CompuCell_intro_2011_Knoxville.ppt-CompuCell3D.ppt

Photoshoot everyone!!! Don’t leave or you’ll be sorry Replacing CC3DML with Python Cell-sorting simulation on square and hexagonal lattices 1000 MCS 1000 MCS The simulation parameters were kept the same for the two runs Cell Attributes CompuCell3D cells have a default set of attributes: Volume, surface, center of mass position, cell id etc… Additional attributes are added during runtime: List of cells neighbors, polarization vector etc… To keep parameters up-to-date users need to declare appropriate plugins in the CC3DML configuration file. For example, to make sure surface of cell is up-to-date users need to make sure that SurfaceTracker plugin is registered: Include : Plugin Name=“SurfaceTracker”/ or use Surface plugin which will implicitly call SurfaceTracker Plugin Name=“Surface” LambdaSurface0.0/LambdaSurface TargetSurface25.0/TargetSurface /Plugin But here surface tracking costs you extra calculation of surface energy term: E=…+l(s-ST)2 +… More Flexible Specification of Surface and Volume Constraints Plugin Name=VolumeFlex VolumeEnergyParameters CellType=“Amoeba TargetVolume=“150 LambdaVolume=10/ VolumeEnergyParameters CellType=“Bacteria TargetVolume=“10 LambdaVolume=“50/ /Plugin Plugin Name=“SurfaceFlex SurfaceEnergyParameters CellType=“Amoeba TargetSurface=“60 LambdaSurface=10/ SurfaceEnergyParameters CellType=“Bacteria TargetSurface=“12 LambdaSurface=“20/ /Plugin You may specify different volume and surface constraints for different cell types. This can be done entirely at the XML level. Type dependent quantities Even More Flexible Specification of Surface and Volume Constraints Plugin Name=VolumeLocalFlex“/ Plugin Name=“SurfaceLocalFlex“/ Notice that all the parameters are local to a cell. Each cell might have different target volume (target surface) and different l volume (surface). You will need to use Python to initialize or manipulate those parameters while simulation is running. There is currently no way to do it from