367–74.